title: Cerebrospinal fluid microRNAs are potential biomarkers of temporal lobe epilepsy and status epilepticus

status: Public on Jun 23 2017

city: Dublin

first: David

last: Henshall

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Temporal lobe epilepsy (TLE) is the most common intractable form of epilepsy in adults and status epilepticus (SE) is the most severe form of seizure that can be non-convulsive and is then difficult to diagnose. Diagnosis of both conditions is principally based on clinical examination and history, often depending on EEG and imaging. A molecular biomarker of these two conditions would be transformational in supporting both diagnoses.Cerebrospinal fluid offers an alternative source of microRNA biomarkers with the advantage of being in closer contact with the target tissue and sites of pathology. The present study indicates cerebrospinal fluid may contain microRNA biomarkers of TLE and SE and offers insights into trafficking mechanisms of biofluid microRNAs that may further enhance diagnostic value.

overall_design: microRNA expression in the CSF of 15 patients with headache, 15 pateints with TLE and 15 pateints with SE was measured by TaqMan OpenArray Human MicroRNA Panel.

first: Rana

last: Raoof

first: Eva

last: Jimenez

first: Sebastian

last: Bauer

first: Felix

last: Rosenow

first: Hajo

last: Hamer

first: Müjgan

last: Dogan

first: Tessa

last: Huchtemann

first: Peter

last: Körtvélyessy

first: Michael

last: Farrell

first: Donncha

last: O'Brien

first: Catherine

last: Mooney


title: Promoter context-specific positive and negative transcriptional regulation of Glucocorticoid Receptor target genes by coregulator GLP.

status: Public on Jun 13 2017

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

country: USA

institute: University of Southern California

summary:
A549 lung cancer cells were not infected (NI), transfected by plasmids containing shGLP (sequence targeting GLP gene) or shNS (non-specific sequence).
These cells were treated with dex to identify subsets of genes regulated by dex (hormone) and GLP (EHMT1). NI and shNS data were submitted on the GSE35962.

overall_design: Cells (NI/shNS/shGLP) were treated with 100nM dex for 24h and total RNA was extracted to identiy differentially expressed genes.

first: M

last: Stallcup

first: D

first: C

last: Poulard

last: Bittencourt


title: Identification of differentially expressed genes and pathways for myofiber characteristics in soleus and extensor digitorum longus muscles between chicken breeds differing in meat quality

status: Public on Jun 16 2017

city: Yangzhou

first: Jingting

last: Shu

address: Cangjie Road 58#

country: China

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

summary: In the modern chicken industry, fast-growing broilers have undergone strong artificial selection for muscle growth, which has led to remarkable phenotypic variations compared with slow-growing chickens. However, the molecular mechanism underlying these phenotypes differences remains unknown. In this study, a systematic identification of candidate genes and new pathways related to myofiber development and composition in chicken Soleus muscle has been made using gene expression profiles of two distinct breeds: Qingyuan partridge (QY), a slow-growing Chinese breed possessing high meat quality and Cobb 500 (CB), a commercial fast-growing broiler line. Agilent cDNA microarray analyses were conducted to determine gene expression profiles of soleus and extensor digitorum longus muscle sampled at sexual maturity age of QY (112 d) and CB (42 d).

overall_design: two chicken breeds, two muscle types, three repeats

first: J

last: Song

first: H

last: Li

first: Y

last: Shan

first: W

last: Xu

last: Zhu

first: Z

last: Tao


title: Comparative transcriptome analysis of Brucella suis 1330 wild-type and DregA mutant

status: Public on Jun 26 2017

city: Montpellier

first: Veronique

middle: Jubier

last: Maurin

address: 1919 route de Mende

country: France

institute: CNRS

summary: Investigation of whole genome gene expression level changes in a B. suis 1330 regA mutant, compared to the wild-type strain. The two-component system RegBA of Brucella suis plays a central role in the control of respiratory systems adapted to oxygen deficiency. The mutant strain  is affected in long-term persistence in  vitro (this study) and in chronic infection in vivo (Abdou, E et al. 2013, Infect.Immun. 81: 2053-61). Using an original “in vitro model of persistence”, we compare large-scale transcriptome of the wild-type and ∆regA strains to identify the RegA-regulon potentially involved in the set-up of the persistence state.

overall_design: six microarrays were hybridized with (ds)cDNAs prepared from total RNA recovered from three independent cultures of the wild-type and DregA B. suis strains. Each array measures the expression level of 3,271 genes from B. suis 1330 with nineteen 60-mer probes per gene, in three replicates.

first: Elias

last: Abdou

first: Véronique

last: Jubier-Maurin

first: Stephan

last: Kohler

last: Pantesco

first: Alessandra

last: Occhialini-Cantet


title: microRNAs regulated by aldosterone/salt in rat left ventricles in vivo

status: Public on Jun 15 2017

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

institute: University of Mississippi Medical Center

summary:
The overall objective of the study was to screen for microRNAs regulated by aldosterone and salt in rat left ventricles .
Primary aldosteronism is characterized by excess aldosterone (ALDO) secretion independent of the renin-angiotensin system and accounts for ~10% of hypertensive patients. Excess ALDO, inappropriate for the salt intake status, causes cardiac hypertrophy, inflammation, fibrosis and hypertension. The molecular mechanisms that trigger the onset and progression of ALDO-mediated cardiac injury are poorly understood. MicroRNAs (miRNAs) are endogenous, small, non-coding RNAs that have been implicated in diverse cardiac pathologies, yet very little is known about their regulation and role in ALDO-mediated cardiac injury.   To elucidate the regulation of miRNAs in ALDO-mediated cardiac injury, we performed a time-series analysis of left ventricle (LV) miRNA expression. Uninephrectomized male Sprague Dawley rats were treated with ALDO (0.75 µg/h) infusion and SALT (1.0% NaCl/0.3% KCl) in the drinking water for up to 8 weeks. ALDO/SALT time-dependently modulated the expression of multiple miRNAs in the LV. miR-21 was the most upregulated miRNA after 2 weeks of treatment and remained elevated until the end of the study.  To elucidate the role of miR-21 in ALDO/SALT-mediated cardiac injury, miR-21 was downregulated using antagomirs in ALDO/SALT-treated rats. miR-21 downregulation exacerbated ALDO/SALT-mediated cardiac hypertrophy, fibrosis and inflammation markers gene expression, interstitial and perivascular fibrosis, OH-proline content and cardiac dysfunction.   These results suggest that ALDO/SALT-mediated cardiac miR-21 upregulation may be a compensatory mechanism that mitigates ALDO/SALT-mediated cardiac deleterious effects. We speculate that miR-21 supplementation would have beneficial effects in reverting or mitigating cardiac injury and dysfunction in patients with primary aldosteronism.

overall_design: Eight-week old male Sprague Dawley rats (Harlan Laboratories) were uninephrectomized and the next day randomly assigned to Control or Aldosterone/Salt (ALDO/SALT) experimental groups. ALDO (0.75 µg/h, Steraloids) was administered in PEG 300 (vehicle, Fluka) by subcutaneously implanted osmotic minipumps (Alzet 2004, Durect). SALT (1.0 % NaCl) was administered in the drinking fluid instead of tap water. ALDO-treated animals were supplemented with 0.3 % KCl in the drinking fluid to avoid hypokalemia. Animals were treated for 2, 7, 14, 28 or 56 days. Three animals per group (treatment, time) were processed individually as biological replicates. At the indicated time points, the left ventricle was excised, total RNA extracted and processed for microRNAs microarrays.

first: Jana

middle: P

last: Ball

first: Maryam

last: Syed

first: Rodrigo

middle: O

last: Maranon

first: Michael

middle: E

last: Hall

first: Roshan

last: KC

first: Jane

middle: F

last: Reckelhoff

first: Licy

middle: L

last: Yanes Cardozo

middle: G


title: Establishment and characterization of a new murine cell line of sarcomatoid hepatocellular carcinoma

city: Kaohsiung

first: Chih-Chung

last: Lai

address: 100,Shih-Chuan 1st Road

country: Taiwan

institute: Kaohsiung Medical University

summary:
Sarcomatoid HCC is a rare and highly malignant type of HCC. A mouse cell line, Ymac-1 was established as a cell model of sarcomatoid HCC. The finding of this study could be useful for developing biomarkers and therapeutic modalities for sarcomatoid HCC.
We used microarrays to delineate the mechnism of action of sarcomatoid HCC in normal mice liver, Gnmt-/- mice liver tumor, and Ymac-1 cell.

overall_design: Tissue and Cells were harvested for RNA extraction and hybridization on Phalanx Microarray. Differentially expression genes between  normal mice liver, Gnmt-/- mice liver tumor, and Ymac-1 cells were identified for functional study.

first: Chia-Hung

last: Yen

first: YiMing

last: Chen


title: Gene expression profiles after injection of zebrafish with NV (non virion) recombinant protein from Viral Hemorrhagic Septicemia Virus (VHSV)

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary:
NV is a viral protein  only present in the genus Novirhabdovirus (fam Rhabdoviridae), its function is not well characterized yet. In this study we try to shed some light in the biological function of this viral protein in the zebrafish.
We describe here  transcripts induced after injection of adult zebrafish with NV recombinant protein of VHSV. Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in zebrafish internal organs (pooled spleen and head kidney).

overall_design: 6 zebrafish were divided in two groups, 3 per group . First group  was injected with recombinant NV protein (tag:polyhistidine tail) and second group was used as a control and injected with polyhistidine protein.  Two days after injection, zebrafish were sacrified and head kidney and spleen of each individual were extracted and pooled between this group. This experiment was repeated three times to get four biological replicates. RNA was  extracted and submitted to quality controls. Lately, RNA was labelled with Cy3 and used in the Agilent  Danio rerio custom  array zfin 2.2 ID: 47562.

first: Blanca

last: Chinchilla

first: Eduardo

last: Gómez-Casado


title: Identification of microRNA biomarkers in the blood of breast cancer patients based on microRNA profiling

status: Public on Jun 28 2017

city: Jinan

first: Ya-Wen

last: Wang

address: Wen Hua Xi Road 107

institute: Shandong University

summary: Accumulating evidence indicates that human circulating microRNAs (miRNAs) could serve as diagnostic and prognostic biomarkers in various cancers. We aimed to explore novel miRNA biomarkers in the blood of breast cancer patients based on miRNA profiling. A miRCURY™ LNA Array was used to identify differentially altered miRNAs in the whole blood of breast cancer patients (n = 6) and healthy controls (n = 6). Levels of candidate miRNAs were quantified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in whole blood specimens of 15 breast cancer patients and 13 age-matched healthy control individuals. The miRWalk database was used to predict miRNA targets and the DAVID tool was used to identify significant enrichment pathways. A total of 171 differentially expressed miRNAs were identified by microarray, including 169 up-regulated and 2 down-regulated miRNAs in breast cancer. Five upregulated miRNAs (miR-30b-5p, miR-96-5p, miR-182-5p, miR-374b-5p, and miR-942-5p) were confirmed by qRT-PCR. The areas under the receiver operating characteristic curve of miR-30b-5p, miR-96-5p, miR-182-5p, miR-374b-5p, and miR-942-5p were 0.9333, 0.7692, 0.7590, 0.8256, and 0.8128, respectively. A total of 855 genes were predicted to be targeted by the five miRNAs, and the one cut domain family member 2 gene (ONECUT2) was a shared target of the five miRNAs. Analysis of publicly available data revealed that these dysregulated miRNAs and target genes were associated with the survival of breast cancer patients. Furthermore, the five miRNAs were significantly enriched in numerous cancer-related pathways, including “MicroRNAs in cancer”, “Pathways in cancer”, “FoxO signaling pathway”, “Ras signaling pathway”, “Rap1 signaling pathway”, “MAPK signaling pathway”, and “PI3K-Akt signaling pathway”. Our data support the potential of the five identified miRNAs as novel biomarkers for the detection of breast cancer, and indicate that they may be involved in breast cancer development and progression.

overall_design: miRNA profiling in blood samples were analyzed by the 7th generation of miRCURYTM LNA Array (v.18.0, Exiqon), as previously described. It contains 3100 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 18.0, as well as all viral microRNAs related to these species.

first: Kai

last: Zhang


title: Identification of critical gene regions in chronic lymphocytic leukemia using high-resolution array comparative genomic hybridization

status: Public on Jun 14 2017

city: Christchurch

first: Christine

last: Morris

state: Canterbury

address: 2 Riccarton Ave

department: Pathology

country: New Zealand

institute: University of Otago Christchurch

type: Genome variation profiling by genome tiling array

summary: With an objective to identify novel copy number alterations (CNAs) critical to CLL pathogenesis, we performed array comparative genomic hybridization (array CGH) on genomic DNA extracted from purified leukemic cells of 51 CLL patients. We used the 1.4 Mb HumArray platform, and analyzed data using a combination of three different statistical algorithms and in full awareness of the copy number variations (CNVs) found in normal populations. Use of reference DNA extracted from matched patient neutrophils in four cases also assisted a more comprehensive interpretation of constitutional versus CLL-specific copy number alterations. A total of 108 clones showed alterations in >10% of the cases. Of these, 25 clones corresponded to known recurrently acquired CNAs for CLL, representing +12 in 8 cases (16%) and del(13)(q14) in 26 cases (51%). For the remaining 83 clones, frequent deletions corresponded to loci within cytobands 17q12 (71% of CLL cases), 9q32 (55%), 8p23 (47%) and 2q21 (33%), and frequent gains corresponded to loci within cytobands 18q22.3 (51%), 20p12 (33%) and 15q13 (31%), most of which have been reported in normal population cohorts.   We further analysed associations between CNV status across the 108  frequently affected clones and CD38 expression status.  Consistent with previous findings, loss of 13q14 (represented in clone RPI-269F22) and gain of chromosome 12 (clones RP11-64J22, RMC12P001 and RP11-282G15) were associated with low and high CD38 expression, respectively.  We also found that loss within the beta-defensin (DEFB) locus at 8p23, and gains across clones CTB-120N12 (17q25) and RP11-118K20 (13q31.1) were associated with the poor prognostic CD38+ subgroup (p<0.05).  Further studies are needed to assess biological relevance of genes located within these regions and prognostic outcomes in CLL.

overall_design:
At the time this study was initiated, array CGH was a relatively new technique that was still under development. In order to establish robust and reliable array CGH protocols, extensive optimization was carried out. Different array platforms (cDNA and BAC arrays) and hybridization protocols were compared, and diverse methods for statistical analysis were explored. After optimization, the University of California San Francisco (UCSF) 2.5K BAC arrays and BlueFuse software for Microarrays were used to analyse CNVs in 51 CLL DNA samples. Genomic DNA was extracted either directly from peripheral blood mononuclear cells (PBMCs), or after further purification of CD19+ B-lymphocytes using a magnetic bead system. Different data analysis approaches that provided varying degrees of sensitivity and specificity were applied for more effective detection of CNVs. Identification of CLL-specific CNVs was maximized by performing array CGH using a single female reference DNA across all experiments, and by using reference DNA extracted from matched patient neutrophils in four cases.

Patients were recruited into the study from a cohort of consenting patients referred for routine assessment to the Clinical Haematology Department at Christchurch Hospital, New Zealand.  Diagnosis of CLL follows clinical assessment for commonly associated symptoms including physical weakness, enlarged spleen or lymph nodes, loss of weight, low immunological tolerance and night sweats.   Follow-up pathological assessment typically includes a repertoire of blood tests (white blood cell count, platelet count, erythrocyte sedimentation rate, blood differential, cytochemistry), a bone marrow aspirate and sometimes lymph node biopsy assessment. At the time of this study, flow cytometry analysis of whole blood collected in either ethylenediaminetetraacetic acid (EDTA) or heparin tubes typically included the following antigens: CD5, CD19, CD20, CD22, CD23, CD11a, CD38, and membrane surface immunoglobulin lambda and kappa light chains. For CLL cases where flow cytometry results were not available at the time of sample collection, flow cytometry was performed to determine leukaemic cell purity.  Conventional G-banded karyotype information was not available for patients recruited to this study.

This study was approved by the New Zealand Upper South Regional Ethics Committee.

first: So-Young

last: Moon

first: Ursula

middle: R

last: Jewell

first: Judith

last: McKenzie

first: Peter

middle: S

last: Ganly


title: Microarray using TNG67, pUbi:AtFD, pHd3a:AtFD, pUbi:AtFDP, pHd3a:AtFDP and pUbi:AtFD+pUbi:AtFDP samples

city: Tainan

first: Seonghoe

last: Jang

state: Tainan

address: No.59, Siraya Blvd. Xinshi Dist.

institute: Academia Sinica

summary: We analyzed transcripts using microarray hybridization between whole parts above the ground samples of  TNG67, pUbi:AtFD, pHd3a:AtFD, pUbi:AtFDP, pHd3a:AtFDP and pUbi:AtFD+pUbi:AtFDP.

overall_design: We used 22k probed rice microarray from Phalanx Biotech.

first: Hsing-Yi

last: Li

first: Lynda

last: Kuo


title: Circular RNA profile of acute myeloid leukemia

first: Wei

state: Shandong

address: #44,West Wenhua Road

summary: Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs, which drew little attention in the past. Recently, limited data showed their promising future to act as biomarkers in human cancer, but the characteristics and functions remain largely unknown in hematopoietic malignancies, especially in leukemia. In this study, with the help of circRNA microarray, we demonstrated the expression profile of circRNAs in acute myeloid leukemia (AML) patients, and identified a large number of circRNAs possibly expressed in a leukemia specific manner. We also described a circRNA signature related to AML risk-status based on the bioinformatics prediction.

overall_design: 4 healthy controls and 6 AML patients (3 as better-risk AML and 3 as poor-risk AML) are selected for circular RNA microarray.

first: Daoxin

last: Ma


title: Real-time quantitative PCR analysis of WT and NOD1 knockout zebrafish (PI3K-AKT)

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Zebrafish larvae from WT and NOD1-1IS-/- collected at 10 dpf were used for Zebrafish PI3K-AKT Signaling Pathway RT2 Profiler PCR Array.

overall_design: qPCR gene expression profiling. Larvae from WT and NOD1-deficient zebrafish were collected at 10 dpf.Three biological replicates were performed for the WT and NOD1-deficient zebrafish. 200~250 larvae per replicate were pooled and used for gene expression analysis.

first: Ming

first: Yi

middle: W

last: Hu


title: Global transcriptome profiling identifies KLF15 and SLC25A10 as regulators of adipocytes insulin sensitivity in obese women [WAT]

status: Public on Jun 29 2017

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

summary:
The aim of this study was to identify new genes controlling insulin sensitivity in adipocytes from obese women with either insulin-resistant (OIR) or -sensitive (OIS) adipocytes.
432 genes were differentially expressed between the OIR and OIS group (FDR <5%). These genes are enriched in pathways related to glucose and amino acid metabolism, cellular respiration, and insulin signaling, and include SLC2A4, AKT2, as well as enzymes in the mitochondria respiratory chain. Two IR-associated genes, KLF15 and SLC25A10, were selected for functional evaluation.

overall_design: Insulin sensitivity was determined by measuring lipogenesis in isolated adipocytes from abdominal subcutaneous white adipose tissue (WAT). We performed microarray-based transcriptome profiling on subcutaneous WAT specimen from 9 lean, 21 OIS and 18 obese OIR women. Patients were examined in the morning after 12 hrs fasting. An abdominal subcutaneous WAT biopsy was obtained by needle aspiration. From WAT specimen we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.1 ST Arrays (Affymetrix Inc., Santa Clara, CA), and then washed, stained and scanned the slides using standardised protocols (Affymetrix Inc.). Significance analysis of microarrays (SAM) was used to compare the difference in gene expression between groups.


title: Physiological response of S. cerevisiae excess cysteine or cystine

city: Mohali

first: Anand

middle: K

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli PO

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education and Research, Mohali

summary: Excess cysteine (and cystine) is known to be toxic in organisms. Due to the absence of cysteine dioxygenase (involved in degradation of excess cysteine in humans and pathogenic fungi) in non pathogenic fungi such as S. cerevisiae, mechanism of cysteine (and cystine) tolerance is yet to be addressed.

overall_design: In order to understand the physiological (transcriptional) response to excess cytosolic cysteine or cystine, S. cerevisiae (MET15 yct1Δ) cells constitutively expressing either cysteine (YCT1) or cystine specific transporter (C. glabrata CgCYN1) were exposed to excess cysteine or cystine (500µM) respectively for 5hrs and analysed with repect to the untreated respective controls  for the transcriptional response.

last: Bachhawat

first: Anup

middle: A

last: Deshpande


title: Multimodal Regulation Orchestrates Normal and Complex Disease States in the Retina

city: Boston

first: Neena

middle: B

last: Haider

state: Massachusetts

address: 20 Staniford Steret

department: Ophthalmology

institute: Schepens Eye Research Institute/MEE/Harvard Medical School

summary: Murine comparison of miRNA expression by array profiling comparing B6 and RD7 across four timepoints

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

overall_design: Comparison of B6 versus RD7 miRNA expression across four timepoints utilizing pooled RNA; timepoints analyzed are E18, P6, P14, and AD (adult)

first: James

last: Reinecke

first: Austin

last: Jelcick


title: Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

institute: CHRU Montpellier

summary:
Background: MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. miRNAs have been involved in fine-tuning critical biological processes, but the potential contribution of miRNAs to human plasma cell differentiation (PCD) has remained largely unknown.
Methods: We analyzed the expression profile of miRNAs and mRNAs during PCD. We developed a method and R package, to infer candidate miRNA-mRNA target interactions that could be active and functional in PCD. Finally, we experimentally validated biologically relevant miRNA – mRNA networks.
Results: Our results reveal 63 miRNAs with significant temporal changes in their expression during normal PCD. We derived a high-confidence network of 295 target relationships comprising 47 miRNAs and 141 targets. These relationships include new examples of miRNAs (miR-30, miR-106b and miR-16) that appear to coordinately regulate multiple members of critical pathways associated with PCD, including IRF4/PRDM1 axis, TGF-b pathway, autophagy, ZBTB4/EZH2 axis and cell cycle. Consistent with this, we have experimentally validated a role for the miRNA-30b/c/d-mediated regulation of key PCD factors (IRF4, PRDM1, ELL2 and ARID3A), which expression was altered significantly upon transfection of pre-miRNA-30 or anti-miR-30 oligunucleotides. Furthermore, we found that 24 PCD stage-specific miRNAs are aberrantly overexpressed in multiple myeloma (MM) tumor cells compared to their normal counterpart and/or are associated with high risk myeloma, suggesting that MM cells frequently acquired expression changes in miRNAs already undergoing dynamic expression modulation during normal PCD.
Conclusions: Our comprehensive analysis of normal PCD miRNome identifies candidate novel key miRNAs regulating networks of significance for normal PCD and malignant plasma cell biology.

overall_design: Global miRNA expression profiling was carried out for in vitro human plasma cell differentiation cell subpopulations, including memory B cells, preplasmablasts, plasmablasts and plasma cells.

first: Alboukadel

last: Kassambara

first: Michel

last: Jourdan

first: Angélique

last: Bruyer

first: Nicolas

last: Robert

first: Veronique

last: Pantesco

first: Olivier

last: Elemento

first: Bernard

last: Klein

first: Jérôme


title: Molecular mechanisms of pulmonary response progression in crystalline silica exposed rats

status: Public on Jun 20 2017

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

institute: National Institute for Occupational Safety and Health

summary: The capability to detect target organ toxicity as well as to determine the molecular mechanisms underlying such toxicity by employing surrogate biospecimens that can be obtained by a non-invasive or minimally invasive procedure has significant advantage in occupational toxicology. Pulmonary toxicity and global gene expression profile in the lungs, peripheral blood and bronchoalveolar lavage (BAL) cells were determined in rats at 44-weeks following pulmonary exposure to crystalline silica (15 mg/m3, 6-hours/day, 5 days). A significant elevation in lactate dehydrogenase activity and albumin content observed in the BAL fluid suggested the induction of pulmonary toxicity in the silica exposed rats. Similarly, the observation of histological alterations, mainly type II pneumocyte hyperplasia and fibrosis, in the lungs further confirmed silica-induced pulmonary toxicity in the rats. A significant increase in the number of neutrophils and elevated monocyte chemotactic protein 1 level in the BAL fluids suggested silica-induced pulmonary inflammation in the rats. Determination of global gene expression profile in the lungs, BAL cells, and peripheral blood of the silica exposed rats identified 144, 236, and 51 significantly differentially expressed genes (SDEGs), respectively, compared with the corresponding control samples. Bioinformatics analysis of the SDEGs demonstrated a remarkable similarity in the biological functions, molecular networks and canonical pathways that were significantly affected by silica exposure in the lungs, BAL cells and blood of the rats. Induction of inflammation was identified, based on the bioinformatics analysis of the significantly differentially expressed genes in the lungs, blood and BAL cells, as the major molecular mechanism underlying the silica-induced pulmonary toxicity. The findings of our study demonstrated the potential application of global gene expression profiling of peripheral blood and BAL cells as a valuable minimally invasive approach to study silica-induced pulmonary toxicity in rats.

overall_design:
Pulmonary toxicity and global gene expression profile in the lungs, peripheral blood and bronchoalveolar lavage (BAL) cells were determined in rats at 44-weeks following pulmonary exposure to crystalline silica.

LUNG:  12 samples were analyzed in this experiment. The RNA from rat lung samples was isolated for gene expression studies. Rats (6) were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days) and air (6). Lung gene expression profiling was performed using RNA isolated from rat lung samples, 6 for silica exposed and 6 for air exposed controls at 44 weeks post-exposure time period.

BLOOD:  12 samples were analyzed in this experiment. The RNA from rat blood samples was isolated for gene expression studies. Rats (6) were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days) and air (6). Blood gene expression profiling was performed using rat blood samples, 6 for silica exposed and 6 for air exposed controls at 44 weeks post-exposure time period.

BALF:  12 samples were analyzed in this experiment. The RNA from rat brancheoalveolar lavage fluid (BALF) cells was isolated for gene expression studies. Rats (6) were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days) and air (6). Gene expression profiling of BALF cells was performed using rat BALF cells samples, 6 for silica exposed and 6 for air exposed controls at 44 weeks post-exposure time period.

first: Christina

last: Umbright

first: Jenny

last: Roberts

first: Shih-Houng

last: Young

first: Diana

last: Richardson

first: Walter

last: McKinney

first: Bean

last: Chen

first: David

last: Frazer

first: Shengqiao

last: Li

first: Michael

last: Kashon

first: Pius

last: Joseph


title: Transcriptomic analysis of liver in sex-linked Dwarf and wild type chickens

city: Jouy en Josas

first: Tatiana

last: Zerjal

address: bat 211

department: Animal Genetics

institute: INRA

summary: The sex-linked Dwarf (SLD) recessive mutation is characterized by a significant reduction of body size in hemizygous females (30%) and homozygous males (40%). The SLD chickens of the Leghorn line are affected by a Growth Hormone (GH) resistance condition due to a missense mutation at the Growth Hormone Receptor (GHR) gene causing a loss of function of the GHR. The sex-linked recessive dwarf mutation has large commercial use in maternal lines of the broiler poultry industry since these hens require less food and less housing space. The SLD chickens are also an interesting model for investigating complex traits such as energy expenditure and heat resistance for which the SLD chickens differ compared to normal size ones. In this study we performed a whole genome microarray expression profiling of liver using a 8x60K custom Agilent microarray. In total we analyzed 24 SLD and 24 wild type birds of 12 weeks of age obtained by crossing a heterozygous “dw” Leghorn cock with 12 females of an inbred Leghorn line to obtain wild type and dwarf sib and half-sib hens. The aim of the study was the fine identification of GH-inducible genes, and the characterization of the GH dependent signalling pathways.

overall_design: A population of Leghorn hens was created by crossing a heterozygote cock Dw/dw with 12 normal Leghorn females to obtain normal (Dw/-)and dwarf (dw/-) sisters and half sisters. In total we analyzed  the liver trascriptomic profile from 24 SLD and 24 wild type birds at 12 weeks of age (Wks).

first: Florence

last: Jaffrezic


title: Gene expression profiles in leaves of rice plants treated with plant-activators in field

city: Nasushiobara

first: Ryo

last: Okada

state: Tochigi

address: 768 Senbonmatsu

department: Forage Crop Research Division

country: Japan

institute: NARO Institute of Livestock and Grassland Science

summary: Plant-activator is known as a chemical inducer to activate disease resistances in plants without direct antibacterial activities. To identify plant-activator responsive genes, we analyzed temporal expression changes of the genes when treated with some plant-activators (e.g., isotianil and probenazole) in Japonica rice cv. Nipponbare in a field at Tsukuba in Japan.

overall_design: The submitted samples were field transcriptome data in rice leaves obtained from chemical treatment experiments. In a paddy field experiment, leaf samples were harvested before treatments (0 day) and in 1, 3, 7, 14 and 30 days after treatments, respectively. Leaf samples from plants transplanted in containers placed in the field were harvested in 1 and 3 days after treatments, respectively.

first: Takeshi

last: Izawa


title: Drawing links from transcriptome to metabolites: the evolution of aroma in the ripening berry of Moscato bianco (Vitis vinifera L.)

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

summary: Flavor and aroma play a major role in the perceived quality of grapes and wines. Among the most important compounds determining the oenological quality are monoterpenes. They confer typical floral notes to ‘Muscat’ varieties and, to a lesser extent, to other aromatic varieties. In recent years an increasing number of studies on the biosynthesis of terpenes in grape led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are not known. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries. In particular, gas chromatography-mass spectrometry analysis of free and bound terpenoid compounds was combined with microarray analysis (14,562 probes) in the skins of berries collected at five developmental stages from pre-véraison to over-ripening. Differentially expressed metabolites and probesets were identified in the pairwise comparison between time points by using the early stage as a reference. Metabolic and transcriptomic data were integrated through pairwise correlation and clustering approaches to discover genes linked with particular metabolites or groups of metabolites. Finally, the candidate transcripts were checked for co-localization with QTLs controlling the level of aromatic compounds. The results provided novel insights into the biological networks of grapevine secondary metabolism, both at the regulatory and catalytic levels, and yielded a collection of previously undescribed genes related to the accumulation of target metabolites.

overall_design:
Berry skin RNA from developmental points 2 to 5 was hybridized competitively with RNA from point 1 (pre-véraison), following the dye-swap experiment design (Churchill, 2002).
Developmental series.

first: Laura

last: Costantini

first: Juri

last: Battilana

first: Francesco

last: Emanuelli

first: Maddalena

last: Sordo

first: Massimiliano

last: Trenti

first: Marco

last: Moretto

first: Céline

last: Camps

first: Roberto

last: Larcher

first: Serge

last: Delrot

first: Maria

last: Grando


title: Real-time quantitative PCR analysis of WT and NOD1 knockout zebrafish (mTor)

first: M

last: Chang

summary: Zebrafish larvae from WT and NOD1-1IS-/- collected at 10 dpf were used for Zebrafish mTOR Signaling RT² Profiler™ PCR Array.

first: Ming

first: Yi

last: Hu


title: Study of the onset of puberty in the European sea bass

city: Barcelona

first: Mercedes

last: Blazquez

address: Passeig Maritim 37-49

institute: Institut de Ciencies del Mar (ICM-CSIC)

summary: Pubertal development in males starts with the onset of spermatogenesis that implies the division of primary spermatogonia and their subsequent entry into meiosis. Whole genome microarray expression profile was used as a means to explore the molecular basis underlying the onset of pubertal development in sea bass. The present study is aimed at the characterization of the expression of genes involved in the onset of spermatogenesis in the European sea bass. The study is focused on the first stages of the process including the appearance of spermatocytes and thus the first meiotic divisions. The transcriptomic study using a sea bass-specific microarray resulted in a number of genes differentially expressed during the onset of spermatogenesis. Among those, genes involved in cell-cycle progression, microtubule assembly during meiosis or retinoic acid signaling pathway indicating that they can be used as potential molecular markers for the onset of spermatogenesis in sea bass.

overall_design: Two different experimental groups (conditions) were used in the study. Condition 1 corresponded to testicular development stage I, whereas condition 2 represented testicular development stage II. Both conditions were compared to reveal differences in gene expression signatures related to the onset of spermatogenesis.

first: Silvia

last: Zanuy


title: miRNA expression profiling divides follicular dendritic cell sarcomas into two groups, related to fibroblasts and myopericytomas or Castleman's disease

status: Public on Jun 21 2017

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

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

summary:
miRNA expression profiling divides 31 follicular dendritic cell (FDC) sarcomas into two subgroups, one group closely related to microdissected FDCs from Castleman´s disease, the other group closely related to fibroblasts and myopericytomas.
miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

overall_design: miRNA expression profiling was performed of 31 FDC sarcomas and appropriate reactive samples

first: Sylvia

last: Hartmann


title: Epigenomic profiling in visceral white adipose tissue (VWAT) of offspring of mice exposed to late gestational intermittemt hypoxia

city: Chicago

first: Riyue

last: Bao

state: IL

address: 900 E 57 Street

department: Center for Research Informatics

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary: BACKGROUND: Epigenetic processes enable the environment to modulate gene transcription during fetal development, ultimately leading to stable phenotypic changes throughout the lifespan. There is a relatively high prevalence of altered sleep patterns during late gestation, especially obstructive sleep apnea (OSA). Intermittent hypoxia (IH) is a hallmark of OSA caused by periodic obstructions of the upper airway, which occurs along with sleep fragmentation (SF). We have previously shown that adult offspring of late gestational SF (LG-SF) mothers exhibited metabolic alterations via epigenomic alterations. The aims of this study were to investigate the effects of LG-IH on metabolic features in offspring and to determine the effects of LG-IH on the epigenome of visceral white adipose tissue (VWAT) in the offspring.  METHODS: Time-pregnant mice were exposed to LG-IH or room air (RA) paradigms conditions during the last 6 days of gestation (LG-IH and LG-RA groups, respectively). Offspring were weaned at 21 days and fed with normal chow diet. At 24 weeks, lipid profiles and metabolic parameters were assessed. We performed large scale DNA methylation analysis using MeDIP coupled to microarrays (MeDIP-chip) in offspring VWAT  (n=8 mice per group). Regions exhibiting differential DNA methylation (DMRs) between the groups were mapped to their corresponding genes and tested for potential overlaps with biological processes and pathways using Ingenuity Pathway Analysis.  RESULTS: We detected 1520 DMRs between the LG-IH and LG-RA groups (p< 0.0001, two-way ANOVA), associated with 693 genes. A significant portion of these genes (n=162) were also associated with previously identified DMRs in LG-SF offspring (p=1.35 x 10-97, hypergeometric test). Pathway analyses showed that genes affected by LG-IH and LG-SF, were mainly associated with molecular processes related to metabolic regulation and inflammatory response. In particular for LG-IH, biochemical pathways related to energy production through amino acid and fatty acid metabolism (i.e. methionine, choline and 2-oxobutanoate degradation pathways, methylmalonyl pathway, cysteine biosynthesis, etc.).   CONCLUSIONS: Our findings suggest a major role for epigenomic alterations in the metabolic dysfunction of adult offspring born to LG-IH and LH-SF mothers. Furthermore, whereas LG-IH may concomitantly act upon metabolic pathways also affected by LG-SF, LG-IH also affects biochemical processes underlying energy production in VWAT of the offspring.

overall_design: 16 mouse VWAT samples were analyzed by MeDIP coupled to microarray analysis: Offspring of mothers exposed to late-gestational intermittent hypoxia (n=8, LG-IH group) and offspring of mothers mouse exposed to room air sleep conditions (n=8, LG-SC group)

first: Rene

last: Cortese

first: Abdelnaby

last: Khalyfa

first: Ryue

first: Jorge

last: Andrade

first: David

last: Gozal


title: A Comparative Study of Global Transcriptomic Responses under Excess or deficient Phosphate (Pi) Regime reveals ethylene mediated signaling in Arabidopsis.

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Phosphorus is an essential macronutrient element, but some time causes problems if present in excess. Unlike the enormous molecular and morphophysiological information available in plants regarding phosphate (Pi) deficiency, little is known about the effect of excess Pi on plants, which is indeed essential for its remediation. Here, we have carried out a comparative study of plant molecular responses under excess Pi (20 mM) or without Pi (0 mM) at transcriptome level. The 1.25 mM treatment concentration of Pi used as a control to obtain differentially regulated genes under above mentioned Pi regimes. A novel whole-transcript expression array, i.e. Arabidopsis Gene 1.0 ST Array, was used to perform these experiments. The most distinctly regulated groups of genes represent modulation in ethylene mediated signaling, Fe deficiency response, and root development. We have also identified some defensin like genes, possessing a gibberellic acid regulated domain (GASA like) under excess Pi treatment. Overall, this study will not only help in dissecting the mechanism of plant responses under excess Pi but also provide the clues about the unknown genes involved in phosphorus homeostasis.

overall_design: A total of eighteen (18) samples with biological triplicates under two tissue types (root and shoot) and three phosphorus treatment conditions.  The treatment groups consist of: (1) root and shoot with 1.25 mM phosporus treatment (control); (2) root and shoot with 20mM phosphorus treatment; and (3) root and shoot without phosporus treatment (P-).

first: Devesh

last: Shukla

first: Claire

last: Rinehart

middle: C

first: Sabine

last: Waigel

first: Shivendra

middle: V

last: Sahi


title: TTF-1-regulated miR-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma [rt-pcr]

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Thyroid transcription factor-1 (TTF-1), also known as NKX2-1, plays a role as a lineage-survival oncogene in lung adenocarcinoma with double-edged sword characteristics. Although previous studies steadily accumulated evidence for roles of TTF-1 in the transcriptional regulation of protein-coding genes, very little is known about its regulatory relationship with miRNAs. In this study, we have identified miR-532-5p as a novel transcriptional target of TTF-1 by an integrative approach, which was designed to extract maximal information from expression profiles of both patient tumors in vivo and TTF-1-inducible cell lines in vitro. Consequently, we have found that miR-532-5p is directly regulated by TTF-1 through its binding to a genomic region 8 kb upstream of miR-532-5p, which appeared to impose transcriptional regulation independent of that of CLCN5, a protein-coding gene harboring miR-532-5p in its intron 3. Further, we have also identified KRAS and MKL2 as novel direct targets of miR-532-5p. Introduction of miR-532-5p mimics markedly induced apoptosis in KRAS-mutant as well as KRAS wildtype lung adenocarcinoma cell lines. Interestingly, miR-532-5p affected the MEK-ERK pathway signaling specifically in cell lines sensitive to siKRAS treatment, while the miR-532-5p-mediated effects were clearly phenocopied by repressing expression or inhibiting function of MKL2 regardless of KRAS mutation status. In summary, our findings demonstrate that miR-532-5p is as novel transcriptional target of TTF-1 and plays a tumor suppressive role by targeting KRAS and MKL2 in lung adenocarcinoma. Novel therapeutic strategies using miR-532-5p or an MKL2 inhibitor may prove effective against this hard-to-cure cancer irrespective of the dependence on KRAS-mediated signaling.

overall_design:
TaqMan Low-Density Array (TLDA) using human miRNA A+B Cards Set v3.0 (Applied Biosystems) were applied to examine the global change of miRNA expression levels. miRNAs with Ct values higher than 32 were excluded from the analysis. Normalization was carried out with the expression level of RNU44. The data was presented as log2 of the relative quantity of each miRNA.
BEAS-2B CTRL and TTF-1 cell lines were treated with 1 ug/ml Doxycycline for 48 h before RNA was harvested

first: Sebastian

last: Griesing

first: Taisuke

last: Kajino

first: Mei

last: Tai

first: Zhuoran

last: Liu

first: Masahiro

last: Nakatochi

first: Yukako

last: Shimada

first: Motoshi

last: Suzuki


title: Influence of manufacturing processes on cell surface properties of probiotic strain Lactobacillus rhamnosus Lcr35®

status: Public on Jun 22 2017

city: Aurillac

first: Stephanie

last: Bornes

address: 100 rue de l'egalite

department: IUT genie biologique

institute: Universite d'Auvergne

summary: Investigation of whole genome gene expression level changes in  Lcr35® pharmaceutical formulations, compared to the native strain.

overall_design: A nine chip study using total RNA recovered from three separate cultures of  Lcr35® native strain or of the two different formulations restituo capsule and packet.  Each chip measures the expression level of 7303 genes from 25 Lactobacillus with 2 or 3 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Adrien

last: Nivoliez

first: Philippe

last: Veisseire

first: Elina

last: Alaterre

first: Caroline

last: Dausset

first: Fabrice

last: Baptiste

first: Olivier

last: Camares

first: Marylise

last: Gachinat

first: Muriel

last: Bonnet

first: Christiane

last: Forestier


title: Integrative omics analysis in HCC samples [lncRNA expression]

city: Beijing

first: Jin

last: Song

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

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

summary:
38 paires of tumor tissues and adjacent non-tumor tissues from HCC patients
The number of known lncRNAs increased sharply upon the tiling microarrays and RNA-sequencing were applied to identify lncRNAs. However, only about a dozen of lncRNAs have been well characterized and demonstrated to be tightly associated with development and progression of HCC. A major challenge remains to identify functional lncRNAs associated with HCC. Previous reports mainly selected differentially expressed lncRNAs in cancer tissue or cell lines as candidates for further validation and characterizing. Here, based on mRNA and lncRNA gene expression profiles data collected from tumor and adjacent normal tissues of thirty-eight HCC patients, we adapted integrative omics strategy to identify HCC-associated lncRNAs.

overall_design:
To systematically discover functional lncRNAs in HCC, we recruited tumor tissues and paired adjacent non-tumor tissues from thirty-eight patients of primary HCC undergoing surgery and acquired the protein-coding genes and lncRNAs expression profiles through microarray assay. Particular attention was paid to obtain the “core” part of the tumor mass to avoid the adjacent non-tumor tissues, each specimen was reviewed by a board-certified pathologist to confirm that the frozen sections was histological consistent with tumor or non-tumor tissues, and tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis. Tissues were kept frozen in liquid nitrogen immediately after separation until they were used for molecular studies. This study was performed with the approval of the Medical Ethical Committee of Beijing Institute of Radiation Medicine (Beijing, China).
Please note that  total RNAs of 38 adjacent non-tumor tissues were mixed with equal amount and used as the  common reference labelled with cy5.

first: Xinyi

last: Tu

first: Xi

last: Chen

first: Fuchu

last: He

first: Gangqiao

last: Zhou


title: Transcriptome profiling of Propionibacterium freudenreichii strains associated with different anti-inflammatory properties.

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

summary:
Propionibacterium freudenreichii, a dairy starter, reaches a population close to 10^9 propionibacteria per gram of Swiss-type cheese at the time of consumption.
Also consumed as a probiotic, it revealed strain-dependent anti-inflammatory properties mediated by proteins inducing IL-10 in leukocytes.
Here, strains with varied anti-inflammatory potentials were compared in terms of transcriptome profiles.

overall_design: Eight strains were analyzed in one growth condition. After visual quality check based on the distribution of probe intensities, most strains were represented by 2 biological replicates (1 biological replicate for one strain, and 3 biological replicates for two strains).

first: Stéphanie-Marie

last: Deutsch

first: Hélène

last: Falentin

first: Julien

last: Burati

first: Valentin

last: Loux


title: Estrogen-like activity in cell signaling of capsaicinoids

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

summary: Comparing the expression profiles of the genes in response to 17b-estradiol (E2) and capsaicinoids (capsaicin (CAP), dihydrocapsaicin (DHCAP), nordihydrocapsaicin (NDHCAP), nonivamide (NV))

overall_design: Two-condition experiment, E2- or each capsainoid-treated vs. control cells. Three biological replicates, independently grown and harvested. Three replicates per array.

first: Yun

last: Zhu

first: Ryoiti

last: Kiyama


title: Shared and unique transcriptomic changes in chickpea in response to concurrent drought stress and Ralstonia solanacearum pathogen

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

institute: National Institute of Plant Genome Research

summary:
Chickpea (Cicer arietinum) is the third largest legume grown worldwide and are prone to drought and various pathogen infections. These stresses often occur concurrently in the field conditions. Previous studies in other plant species indicated that plant senses concurrently occurring stresses as new state of stress however, the molecular events in response to that is largely unknown. In the present study, we studied the transcriptome changes in chickpea plants exposed to combination of drought stress and a potential wilt pathogen, Ralstonia solanacearum by microarray analysis. Chickpea plants were exposed to short duration individual drought (SD-drought, soil field capacity, FC-35%), long duration individual drought (LD-drought, FC-30%), short duration individual pathogen stress (SD-pathogen = 2 days pathogen infection), long duration individual pathogen stress (LD-pathogen = 4 days of infection) and short duration and long duration combined stress, SD-combined = 2 days of pathogen infection with progressive drought (FC-40% to FC- 35%), LD combined = 4 days of pathogen infection with progressive drought (FC-35% to 30%).Transcriptome analysis for the leaf samples from above treatment were done by microarray analysis using Agilent ChickpeaGXP_8X60K chip. Result indicated presence of specific molecular events and also some common but tailored events in response to combined stress.
Global transcriptional analysis in chickpea leaves exposed to individual and combined drought stress and Ralstonia solanacearum infection.

overall_design: Transcriptome analysis was done in the leaf samples of individual and combined stress treated plants by microarray analysis using Agilent ChickpeaGXP_8X60K chip. Chickpea plants were exposed to short duration individual drought (SD-drought, soil field capacity, FC-35%), long duration individual drought (LD-drought, FC-30%), short duration individual pathogen stress (SD-pathogen = 2 days pathogen infection), long duration individual pathogen stress (LD-pathogen = 4 days of infection) and short duration and long duration combined stress, SD-combined = 2 days of pathogen infection with progressive drought (FC-40% to FC- 35%), LD combined = 4 days of pathogen infection with progressive drought (FC-35% to 30%). Two biological replicates were hybridized for each treatment.

first: Ranjita

last: Sinha

first: Muthappa

last: Senthil-Kumar


title: Exposure to different nickel nanoparticles and nickel salt: gene expression profile in Enchytraeus crypticus

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary: The effect of nanomaterials (NMs) is less understood in light of the implemented and existing methodologies for regular chemicals. To understand the mode of action of NMs is one of the alternatives to improve predictions and environmental risk assessment (ERA). In the present work the high-throughput gene expression tool (4x44K microarray for Enchytraeus crypticus) was used to investigate the mechanisms activated by Ni exposure. Ni nanoparticles (Ni-NPs) were investigated together with Ni-salt (NiNO3). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 3 and 7 days of exposure to the EC20 and EC50 (effect concentrations on reproduction) of nickel nanoparticles (Ni-NPs) and nickel salt (NiNO3) in LUFA 2.2 soil. Three biological replicates per test treatment and control (un-spiked LUFA soil) were used.

first: Carlos

middle: P

last: Roca

first: Janeck

middle: J

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: mRNA expression analysis of AR, HOXC6 and NKX2-2 overexpression

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

summary: Investigation of mRNA expression level changes in RWPE1 cells with AR,HOXC6 and NKX2-2 overexpression. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

overall_design: The Human 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 45033 genes were collected from the authoritative data source including NCBI.

first: Haiyue

last: Liu


title: Exposure to UV radiation: gene expression profile in Enchytraeus crypticus

summary: Negatives effects induced by exposure to ultra-violet (UV) radiation are well known. Nevertheless the modes of action of UV radiation are not well understood, in particular in soil invertebrates. In the present work, the effects of two UV doses (mimicking worst case scenarios in earth crust) on gene expression profile of Enchytraeus crypticus (Enchytraeidae, Oligochaeta) were investigated using the high-throughput 4 x 44K microarray developed for the species.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 5 days of exposure to UV radiation, in two different doses. To maximise UV exposure, the test media was reconstituted water (ISO 1). Three biological replicates per test treatment (two UV radiation doses) and control (standard laboratory light) were used.


title: LncRNA and mRNA expression profiles of 3 prostate cancer tumor tissues and 3 normal prostate tissues

status: Public on Jun 12 2017

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

institute: GEORGE WASHINGTON UNIV

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

summary: LncRNA and mRNA expression profiles of 3 prostate cancer tumor samples and 3 normal prostate samples were measured by microarray

overall_design: In the study presented here, we compared lncRNA and mRNA expression profiles between 3 prostate cancer samples and 3 normal prostate samples using a microarray containing 41531 lncRNA probes and 33352 mRNA probes.

first: Tao

last: Li

first: Xuechao

last: Wan


title: PARP1 expression drives the synergy between trabectedin and PARP1 inhibitors

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary: Trabectedin is a DNA-damaging agent with a peculiar mechanism of action; it traps the DNA repair machinery leading to DNA single- and double-strand breaks, particularly in BRCA1/2-deficient tumors. We hypothesized that trabectedin-induced DNA damage might activate PARP1 (a DNA-repair machinery key player), and consequently, PARP1 inhibition would perpetuate trabectedin-induced DNA damage. In several tumor histotypes, we demonstrated a different degree of synergism between trabectedin and PARP1 inhibitors (PARP1-Is). Independent of BRCA1/2 status, PARP1 expression dictated the degree of synergism. Namely, silenced PARP1 reduced trabectedin-PARP1-Is synergism, whereas overexpressed PARP1 increased combination efficacy. High-PARP1 expression and specific gene signatures associated with DNA damage response and repair (DDR-R) were predictive of trabectedin+PARP1-I synergy. These findings pave the way for the clinical development of this novel combination therapy, as well as evaluation of PARP1 expression and DDR-R signatures in tumor samples as predictive biomarkers of response

overall_design: A first panel of bone and soft tissue sarcoma cell lines were analyzed in terms of response and sensitivity to trabectedin and olaparib combination. A group of cells displaying high synergism of the combination was then compared with a group of cells with low synergism of the combination. Validation of PARP1 role was then performed in a second panel of non sarcoma cells ( mesotheliomas, colon  breast, prostate, cholangio and lung carcinomas)

first: Ymera

last: Pignochino

first: Federica

last: Capozzi

first: Lorenzo

last: D'Ambrosio

first: Carmine

last: Dell'Aglio

first: Marco

last: Basiricò

first: Marta

last: Canta

first: Sandra

last: Aliberti

first: Erica

last: Palesandro

first: Paola

last: Boccone

last: Ostano

first: Ilaria

last: Gregnanin

first: Danilo

last: Galizia

first: Loretta

last: Gammaitoni

first: Dario

last: Sangiolo

first: Annalisa

last: Lorenzato

first: Francesca

last: Lutati

first: Maria

last: Benassi

first: Giovanna

last: Chiorino

first: Barbara

last: Pasini

first: Massimo

last: Aglietta

first: Giovanni

last: Grignani


title: Globally construct ceRNA regulation network based on comparison with SHEE and SHEEC cell lines

city: Luoyang

first: Jiachun

last: Sun

state: Henan

address: 24 Jinghua road, Jianxi district

institute: Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology

summary: Long non-coding RNAs (lncRNAs), new star ncRNA class of mRNA-like transcripts, play complicate and critical roles in regulating various key biological processes including chromatin modification, transcription and post-transcriptional processing. Remarkably, some lncRNAs serve as a miRNA “sponge” to inhibit mediation of the differentiation of miRNA target in post-transcriptional regulation. Here, we firstly constructed the putative ceRNA network by integrating lncRNAs, miRNAs and mRNAs expression in compared with SHEE and SHEEC cell lines based on the high-though RNA sequencing data and microarray data. Though the biology function analysis, the result showed that ceRNA network mainly participate in PI3K-Akt pathway and may play a modulating role in regulation of essential signal molecules including SYK, FGF11, IL7R, MET, LAMB3, PRS6KB1, ITGB6, ITGB4, ITGA2, ITGA6, EPHA2, SOS2, VEGFA, GRB2, KRAS, CCDN1 and TP53 in primary ESCC. These results could provide us more essential clues for the development of novel therapeutic strategies and efficient drugs target in primary ESCC.

overall_design: The SHEEC and SHEE cell lines were pooled with 5 cell lines respectively.


title: Transcriptomic changes in maize roots in response to Fe deficiency

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

institute: University of Verona

summary: Iron deficiency is a yield-limiting factor and a worldwide problem for crop production in many agricultural regions, particularly in aerobic and calcareous soils. Graminaceous species, like maize, improve Fe acquisition through the release of phytosiderophores (PS) into the rhizosphere and the following uptake of Fe(III)-PS complexes through specific transporters. Transcriptional profile obtained by roots 12-d-old maize plants under Fe starvation for 1 week (Fe-deficient; 19-d-old plants) were compared with the transcriptional profile obtained by roots of 12-d-old maize plants grown in a nutrient solution containing 100 μM Fe-EDTA for 1 week (Fe-sufficient; 19-d-old plants).

overall_design:
12-d-old maize plants were treated for 7 days with nutrient solution  containing 100 μM Fe-EDTA (Fe-sufficient plants) while roots of an other part of 12-d-old maize plants were exposed for 7 days to nutrient solution without 100 μM Fe-EDTA (Fe-deficient plants).
Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants.

first: Laura

last: Zanin

first: Nicola

last: Tomasi

first: Silvia

last: Venuti

first: Stefano

last: Cesco

first: Zeno

last: Varanini

first: Roberto

last: Pinton


title: Hyperactivation of Nrf2 in early tubular development induces nephrogenic diabetes insipidus

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: NF-E2-related factor-2 (Nrf2) regulates the cellular response to oxidative/electrophilic stresses, and loss of Keap1 increases the Nrf2 protein level. As Keap1-null mice die of esophageal hyperkeratosis, whole-body phenotypes of Nrf2 hyperactivation in adult animals remain to be delineated. Here we show that deleting esophageal Nrf2 in Keap1-null mice the mice survive until adulthood, but develop polyuria with low osmolality and bilateral hydronephrosis. This novel phenotype is to be attributable to defects in water reabsorption caused by a reduction in the level of the aquaporin 2 (AQP2) channel in the kidney. In line, renal tubular deletion of Keap1 generates symptoms of nephrogenic diabetes insipidus, demonstrating that Nrf2 activation in developing tubular cells causes a water reabsorption defect. The rescue of mice from the lethal first hit of Keap1 ablation serves as a useful tool to study novel functions of Nrf2.

overall_design: Gene expression in the kidneys of NEKO and control mice. In the organs from NEKO (Keap1–/–::Nrf2Flox/Flox::K5-Cre) mice, except for esophagus, Nrf2 transcription factor is activated due to Keap1-deficiency. Control mice include K1 (Keap1+/–::Nrf2Flox/Flox) and K1Cre (Keap1+/–::Nrf2Flox/Flox::K5-Cre) mice. Samples were obtained from 4 NEKO mice and 4 control mice.

first: Takafumi

last: Suzuki

first: Shiori

last: Seki

first: Keiichiro

last: Hiramoto

first: Eriko

last: Naganuma

first: Ayaka

last: Yamaoka

first: Liam

last: Baird

first: Nobuyuki

last: Takahashi

first: Hiroshi

last: Sato

first: Masayuki

last: Yamamoto


title: Role of differentially expressed microRNA-139-5p in the regulation of phenotypic internal anal sphincter smooth muscle tone

city: Philadelphia

first: Satish

last: Rattan

state: PA

address: 1025 Walnut St., Room 320 College

department: Medicine

institute: Thomas Jefferson University

summary: The present study focused on establishing the role of microRNA-139-5p (miRNA-139-5p) in the phenotypic expression of basal tone in rat internal anal sphincter (IAS) vs. lack of tone in truly phasic smooth muscle of anococcygeus (ASM), via RhoA-associated kinase (RhoA/ROCK2).

overall_design: miRNA expression profiling of smooth muscle from internal anal sphincter (IAS), rectum (RSM), or anococcygeus (ASM).

first: Jagmohan

last: Singh

first: Ipsita

last: Mohanty

first: Sankar

last: Addya

first: Benjamin

last: Phillips

first: Hwan

last: Yong

first: Steven

last: An

first: Raymond

last: Penn


title: Transcriptional Responses to Pre-flowering Leaf Defoliation in Grapevine Berry from Different Growing Sites, Years, and Genotypes

first: Silvia

last: Dal Santo

department: Department of Biotechnology

summary: Leaf removal is a grapevine canopy management technique widely used to modify the source-sink balance and/or microclimate around berry clusters to optimize fruit composition. In general, the removal of basal leaves before flowering reduces fruit set, hence achieving looser clusters, and improves grape composition since yield is generally curtailed more than proportionally to leaf area itself. Albeit responses to this practice seem quite consistent, overall vine performance is affected by genotype, environmental conditions, and severity of treatment. The physiological responses of grape varieties to defoliation practices have been widely investigated, and just recently a whole genome transcriptomic approach was exploited showing an extensive transcriptome rearrangement in berries defoliated before flowering. Nevertheless, the extent to which these transcriptomic reactions could be manifested by different genotypes and growing environments is entirely unexplored. To highlight general responses to defoliation vs. different locations, we analyzed the transcriptome of cv. Sangiovese berries sampled at four development stages from pre-flowering defoliated vines in two different geographical areas of Italy. We obtained and validated five markers of the early defoliation treatment in Sangiovese, an ATP-binding cassette transporter, an auxin response factor, a cinnamyl alcohol dehydrogenase, a flavonoid 3-O-glucosyltransferase and an indole-3-acetate beta-glucosyltransferase. Candidate molecular markers were also obtained in another three grapevine genotypes (Nero d'Avola, Ortrugo, and Ciliegiolo), subjected to the same level of selective pre-flowering defoliation (PFD) over two consecutive years in their different areas of cultivation. The flavonol synthase was identified as a marker in the pre-veraison phase, the jasmonate methyltransferase during the transition phase and the abscisic acid receptor PYL4 in the ripening phase. The characterization of transcriptome changes in Sangiovese berry after PFD highlights, on one hand, the stronger effect of environment than treatment on the whole berry transcriptome rearrangement during development and, on the other, expands existing knowledge of the main molecular and biochemical modifications occurring in defoliated vines. Moreover, the identification of candidate genes associated with PFD in different genotypes and environments provides new insights into the applicability and repeatability of this crop practice, as well as its possible agricultural and qualitative outcomes across genetic and environmental variability.

overall_design: Grapevine (Vitis vinifera cv Sangiovese) samples were collected from control vines and vines subjected to Pre-Flowering Defoliation (PFD) treatment in two different terroirs (Ancona and Bologna). Berry sampling at each site x cultivar combination was performed on either control and PFD treatments at four different development stages as it follows:  20 days after leaf removal (Stage 1); hard and green berries at veraison (Stage 2); soft, yet still not colored berries at veraison (Stage 3), berries at a total soluble solid concentration of about 18 °Brix (Stage 4).The above-described procedure was followed for each stage, treatment and terroir, thus the experiment entailed the collection and the analysis of 48 pooled berry pericarp (berry without seeds) samples (2 Treatment X 4 stages X  2 Terroirs X 3 replicates).

first: Sara

last: Zenoni

first: Giovanni Battista

last: Tornielli

first: Erica

last: D'Incà

first: Ilaria

last: Filippetti

first: Chiara

last: Pastore

first: Gianluca

last: Allegro

first: Oriana

last: Silvestroni

first: Vania

last: Lanari

first: Antonino

last: Pisciotta

first: Rosario

last: Di Lorenzo

first: Alberto

last: Palliotti

first: Sergio

last: Tombesi

first: Matteo

last: Gatti

first: Stefano

last: Poni


title: cDNA expression profiling of MDA-MB-231 breast cancer cells upon β-hydroxybutyrate treatment

city: Taipei

first: Chun-Kai

last: Huang

address: 128 Academia Road, Section 2, Nankang

institute: Genomics Research Center, Academia Sinica

summary: Investigating the gene expression profile changes upon β-hydroxybutyrate treatment in MDA-MB-231 breast cancer cells w/ or w/o MCT2 expression

overall_design: MDA-MB-231 shLacZ and MCT2-depleted cells were cultured in the presence of 10 mM β-hydroxybutyrate. The total RNAs were extracted and subjected to microarray analyses.

first: Wen-Hwa

last: Lee


title: Transcriptional profile Lactobacillus plantarum WCFS1 : olive oil (OO) treated cells

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with olive oil (OO). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals the downregulation of processes associated with rapid growth and the induction of stress-related pathways indicating the involvement of the stringent response. The fatty acid biosynthetic pathway is thoroughly downregulated at the transcriptional level and genes involved in host-cell signalling are differentially regulated.

overall_design: Biological triplicates: untreated cells: Control vs. Olive oil treated cells: Experimental

first: María

last: del Mar Esteban-Torres

first: Inés

last: Reverón

first: Laura

last: Plaza

first: Blanca

last: de las Rivas

last: Muñoz

first: Félix

last: López de Felipe


title: Abberant miRNA expression profiles in recurrent implantation failure endometrium

first: Fan

middle: Li

last: juan

state: Beijing

address: 11th Xizhimen south street,Xicheng district

department: Reproductive medical Center

institute: Peking University Peoples' Hospital

summary:
A microarray study about miRNA expression profiles in recurrent implantation failure patients as compare with who had got pregnancy after embryo implantation no more than three times
To detect the miRNAs that may regulate endometrial receptivity by microarray study

overall_design: A microarray profile comparision between RIF and control endometrium at window of implantation

first: Lijuan

last: Fan

first: Cheng

last: Shi


title: Expression data from Caenorhabditis elegans fed with a Lactoferrin-based product

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

summary:
Lactoferrin is a highly multifunctional protein. Indeed, it is involved in many physiological functions, including regulation of iron absorption and immune responses.
We use microarrays to study the global genome expression of C. elegans fed with a nutraceutical product based on encapsulated lactoferrin.

overall_design: Wild type strain N2 of C. elegans was cultured in  Nematode Growth medium (MGM, control fed) or NGM supplemented with Lactoferrin-based product. Young adult worms were age-synchronized. RNA was isolated from each populations (control and treated) using RNAasy Kit (Qiagen) and hybridizated on Affymetrix microarrays.

first: Salvador

last: Genovés

first: Daniel

last: Ramón


title: Gene expression profiling of Nedd4- or control-knockdown Hep3B cells

city: New York

first: Xian

last: Zhang

address: 580 main st apt 138

institute: MSKCC

summary: Gene expression profiling of Nedd4 or control knockdown Hep3B cells

first: Hui-Kuan

last: Lin


title: microRNA profiling of murine wt and MyD88-/- deficient bone marrow derived macrophages upon infection with Legionella Pneumophila

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
wt and MyD88-/- murine bone marrow derived macrophages were infected with Legionella Pneumophila for 24h. RNA was isolated by phenol/chloroform precipitation.
400 ng RNA per sample were then reverse transcribed with the Life Technologies miR RT kit with megaplex primers. Reverse transcribed RNA was then loaded on the rodent Taqman Low Density Array (TLDA) Cards and run according to manufacturer´s recommendations

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Uninfected MyD88-/- and wt cells were used as control to evaluate the impact of infection. Normalized infected MyD88-/- samples were then compared against normalized infected wt samples.

first: Elisa

last: Jentho


title: Circulating microRNAs as a signature predicting the occurrence of Acute Mountain Sickness before exposure to high altitude

status: Public on Jun 10 2017

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

summary: Acute mountain sickness (AMS) is a common disabling condition in individuals experiencing high altitudes, which may progress to life-threatening high altitude cerebral edema. Today, no established biomarkers are available for prediction of AMS and Non-AMS individuals before exposure to high altitude.MicroRNAs emerge as promising sensitive and specific biomarkers for a variety of diseases. Thus, we sought to identify circulating microRNAs suitable for prediction the susceptible of AMS before exposure to high altitude. A total of 31 microRNAs were differentially expressed between AMS and Non-AMS groups, 15 up-regulated and 16 down-regulated. Up-regulation of miR-369-3p, miR-449b-3p, miR-136-3p, and miR-4791 in patients with AMS compared with Non-AMS individuals were quantitatively confirmed using qPCR (all, P < 0.001).  A unique signature encompassing miR-369-3p, miR-449b-3p, and miR-136-3p discriminate AMS from Non-AMS (area under the curve 0.986, 95%CI 0.970-1.000, P < 0.001, LR+: 14.21, LR-: 0.08). This signature yielded a 92.68% sensitivity and a 93.48% specificity for AMS vs. Non-AMS.The study here, for the first time, describes a signature of three circulating microRNAs as a robust biomarker to differentiate AMS from Non-AMS individuals.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: we enrolled 109 healthy man adults, 22 individuals randomly selected for microarray assay, the remained 87 volunteers for quantitative reverse-transcription polymerase chain reaction test. A total of 31 microRNAs were differentially expressed between AMS and Non-AMS groups, 15 up-regulated and 16 down-regulated. After microRNA profiling, up-regulation of miR-369-3p, miR-449b-3p, miR-136-3p, and miR-4791 in patients with AMS compared with Non-AMS individuals were quantitatively confirmed using quantitative reverse-transcription polymerase chain reaction (all, P < 0.001).

first: Bao

last: Liu

first: YuQi

last: Gao


title: Microarray expression profiling of dysregulated long non-coding RNAs between RCC tumor tissues and corresponding adjacent tissues

city: chongqing

first: Jing

last: Xiong

state: chongqing

address: Medical College Road, Yuzhong District, Chongqing, No. 1

institute: chongqing medical university

summary: During the past decade, increasing evidence has shown that lncRNAs play important roles in oncogenesis and tumor suppression; however, the roles of lncRNAs in RCC are poorly understood. To address this issue, we used Agilent human lncRNA microarray chips and bioinformatics tools to assess lncRNA expression in 5 pairs of RCC tissues. A dysregulated lncRNA expression profile was identified by microarray and verified by qRT-PCR in 60 pairs of renal cell carcinoma.

overall_design: 5 pairs of RCC tissues were analyzed by lncRNA microarray chips, parts of the dysregulated lncRNAs were further validated in an additional cohort of 55 samples by qRT-PCR.

first: Ying

first: Jun

last: Luo

first: Li

last: Jiang

first: Yang

last: Zeng

first: Xiong

middle: Z

last: Chen

first: Bo

last: Lv

first: Wei

last: Tang


title: LncRNA expression profiles of LNCaP cells treated with 10 nM DHT for 0 and 2 hr.

first: Shu

last: Yang

summary: We have employed human lncRNA microarray expression profiling as a discovery platform to identify differential expression lncRNAs between DHT treated LNCaP cells and untreated cells.

overall_design: Androgen induced lncRNA expression in LNCaP, human prostate cancer cell, was measured at 0 and 2 hours after exposure to 10 nM DHT.

first: Xuechao

last: Wan


title: Whole-genome microarray of Caenorhabditis elegans strains DA650 and RC301 exposed to Pseudomonas aeruginosa PA14

city: Durham

first: Alejandro

last: Aballay

state: NC

address: 265 Jones Building

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

summary: To gain insights into the mechanisms by which RC301 compensates for the deficiency in the NPR-1 controlled immune and behavioral responses of strain DA650, we determine the whole-genome expression profile of these two strains upon exposure to Pseudomonas aeruginosa strain PA14

overall_design: DA650 and RC301 animals were synchronized to developmental stage L1. These animals were grown at 20°C on nematode growth media plates seeded with Escherichia coli OP50 until L4 stage (48 hours). At 48 hours, animals were transferred to plates containing Pseudomonas aeruginosa strain PA14. After 4 hours of incubation at 25°C, animals were rinsed off the plates and total RNA from three biological replicates was extracted. C. elegans Gene Expression Microarray (Agilent Technologies, Santa Clara, CA) were used.were used.

first: Natalia

last: Martin

first: Jogender

last: Singh


title: Frequent silencing of the candidate tumor suppressor TRIM58 by promoter methylation in early stage lung adenocarcinoma

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

summary: We performed a systematic, genome-wide screening of aberrantly methylated CGIs in stage I LADC from NS and S to identify tumor-associated genes commonly dysregulated through aberrant DNA methylation in early stage of LUAC regardless of smoking status. A series of criteria targeting novel genes frequently silenced in LADC tumors and cell lines possibly through hypermethylation were applied to prioritize the selection of top candidates for validation. As the result, we identified TRIM58 for further detailed analyses of methylation status and its relation with gene expression using a larger set of LADC tumors and cell lines.  Our functional analyses demonstrated the growth suppressive effect of restored TRIM58 expression on LADC cell in vitro and in vivo, suggesting that this gene exerts TSG.

overall_design: To investigate the molecular pathways involved by TRIM58-overexpression, the expression levels of mRNAs in TRIM58-stably transfectants were analyzed using microarray

first: Koichiro

last: Kajiura

first: Takuya

last: Naruto

first: Tomohiro

last: Kohmoto

first: Miki

last: Watanabe

first: Mitsuhiro

last: Tsuboi

first: Hiromitsu

last: Takizawa

first: Kazuya

last: Kondo

first: Akira

last: Tangoku

first: Issei

last: Imoto


title: Gene and microRNA modulation upon ET-743 treatment in a human intrahepatic cholangiocarcinoma paired patient derived xenograft and cell line [miRNA expression]

first: giovanna

last: chiorino

summary:
Transcriptional profiling and microRNA profiling of paired PDX and derived cell line MT-CHC01 upon ET-743 treatement
Intrahepatic cholangiocarcinoma (ICC) is an aggressive and lethal malignancy with limited therapeutic options.  ET-743 has a high antitumor activity in preclinical models of biliary tract carcinoma (BTC), being a promising alternative treatment. Here, we studied the effect of ET-743 at transcriptomic level on an ICC patient derived xenograft (PDX) and on the derived cell line, MT-CHC01. Further, putative targets of ET-743 were explored in the in vitro model. In vitro, ET-743 inhibited genes involved in protein modification, neurogenesis, migration, and motility; it induced the expression of genes involved in keratinization, tissues development, and apoptotic processes. In the PDX model, ET-743 affected ECM-receptor interaction, focal adhesion, complement and coagulation cascades, Hedgehog, MAPK, EGFR signaling via PIP3 pathway, and apoptosis. In MT-CHC01, 24 microRNAs were deregulated upon drug treatment. Only 5 microRNAs were perturbed by ET-743 in PDX; 2 up and 3 down-regulated. Among down- regulated genes, we selected SYK and LGALS1; their silencing caused a significantly reduction of migration, but did not affect proliferation in MT-CHC01 and WITT cells. In conclusion, we described that ET-743 affected genes and microRNAs involved in tumor progression and metastatic processes, reflecting data previously obtained at macroscopically level; in particular, we identified SYK and LGALS1 as new putative targets of ET-743.

overall_design:
MicroRNA alterations upon ET-743 treatement
MT-CHC01 cell line treated with ET-743 at the dose of 5 nM for 24 hours vs MT-CHC01 cell line untreated;ICC PDX treated with ET-743 at the dose of 0.15 mg/Kg/weekly for three weeks vs ICC PDX untreated

first: Caterina

last: Neia

first: Giuliana

last: cavalloni

first: Giovanna

last: Chiorino

first: Paola

last: Ostano

first: Francesco

last: Leone

first: Massimo

last: Aglietta


title: The human pericardial fluid is enriched with cardiovascular-expressed microRNAs

city: Bristol

first: Costanza

last: Emanueli

address: Research Floor Level 7, Bristol Royal Infirmary, Upper Maudlin Street

department: School of Clinical Science

country: United Kingdom

institute: Bristol Heart Institute, University of Bristol

summary: The pericardial fluid (PF) surrounds the heart and it  is contained in the pericardial sac. PF contains myocardial-derived factors. MicroRNAs (miRNAs) are negative post-transcriptional regulators of their target genes and they can be released into extracellular vesicles (EVs) contributing to cell-to-cell communication. We hypothesize that the PF contains miRNAs of myocardial origin and that represents a niche for the exchange of miRNAs between heart cells.  In order to investigate whether PF contains functionally active miRNAs,  miRNA expression profiles on PF samples  collected from three patients undergoing aortic valve replacement (AVR) surgery performed during cardiopulmonary-bypass (CPB), were genereted.

overall_design: PF samples were collected from three patients undergoing aortic valve replacement (AVR) surgery performed during cardiopulmonary-bypass (CPB).

first: Saran

last: Shantikumar

first: Cristina

last: Beltrami


title: Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) [exon level]

city: London

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

summary:
Alternative splicing is a key event to human transcriptome and proteome diversity and complexity. Recent evidence suggests that pancreatic cancer might possess particular patterns of splice variation that influence the function of individual genes contributing to tumour progression in this disease. The identification of new pancreatic cancer-associated splice variants would offer opportunities for novel diagnostics and potentially also represent novel therapeutic targets.
In this dataset, we investigated the alterations in the splicing machinery in pancreatic adenocarcinoma (PDAC) specimens with full clinicopathological details, in comparisons to adjacent pancreatic tissues and normal tissues from donors.

overall_design:
We extracted total RNA from 28 PDAC specimens, 4 adjacent tissues and 2 normal pancreatic tissues from donors, and hybridized them to Affymetrix exon arrays. Affymetrix GeneChip® Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) were used for gene expression and alternative splicing analysis. Labelling and hybridization were performed according to the manufacturer's instructions. After scanning, .CEL files were checked for quality and analysed following the pipeline based on aroma.affymetrix R package, to produce transcript, probeset and probe-level intensities. This was followed by intensity filtering as recommended by Affymetrix.

This submission includes the exon-level analysis.

first: Claude

last: Chelala

first: Tatjana

last: Crnogorac-Jurcevic

first: Aldo

last: Scapra

first: Nick

last: Lemoine


title: Correction of the exon 2 duplication in DMD myoblasts by a single CRISPR/Cas9 system

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

institute: University of Ferrara

summary: Exonic duplications account for 10-15% of all mutations in Duchenne muscular dystrophy (DMD), a severe hereditary neuromuscular disorder. We report a novel CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/Cas9-based strategy to correct the most frequent (exon 2) duplication in the DMD gene by targeted deletion, and tested the efficacy of such an approach in patient-derived myogenic cells. We demonstrate restoration of wild-type dystrophin expression at transcriptional and protein level in myotubes derived from genome-edited myoblasts in the absence of selection. Removal of the duplicated exon was achieved by the use of only one gRNA directed against an intronic duplicated region, thereby increasing editing efficiency and reducing the risk of off-target effects. This study opens a novel therapeutic perspective for patients carrying disease-causing duplications independently from the duplication extension.

overall_design: CGH analysis of the Dystrophin gene in eight DMD patients with exon 2 duplications


title: Identification of miRNAs correlated with Rb-depletion induced spherogenesis.

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

type: Non-coding RNA profiling by high throughput sequencing

summary: We found that Rb inactivation induces sphere-forming activity under 3D culture condition in primary soft tissue sarcoma cells derived from p53 null mice. To elucidate molecular mechanism, we employed microRNA array as a discovery platform to identify miRNAs correlated with Rb-depeltion induced sphere-forming cells. To enrich sphere-forming cells and make the culture condition equivalent to that of parental cells (Primary cells), we replated sphere-forming cells on normal dishes (Rb shRNA Secondary cells), and obtained total RNA soon after replating.

overall_design: In p53 null mice derived soft tissue sarcoma cells, control cells, Rb depleted cells and sphere forming cells derived from Rb depleted cells were measured. Two or three independent experiments were performed at each condition.

first: Akiyo

last: Yoshida

first: Shunsuke

last: Kitajima

first: Chiaki

last: Takahashi


title: Exposure to different copper forms – nanoparticles, nanowires, salt and field aged: gene expression profiling in Enchytraeus crypticus

city: Aveiro

first: Susana

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

institute: CESAM & University of Aveiro

summary: The testing of NMs under the currently available standard toxicity tests does not cover many of the NMs specificities. One of the current recommended approaches forward lays on understanding the mechanisms of action as these can help predicting long term effects and safe-by-design production. Copper nanomaterials (Cu-NMs) usage has been highly increasing with the concern in terms of exposure, effect and associated risks. In the present study we used the high-throughput gene expression tool developed for Enchytraeus crypticus (44Kx4 Agilent microarray) to study to the effect of exposure to several copper forms. The copper treatments include two NMs (spherical and wires) and two copper-salt treatments (CuNO3 spiked and Cu field historical contamination). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 3 and 7 days of exposure to the EC20 and EC50 (effect concentrations on reproduction) of several copper forms (nanoparticles, nanowires, salt and field aged) in a natural soil from Hygum site (Denmark). Three biological replicates per test treatment and control (Hygum soil from control area) were used.

middle: L

first: Carlos

last: Roca

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: Affymetrix SNP array data for esophageal squamous cell carcinoma samples

city: Beijing

first: Jianming

last: Ying

address: Panjianyuan Nanli 17, Chaoyang District, Beijing, China

department: Pathology

institute: Cancer Hospital Chinese Academy of Meidcal Sciences

summary: A proportion of superficial esophageal squamous cell carcinoma, a type of less invasive esophageal squamous cell carcinoma (ESCC), would have metastasis after esophagectomy or endoscopic resection with poor prognosis. The purpose of this study was to discover the whole-genome copy number alteration (CNA) profiles of superficial ESCC and compare the CNAs of superficial ESCC patients with and without metastasis after surgery. Thirty eight superficial ESCC cases, including 19 cases with metastasis and 19 cases without metastasis within 5 years after surgery, were analyzed CNAs by Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was initially constructed to identify high risk of metastasis in superficial ESCC patients. In addition, amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were identified as recurrent CNAs across all 38 superficial ESCC cases. And amplifications of 3p26.33 (SOX2-OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were identified as recurrent CNAs among metastasis cases only. Our study provided a 39-gene signature tool to identified high risk metastasis in superficial ESCC and suggested that amplifications of SOX2-OT, MYC, FOXA1 genes and deletion of GBE1 gene might play a vital role in metastasis among superficial ESCC.

overall_design: Copy number analysis of Affymetrix FFPE Oncoscan Array was performed for 38 superficial esophageal squamous cell carcinoma (pT1N0M0) samples, including 19 cases with metastasis after surgery within 5 years after surgery and 19 cases without metastasis.

first: Ning

last: Lu

first: Ling

last: Shan

first: Pengjiao


title: Chinese lung ADC exon-level expression

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

institute: SIBCB

summary: Chinese lung adenocarcinomas exon-level expression

overall_design: In order to search for novel gene fusions which may play important roles in lung adenocarcinoma initiation and progression, we performed Exon array in lung adnocarcinoma samples.

first: Fei

last: Li

first: Zhaoyuan

last: Fang


title: Gene expression profiles in fins after infection of zebrafish with Spring Viremia Carp Virus (SVCV)

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

summary: Because fin base is supposed to be the entry zone of some fish virus, we wanted to know which  transcripts are induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in zebrafish fins. Also transcripts from resistant fishes to viral infection one month after inoculation were studied.

overall_design: Three different experiments were performed to get three biological replicates. Fishes were divided in two groups in each experiment. First group was infected by immersion with SVCV 107 pfu/ml, second group was used as a control of non-infected fishes. 6 fishes per group were sacrified two days post infection, whereas the rest of infected fishes from the three experiments were maintained for 30 days in the aquariums and then survivors (six for experiment)  were sacrified.

first: Paloma

last: Encinas

first: Pablo

last: García-Valtanen


title: Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

status: Public on Jun 09 2017

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: Excessive accumulation of adipose tissue in cultured fish is an outstanding problem in aquaculture. To understand the development of adiposity, it is crucial to identify the genes which expression is associated with adipogenic differentiation. Therefore, the transcriptomic profile at different time points (days 3, 8, 15 and 21) along primary culture development of rainbow trout preadipocytes has been investigated using an Agilent trout oligo microarray. Our analysis identified 4026 genes differentially expressed (fold-change >3) that were divided into two major clusters corresponding to the main phases observed during the preadipocyte culture: proliferation and differentiation. Proliferation cluster comprised 1028 genes up-regulated from days 3 to 8 of culture meanwhile the differentiation cluster was characterized by 2140 induced genes from days 15 to 21. Proliferation was characterized by enrichment in genes involved in basic cellular and metabolic processes (transcription, ribosome biogenesis, translation and protein folding), cellular remodelling and autophagy. In addition, the implication of the eicosanoid signalling pathway was highlighted during this phase. On the other hand, the terminal differentiation phase was enriched with genes involved in energy production, lipid and carbohydrate metabolism. Moreover, during this phase an enrichment in genes involved in the formation of the lipid droplets was evidenced   as well as the activation of the TR/RXR and the PPARs signalling pathways. The whole adipogenic process was driven by a coordinated activation of transcription factors and epigenetic modulators. Overall, our study demonstrates the coordinated expression of functionally related genes during proliferation and differentiation of rainbow trout adipocyte cells. Furthermore, the information generated will allow future investigations of specific genes involved in particular stages of fish adipogenesis.

overall_design: Samples were collected at day 3 (mesenchymal stem cells), day 8 (proliferated cells), day 15 (committed preadipocytes) and day 21 (mature adipocytes).

first: Marta

last: Bou

first: Jerôme

last: Montfort

first: Aurélie

last: Le Cam

first: Cécile

last: Rallière

first: Véronique

last: Lebret

first: Jean-Charles

last: Gabillard

first: Claudine

last: Weil

first: Joaquim

last: Gutiérrez

first: Pierre-Yves

last: Rescan

first: Encarnación

last: Capilla

first: Isabel

last: Navarro