title: Sucrose accumulation regulation revealed through studies of the transcriptome and physiology in breeding populations of sugarcane

status: Public on Dec 31 2016

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

summary: Background: Sugarcane is an important sugar and energy crop largely used for bioethanol production in the world. The development of sugarcane cultivars with high sucrose content and yield is one of the biggest challenges of breeding programs nowadays. To identify genes networks that underlie sucrose content and yield, we used a custom designed oligonucleotide array with 21,901 different probes to study the transcriptome from breeding populations of sugarcane contrasting to sucrose content and genotypes contrasting to photosynthesis rate. Results: Physiological and biochemical data reveals that the transcriptome profiles described here showed a close relationship between sucrose content and stem development. A total of 2135 genes were differentially expressed in at least one experimental hybridization. We identified genes related to carbohydrate metabolism, cell wall metabolism and signal transduction. The same oligoarrays was used to detect transcription in both sense and antisense orientation. The enriched functional category from antisense expressed genes reveals light harvesting and circadian clock as the two top categories that can be related to photosynthesis and yield in sugarcane. Conclusions: Knowledge on the mechanisms underlying carbon partitioning and its relationship with sucrose accumulation in sugarcane stems would help defines routes to increase yield. Our findings showed for instance that sucrose accumulation and yield in sugarcane may be regulated by hormone signaling pathways, light harvesting and circadian clock genes. Analysis of the expression data and gene category enrichment provided an insight into signaling pathways and transcriptional control contrasting in high brix and low brix plants as well as differing photosynthesis rates and yield.

overall_design: various crosses and phenotypes

first: Sato

middle: M

last: Paloma

first: Andrade

middle: F

last: Rodrigo

first: Nishiyama-Jr

middle: Y

last: Milton

first: Lembke

middle: G

last: Carolina

first: Siqueira

middle: S

last: Savio

first: Silveira

middle: P

last: Ana

first: Labate

middle: A

last: Carlos

first: Hoffmann

last: Hermann

first: Sampaio

middle: C

last: Monalisa

first: Souza

last: Glaucia


title: miRNA profiles of hydroquinone-induced CD34+ cells in 5days, 8days, 12days

status: Public on Dec 23 2016

city: Guangzhou

first: Boxuan

last: Liang

state: Guangdong

address: Zhongshan second road

country: China

institute: Sun Yat-sen University

summary: To identify hydroquinone-associated miRNAs during blood cell development, CD34+ cells which isolated from human cord blood were tread with different dosese of hydroquinone(0, 1, 2.5 5μM) for 5days, 8days, and 12days.

overall_design: In total of 12 samples were analyzed, four different dosese of hydroquinone in three different time-point.

first: Yongmei

last: Xiao


title: Transcriptome differences between a transgenic poplar tolerant to drought and the control in different growth conditions

status: Public on Dec 30 2016

city: Málaga

first: Juan Jesus

last: Molina-Rueda

state: Spain

address: Facultad de ciencias, campus universitario de teatinos, SN

department: Molecular biology and Biochemistry

country: Spain

institute: University of Málaga

summary:
Transgenic hybrid poplars engineered to express ectopically the heterologous pine cytosolic GS1a display a number of significant pleiotropic phenotypes including enhanced growth, enhanced nitrogen use efficiency (NUE), and resistance to drought stress.  The present study was undertaken in order to assess mechanisms whereby ectopic expression of pine GS1a in transgenic poplars results in enhanced agronomic phenotypes.  Microarray analysis using the Agilent Populus whole genome array has allowed identification of genes differentially expressed between wild type and GS transgenics in four tissues (sink leaves, source leaves, stems, and roots) under three growth conditions (well-watered, drought, and recovery).
Genes whose expression is significantly altered showing a minimum of 2‐fold differential expression between transgenic and wild type samples were selected for further analysis.  Significantly over-represented functional categories among differentially-expressed genes have been identified.  Two weighted co-expression networks were constructed analyzing separately GS transgenic and wild type transcript profile data.  Differential network behavior and differential gene connectivities between GS and the wild type (WT) expression profiles have been analyzed.  Transcript levels for some differentially expressed candidates were validated by q-PCR. The results show that ectopic expression of the pine GS1a in poplars results in transcriptomic rewiring affecting expression of genes belonging to relevant functional categories, including hormone metabolism, regulation of transcription, and stress related genes.

overall_design: Two different genotypes were used, hybrid poplar (Populus tremula X P. alba, INRA 717-1B4) expressing ectopically the pine glutamine synthetase gene (GS1a)(transgenic line 4-29), and the wild type (non-transformed control). RNA was extracted from two biological replicates consisting of pooled samples from 5 individual plants from two replicate experiments.  Four tissues were collected, young sink leaves (leaves in positions 2, 3 and 4, numbered from the top of the plant, considering leaf 1 the first leaf with at least 1 cm width), mature source leaves (second and third fully expanded leaves, corresponding to leaves in positions 8 and 9), stem (from nodes 4 to 8), and root. Three growth conditions were performed, well-watered, drought and recovery from drought.  Genotypes (2), tissues (4), conditions (3) and replicates (2) made a total of 48 samples.

first: Juan-Jesús

first: Hong-Qiang

last: Wang

first: Lei

last: Du

first: Chung-Jui

last: Tsai

first: Edward

last: Kirby


title: Differential gene expression in lymph nodes from rhesus macaque subject to unstable social condition vs. control

city: Los Angeles

first: Katie

last: Chun

state: CA

address: 300 Medical Plaza

country: USA

institute: University of California, Los Angeles

summary: Differences in lymph node gene expression profiles between animals in stable vs. unstable social conditions

overall_design: Gene expression profiling was carried out on lymph node mRNA samples collected from 5 animals subject to unstable social conditions and 5 animals subject to stable social conditions.  The primary research question is whether gene expression differs in lymph nodes from animals exposed to unstable social conditions vs. stable social conditions.


title: Comparison of gene expression profile of testis samples from prednisolone-treated and control cows

status: Public on Dec 22 2016

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

country: Italy

institute: university of padua

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) testis samples from prednisolone-treated cows and seven (7) from control animals. T-test found 84 up-regulated and 49 down-regulated transcripts in the prednisolone-treated animal group respect to the controls.

overall_design: In this study, we analyzed fifteen (15) bovine testis samples, eight (8) from prednisolone-treated cows and seven (7) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: Comparison of radiation-induced rat mammary carcinomas from individuals with different sensitivity to diet-induced obesity

status: Public on Dec 25 2016

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

summary: Understanding the relationship between radiation-induced breast cancer and obesity, together with information on underlying mechanisms, are potentially useful in risk management and prevention of second cancer in patients receiving radiotherapy. The present study aims to develop a novel animal model to study the relationship by combining two Sprague-Dawley rat models of radiation carcinogenesis and diet-induced obesity. Mammary carcinomas were induced in female obese and lean rats by irradiation with 4 Gy of gamma rays. Gene expression of mammary carcinomas and normal mammary tissues were analyzed with Agilent Whole Rat Genome DNA microarray. The result indicated that genes related to translation and oxidative phosphorylation were upregulated in carcinomas of obese rats.

overall_design: Female Sprague-Dawley (Jcl:SD) rats fed on a high fat diet (45 kcal% fat) were divided into obesity prone (OP, n = 30) and resistant (OR, n = 30) individuals based on the body weight at 7 weeks of age, when they were whole-body irradiated with 4 Gy of Cs-137 gamma rays at 0.5 Gy/min; lean control (LC, n = 30) rats were fed on a standard diet (10 kcal% fat) and irradiated in the same manner; these groups of rats were observed for development of palpable mammary cancer, while kept on the same diet, for 30 weeks. Mammary adenocarcinomas with homogeneous histology without necrosis or marked infiltrating cells were selected for microarray analysis (OP, n = 6; OR, n = 3; LC, n = 3) as well as normal tissues (OP, n = 3; OR, n = 2; LC, n = 3). Microarray analysis was performed as described previously (T. Imaoka, M. Nishimura, D. Iizuka, et al. Mol Carcinog 50, 539-552, 2011). In brief, total RNA was extracted from frozen tissues and cyanine 3-labeled complementary RNA was generated from total RNA and hybridized to DNA microarrays (Whole Rat Genome Microarray Kit, Agilent Technologies, Inc., Santa Clara, CA, USA). Scanned microarray images were processed with the Feature Extraction 10 software (Agilent Technologies), normalized by the Robust Multi-array Average method and analyzed on GeneSpring GX 12 (Agilent Technologies).

first: Mayumi

last: Nishimura

first: Kazuhiro

last: Daino

first: Takamitsu

last: Morioka

first: Yukiko

first: Hiroji

last: Uemura

first: Kenta

last: Akimoto

first: Yuki

last: Furukawa

first: Masahiro

last: Fukushi

first: Keiji

last: Wakabayashi

first: Michihiro

last: Mutoh

first: Yoshiya

last: Shimada


title: Identification of genetic loci involved in iron metabolism by Bifidobacterium breve UCC2003

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

summary: Phenotypic screening of a random mutant library combined with microarray analysis of the transcriptional response of B. breve UCC2003 to iron limitation, allowed the identification of a number of genes implicated in the survival of Bifidbacterium breve UCC2003 under iron-limiting conditions. Of the identified genes, two putative iron-uptake systems, were further characterised: (i) a presumed ferrous iron uptake system, designated here as bfeUO, and (ii) a predicted ferric iron/siderophore uptake system, designated sifABCDE. In silico analysis also illustrated that these two clusters are highly conserved across members of the genus Bifidobacterium and are invariably co-located. Murine colonization studies demonstrated that B. breve UCC2003-bfeU and B. breve UCC2003-sifA insertion mutants are able to colonize a healthy murine gut as efficiently as the wild type B. breve strain, indicating that these genes are not crucial for gut survival or colonization in a healthy host.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Douwe

last: van Sinderen


title: SIMVASTATIN ATTENUATES LIVER INJURY IN RODENTS WITH BILIARY CIRRHOSIS SUBMITTED TO HEMORRHAGE/RESUSCITATION

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: In variceal bleeding liver function deterioration is a major cause of death. The effects of bleeding on intrahepatic microvascular dysfunction, which contributes to liver injury in cirrhosis, are largely unknown. The aims of this study were to evaluate the impact of hemorrhage/resuscitation (H/R) on cirrhotic microcirculation, and whether simvastatin, a drug that improves liver microcirculation, has hepatoprotective effects. The study was performed in three groups of rats: controls, rats with biliary cirrhosis (CBDL) and CBDL rats pre-treated with 3 doses (5 mg*Kg-1*day-1) of simvastatin. Rats were submitted to H/R or sham procedure. Subsequently, livers were isolated and perfused for functional assessment of liver microcirculation. Liver transcriptome was assessed with microarrays.  H/R significantly impaired endothelial-dependent vasorelaxation in cirrhotic (p=0.035) but not control livers. H/R induced a similar increase in ALT in control and cirrhotic rats, whereas the increase in AST was 10 times higher in cirrhotic than in control rats (p=0.007). Simvastatin prevented the impairment in endothelial-dependent vasorelaxation induced by H/R, and reduced by half the increase in ALT and AST (p<0.05). Transcriptomics showed a marked upregulation of genes related to inflammatory response after H/R in cirrhotic livers, but not in controls, and this was blunted by simvastatin.  In conclusion, H/R aggravates liver microvascular dysfunction in cirrhosis, and upregulates liver inflammatory pathways. This does not occur in control livers. Simvastatin prevented H/R-induced liver endothelial dysfunction, and attenuated liver injury and liver inflammatory response, suggesting that it might have potential for protecting the cirrhotic liver during bleeding complications.

overall_design: Transcriptome analysis from  CBDL (Common biliar duct ligation) rats submitted to a sham hemorrhage/resuscitation procedure (CBDLpS: n=5),  CBDL rats submitted to hemorrhage/resuscitation (CBDLpH:n=6),  CBDL rats pre-treated with simvastatin submitted to a sham hemorrhage/resuscitation procedure (CBDLpSS:n=5) and CBDL rats pre-treated with simvastatin submitted to hemorrhage/resuscitation (CBDLpSH:n=8). Also we included Controls submitted to a sham hemorrhage/resuscitation procedure (CONTROLS:n=5) and  Controls submitted to hemorrhage/resuscitation (CONTROLH:n=6)

first: C

last: Zimmermann-Meireles

first: M

last: Pasarin

first: J

middle: J

first: H

last: García-Calderó

last: Gracia-Sancho

last: García-Pagan

last: Bosch

last: González-Abraldes


title: Characterization of an abiraterone ultra-responsive phenotype in castration-resistant prostate cancer patient-derived xenografts

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: To identify the molecular signature associated with abiraterone acetate (AA) response and mechanisms underlying AA resistance in castration-resistant prostate cancer patient-derived xenografts (PDXs).

overall_design: SCID mice bearing LuCaP 136CR, 77CR, 96CR, and 35CR PDXs were treated with AA. Tumors response were followed, and tumors were harvested 7 days post-treatment (D7) and at end of study (EOS) for gene expression profiling using the Affymetrix Human Genome U219 Array Plate platform.  Four replicates per PDX, treatment, and timepoint were profiled.

first: Hung-Ming

last: Lam

first: Ryan

last: McMullin

first: Holly

last: Nguyen

first: Michael

last: Gormley

first: Roman

last: Gulati

first: Lisha

last: Brown

first: Sarah

middle: K

last: Holt

first: Weimin

last: Li

first: Deborah

last: Ricci

first: Karin

last: Verstraeten

first: Shibu

last: Thomas

first: Elahe

last: Mostaghel

first: Peter

last: Nelson

first: Robert

middle: L

last: Vessella

first: Eva

last: Corey


title: Comparison of gene expression profile of different tissue samples from prednisolone-treated and control cows

first: sara

last: pegolo

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

overall_design: Refer to individual Series

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: Gene expression profile in rat frontal cortex during the secondary phase of trauma injury

city: Marseille

first: PABAN

last: Veronique

address: 3 place V. Hugo

country: France

institute: Aix-Marseille Universite

summary: The pathophysiology of TBI is complex and can be divided into primary damage resulting from mechanical impact and secondary damage, which comprises complex interconnecting structural, functional, cellular and molecular changes. The current study was performed to evaluate gene expression profiles in the frontal cortex at 1 month, a time at which secondary damaged can be detected, following lateral fluid percussion induced TBI (lfp-TBI) and rotational acceleration induced TBI (rot-TBI) in rats. After lfp-TBI, genes significantly expressed belong to metabolic process, immune system, cellular process, and morphogenesis. After rot-TBI, genes were related to apoptosis response, morphogenesis, angiogenesis, extracellular matrix, metabolic process, and transport and localization. Interestingly, we found that the molecular signature of secondary TBI share similar alterations to pathologies related to ischemia stroke and depression. Overlapped genes belong to immune/inflammation processes, extracellular organization, and intracellular trafficking. Their biological implications in multiple brain pathologies remain to be further examined. Nonetheless, these genes homologies may indicate that therapeutic strategies following stroke and depression may also be beneficial after trauma.

overall_design: Two rat models of trauma were used: lateral fluid percussion injury (N=3) and head acceleration rotational injury  (N=3).  Total RNA was extracted from  frontal cortex 1 month after trauma. Trauma rats were compared to sham rats. Sham animals were subjected to anesthesia and all surgery but were not subjected to trauma.

first: Paban

first: Fernandez

last: Nicolas


title: Listeria monocytogenes J0161 shows altered resistance characteristics when grown at low temperature and under anaerobic conditions.

city: Northampton

first: Stuart

last: Allen

state: Northamptonshire

address: Boughton Green Road

department: Faculty of Health and Society

country: United Kingdom

institute: University of Northampton

summary: Listeria monocytogenes is a food-borne pathogen and the causative agent of listeriosis, an infection which typically arises through the consumption of contaminated foodstuffs. L. monocytogenes is a psychotrophic and facultatively anaerobic; properties which permit growth under refrigeration conditions and within modified atmosphere packaging. Through transcriptional changes L. monocytogenes is able to mount adaptive responses against stressors. Such responses typically cross protect against subsequent stresses.

overall_design: Gene expression profiles were analysed in Listeria monocytogenes subjected to oxygen limitation and low temperature (7ºC) alone and in combination. Four independent experiments were conducted for each variation of condition.

first: Danny

last: Sewell

middle: H

first: Carol

last: Phillips


title: Comparative toxicogenomic response in developing zebrafish to the flame retardant, mono-substituted isopropylated triaryl phosphate

status: Public on Dec 24 2016

city: Corvallis

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: mITP-induced transcriptional changes were measured in 48 hpf wild-type or ahr2hu3335 embryos exposed to 0 or 0.2 uM mITP from 6-48 hpf.

overall_design: Three biological replicates of at least 9 pooled whole embryos were used for each sample group, which included control and treated groups in either wild-type or ahr2hu3335 zebrafish

first: Derik

middle: E

last: Haggard


title: Comparison of gene expression profile of biceps brachii muscle samples from prednisolone-treated and control cows

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) muscle samples from prednisolone-treated cows and seven (7) from control animals. T-test found 64 up-regulated and 69 down-regulated transcripts in the prednisolone-treated animal group respect to the controls.

overall_design: In this study, we analyzed fifteen (15) bovine biceps brachii muscle samples, eight (8) from prednisolone-treated cows and seven (7) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.


title: Comparative analysis of time-dependent effects of dynamic stretch on gene expression in neonatal rat cardiomyocytes

status: Public on Dec 29 2016

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

country: Germany

institute: University Medical Center Kiel

summary: The present study focuses on the identification of the gene expression profile of neonatal rat cardiomyocytes (NRVCMs) after dynamic mechanical stretch through microarrays of RNA isolated from cells stretched for 2, 6 or 24 h.

overall_design: mRNA microarray and subsequent bioinformatics analysis was performed commercially from Comprehensive Biomarker Center (Heidelberg, Germany) on Agilent’s high-performance mRNA microarray platform. Briefly, mRNA expression profile was determined using RNA isolated from either unstretched (control group), or stretched cardiomyocytes for 2, 6, or 24 h using Agilent’s standard Rattus norvegicus 8x60K_60mer mRNA microarrays printed by Agilent’s 60-mer SurePrint technology. Each study group consisted three biological replicates. The generated microarray data were exploited bioinformatically to compare mRNA profiles of individual samples as well as grouped samples to identify significantly deregulated candidates.

first: Jost

last: Pott

first: Annika

last: Kluge

last: Frauen

first: Katharina

last: Stiebeling

first: Phillip

last: Hoppe

first: Samuel

last: Sossalla

first: Norbert

last: Frey

first: Derk

last: Frank


title: Global analysis of the molecular targets of MBNL1 and CELF1 proteins and their potential role in DM1

status: Public on Dec 21 2016

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

summary: Myotonic dystrophy type 1 (DM1) is caused by the nuclear accumulation of mutant DMPK mRNA containing CUG-repeat expansions, resulting in a trans-dominant effect on RNA processing by sequestration of MBNL1 and activation of CELF1 splicing regulators. Here, we present a comprehensive study of the MBNL1 and CELF1-regulated splicing in the HeLa cell line that may participate in the complex phenotype of the DM1 disease. We have performed human GeneChip Exon array experiments with RNAs extracted from HeLa cells in which MBNL1 or CELF1 were silenced or over-expressed. MBNL1 or CELF1-silenced HeLa cells showed changes in the expression of 170 probe sets (150 genes) and 893 probe sets (613 genes), whereas MBNL1 or CELF1 over-expression on these cells had 812 probe sets (589 genes) and 684 probe sets (531 genes) altered, respectively. In MBNL1-silenced cells we have found and validated by RT-qPCR the exclusion of RASIP1 exon 4 and of KIF13A exon 26 and the inclusion of MBNL2 exon 5. Furthermore, we have found exclusion of LCOR exon 6 and PIP4K2C exon 1, and inclusion TCF12 exon 16, with dependence on the silencing degree of MBNL1, In MBNL1 over-expressed HeLa cells we have found and validated by RT-qPCR a potent inclusion of CD44 exon 8, CD44 exon 11 and the 3´UTR of TRAF2. We have then mimicked the misregulation of MBNL1 and CELF1 protein levels of DM1 in HeLa cells, finding new altered splicing events. These alterations were found in genes that encode proteins involved in myoblast differentiation and migration (CD44, RASIP1) and muscle development (TCF12 transcription factor), estrogen and thyroid receptor interactor (LCOR), as well as proteins involved in transduction signaling pathways (PIP4K2C, TRAF2) and intracellular trafficking (KIF13A). These results provide potential contributing genes that could help to explain the complex phenotype of the DM1 disease.

overall_design: In this study, we used exon array profiling to investigate splicing events when comparing MBNL1, CELF1 and control group  in two scenarios: silencing or over-expression.

first: F

last: Hernandez-Torres

first: E

middle: D

last: Hernandez

first: A

last: Rastrojo

first: M

last: Mata

last: Garcia-Garcia

first: J

last: Dopazo

first: R

last: Artero

first: B

last: Aguado


title: Comparison of gene expression profile of lymphocytes samples from prednisolone-treated and control cows.

first: sara

last: pegolo

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) lymphocytes samples from prednisolone-treated cows and seven (7) from control animals at two sampling times (T1 and T2). T-test found 539 up-regulated and 368 down-regulated transcripts at T1 sampling time (31 days treatment) and 768 up-regulated and 648 down-regulated transcripts at T2 sampling time (6 days after drug withdrawal) in the prednisolone-treated animal group respect to the controls.

overall_design: In this study, we analyzed a total of thirty (30) bovine lymphocytes samples, eight (8) from prednisolone-treated cows  and seven (7) from control animals at each sampling time (T1 and T2). Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: Optimization of a toxicogenomics-based comparison approach to categorize chemicals  based on their modes of action

city: Bilthoven

first: Mirjam

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

summary:
The current test strategy for carcinogenicity consists initially of in vivo and in vitro genotoxicity tests. Non-genotoxic carcinogens do not directly induce DNA damage and, as such, go undetected under this test strategy.
In a previous study we setup a comparison approach to categorize chemicals having similar modes of action, according to similarity in gene expression. In the current study we will investigate whether this comparison approach can be improved by omptimizing the concentration selection procedure and by testing a concentration range per chemical.

overall_design: Primary mouse hepatocytes were exposed to a concentration range of Cyclosporin A and Tacrololimus. Cytotoxicty was measured using two different tests. Based on these tests a concentration range was selected for gene expression profiling. The previously described comparison approach was applied and pathway and GSEA analyses were used to biologically confirm the results of the comparison approach.

first: Edwin

last: Zwart

first: Paul

last: Wackers

first: Alexa

last: Vitins

first: Anne

last: Kienhuis

first: Timo

last: Breit

first: Harry

last: van Steeg

last: Luijten


title: Macrophage reponse to triple-negative breast cancer cells in vitro

status: Public on Dec 28 2016

city: Oxford

first: Zhichao

last: Ai

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: Gene expression profiling of monocyte-derived macrophage polarised by triple-negative breast cancer cell conditioned medium

overall_design: Human donor monocyte-derived macrophage, MDA-MB-231(ATCC® HTB-26™) and MDA-MB-468(ATCC® HTB-132™) were maintained in the respective medium with the harvestation of the medium for 24 hours before exposing the cancer cell conditioned mediums on monocytic-derived macrophage. Total RNAs were extracted and expression profiles were generated for each sample by RT² Profiler™ PCR Arrays(Qiagen).

last: Cassetta


title: The Microbial Gene Diversity along time and space of the wastewater treatment plant

city: Beijing

first: Tengxu

last: Wang

address: Tsinghua Yuan Street, No.1

department: School of Environment

institute: Tsinghua University

summary: Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. Nonetheless, there were significant correlations in their α- and β-diversities between phage and prokaryotes. Phages explained 40.6% of total prokaryotic community composition, much higher than the explainable power by abiotic factors (14.5%). Consequently, phages were significantly (P<0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed that phage-prokaryote pairs were deeply rooted, and two network modules were exclusively comprised of phages, suggesting a possibility of co-infection. Those results collectively demonstrate phages as a major biotic factor in controlling bacterial composition. Therefore, phages may play a larger role in shaping prokaryotic dynamics and process performance of WWTPs than currently appreciated, enabling reliable prediction of microbial communities across time and space.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: 48 samples were monthly collected from 4 anaerobic tanks in 3 wastewater treatment plants (Ninghai WWTP has 2 tank applying mesophilic and thermophilic technology respectively) during a year.

first: Yunfeng

last: Yang

first: Qiuting

last: Zhang


title: microRNA deregulation in Hepatocellular Carcinoma

city: Singapore

first: Yu

address: 11 Hospital Drive

country: Singapore

institute: National University of Singapore

summary: microRNA microarray expression profiling comparing tumor versus paired adjacent non-tumor from 100 HCC patients

overall_design: Two-color tumor versus paired adjacent non-tumor

first: Caroline

last: Lee


title: Chronic sublethal exposure to silver nanoparticles disrupts thyroid hormone signaling during Xenopus laevis metamorphosis

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

summary: Nanoparticles (NPs) are engineered in the nanoscale (<100nm) to have unique physico-chemical properties from their bulk counterparts. Nanosilver (nAg) is the most prevalent nanoparticle in consumer products due to its strong antimicrobial action. While nAg toxicity at high concentrations has been well described, the sublethal effects at or below regulatory guidelines are relatively unknown. Amphibian metamorphosis is mediated by thyroid hormone (TH), and initial studies indicate that low concentrations of nAg disrupt TH-dependent responses in precociously induced premetamorphic bullfrog (Rana catesbeiana) tadpoles. The present study examined the effects of environmentally-relevant nAg concentrations (LoAg, 0.018 µg/L; MedAg, 0.18 µg/L; HiAg, 1.8 µg/L) on naturally metamorphosing Xenopus laevis tadpoles in two 28-day chronic exposures beginning with pre- and prometamorphic stages, respectively. nAg was found to significantly bioaccumulate in tadpoles after 28 days. While nAg didn’t alter metamorphic timing, it increased hindlimb length during early premetamorphosis and in post-metamorphic juvenile tadpoles. Using MAGEX microarray and QPCR transcript analyses, 7 markers of nAg exposure were discovered and validated, 5 of which showed nAg-induced disruption of their TH-response. The increased mRNA abundance of two peroxidase genes suggests that nAg could generate reactive oxygen species (ROS) even at low, environmental concentrations. Furthermore, differential responsiveness to nAg was observed between developmental stages. Therefore, low concentrations of nAg had endocrine disruptive effects at both the physiological and molecular level, indicating that regulatory guidelines for silver may need revision.

platform_organism:
Xenopus laevis
Aquarana catesbeiana
Lithobates pipiens

overall_design: Six pre- or prometamorphic tadpoles were selected from each treatment and examined for the status of the hepatic transcriptome using MAGEX cDNA array analysis.

first: Amanda

last: Carew

first: Caren

last: Helbing


title: DNA methylation in systemic lupus erythematosus patients

status: Public on Dec 27 2016

city: Seoul

first: Yeong-Wook

last: Song

address: Yungon-dong, Chongro-gu

department: Internal Medicine

country: South Korea

institute: Seoul National University College of Medicine

summary: To screen specific DNA methylation markers  in systemic lupus erythematosus (SLE) patient's blood DNA, whole-blood DNAs from 6 female SLE patients and 6 female controls were analyzed by methylation microarray.

overall_design: Twelve whole-blood DNA samples from six SLE patients and six controls were analyzed by Illumina HumanMethylation27 BeadChip.

first: Kyeong-Man

last: Hong


title: Sequential global gene expression analysis of glucose stimulated human islets

status: Public on Dec 26 2016

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Islet transplantation has the potential to benefit patients with type I diabetes, but this cellular therapy is limited by a shortage of islets, which necessitates the collection or production of islets from alternative sources. If islets produced from stem cells are to be used for transplant therapy they should precisely replicate beta-cell function. Characterization of the unique molecular mechanisms underlying the beta-cell’s response to glucose stimulation will allow a better understanding of critical elements that the alternative cells must possess. Human islets from five donors were stimulated with glucose for various durations of time to discover the glucose-responsive pathways operating at a molecular level in islets. Compared with human hepatocytes, fibroblasts and peripheral blood mononuclear cells, human islets displayed distinct gene expression signatures. Seven hundred and forty genes were differentially expressed in islets during short-term glucose stimulation and 42 of these genes were exclusively expressed in terms of tissue specificity and exposure duration. One thousand six hundred and thirty five genes were differentially expressed in islets during long-term glucose stimulation and 148 of these genes were exclusively expressed. The expression of two important glucose-responsive genes TSC2 and ARF1 were measured by real-time PCR in mouse MIN6 beta-cell line. Insulin secretion from ARF1 knockdown MIN6 cells decreased by 1-fold compared with controls, and TSC2-knockdown MIN6 cells decreased by 2-fold. These findings may allow for better direction of the differentiation of other types of cells such as embryonic and induced pluripotent stem cell into insulin-producing cells.

overall_design: We performed gene expression profiling on samples of human pancreatic islets from 5 donors stimulated by 300 mg/dl glucose for 1 hr (5 biological repeats), 2 hr (3 biological repeats) and 24 hr (5 biological repeats) for a total of 13 arrays. For comparison, gene expression profiling was conducted on unstimulated pancreatic islets for 1 hr (4 biological repeats), 2 hr (5 biological repeats) and 24 hr (4 biological repeats) for a total of 13 arrays. Single samples of fibroblasts were treated for 1 hr and 24 hr and untreated for 1 hr, 2 hr and 24 hr periods for a total of 5 arrays. Hepatocytes were treated for 1 hr (1 sample), 2 hr (1 sample) and 24 hours (2 technical repeats) and untreated for 1 hr (1 sample), 2 hr (2 technical repeats) and 24 hr (2 technical repeats) for a total of 9 arrays. PBMC were treated for 1 hr (2 technical repeats), 2 hr (2 technical repeats) and 24 hr (2 technical repeats) and untreated for 1 hr (2 technical repeats), 2 hr (2 technical repeats) and 24 hrs (2 technical repeats) for a total of 12 arrays. Total RNA from PBMCs pooled from six normal donors was amplified into aRNA to serve as the reference.


title: Serum microRNA signatures are indicative of skeletal fractures in post-menopausal women with and without type 2 diabetes and influence osteo-genic differentiation of mesenchymal stem cells

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: The objective of this study was the identification of serum microRNAs that can differentiate osteoporotic fracture patients with and without type-2 diabetes from healthy control subjects. For that purpose circulating microRNAs were profiled by real-time quantitative PCR using a custom 384-well panel in 200 µl serum samples. Univariate and multivariate statistical tools were used in order to identify single as well as combinations of circulating microRNas that were characteristic of patients with prevalent osteoporotic fractures: a qRT-PCR-based classifier consisting of miR-550a-5p, miR-96-5p, miR-32-3p and miR-486-5p can distinguish T2D women with (DMFx) and without fragility fractures (DM) with high specifitiy and sensitivity (AUC = 0.93). A classifier consisting of miR-188-3p, miR-382-3p, miR-942 and miR-155-5p was capable of differentiating between postmenopausal women with osteoporotic fractures and fracture-free controls with an AUC of 0.98.

overall_design: qPCR circulating microRNA profiling.  Four groups were defined: postmenopausal women without type-2 diabetes and no history of osteoporotic fractures (CO); postmenopausal women without type-2 diabetes and a history of at least one (non-recent) osteoporotic fractures (FX); postmenopausal women with type-2 diabetes and no history of osteoporotic fractures (DM); postmenopausal women with type-2 diabetes and a history of at least one (non-recent) osteoporotic fractures (DMFX)

first: Ursula

last: Heilmeier

first: Susanna

last: Skalicky

first: Sylvia

last: Weilner

first: Fabian

last: Schröder

first: Klemens

last: Vierlinger

first: Janina

middle: M

last: Patsch

first: Thomas

last: Baum

first: Andrew

last: Burghardt

first: Ann

middle: V

last: Schwartz

first: Johannes

last: Grillari

last: Link


title: MeDIP-chip from livers of cloned and not cloned cattle at two stages (perinatal period, adulthood), using anti-methylcytosine antibody.

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

institute: INRA

type: Methylation profiling by genome tiling array

summary: Background: It is postulated that the developmental defects frequently observed in somatic clones arise from inappropriate reprogramming of the donor epigenome by the oocyte. We used cattle clones as a model to investigate the long-term effects of nuclear reprogramming on both DNA methylation and the phenotype of a differentiated organ, the liver. Pathological perinatal clones and apparently normal adult clones, both produced within one decade, were studied, together with age-matched controls.  Results: Using MeDIP-chip, we identified differentially methylated regions (DMRs) in gene promoters displaying variations according to age and to the clone status of the animals. Strikingly, whereas adult clones did not differ significantly from adult controls, perinatal clones showed a demethylation at DMRs inconsistent with their chronological age. Pathological features were found in the liver of perinatal clones only, with histological lesions and modifications to both histomorphometrical and metabolic parameters. The integration of DMRs with phenotypic datasets led to the identification of epigenetic alterations correlated to phenotypic abnormalities in perinatal clones. Genes important to the antioxidant response and energy metabolism were targeted by these alterations. For at least one DMR, the aberrant methylation profile in perinatal clones was associated with altered gene expression.  Conclusions: The liver defects encountered in pathological perinatal clones could be associated to the aberrant age of DNA methylation, at genes indicating potential deficits in oxidative metabolism. We propose that epigenetic ageing is an adaptation to the excessive oxidative stress induced by reprogramming that the pathological clones were not able to counteract during subsequent developmental stages.

overall_design: Comparison of MeDIP DNA and input DNA with a dye-swap technical repetition for every sample; 26 samples in total, including 4 perinatal controls, 7 perinatal clones, 8 adult controls and 7 adult clones.

first: Hélène

first: Luc

last: Jouneau

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Ewing's sarcoma: an analysis of miRNA expression profiles and target genes in paraffin-embedded primary tumor tissue

city: Pescara

first: Anna

middle: Concetta

last: Berardi

address: Via Fonte Romana 8

institute: Hospital Santo Spirito

summary: The molecular mechanism responsible for Ewing Sarcoma (ES) remains largely unknown. This study compared global miRNA expression in biopsies from 20 ES patients, affected by primary untreated tumors, with miRNA expressed in normal human mesenchymal stromal cells (MSCs) by microarray analysis.  A miRTarBase database was used to identify the predicted target genes for differentially-expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNA expression between ES biopsies and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis, carried out on three selected miRNAs, showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly-regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-Let-7a, miR-34a. Using paraffin-embedded tissues from ES, this study has identified several potential target miRNAs and one gene that might be considered novel critical biomarkers for ES pathogenesis.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Biopsies from 20 ES patients using paraffin-embedded tissues and normal human mesenchymal stromal cells as controls.

first: Antonina

last: Parafioriti

first: Caterina

last: Bason

first: Elisabetta

last: Armiraglio

first: Lucia

last: Calciano

first: Primo

last: Daolio

first: Martina

last: Berardocco

first: Andrea

last: Di Bernardo

first: Alessia

last: Colosimo

first: Roberto

last: Luksch


title: caArray_topal-00242: MicroRNA  Analysis of TCGA Ovarian samples using Agilent MicroRNA array

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: MicroRNA  Analysis of TCGA OVA samples using Agilent MicroRNA array

overall_design:
topal-00242
Assay Type: microRNA
Provider: Agilent
Array Designs: H-miRNA_8x15K
Organism: Homo sapiens (ncbitax)
Tissue Sites: Ovary, NOT SPECIFIED, PERITONEUM (OVARY), OMENTUM
Material Types: Recurrent Solid Tumor, Primary solid_tumor, whole_organism, Solid normal_tissue
Disease States: Serous Cystadenocarcinoma, NOT SPECIFIED


title: ChIP-chip and transcriptomic analysis of Arabidopsis BRM chromatin remodeler

status: Public on Dec 20 2016

city: Warsaw

first: Rafal

last: Archacki

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Genome-wide profiling of BRM chromatin remodeler in Arabidopsis thaliana

summary: Chromatin, in addition to its purely structural functions, is considered a major regulatory system coordinating various genetic networks in eukaryotes. Constant changes of gene expression programs are especially important for plants, which have to respond to environment by modulating their growth and development during whole lifetime. External and developmental signals can be transmitted through signaling cascades to chromatin remodeling complexes like SWI/SNF, which alter chromatin structure by moving, ejecting or restructuring nucleosomes. Genetic studies in Arabidopsis thaliana revealed that SWI/SNF chromatin remodeling complexes are critical for proper plant development and growth. Especially, BRM, a catalytic subunit of the complex, was shown to directly regulate several genes with important functions in leaf development, flowering initiation, as well as gibberellin and abscisic acid signaling. In this study, we profiled BRM global binding regions in Arabidopsis genome by ChIP-chip analysis. We found that BRM can bind to thousands of genes, many of which have key functions in hormone and stress signaling.

overall_design: In total 4 samples; 2 Input with the corresponding 2 ChIP samples

first: Daniel

last: Buszewicz

first: Roksana

last: Iwanicka-Nowicka

first: Marta

last: Koblowska

first: Bartek

last: Wilczyński


title: Expression data from 3-week old Arabidopsis seedlings of WT and brm-1 mutant

summary:
Chromatin, in addition to its purely structural functions, is considered a major regulatory system coordinating various genetic networks in eukaryotes. External and developmental signals can be transmitted through signaling cascades to chromatin remodeling complexes like SWI/SNF, which alter chromatin structure by moving, ejecting or restructuring nucleosomes. Genetic studies in Arabidopsis thaliana revealed that SWI/SNF chromatin remodeling complexes are critical for proper plant development and growth. Especially, BRM, a catalytic subunit of the complex, was shown to directly regulate several genes with important functions in leaf development, flowering initiation, as well as gibberellin and abscisic acid signaling. In addition, SWI/SNF complexes were also shown to be involved in regulation of enhancer activity in animal cells and RNA-mediated transcriptional silencing in plants.
In this study we performed transcript profiling of WT and brm-1 mutant using Agronomics microarrays for detecting changes in expression of both sense and antisense transcripts.

overall_design: 3-week old Arabidopsis seedlings of WT and brm-1 null mutant were selected for RNA extraction and hybridization on Affymetrix Agronomics microarrays.


title: Transcriptional changes in innate immunity genes in head kidney associated with Aeromonus salmonicida infection in polycyclic aromatic hydrocarbon mixture-fed rainbow trout

first: Susan

middle: C.

last: Tilton

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

summary: Responses of salmonid populations to ecosystem degradation often, if not typically, involve multiple stressors. The interaction of disease and contaminant exposure is of potential relevance to persistence of salmonid populations. The duration of PAH exposure and the life stage of exposure in the trout reflect a likely exposure scenario for some stocks of anadromous salmonids (sub-yearling ocean-type Chinook salmon) during emigration to the ocean.  This current study focuses on the genes expressed in rainbow trout after exposure to both the high molecular weight PAH mixture and to the A. salmonicida pathogen.

overall_design: Rainbow trout (Oncorhynchus mykiss) were fed a mixture of ten high molecular weight polycyclic aromatic hydrocarbons (PAH) at an environmentally relevant concentration (400ppm) for 50 days. After 50 days of PAH exposure, fish were challenged with Aeromonas salmonicida (A. Salmonicida), the causative agent of furunculosis, at a lethal concentration 30 (LC30) or growth media without the pathogen (mock challenge). There were a total of four treatment combinations: (1) mock-challenged, control-fed fish; (2) A. salmonicida-challenged, control-fed fish; (3) mock-challenged, PAH-fed fish; (4) A. salmonicida-challenged, PAH-fed fish. Head kidney was collected 2, 4, 10 and 20 days after challenge.

first: Lawrence

last: Curtis


title: Mechanism of gene regulation by a Staphylococcus aureus toxin

status: Public on Dec 19 2016

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Virulence of many bacterial pathogens, including the important human pathogen Staphylococcus aureus, depends on the secretion of frequently high amounts of toxins. Toxin production involves the need for the bacteria to make physiological adjustments for energy conservation. While toxins are primarily known to be targets of gene regulation, such changes may be accomplished by regulatory functions of the toxins themselves. However, mechanisms by which toxins regulate gene expression have remained poorly understood. We show here that the phenol-soluble modulin toxins have gene regulatory functions, which in particular include regulation of their own export by direct interference with a GntR-type repressor protein. This capacity was most pronounced in PSMs with low cytolytic capacity, demonstrating functional specification among closely related members of that toxin family. Our study presents a paradigmatic example of how bacterial toxins may regulate gene expression to adapt to the physiological needs in situations of enhanced toxin production.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: strain vs. different strain, 3 replicates

first: Hwang-Soo

last: Joo

first: Som

middle: S

last: Chatterjee

first: Amer

last: Villaruz

first: Seth

middle: W

last: Dickey

first: Vee

middle: Y

last: Tan

first: Yan

last: Chen

first: Stacy

last: Ricklefs

first: Michael

last: Otto


title: Gene expression signature of the T-ALL cell line LOUCY treated with 1µM (+)-JQ1 for 48h

status: Public on Dec 15 2016

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

summary:
We analyzed the transcriptional consequences of the BET bromodomain inhibitor JQ1 in the T-ALL cell line LOUCY by microarray analysis. Sustained exposure at a high concentration (48h, 1µM) revealed broad transcriptional effects with more than half of the expressed probesets showing significant up- or downregulation (adj. p-value<0.05).
Significantly downregulated genes included stem-cell associated genes and putative oncogenes such as BAALC, WT1, MN1, MEF2C, LMO1, LMO2, BCL2, IGFBP7, ZEB2, GFI1B, MYB and LYL1.

overall_design: LOUCY cells were treated with 1µM (+)-JQ1 or DMSO for 48h. Three biological replicates of this treatment were performed.

first: Pieter

last: Van Vlierberghe


title: Functional Subclone Profiling for Prediction of Treatment-Induced Intratumor Population Shifts and Discovery of Rational Drug Combinations in Human Glioblastoma [SNP]

city: Bonn

first: Roman

last: Reinartz

address: Sigmund Freud Strasse 25

department: Institute of Reconstructive Neurobiology

institute: University of Bonn

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

summary:
Purpose: Investigation of clonal heterogeneity may be key to understanding mechanisms of therapeutic failure in human cancer. However, little is known on the consequences of therapeutic intervention on the clonal composition of solid tumors.
Experimental Design: Here, we used 33 single cell–derived subclones generated from five clinical glioblastoma specimens for exploring intra- and interindividual spectra of drug resistance profiles in vitro. In a personalized setting, we explored whether differences in pharmacologic sensitivity among subclones could be employed to predict drug-dependent changes to the clonal composition of tumors.
Results: Subclones from individual tumors exhibited a remarkable heterogeneity of drug resistance to a library of potential antiglioblastoma compounds. A more comprehensive intratumoral analysis revealed that stable genetic and phenotypic characteristics of coexisting subclones could be correlated with distinct drug sensitivity profiles. The data obtained from differential drug response analysis could be employed to predict clonal population shifts within the naïve parental tumor in vitro and in orthotopic xenografts. Furthermore, the value of pharmacologic profiles could be shown for establishing rational strategies for individualized secondary lines of treatment.
Conclusions: Our data provide a previously unrecognized strategy for revealing functional consequences of intratumor heterogeneity by enabling predictive modeling of treatment-related subclone dynamics in human glioblastoma

overall_design: SNP profiling of 7 cultured glioblastoma-samples from one surgical specimen. 5 subclones (GNV019_CL1/2/3/6/7) were derived from a parental culture (GNV019; in an early (3) and late (10) passage).

first: Björn

last: Scheffler


title: Gene expression signature of the T-ALL cell line LOUCY treated with 250nM (+)-JQ1 for 4h

summary:
We analyzed the transcriptional consequences of the BET bromodomain inhibitor JQ1 in the T-ALL cell line LOUCY by microarray analysis. Short-term exposure to a low dose of JQ1 (4h, 250nM) provided insights in the genes whose expression was immediately affected by BET bromodomain inhibition.
Significantly downregulated genes upon short-term drug treatment included stem-cell associated genes and putative oncogenes such as BAALC, WT1, MN1, MEF2C, LMO1 and LMO2. Genes associated with the 500 highest ranked enhancer regions in LOUCY, were significantly enriched in genes downregulated after JQ1 treatment.

overall_design: LOUCY cells were treated with 250nM (+)-JQ1 or DMSO for 4h. Three biological replicates of this treatment were performed.


title: Transcriptomic profiling of peripheral blood CD4+ T cells in asthmatics with and without depression

status: Public on Dec 09 2016

city: Chengdu

first: Ting

last: Wang

state: Sichuan

address: No. 37 Guo Xue Xiang

department: Respiratory and Critical Care Medicine

country: China

institute: West China Hospital, Sichuan University

summary: The aim of this study was to determine whether asthma with depression is characterized by unique pathophysiological pathways by analyzing the global gene expression patterns of CD4+ lymphocytes from asthmatics with or without depression.

overall_design: Four groups of subjects (non-depressive asthmatics, depressive asthmatics, depression patients, and healthy controls) consisting of 6 participants in each group were studied. Peripheral CD4+ 4 lymphocytes were isolated and the global transcriptomic profiles were defined by using the Agilent SurePrint G3 Human GE 8x60K Microarray.


title: mRNA expression analysis in  glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals

status: Public on Dec 08 2016

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: To determine mRNA expression levels  glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals, RNA was purified from total worms collected at late L4 stage using TRI Reagent (MRC).

overall_design: A total of 6 samples was analyzed (triplicates of glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals respectively)

first: Magdalene

last: Rausch

first: Stephane

last: Thiry

first: Helge

last: Grosshans


title: MicroRNA expression profile of human umbilical vein endothelial cells treated with Angiogenin (ANG)

status: Public on Dec 13 2016

city: Hangzhou

first: Chunhua

last: Weng

address: 866 Yuhang-Tang Road

department: School of Medicine

institute: Zhejiang University

summary: We quantified differential microRNA (miRNA) expression in Human umbilical vein endothelial cells （HUVECs）response to Angiogenin (ANG) treatment.These data were used to determine which miRNAs are altered on ANG in Human umbilical vein endothelial cells.

overall_design: Each group had a n=2 and ANG response miRNA levels post incubations were compared to no treatment with ANG.

first: Haojie

last: Dong

first: Zhengping

last: Xu


title: Whole-genome DNA methylation profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes.

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

country: Spain

institute: Hospital Universitario Central de Asturias

summary: The loss of the CD28 co-stimulatory molecule by CD4+ lymphocytes (CD28null T cells) is accompanied by the acquisition of new biological and functional properties that lead to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset in several inflammatory disorders and in healthy individuals, mainly in aging, are yet a controversial point. Here, we provide the whole-genome DNA methylation profile of CD28null T cells and its CD28+ counterpart. A comparative analysis reveals that 296 genes are differentially methylated between both cell subsets. One hundred sixty (160 genes) associated with the cytotoxicy ability (e.g., GRZB, TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g., CX3CR1, CD27, and IL1R) are demetylated in CD28null T cells, whilst 136 de-novo methylated genes matched with defects in the TCR signaling pathway (e.g., ITK, TXK, CD3G, and LCK). Overall, our results reveal that CD28null T cells have a unique DNA methylation landscape, which is associated with alteration in gene expression and contributes to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could provide novel therapeutic strategies to prevent the accumulation and activation of these cells in aging and inflammatory disorders.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation from 24 healthy donors. Further, CD4+CD28null and CD4+CD28+ T lymphocytes were purified using CD4 Multisort kit and CD28 MicroBead kit (Miltenyi Biotec) following the manufacturer´s instructions or sorted with a BD FACSARIA II cytometer (BD Bioscience) after staining with CD4-APC and CD28-FITC monoclonal antibodies (mAbs) (BioLegend). Purity was always higher than 95% for all samples. Datasets were generated from two biological replicates per each cell type (CD28null and CD28+) obtained from a pool of twelve healthy donors each one. Samples were pooled using the same DNA quantity by donor. Bisulphite converted DNA from the two pools were hybridised to the Illumina Infinium 27k Human Methylation Beadchip.

first: Ramón

last: Rodriguez

first: Karin

last: Schlangen

first: Aroa

middle: B

last: Raneros

first: Leonardo

last: Márquez

first: Agustín

middle: F

last: Fernandez

first: Carmen

last: Díaz-Corte

first: Ana

last: Aransay

first: Carlos

last: López-Larrea


title: Comparison of bovine 16-cell (96 hpi) embryo transcriptome in presence of co-culture systems (BOEC or VERO) in SOF medium

city: Jouy-en-Josas

first: Anaïs

last: Vitorino Carvalho

address: Domaine de Vilvert

department: BDR

summary: To analyze impact of co-culture presence and type of feeder cell lines, we compared the transcriptome of bovine 16-cell (96 hpi) using a new custom bovine microarray.

overall_design: In vitro produced putative zygotes were cultured in 500 µl weel (25 embryos per well) in control condition (5% O2, 5%, 4 replicates), in high level of oxygen (20% O2, 20%, 3 replicates), in presence of BOEC at 20%O2 (BOEC, 3 replicates) or in presence of VERO (VERO, 4 replicates). Embyos were sampled at 16-cell stage (96 hours post insemination).

first: Veronique

last: Duranthon


title: Comparison of bovine blastocysts (192 hpi) embryo transcriptome in presence of co-culture systems (BOEC or VERO) in SOF medium

summary: To analyze impact of co-culture presence and type of feeder cell lines, we compared the transcriptome of bovine blastocyst (192 hpi) using a new custom bovine microarray.

overall_design: In vitro produced putative zygotes were cultured in 500 µl weel (25 embryos per well) in control condition (5% O2, 5%, 3 replicates), in high level of oxygen (20% O2, 20%, 3 replicates), in presence of BOEC at 20%O2 (BOEC, 3 replicates) or in presence of VERO (VERO, 4 replicates). Embyos were sampled at 16-cell stage (96 hours post insemination).


title: Comparison of bovine embryo transcriptome at 16-cell (96 hpi) and blastocysts (192 hpi) stages in presence of co-culture systems (BOEC or VERO) in SOF medium


title: Whole-Cell Cancer Vaccines Induce Large Antibody Responses to Carbohydrates and Glycoproteins

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

country: USA

institute: National Cancer Institute

summary:
Purpose:  This study uses a high-throughput glycan microarray to profile anti-glycan immune responses to whole-cell vaccines: GVAX Pancreas, K562-GM and H1299. The aim was to indentify anti-glycan antibody responses relevent to patient clinical outcomes
Results:  Immune responses to non-human antigens bovine fetuin and alpha-Gal antigens were identified induced by GVAX Pancreas. The magnitude of these responses inversely correlate with patient survival. The non-human antigens were likely incorporated from cell media used for vaccine production. Their presence distracted immune system, resulting in decreased immune response to vaccine antigens.
Conclusion: This study highlighted the importance of anti-glycan immune response in vaccine development. Whole-cell vaccinesderived from human cell lines could incorporate non-human antigens from cell media. These xeno-antigens may have negative impact on the vaccine efficacy.

platform_organism:
Quercus alba
Gossypium hirsutum
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design: Anti-glycan antibodies in Pre- and Post-vaccination sera from 62 patients treated with GVAX Pancreas (n=28), K562-GM vaccine (n=26) and H1299 vaccine (n=8) were profiled with glycan microarrays. Responses in anti-glycan IgG and IgM antibodies were quantified by calculating the fold-changes to indivudal antigens before and after vaccination. The magnitude of antibody response was used to evaluate the correlation with patient survival. The results from Kaplan-Meier estimate and Cox regression analysis were further validated with permutations.Finally, mechanistic studies were performed to rationalize the observed inverse correlations between anti-glycan immune responses and patient survival.

first: Li

last: Xia

first: David

last: Schrump

first: Jeffrey

middle: C


title: Integrated analysis of long non-coding RNAs and mRNA expression profiles in human pulmonary artery smooth muscle cells reveals the potential role of lncRNAs in the pathogenesis of pulmonary artery hypertension

status: Public on Dec 07 2016

city: Nanjing

first: Yue

last: Yu

state: Jiangsu

address: No. 300, Guangzhou Road

department: Department of Thoracic Surgery

institute: the First Affiliated Hospital of Nanjing Medical University

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

summary: Background: Long noncoding RNAs (lncRNA) may play critical regulatory role in pulmonary arterial hypertension (PAH). In this study, we used microarray and bioinformatics analysis to find potential lncRNAs which may be useful in PAH.  Methods: Human pulmonary arterial smooth muscle cells (HPASMCs) were cultured and stimulated by endothelin (ET)-1 to establish as a PAH cellular model. We examined the two cells’ status of proliferation and apoptosis, and identifying their expression patterns of lncRNAs and mRNAs via microarray analysis. Bioinformatics analysis were performed to analyze lncRNA related coding genes involved in different biological responses.   Results: After treated by ET-1, proliferation and apoptosis resistance of HPASMCs were enhanced. Microarray data showed that 1296 lncRNAs were significantly induced and 972 lncRNAs were suppressed in HPASMCs after ET-1 treatment. Meanwhile, 325 mRNAs were up-regulated and 335 mRNAs were down-regulated. Gene Ontology analysis results showed that up-regulated mRNAs were mainly involved positive regulation of angiogenesis and extracellular space, while down-regulated mRNAs were involved in low-density lipoprotein particle clearance and extracellular space. Kyoto Encyclopedia of Genes and Genomes analysis showed pathways of up-regulated mRNAs included cytokine-cytokine receptor interaction and transcriptional misregulation in cancer, while down-regulated mRNAs were related to fat digestion and absorption, sphingolipid metabolism and nitrogen metabolism. The most significantly up- and down-regulated lncRNA were validated by RT-PCR. 192 differentially expressed lncRNAs were found may play cis roles for the closest differentially expressed mRNAs.  Conclusion: This preliminary study indicated that the identified aberrantly expressed genes and hub lncRNAs which might play important roles in PAH.

overall_design: Examine the different of mRNA and lncRNA expression profiles between endothelin-1 treated and untreated human pulmonary arterial smooth muscle cells

first: Junjie

last: Du


title: Curcumin mediates oxaliplatin-acquired resistance reversion in colorectal cancer cell lines through modulation of CXC-Chemokine/NF-kB signaling pathway

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Resistance to oxaliplatin (OXA) is a complex process affecting the outcomes of metastatic colorectal cancer (CRC) patients treated with this drug. The NF-kBsignalling pathway deregulation has been proposed as an important mechanism involved in this phenomenon. Here, we show that NF-kBwas hyperactivated in in vitro models of OXA-acquired resistance but was attenuated by the addition of Curcumin, a non-toxic NF-kB inhibitor. The concomitant combination of Curcumin+OXA was more effective and synergistic in cell lines with acquired resistance to OXA, leading to the reversion oftheir resistant phenotype, through the inhibition of the NF-kBsignalling cascade. Transcriptomic profiling revealed the up-regulation of three NF-KB-regulated CXC-chemokines, CXCL8, CXCL1 and CXCL2, in the resistant cells thatwere more efficiently down-regulated after OXA+Curcumin treatment as compared to the sensitive cells. Moreover, CXCL8 and CXCL1 gene silencing made resistant cells more sensitive to OXA through the inhibition of the Akt/NF-kBpathway. High expression of CXCL1 in FFPE samples from explant cultures of CRC patients-derived liver metastaseswas associated with response to OXA+Curcumin.In conclusion, we suggest that combination of OXA+Curcumincould be an effective treatment in CRC patients after progression to OXA-based chemotherapy being CXCL1a good candidate predictive marker to this treatment.

overall_design:
Stable colorectal cancer-derived cell lines sensitive to oxaliplatin (HT29) and resistant to oxaliplatin (HTOXAR3) were cultured under basal conditions (without treatment) or in the presence of oxaliplatin or oxaliplatin and curcumin in triplicate.

cell type comparison; treatment comparison

first: Vicenç

last: Ruiz de Porras

first: Sara

last: Bystrup

first: Anna

last: Martinez-Cardús

first: Raquel

last: Pluvinet

first: Lynne

last: Howells

first: Mark

middle: I

last: James

first: Chinenye

last: Iwuji

first: José-Luis

last: Manzano

first: Laura

last: Layos

first: Cristina

last: Bugés

first: Eva

last: Martinez-Balibrea


title: caArray_socci-00214: TCGA Analysis of Copy Number for OV Using Agilent Human Genome CGH Microarray Kit 244K

first: Mervi

last: Heiskanen

type: Genome variation profiling by genome tiling array

overall_design:
socci-00214
Assay Type: aCGH
Provider: Agilent
Array Designs: TCGA__HG-CGH-244A_v081008.ADF
Organism: Homo sapiens (ncbitax)
Tissue Sites: Ovary, Blood
Material Types: normal_Blood, genomic_DNA, synthetic_DNA, organism_part, solid_tumor, cell, normal_tissue
Disease States: Serous cystadenocarcinoma


title: A novel HbA1c-lowering traditional Chinese medicinal formula, identified by translational medicine study

status: Public on Dec 05 2016

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: CYSKT affected the expressions of genes associated with insulin signaling pathway, increased the amount of phosphorylated insulin receptor in cells and tissues, and stimulated the translocation of glucose transporter 4 to the cell membrane. Moreover, CYSKT affected the expressions of genes related to diabetic complications, improved the levels of renal function indexes, and increased the survival rate of diabetic mice.

overall_design: Type 2 diabetic mice were treatedwithout or with 200 mg/kg CYSKT for 30 consecutive days and RNAs from muscle tissuess were extracted for microarray analysis. Number of replicate was three.


title: Identification of Eda targets during Meibomian gland development

city: Baltimore

first: Yong

last: Qian

address: 251 Bayview Blvd, Suite 100

department: NIA

summary: Eda signaling plays critical role for Meibomian gland dvelopment, however, the crosstalk of Eda with other signaling is largly unknown.  By comparing expreession profilings between wild-type and Eda mutant Tabby eyelids,  we identified Dkk4 and Lrp6 highly expressed during mouse Meibomian gland development.

overall_design: Total RNAs isolated from microdissected wild-type and Tabby eyelids were profiled with Agilent 44K NIA mouse microarrays.

first: Jian

last: Sima


title: Tissue-specific metabolic reprogramming drives nutrient flux in diabetic complications

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

summary: Diabetes is associated with altered metabolism, but how altered metabolism contributes to the development of complications such as diabetic kidney disease is unknown. We used a systems approach with transcriptomics and mass spectrometry (MS)-based metabolomics to determine alterations in carbohydrate and lipid metabolism in kidney cortex tissue from 24-week-old BKS db/db diabetic mice and db/+ controls. Glomerular-deprived kidney cortex (kidney proximal tubule) gene expression was profiled and compared with metabolite data. Transcriptomic and metabolomic profiling demonstrated an increase in both glycolysis and fatty acid beta-oxidation,

overall_design: Glomerular-deprived kidney cortex RNA was extracted using the RNeasy Mini Kit and processed for hybridization on Affymetrix GeneChip Mouse Genome 430 2.0 microarrays.

first: Kelli

last: Sas

first: Pradeep

last: Kayampilly

first: Jaeman

last: Byun

first: Lucy

last: Hinder

first: Junguk

last: Hur

first: Hongyu

last: Zhang

first: Chengmao

last: Lin

first: Nathan

middle: R

last: Qi

first: George

last: Michailidis

first: Per-Henrik

last: Groop

first: Robert

middle: G

last: Nelson

first: Manjula

last: Darshi

first: Kuman

last: Sharma

first: Jeffrey

last: Schelling

first: John

last: Sedor

first: Rodica

last: Pop-Busui

first: Joel

last: Weinberg

first: Scott

middle: A

last: Soleimanpour

first: Steven

last: Abcouwer

first: Thomas

last: Gardner

first: Charles

last: Burant

middle: L

last: Feldman

first: Matthias

last: Kretzler

first: Frank

last: Brosius

first: Subramaniam

last: Pennathur


title: Glycogene expression profiles based on microarray data of cervical carcinoma HeLa cells partially silenced in E6 and E7 HPV oncogenes

city: Atlixco

first: Verónica

last: Vallejo-Ruiz

state: Puebla

address: Km 4.5 Carretera Federal Atlixco-Metepec

department: Centro de Investigación Biomédica de Oriente

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: Aberrant glycosylation is a characteristic of tumor cells. The expression of certain glycan structures has been associated with poor prognosis. In cervical carcinoma has been reported changes in the gene expression level of some glycogenes that has been associated with lymph invasion. Human papilloma virus (HPV) infection is one of the most important factors to develop cervical cancer. HPV oncoproteins E6 and E7 have been implicated in cervical carcinogenesis. The role of these oncoproteins in glycosylation changes has not been reported. To know the effect of these oncoproteins on glycogene expression we realized a partial silencing of oncogenes E6 and E7 in HeLa cells, we made a microarray expression assay and we identified glycogenes that modified its expression. The analysis showed alteration in some glycosylation pathways, like glycosphingolipid, O-glycan mucin-type, and O-glycan non mucin-type glycosylation.  Our results suggest that E6 and E7 oncoproteins could modified glycosylation of structures implicated in proliferation, adhesion, and apoptosis.

overall_design: Two-condition experiment,  HeLa cell groups (shE6/E7, and shControl) One replicate array. 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 (for shE6/E7) or dUTP-Alexa647 (for shControl) employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

first: Miguel

last: Aco-Tlachi


title: Role of MYC target lncRNA DANCR in cancer

city: Philadelphia

first: Zhongyi

last: Hu

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

summary:
Expression profiling by array
Effects of DANCR siRNA on gene expression

overall_design: PC3 cells were seeded in 6-well plates in antibiotic-free media overnight, and then transfected with DANCR siRNA. Arrays were performed to determine the repertoire of genes that change following knock-down of DANCR.

first: Chi

last: Dang


title: Differentially expressed mRNAs in bladder cancer stem cells

status: Public on Dec 06 2016

city: Beijing

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Using the highly sensitive lncRNA array (Arraystar human lncRNA microarray), we screened the lncRNAs and mRNA abundant in bladder cancer stem cells sorted from three bladder cancer cell lines, compared to the bladder cancer cells. And the functions of lncRNAs in bladder cancer stem cells were analyzed along the following research.

overall_design: Bladder cancer stem cells sorted from 3 bladder cancer cell lines were individually profiled the lncRNA and mRNA expression

first: Guoqing

last: Wang


title: Islet Inflammation and Ductal Proliferation, a Link to Pancreattisin Type-2 Diabetes?

status: Public on Dec 02 2016

city: Los Angeles

first: Alexandra

last: Butler

address: 900 Veteran Ave

department: Medicine/Endocrinology

institute: UCLA

summary: Pancreatitis is more frequent in type 2 diabetes (T2DM) although the underlying cause is unknown. We tested the hypothesis that ongoing beta-cell stress and apoptosis in T2DM induces ductal tree proliferation, particularly the pancreatic duct gland (PDG) compartment, and thus potentially obstructs exocrine outflow. PDG replication was increased two-fold in human pancreas from individuals with T2DM (P<0.01), and was associated with increased pancreatic intraepithelial neoplasia (PanINs) (P<0.05), lesions associated with pancreatic inflammation and with the potential to obstruct pancreatic outflow. Increased PDG replication (p<0.05) in the prediabetic HIP rat model of T2DM was concordant with increased beta-cell stress but preceding metabolic derangement. Moreover, the most abundantly expressed chemokines released by the islets in response to beta-cell stress in T2DM, CXCL1, 4 and 10, induced proliferation in human pancreatic ductal epithelium (p<0.05). Also, the diabetes medications that are reported as potential modifiers for the risk of pancreatitis in T2DM modulated PDG proliferation accordingly. We conclude that chronic stimulation and proliferation of the PDG compartment of the pancreas in response to islet inflammation in T2DM is a novel mechanism that serves as a link to the increased risk for pancreatitis in T2DM and may potentially be modified by currently available diabetes therapy.

overall_design: HIP rats vs nondiabetic WT rats ( 4 samples total [2 HIP and 2 WT], so 2 replicates)

first: Belinda

last: Schludi

first: Aleksey

last: Matveyenko

first: David

last: Kirakossian

last: Dawson

first: Sarah

last: Dry

first: Peter

middle: E


title: Effect of vitrification on the microRNA transcriptome in mouse blastocysts

status: Public on Dec 31 2016

first: xueming

last: zhao

address: No.2 Yuanmingyuanwestern road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: Vitrification is commonly used in the cryopreservation of mammalian blastocysts to overcome the temporal and spatial limitations of embryo transfer. Previous studies have shown that the implantation ability of vitrified blastocysts is impaired and that microRNAs (miRNAs) regulate the critical gene for embryo implantation. However, little information is available about the effect of vitrification on the miRNA transcriptome in blastocysts, which partially explains the impaired implantation ability of vitrified blastocysts. In the present study, the miRNA transcriptomes in fresh and vitrified mouse blastocysts were analyzed by microRNA Taqman assay based method, and the results were validated using quantitative real-time PCR (qRT-PCR). Then, the differentially expressed miRNAs were assessed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Overall, 760 known mouse miRNAs were detected in the vitrified and fresh mouse blastocysts. Of these, the expression levels of five miRNAs differed significantly: in the vitrified blastocysts, four miRNAs (mmu-miR-199a-5p, mmu-miR-329-3p, mmu-miR-136-5p and mmu-miR-16-1-3p) were upregulated, and one (mmu-miR-212-3p) was downregulated. The expression levels of all miRNAs measured by the microRNA Taqman assay based method and qRT-PCR were consistent. The four upregulated miRNAs were predicted to regulate 877 candidate target genes, and the downregulated miRNA was predicted to regulate 231 genes. The biological analysis further showed that the differentially expressed miRNAs mainly regulated the implantation of embryos. In conclusion, the results of our study showed that vitrification significantly altered the miRNA transcriptome in mouse blastocysts, which may decrease the implantation potential of vitrified blastocysts.

overall_design: The TaqMan® Array Rodent MicroRNA A+B Cards Set v3.0 with an Applied Biosystems 7900 HT Fast Real-time PCR system was utilized to detect the miRNA transcriptome in fresh and vitrified mouse blastocysts.6 samples were analyzed, including 3 vitrification samples and 3 fresh samples.

first: Xueming

last: Zhao


title: caArray_staud-00261: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

institute: NCI

summary: The survival of patients with diffuse large-B-cell lymphoma after chemotherapy is influenced by molecular features of the tumors. We used the gene-expression profiles of these lymphomas to develop a molecular predictor of survival. METHODS: Biopsy samples of diffuse large-B-cell lymphoma from 240 patients were examined for gene expression with the use of DNA microarrays and analyzed for genomic abnormalities. Subgroups with distinctive gene-expression profiles were defined on the basis of hierarchical clustering. A molecular predictor of risk was constructed with the use of genes with expression patterns that were associated with survival in a preliminary group of 160 patients and was then tested in a validation group of 80 patients. The accuracy of this predictor was compared with that of the international prognostic index. RESULTS: Three gene-expression subgroups--germinal-center B-cell-like, activated B-cell-like, and type 3 diffuse large-B-cell lymphoma--were identified. Two common oncogenic events in diffuse large-B-cell lymphoma, bcl-2 translocation and c-rel amplification, were detected only in the germinal-center B-cell-like subgroup. Patients in this subgroup had the highest five-year survival rate. To identify other molecular determinants of outcome, we searched for individual genes with expression patterns that correlated with survival in the preliminary group of patients. Most of these genes fell within four gene-expression signatures characteristic of germinal-center B cells, proliferating cells, reactive stromal and immune cells in the lymph node, or major-histocompatibility-complex class II complex. We used 17 genes to construct a predictor of overall survival after chemotherapy. This gene-based predictor and the international prognostic index were independent prognostic indicators.

overall_design:
staud-00261
Assay Type: Gene Expression
Provider: GenePix
Organism: Homo sapiens (ncbitax)


title: Plasma microRNA biomarker detection for mild cognitive impairment using differential correlation analysis

status: Public on Dec 10 2016

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

country: Japan

institute: National Center for Geriatrics and Gerotology

summary: Background: Mild cognitive impairment (MCI) is an intermediate state between normal aging, and Alzheimer’s disease, and other dementias. Early detection of dementia, and MCI, is a crucial issue in terms of secondary prevention. Blood biomarker detection is a possible way for early detection of MCI. Although disease biomarkers are detected by, in general, using single molecular analysis such as t-test, another possible approach is based on interaction between molecules.  Results: Differential correlation analysis, which detects difference on correlation of two variables in case/control study, was carried out to the dataset with 745 microRNAs (miRNAs) from plasma samples of 30 age-matched controls and 23 MCI patients in Japan. The 20 pairs of miRNAs, which consist of 20 miRNAs, were selected as MCI markers. Two pairs of miRNAs (hsa-miR-191 and hsa-miR-101, and hsa-miR-103 and hsa-miR-222) out of 20 attained the highest area under the curve (AUC) value of 0.962 for MCI detection. Other two miRNA pairs that include hsa-miR-191 and hsa-miR-125b also attained high AUC value of ≥ 0.95. Pathway analysis was performed to the MCI markers for further understanding of biological implications. As a result, collapsed correlation on hsa-miR-191 and emerged correlation on hsa-miR-125b may have key role in MCI, and dementia progression.  Conclusion: Differential correlation analysis, a bioinformatics tool to elucidate complicated and interdependent biological systems behind diseases, detects effective MCI markers that cannot be found by single molecule analysis such as t-test.

overall_design: To detect plasma miRNA biomarker for MCI, the blood samples were collected from 30 age-matched controls (Normal, 12 males and 18 females, mean age of 70.4) and 23 MCI patients (11 males and 12 females, mean age of 72.8).Total RNA was extracted from plasma using the miRNeasy Mini Kit (Qiagen). Then, the miRCURY LNA™ Universal RT microRNA PCR System, Ready-to-Use Human panel I and panel II, V2. were performed to profile miRNAs differential expression in these plasma samples. Processed data were compared between control and MCI groups.

first: Mitsunori

last: Kayano

first: Sayuri

last: Higaki

first: Jun-ichi

last: Sato

first: Kenji

last: Matsumoto

first: Etsuro

last: Matsubara

first: Osamu

last: Takikawa

first: Shumpei

last: Niida


title: caArray_topal-00039: TCGA (GBM): MicroRNA  Analysis of TCGA GBM samples using Agilent MicroRNA array (UNC)

overall_design:
topal-00039
Assay Type: microRNA
Provider: Agilent
Array Designs: H-miRNA_8x15K
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain, NOT SPECIFIED
Material Types: Primary solid_tumor, organism_part, synthetic_RNA, organism_part, solid_tumor, total_RNA, Solid normal_tissue
Disease States: Untreated primary (de novo) GBM, Treated primary GBM, NOT SPECIFIED, GLIOBLASTOMA MULTIFORME, Untreated primary (De Nova) GBM


title: MicroRNA mir-34 provides robustness to environmental stress response in C. elegans

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

institute: University Medical Center Groningen

summary: Diverse stresses and aging result in changes in expression levels of microRNAs, suggesting a role for these posttrancriptional regulators of gene expression in stress modulation and longevity. Earlier studies demonstrated a central role for the miR-34 family  in promoting cell cycle arrest and cell death following stress in human cells. However, the biological significance of this response was unclear, because wildtype and miR-34 family knockouts tested under a variety of stress conditions showed no difference in cell survival in vitro or in vivo. Here, we addressed this question in C. elegans by analyzing the effect of different stress conditions on phenotype, transcriptome and mir-34 expression in animals deficient in or overexpressing mir-34. We showed that mir-34 upregulation is necessary for developmental arrest, correct morphogenesis, and adaptation to a lower metabolic state to protect animals against stress-related damages. Either deletion or overexpression of mir-34 lead to impaired stress response, which can largely be explained by perturbations in a DAF-16/FOXO target genes. We demonstrate that mir-34 expression is regulated by the insulin signaling pathway via a negative feedback loop between miR-34 and DAF-16/FOXO. We propose that mir-34 provides robustness to stress response programs by controlling noise in the DAF-16/FOXO-regulated gene network.

overall_design: Gene expression levels at different temperatures and in different genetic backgrounds (wild-type, mir-34 deletion or overxepression, daf2) in adult animals or in daures were measured. Three replicates were performed for most conditions.

first: Meltem

last: Isik


title: Expression profile of Parathyroid hormone-related protein (PTHrP) induced miRNAs during TGF-beta mediated chondrogenesis of marrow derived human mesenchymal stem cells

status: Public on Dec 01 2016

city: Goyang

first: Jong-Min

last: Lee

address: 814 Siksa-dong

department: College of Medicine

institute: Dongguk University

summary: A miRNA microarray was used to identify candidate miRNAs regulated by PTHrP treatment in chondrogenic hMSC differentiation. miRNA-expression patterns after PTHrP treatment for 1 week (CM-T-Pt-L1) or 3 weeks (CM-T-Pt-3) in chondrogenic culture were compared with reference levels obtained from cell pellets treated with TGF-β only (CM-T). Under identical chondrogenesis conditions (except for PTHrP treatment), miRNA-expression patterns were relatively unchanged when compared with the TGF-β-only control, which simplified the selection of candidate miRNAs. Microarray analysis revealed that only 4 miRNAs in CM-T-Pt-L1 cells and 7 miRNAs in CM-T-Pt-3 cells were differentially expressed following PTHrP treatment. Hsa-miR-590-5p and hsa-miR-892b were commonly down-regulated or up-regulated in both PTHrP-treated groups. Interestingly, hsa-miR-892b expression was not detected in the TGF-β-only control, while hsa-miR-877*, hsa-miR-1288, and hsa-miR-1305 were up-regulated. Therefore, PTHrP treatment induced hsa-miR-892b expression during TGF-β-mediated hMSC chondrogenesis. hsa-miR-892b expression in CM-T-Pt-L1 cells was 2.43-fold higher than that in CM-T-Pt-3 cells.

overall_design: PTHrP induced miRNA expression in human MSC was measured at 21 days of chondrogenic induction after exposure for last 1 week or all 3 weeks to dose of 100 ng/ml PTHrP.  Four independent experiments were performed depending on PTHrP-exposure times (0, 1, and 3 weeks) using two different donors for each experiment.

first: Gun-Il

last: Im


title: Human Parathyroid Gland: Normal vs. Adenoma

first: Nariman

last: Balenga

address: 655 W. Baltimore St, Room 10-010B

department: Surgery

institute: University of Maryland School of Medicine

summary:
Transcriptional profiling of genes expressed in normal parathyroid glands (Normal) and adenomatous parathyroid glands from patients with primary hyperparathyroidism (PHPT).
Stratagen Human Refernece RNA, pooled from 10 human cell lines, was used to identify genes, which are specifically expressed or suppressed in parathyroid tissue. Comparison between normal and tumor parathyroids shows genes that might be involved in hyperproliferation and PTH hypersecretion in tumors.

overall_design: 6 Normal parathyroid glands and 25 adenoma from PHPT patients.

first: John

last: Olson

first: Holly

last: Dressman


title: albumen vitreux vs albumen farineux-FUI GranoFlakes

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 4plex_maize_2015_02 - albumen vitreux vs albumen farineux - Delineation of the metabolic pathways involved in maize endosperm vitreousness. - Comparison of vitreous (outer) and floury (inner) endosperm from flint and dent maize inbred lines harvested at 15 and 20 day after pollination.

overall_design:
Delineation of the metabolic pathways involved in maize endosperm vitreousness.
8 dye-swap - null

first: ISABELLE

last: GAILLARD

first: Didier

last: MARION

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Overexpression of SSZ1 suppresses temperature sensitivity phenotype of yeasts indicating its novel function to maintain cellular robustness

city: Zhenjiang

first: Huang

last: Guoping

state: Jiangsu province

address: Xuefu Road 301#

department: Institute of Life Sciences

institute: Jiangsu University

summary: Ssz1p plays multifunctional roles in diverse cellular activities including forming a ribosome-associated complex to assist new protein synthesis and activating pleiotropic drug resistance (PDR) pathway. Here we report a novel function of SSZ1 to maintain cellular robustness when it is overexpressed. We found overexpression of SSZ1 can suppress the death phenotype of the double mutant Δire1Δscj1 and the temperature sensitivity (TS) phenotype of scj1-1Δire1. Microarray analyses showed that overexpression of SSZ1 induced up-regulation of the genes involved in the PDR pathway and the cell wall integrity (CWI) pathway, but not the unfolded protein response (UPR) pathway. However, overexpression of PDR1 and PDR5 cannot significantly suppress the TS phenotype of scj1-1Δire1, and overexpression of SSZ1 cannot up-regulate the gene expression of lacZ under the control of the unfolded protein response element in SSZ1OEΔire1 compared with that in Δire1. We infer that the suppression is not through the PDR pathway or through the UPR pathway. It may be through regulating downstream genes of the CWI pathway. Moreover, the peptide-binding domain of Ssz1p is necessary for its suppression of TS phenotype of scj1-1Δire1.

overall_design: Genes expression from early log phase of three strains, that is,  Δire1, SSZ1OEΔire1,  and  SSZ1OEΔire1Δscj1. RNA was prepared from independent duplicate or triplicate samples.

last: Davis