title: Expression data from Saccharomyces cerevisiae upon honokiol treatment

status: Public on May 22 2017

city: Wuhu

first: xiao

middle: long

last: zhu

state: Anhui

address: 2 Zheshan western road

country: China

institute: Yijishan Hospital

summary:
Honokiol (HNK), one of the main medicinal components in Magnolia officinalis, possesses antimicrobial activity against a variety of pathogenic bacteria and fungi.S. cerevisiae is a model eukaryote used for investigating the cellular and  molecular mechanisms of anti-fungal drugs.
To explore the molecular mechanism of its anti-fungal activity, we determined the effects of HNK on the mRNA expression profile of Saccharomyces cerevisiae using a DNA microarray approach.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Wild-type S. cerevisiae (BY4741) cells were treated with 12 μg/mL HNK for 2 h (or an equal volume of ethanol for controls) and for RNA extraction and hybridization on Affymetrix microarrays. Biological replicates: 2 control replicates, 2 HNK treated replicates.

first: Xiaolong

last: Zhu

first: Shenshen

last: Zou


title: Global gene expression in muscle from fasted/refed trout reveals up-regulation of genes promoting myofibre hypertrophy but not myofibre production

status: Public on May 18 2017

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: To learn more about the contribution of genes regulating hypertrophy (increase in muscle fibre size) and hyperplasia (generation of new muscle fibres) in the compensatory muscle growth response in fish, we used high-density trout microarray to investigate the global gene expression in trout muscle during a fasting-refeeding schedule and in control-fed trout displaying normal growth.

first: Pierre-Yves

last: Rescan

last: Le Cam

first: Cécile

last: Rallière

first: Jérôme

last: Montfort


title: ChIP-chip in RNA Pol II mutants

status: Public on May 02 2017

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

country: USA

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific “readers.” While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we investigate the genome-wide occupancy of Pol II, phospho-Thr4, and key reader Rtt103 in WT and CTD-mutant strains of S. cerevisiae.

overall_design: ChIP of Rpb3, phospho-Thr4, and Rtt103 in WT or CTD-mutant strains of S. cerevisiae.

first: C

middle: M

last: Nemec

first: A

middle: Z


title: Expression data from human infant kidney derived-CD133+GFP+ and CD133-GFP+

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Previous studies have suggested that CD133+ cells isolated from human kidney biopsies have the potential to ameliorate injury following intravenous (IV) administration in rodent models of kidney disease by integrating into damaged renal tissue and generating specialised renal cells.  However, whether renal engraftment of CD133+ cells is prerequisite for ameliorating injury has not yet been unequivocally resolved. Here, we have established a cisplatin-induced nephropathy model in immunodeficient rats to assess the efficacy of CD133+ human kidney cells in restoring renal health, and to determine the fate of these cells after systemic administration. Specifically, following IV administration, we evaluated the impact of the CD133+ cells on renal function by undertaking longitudinal measurements of the glomerular filtration rate using a novel transcutaneous device. Furthermore, using histological assays, we assessed whether the human kidney cells could promote renal regeneration, and if this was related to their ability to integrate into the damaged kidneys. Our results show that both CD133+ and CD133- cells improve renal function and promote renal regeneration to a similar degree. However, this was not associated with engraftment of the cells into the kidneys. Instead, after IV administration, both cell types were exclusively located in the lungs, and had disappeared by 24 hours. Our data therefore indicate that renal repair is not mediated by CD133+ cells homing to the kidneys and generating specialised renal cells. Instead, renal repair is likely to be mediated by paracrine or endocrine factors.

overall_design: Human infant kidney-derived cells were isolated, sorted by FACS for the expression of CD133. Both CD133+/GFP+ and CD133-/GFP+ were maintained in culture for 2 additional passages. Afterward the expression of CD133 in both populations was measured with a microarray analysis.

first: Ilaria

last: Santeramo

first: Zeneida

middle: H

last: Perez


title: RNA Pol II CTD mutants

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: RNA expression data from mouse endothelial cells isolated from tumors that were exposed to interferon gamma (IFNγ) in vivo

status: Public on May 04 2017

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary:
While it is clear that T cell derived IFNγ has to act on tumor stroma cells for rejection of solid tumors, it is not clear which tumor stroma cells are targets. We studied how IFNγ affects gene expression in tumor blood vessels in vivo. To study the effect on endothelial cells, we either used a model of ectopic IFNγ (MCA313 tumors) or IFNγ-GFP fusion protein (J558L tumors) expression in tumors, or we used T cell derived IFNγ in large vascularized 16.113 tumours. Tumors were grown in mice that were expressing the IFNγ receptor ubiquitously (J558L tumors + IFNγ-GFP treatment and 16.113 tumors + T cell treatment) or in some experiments the IFNγ-receptor was expressed exclusively in endothelial cells (MCA313 tumor + IFNγ treatment).
We compared RNA expression profiles from mouse endothelial cells exposed to IFNγ (IFNγ-GFP) or not exposed to IFNγ (IFNγ-GFP). Endothlial cells were drived from tumors (or in one experimantal situation -J558L- as a control also from kidney)

overall_design: Tumors were grown in mice (either with ubiquitous IFNγ-receptor expression -WT mice- or in transgenic mice with endothelial cell specific IFNγ-receptor expression - PIG x Pdgfb-Cre x IFNγ-del mice) to ca. the size of ca. 1.0 cm in diameter. Then tumors were exposed for 24h or 48h to IFNγ (MCA313-IFNγ-IND tumors) or IFNγ-GFP (J558L-IFNγ-GFP-IND tumors) by ectopic expression from the tumor cells. As controls we used endothelial cells from tumors which were not induced to express IFNγ(0h). To confirm that T cell derived IFNγ acts similar as in our ectopic models, we used T cells for T cell therapy of 16.113 tumors that could express IFNγ (IFNγ+/+ T cells) or could not express IFNγ (IFNγ-/- T cells).

first: Thomas

last: Kammertoens

last: Blankenstein

first: Christian

last: Friese

first: Giannino

last: Patone


title: RNA expression analysis in RNA Pol II CTD mutants

summary: The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific “readers.” While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we investigate the RNA expression profile in WT and CTD-mutant strains of S. cerevisiae.

first: Y

last: Ho

middle: P

last: Gasch


title: The global transcriptional effect of exogenously added butyrolactone I on Aspergillus terreus under submerged culture

status: Public on May 08 2017

city: Åbo

first: Elina

last: Palonen

address: Artillerigatan 6

department: Biochemistry, Faculty of Science and Engineering

country: Finland

institute: Åbo Akademi University

summary: The filamentous fungus Aspergillus terreus is known to produce both industrially and pharmaceutically important secondary metabolites. The objective of this study is to investigate the effect of exogenously added butyrolactone I (BI) on the submerged culture of A. terreus, especially on the possible regulation of the secondary metabolism on the transcriptional level. In order to elucidate the presumed regulative role of butyrolactone I, a large-scale microarray gene expression study was designed and conducted with an industrially utilised A. terreus strain MUCL38669. A. terreus MUCL38669 was cultured in secondary metabolism inducing submerged conditions for nine days, where butyrolactone I was added at the beginning of the growth phase (at 24 hours p.i.), in the middle of the growth phase (at 96 hours p.i.) or in the late growth phase (at 120 hours p.i.), in addition to the control culture where no exogenous butyrolactone I was added. To obtain comprehensive gene expression profiles over the whole culture time, samples were taken at six time points: 24 hours, 48 hours, 96 hours, 120 hours, 144 hours and 216 hours post inoculation.

overall_design: This study is composed of three treated A. terreus strain MUCL38669 submerged cultures where butyrolactone I (BI) was exogenously added at the following time points: 24 hours, 96 hours and 120 hours post inoculation, and one control culture where no BI was added. All these four submerged culture sets were incubated simultaneously in three biological replicates. The samples to be analysed were taken at 24 hours, 48 hours, 96 hours, 120 hours, 144 hours and 216 hours post inoculation. This generates the 72 samples to be analysed in total.The available A. terreus NIH2624 genome was utilised in the custom probe design.

middle: K

first: Sheetal

last: Raina

first: Annika

last: Brandt

first: Tajalli

last: Keshavarz

first: Juhani

last: Soini


title: Real-time quantitative PCR analysis of gene expression in mechanical stimulated invasion assay

status: Public on May 15 2017

city: Detroit

first: Karen

last: Beningo

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University


title: The induction of an epithelial gene program promotes traits of mammary progenitor luminal cells

status: Public on May 01 2017

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: MicroRNAs are critical regulators of gene networks in normal and abnormal biological processes. Focusing on invasive ductal breast cancer (IDC), we have found dysregulated expression in tumor samples of several microRNAs, including the miR-200 family, along progression from primary tumors to distant metastases, further reflected in higher blood levels of miR-200b and miR-7 in IDC patients with regional or distant metastases relative to patients with primary node-negative tumors. Forced expression of miR-200s in MCF10CA1h mammary cells induced an enhanced epithelial program, aldehyde dehydrogenase (ALDH) activity, mammosphere growth and ability to form branched tubuloalveolar structures while promoting orthotopic tumor growth and lung colonization in vivo. Knockdown of the miR-200 target, ZEB2, partially phenocopied the expression of miR200s with a strong enhancement of mammosphere growth and ALDH activity. Interestingly, the morphology of tumors formed in vivo by cells expressing miR-200s was reminiscent of metaplastic breast cancer (MBC). Indeed, the epithelial components of MBC samples expressed significantly higher levels of miR-200s than their mesenchymal components and displayed a marker profile compatible with luminal progenitor cells. We propose that microRNAs of the miR-200 family promote traits of highly proliferative breast luminal progenitor cells, thereby exacerbating the growth and metastatic properties of transformed mammary epithelial cells.

overall_design: Microarray expression screening was performed using tissue samples from 8 ductal carcinomas in situ (DCIS), 20 primary IDC without LN involvement (PNM), 20 primary IDC with regional LN involvement (PM), 20 LN metastases matched to the node-positive primary tumors (LNM) and 20 distant metastases (DM) and a pool of 10 normal breast epithelial tissues (N).

first: L

last: Sanchez-Cid

first: M

last: Pons

first: J

middle: J

first: N

last: Rubio

last: Guerra-Rebollo

last: Soriano

last: Paris-Coderch

middle: F

last: Segura

first: R

last: Fueyo

last: Bermudo

first: I

last: Alonso

first: X

last: Caparrós

last: Rafii

last: Kang

last: Martínez-Balbás

first: S

last: Weiss

last: Blanco

last: Muñoz

first: P

middle: L

last: Fernández

first: T

last: Thomson


title: Gene expression profile in the small Maf-deficient livers.

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: To elucidate the functional roles of sMafs in the adult liver, we conditionally targeted the sMaf genes using a transgenic complementation rescue approach. MafF-/-::MafG-/-::MafK-/- (F0G0K0) mice are embryonic lethal but can be rescued by complementation of transgenic MafG expression under the regulation of the MafG regulatory domain (MGRD). Therefore, we rescued F0G0K0 mice using a MGRD transgenic mouse line with a MafG gene flanked with loxP (fMafG) sequences so that the MafG gene could be deleted by Cre-mediated recombination. The Albumin(Alb)-Cre transgenic mice were used to delete fMafG gene specifically in the liver. The genotype used are MafF-/-::MafG-/-::MafK-/-::MGRD-fMafG::Alb-Cre (liver-specific sMaf CKO) and MafF-/-::MafG+/-::MafK-/-::MGRD-fMafG::Alb-Cre (control).

overall_design: The microarray analyses were performed using three independent RNA samples from livers of liver-specific sMaf CKO and control mice at 5 weeks of age.

first: Fumiki

last: Katsuoka

first: Hiromi

last: Yamazaki


title: Characterization of stem cell-derived liver and intestinal organoids as a model system to study nuclear receptor biology.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Nuclear receptors (NRs) are ligand-activated transcription factors regulating a large variety of processes involved in reproduction, development, and metabolism. NRs are ideal drug targets. Immortalized cell lines recapitulate NR biology very poorly and primary cultures are laborious and require a constant need for donor material. There is a clear need for development of novel preclinical model systems that better resemble human physiology since technical uncertainty early in drug development is the cause of many preclinical drugs not reaching the clinic. Here, we studied whether organoids, mini-organs derived from the respective tissue’s stem cells, can serve as a novel (preclinical) model system to study NR biology and targeteability. We characterized mRNA expression profiles of the NR superfamily in mouse liver, ileum, and colon organoids. NR mRNA expression patterns were similar to the respective tissues, indicating their suitability for NR research. Metabolic NRs Fxrα, Lxrα, Lxrβ, Pparα, and Pparγ were responsive to ligands in an NR-dependent fashion, as demonstrated by regulation of expression and binding to endogenous target genes. Transcriptome analyses of wildtype colonic organoids stimulated with Rosiglitazone showed that lipid metabolism was the highest significant changed function, greatly mimicking the known function of PPARs and Rosiglitazone in vivo.  In conclusion, our results demonstrate that organoids constitutes a versatile and promising in vitro system to study NR biology and targeteability.

overall_design: Microarray analysis was performed on colonic organoids isolated from wildtype and intestinal epithelium-specific PPARγ mice that were treated with the PPARγ agonist Rosiglitazone or vehicle for 24 hrs.

first: Katja

last: Lange

first: Noortje

last: IJssennagger

first: Ingrid

middle: T

last: Bijsmans

first: Saskia

middle: W

last: van Mil

first: Johan

last: Jonker


title: Transcriptional signature of SPCH mutants compromised in the bHLH domain in response to brassinosteroids

status: Public on May 19 2017

city: Toledo

first: Alberto

last: de Marcos Serrano

state: Toledo

address: Av carlos III s/n, Edificio Sabatini Lab 0.8 F.V

institute: Universidad de Castilla-La Mancha

summary: In order to describe the molecular phenotype of spch-5 and to explore possible changes in gene expression underlying the effects on its epidermal development of BL treatment, we performed a microarray-based transcriptomic analysis. Using 3-days old seedlings grown in the absence or presence of BL, we compared the transcriptomic profiles of wild type (Col-0) and spch-5 plants. In addition, we analyzed a SPCHPPP-complemented spch-3 line to identify gene expression changes distinct of spch-5 or common to the two SPCH variants. We thus obtained six data sets (3 genotypes in two growth conditions).

overall_design: 3 days-old Arabidopsis plants grown in mock medium (DMSO) and brassinosteroids treatment (BL 50 nM) were used. Three genotypes were used: Col-0, spch-5 and SPCHPPP

last: de Marcos

first: Montaña

last: Mena

first: Carmen

last: Fenoll


title: Expression profiling in cellular miRNAs of human bone marrow stromal cells

status: Public on May 12 2017

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: The aging of bone marrow stromal cells (BMSCs) lead to decreased ability to maintain hematopoiesis. The aim of this study is therefore to determine the age-related change of cellular miRNAs in BMSCs.

overall_design: Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors:  62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. The Cellular miRNA profiling was done using a TaqMan low-density array (ABI), and Student’s t-test was used to determine statistical significance for comparisons between young and old groups using R software.


title: Viral Profiles in Sjogren's Syndrome

city: Bethesda

first: John

middle: A

last: Chiorini

state: Maryland

address: 10 Center Drive, Bldg 10, MSC1190

department: Molecular Physiology and Therapeutics Branch

institute: National Institute of Dental and Craniofacial Research, National Institutes of Health

summary: A study was designed to further define the viral landscape within Sjogren's Syndrome (pSS) affected salivary gland tissue to identify potential viral-mediated triggers in the pathogenesis of this autoimmune disease.

overall_design: Viral Probes for Vertebrate Infecting Viral Families

first: Melodie

last: Weller

first: Jay


title: NTRK3 kinase fusions in melanocytic tumors

city: San Francisco

first: Iwei

last: Yeh

state: California

address: 1701 Divisadero St. Ste 280

department: Dermatology

institute: UCSF

type: Genome variation profiling by genome tiling array

summary:
We analyzed the copy number profiles of clinical samples of diagnostically difficult melanocytic tumors. Of 1202 cases, 22 cases demonstrated relative gain of the 5' portion of NTRK3.  We further performed DNA or RNA sequencing on 12 of these cases and identified ETV6-NTRK3, MYO5A-NTRK3 and MYH9-NTRK3 fusions in the 8 cases in this cohort.
Analysis of genomic copy number of melanocytic tumors versus commericial pooled normal control.

overall_design: Select cases from clinical array comparative genomic hybridization with confirmed NTRK3 fusions.


title: HF001-A: Gene expression patterns in the progression towards canine copper-associated chronic hepatitis

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Copper is an essential trace element, but can become toxic when present in abundance. The severe effects of copper-metabolism imbalance are illustrated by the inherited disorders Wilson disease and Menkes disease. The Labrador retriever dog breed is a novel non-rodent model for copper-storage defects displaying identical phenotypic alterations and carrying mutations in genes known to be involved in copper transport. Besides disease initiation and progression of copper accumulation, the molecular mechanisms and pathways involved in copper accumulation and eventually progression towards copper associated chronic hepatitis still remains unclear. Using liver tissue of Labrador retrievers in different stages of copper-associated hepatitis, expression levels targeted at candidate genes as well as transcriptome microarrays, have shed light on involved molecular pathways. At the initial phase, viz. increased hepatic copper levels, transcriptomic alterations in livers revealed enrichment for cell adhesion, developmental, inflammatory, and cytoskeleton pathways. Upregulation of targeted MT1A and COMMD1 mRNA shows the livers first response to rising intrahepatic copper concentrations. In livers with copper-associated hepatitis mainly an activation of inflammatory pathways is detected. Once the hepatitis is in the chronic stage, transcriptional differences are found in cell adhesion adaptations and cytoskeleton remodelling. In view of the high similarities in hepatopathies between men and dog extrapolation of these dog data into human biomedicine seems feasible.

overall_design: Canine Gene Expression Microarrays V1 (Agilent Technologies, Belgium) representing 42,034 canine 60-mer probes in a 4x44K layout were used. The experiment was carried out in dye swap set-up in 18 Labrador retriever dogs (N: n=4, HC: n=5, HCH: n=4, HCCH: n=5, random samples per group). As reference material a pool of 10 healthy dogs were used. N: normal liver; HC: high copper group; HCH: high copper hepatitis group; HCCH: high copper chronic hepatitis group.

first: Karen

last: Dirksen

first: Bart

last: Spee

first: Louis

middle: C

last: Penning

first: Ted

middle: S

last: van den Ingh

first: Iwan

last: Burgener

first: Adrian

last: Watson

first: Jan

last: Rothuizen

first: Frank

middle: G

last: van Steenbeek

first: Hille

last: Fieten


title: Transcriptional profiling of Escherichia coli after addition of CORM-401 to aerobically and anaerobically growing cells

status: Public on May 31 2017

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min.
Samples were taken immediately prior to the addition of CORM-401 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CORM-401 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of CORM-401 under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for the aerobic condition with 2 technical (dye swap) repeats per biological repeat, and two biological repeats were perfomed for the anaerobic condition with 2 technical (dye swap) repeats per biological repeat.

first: Lauren

last: Wareham

first: Samantha

last: McLean


title: miRNA expression profiles of TIE2 expressing Monocytes (TEMs)

city: Shanghai

first: Xinjing

last: Wang

address: 536 Changle Road

institute: Shanghai First Maternity and Infant Hospital Corporation

summary: To identify the miRNA expressing profiles of TIE2 expressing Monocytes (TEMs), we have employed the Agilent Human miRNA 8×60K (Design ID:046064) microarray. Human peripheral blood mononuclear cells (PBMCs) in venous blood from healthy donors were isolated by Lymphoprep (Axis-Shield, Norway). Human monocytes in PBMCs, identified as cells that expressed CD14, were enriched by positive immunomagnetic selection using anti-CD14 MicroBeads (Miltenyi, Germany). TEMs (TIE2+CD14+) and TIE2-Monocytes (Tie2-CD14+) were then isolated by FACS-sorting (Aria II, BD Biosciences) using FITC-conjugated anti-CD14 (BD Biosciences, USA) and APC-conjugated anti-TIE2 (R&D System, USA) antibodies.Three TEMs samples together with their paried TIE2-Monocytes were detected.

overall_design: The gene expressions of three independent paried TEMs and TIE2- Monocytes samples from different donors were measured.

first: Xipeng


title: Targeting of WEE1 suppresses tumorigenecity and cancer stem cell-like phenotype in hepatocellular carcinoma

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: The current standard-of-care for advanced liver cancer is limited. Therefore, there is an urgent need for development of novel molecular targeted therapy. Increase of WEE1 kinase activity through an epigenetic regulation plays an important role in the development of hepatocellular carcinoma (HCC). Here we demonstrated that WEE1 siRNA silencing caused inhibition of HCC cell growth through blockade of cell cycle progression and induction of apoptosis. The anti-proliferative effects were driven by a subset of molecular alterations including the upregulation of cdk inhibitor p21 and the downregulation of AKT1, CDK2, cyclin B1 (CCNB1), PARP1 and GPAM which are functionally involved in control of cell cycle, apoptosis and lipid metabolism. Systemic delivery of a modified WEE1 siRNA encapsulated in lipid nanoparticles significantly inhibited human HCC growth in murine xenograft models, and increased mice survival. Wee1 silencing in tumor cells also resulted in a strong inhibition of lipogenesis (SREBP1C, FAS) and caused a marked decrease in fat accumulation. Of importance, knockdown of WEE1 dramatically reduced the portion of liver cancer stem cells (CSCs) population through co-downregulation of cancer stemness genes and weakened the capacity of sphere formation and the ability of cancer cell migration. Our findings suggest that the epigenetic modifier WEE1 functionally involve to HCC lipid metabolism and CSC-like phenotype maintenance and that molecular targeting of WEE1 may be an effective systemic therapy for prevention of tumor recurrence via elimination of CSCs in liver tumor microenvironment.

overall_design: HepG2 cells were treated with WEE1 siRNA and negative control siRNA for 48 hours and subjected to illumina microarray analysis.

first: Yun-Han

last: Lee

first: Deakwan

first: Snorri

last: Thorgeirsson


title: Genome-wide transcriptome and proteome analysis of the global GATA transcription factors AreA and AreB in Fusarium fujikuroi

status: Public on May 10 2017

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary: We performed genome-wide transcriptome and proteome analyses of the Fusarium fujikuroi wild type and ΔAREA and ΔAREB mutants under nitrogen limitation and excess. Microarray analysis revealed that each transcription factor regulates a total set of about 4200 genes under nitrogen limiting conditions with an enrichment of genes belonging to functional classes of primary/secondary metabolism, transporters, cell defense/virulence and transcription. Under nitrogen excess, AreA is not active as a transcriptional regulator, while AreB affects expression of about 4400 genes. Both transcription factors regulate a common set of about 2100 genes and most of the time work together either as positive or as negative regulators. Our proteomics analysis identified 446 AreA-regulated and 386 AreB-regulated proteins at nitrogen limitation and 138 AreA-regulated and 447 AreB-regulated proteins at nitrogen excess, respectively. Comparison of the proteome and transcriptome data indicates that many post-transcriptional regulations are facilitated by both GATA-factors, for example on enzymes involved in the TCA and glyoxylate cycle and the main glutamate/glutamine cycling.

overall_design: 3 strains were analysed, each with 2 biological replicates, low and high nitrogen condition

first: Andreas

last: Pfannmueller

first: Johannes

last: Leufken

first: Lena

last: Studt

first: Caroline

middle: B

last: Michielse

first: Christian

last: Sieber

last: Güldener

first: Susan

last: Hawat

first: Michael

last: Hippler

last: Fufezan

first: Bettina

last: Tudzynski


title: K562 ctrl vs K562  Saha  (Vorinostat; suberoylanilide hydroxamic acid) 6h

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

country: Italy

institute: IGB - Institute of Genetics and Biophysics - CNR

summary: miRNA expression profiling of K562  ctrl vs K562  treated Saha 5 µM 6h

overall_design: Two-condition experiment,  K NT (K562  ctrl)  vs K 6h s (K562  treated Saha 5 µM 6h) Biological replicates: 3 control, 3 treated, independently grown and harvested at 6 hours. One replicate per array.   LC sciences service

first: Carmela

last: Dell'aversana

first: Christopher

last: Eicken


title: Gene expression signatures for TCM Suduxing treated HepG2.2.15 cells compared to  Suduxing untreated HepG2.2.15 cells

status: Public on May 24 2017

city: Beijing

first: dongping

last: xu

address: #100 Xisihuan Middle Road, Beijing

institute: Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing

summary: To further analyze the gene expression profile regulated by TCM Suduxing, we employed whole genome microarray expression profiling as a discovery platform to identify the differentially expressed genes. Human hepatocellular carcinoma cell lines HepG2.2.15 cells were treated for 48 hr with 0.001 μg/ml and 0.01μg/ml Suduxing or without Suduxing(control samples) in vitro. The differentially expressed genes including all detected and normalized signal more than 8 were selected and 538 upregulated- and downregulated- genes  were identified between 0.01μg/ml dose and control samples.Afterwards, the differentially-expressed genes were analyzed using KEGG database (http://www.genome.jp/kegg/) and 10 genes related to HBV infection-related molecular interaction network were identified.

overall_design: Suduxing-regulated genes in HepG2.2.15 cells was measured at 48 hours after exposure to doses of 0 μg/ml, 0.001 μg/ml,and 0.01 μg/ml.Three independent experiments were performed at each time (48 hours) using different doses for each experiment.

first: Yan

last: Liu

first: Weiming

last: Yao

first: Dongping

last: Xu


title: Tight Regulation of the Interaction between Brassica napus and Sclerotinia sclerotiorum at the MicroRNA Level [array]

status: Public on May 16 2017

city: Hangzhou

first: cao

last: jiayi

address: 866 Yu Hang Tang Road

institute: Zhejiang University

summary: MicroRNAs are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MicroRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as NBS-LRR R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.

overall_design: To identify the miRNAome in B.napus, especially those involved in S. sclerotiorum response, one small RNA library was constructed from an equivalent mix of total RNA from S. sclerotiorum-inoculated and uninoculated B. napus leaves and was sequenced via the high-throughput Illumina Solexa platform.Target genes of the miRNAs were further identified by sequencing of degradomes.To understand response of oilseed rape miRNA to S. sclerotiorum, miRNA microarray analyses were performed to obtain miRNA expression profiles at both early (3 hpi) and late (12 hpi) stage after inoculation with S. sclerotiorum.

first: Xin-Zhong

last: Cai

first: Jia-Yi

last: Cao


title: Intra-macrophage Expression data of Francisella tularensis novicida U112

city: Hannibal

first: Siva

middle: Tej

last: Sarva

state: Missouri

address: 6500 Hospital Dr

department: Division of Pulmonary Critical Care

institute: Hannibal Regional Medical Group

summary: These samples are part of an experiment comparing the expression profiles of Francisella tularensis novicida grown in chemically defined medium and bacteria isolated 24 hours post infection of J774 macrophages to identify virulence factors

sample_organism: Francisella tularensis subsp. novicida U112

overall_design: Custom microarray submitted previously was used as the platform (GPL20119). The samples submitted here were compared with samples submitted previously (GSM1673555-57 in GSE68478) and differentially expressed genes during the intra-macrophage growth were identified.


title: U937 ctrl vs U937 Saha (Vorinostat; suberoylanilide hydroxamic acid) 6h

summary: miRNA expression profiling of U937 ctrl vs U937 treated Saha 5 µM 6h

overall_design: Two-condition experiment,  U NT (U937 ctrl)  vs U 6h s (U937 treated Saha 5 µM 6h) Biological replicates: 3 control, 3 treated, independently grown and harvested at 6 hours. One replicate per array.   LC sciences service


title: Human TNBC Cells 72h Treatment with 45nM OTSSP167 MELK Inhibitor vs. DMSO Control (SUM159)

city: Houston

first: Cecilia

middle: M.

last: Williams

state: Texas

address: 3605 Cullen Blvd

department: Center for Nuclear Receptors & Cell Signaling

institute: The University of Houston

summary: Microarray comparing TNBC cells treated for 72 hours with OTSSP167 MELK Inhibitor and control (DMSO)

overall_design: Two-condition arrays: SUM159 cells were treated with either 45nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).

first: Fahmi

last: Mesmar

first: Marisa

last: Simon


title: Human TNBC Cells 72h Treatment with 4.5nM OTSSP167 MELK Inhibitor vs. DMSO Control (SUM159)

overall_design: Two-condition arrays: SUM159 cells were treated with either 4.5nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).


title: Comparative ovarian microarray analysis of juvenile hormone-responsive genes in water flea Daphnia magna

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

summary: The freshwater zooplankton Daphnia magna has been used for the validation of chemical toxicity tests such as OECD Test Guideline 202 and 211. Previously, it has been demonstrated that treatment of juvenile hormones (JHs) or their analogs to mother daphnids could induce male offspring production. Based on this funding, a rapid screening method for detection of chemical with JH-activity was recently developed by using adult D. magna. This screening system can validate whether arbitrary chemical has JH-activity by investigating the male offspring inducibility. Although this short-term screening system will be possible to enhance a throughput of detection efficiency, JH-responsive genes in the ovary including developing oocytes at JH-sensitive period for male sex determination are still largely undescribed. Here, we conducted comparative microarray analyses using ovary treated by fenoxycarb (Fx; artificial JH agonist) and methyl farnesoate (MF; a putative innate JH in daphnids) to make the comprehensive gene catalogs in response to JH molecules in ovary including developing oocytes at JH-sensitive period for male sex determination. We successfully created the comprehensive ovarian gene catalogs in response to Fx and MF. Furthermore, we demonstrated that the hemoglobin genes are well-conserved JH-responsive element even in the ovary, and a potential toxic effect of JH agonist is suppression of vitellogenin gene expression that might cause reduction of offspring number. This is first report demonstrating the differential transcriptomics profiles between MF and artificial JH agonist in D. magna ovary, making it possible for understanding the tissue-specific mode-of-action of JH molecule.

overall_design: Microarray analyses using ovary treated by fenoxycarb and methyl farnesoate were conducted. Ovary samples consisted of three individuals per replicate, and quadruplicates were prepared for both treatments.

first: Timothy

first: Tomomi

last: Sato

first: Taisen

last: Iguchi


title: Gene expression profiles of TIE2 expressing Monocytes (TEMs)

status: Public on May 17 2017

first: Xinjing

last: Wang

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

summary: To identify the gene expressing profiles of TIE2 expressing Monocytes(TEMs), we have employed the Agilent lncRNA Gene Expression 4×180K(Design ID:042818) microarray. Human peripheral blood mononuclear cells (PBMCs) in  venous blood from healthy donors were isolated by Lymphoprep (Axis-Shield, Norway). Human monocytes in PBMCs, identified as cells that expressed CD14, were enriched by positive immunomagnetic selection using anti-CD14 MicroBeads (Miltenyi, Germany). TEMs (TIE2+CD14+) and TIE2-Monocytes (Tie2-CD14+) were then isolated by FACS-sorting (Aria II, BD Biosciences) using FITC-conjugated anti-CD14 (BD Biosciences, USA) and APC-conjugated anti-TIE2 (R&D System, USA) antibodies.Three TEMs samples together with their paried TIE2-Monocytes were detected.Expressions of sixteen genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

first: Xipeng


title: KASUMI-1ctrl vs KASUMI-1 Saha  (Vorinostat; suberoylanilide hydroxamic acid) 6h

first: carmela

last: dell'aversana

summary: miRNA expression profiling of KASUMI-1 ctrl vs KASUMI-1 treated Saha 5 µM 6h

overall_design: Two-condition experiment, KA NT (KASUMI-1 ctrl) vs KA 6h s (KASUMI-1 treated Saha 5 µM 6h) Biological replicates: 3 control, 3 treated, independently grown and harvested at 6 hours. One replicate per array.  LC sciences service

first: Carmela

last: Dell'aversana

first: Christopher


title: Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly [Array]

status: Public on May 06 2017

city: Nanning

first: Wang

last: Yikui

address: north road

institute: Institute Of Vegetable Research, Guangxi Academy Of Agricultural Sciences

summary: MicroRNAs (miRNAs), a class of endogenous, non-coding, ~21 nucleotide RNAs, regulate the expression of their target genes by mRNA cleavage or translation inhibition. In plants, miRNAs have been demonstrated to play crucial roles in regulating diverse cellular, physiological, and developmental processes. The identification of all the miRNAs is not yet complete; there are no studies on their possible links with the difference in heterostyly observed in eggplant (Solanum melongena L.).

overall_design: In the present study, small RNAs and their targets were identified in S-morph and L-morph styles during the development of eggplant pistil, using high-throughput small RNA microarray and degradome sequencing. Most of the miRNAs were found to be highly conserved in comparison to other plants. Among the 686 miRNAs on the microarray chip, 10 were demonstrated to be differentially expressed, among which ten were identified as pistil development-related miRNAs. The expression profiles of the eggplant miRNAs obtained through the microarray assays were validated by quantitative real-time polymerase chain reaction (qRT-PCR) for randomly selected miRNAs. We also annotated the target genes for differentially expressed miRNAs taking advantage of GO annotations and KEGG pathway analysis. And the pathway Cysteine and methionine metabolism, with a minimal P value, involved the largest number of miRNA target genes. The profiling of the miRNAs and their target genes described in the present study provides new information on the miRNA network during the development of eggplant pistil.

first: Yikui


title: Electroacupuncture mobilized cells demonstrate mesenchymal properties and potency in an equine model

status: Public on May 26 2017

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

summary: Electroacupuncture is the combination of traditional acupuncture and modern electrotherapy. Here we provide a mechanism for the beneficial effects of electroacupuncture and show that stimulation of the equine acupoints LI-4, LI-11 and GV-14 and Bai-hui results in mobilization of mesenchymal stem cells (MSCs) into the systemic circulation, which was accompanied by a time-dependent increase in plasma levels of norepinephrine (p=0.02). MSC differentiation was preferentially directed towards osteogenic rather than adipogenic lineages. Additionally, MSCs enhanced arterialization of blood vessels in vivo when implanted with human endothelial colony forming cells in oligomeric collagen matrices in NOD/SCID mice. When compared to equine bone marrow-derived MSCs or to equine adipose-tissue-derived MSCs, through the use of a microarray, these cells clustered separately. The electroacupuncture -mobilized cells showed increased expression of genes involved in cell growth and proliferation, compared to the bone marrow cells. These findings provide a new insight into the mechanism of the beneficial effects of acupuncture. Our findings suggest the involvement of neuronal regulation in the mobilization of reparative MSCs, and use of electroacupuncture at these designated points may be considered to treat acute and chronic inflammation following injury for which MSCs have been deemed beneficial.

overall_design: MSC mobilized and isolated from the blood of three horses that had been treated by electroacupuncture were compared to (i) control MSC, obtained from the bone marrow of three healthy horses and cultured under the identical conditions, and (ii)  adipose tissue-derived MSC from three healthy, control horses.

first: Tatiana

last: Salazar

first: Matthew

middle: R

last: Richardson

first: John

last: George

first: Ashay

last: Bhatwadekar

first: Yuanquin

last: Yan

first: S

last: McGorray

first: Alicia

last: Bertone

first: D

middle: O

last: Traktuev

first: K

last: March

last: Deng

first: M

last: Kim

first: B

last: McDavitt

first: Lung

last: Chang

first: Huisheng

last: Xie

first: Mervin

last: Yoder

first: Maria

last: Grant


title: Cyflumetofen resistance in the two-spotted spider mite Tetranychus urticae

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
Cyflumetofen is a novel acaricide on the international market with an unknown mode of action.
Under laboratory conditions, we selected for high levels of cyflumetofen resistance in a susceptible mite strain and performed genome-wide gene-expression analysis.
Differential expression between the resistant and susceptible strain was identified to study on the molecular level how mites develop resistance to this novel acaricide.
Our results show that in T. urticae, the selection for cyflumetofen resistance resulted in a differential expression in only a limited number of genes.
This transcriptomic study provides an unbiased look how cyflumetofen resistance triggers selection on the transcriptional level in T. urticae.

overall_design: 4 replicates for one comparison; per replicate 150 mites were pooled. Mites of the derived cyflumetofen resistant spider mite (cy5-labelled) were directly compared to mites of the ancestral susceptible strain (cy3-labelled).

first: Mousaalreza

last: Khalighi

first: Wannes

last: Dermauw

first: Thomas

last: Van Leewen


title: miRNA expression analysis of SAHA-treated leukemia cell lines

first: carmela

last: dell'aversana

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

overall_design: Refer to individual Series


title: Isocaloric intake of diets differing in macronutrient content (high protein or high fat) in adult rats indicate adverse effects as analysed by hepatic transcriptomics

city: Wageningen

first: Evert

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Intake of high-protein (HP) diets has increased over the last years, mainly due to their popularity for body weight control. Liver is the main organ handling ingested macronutrients and it is associated with the beginning of different pathologies. We aimed to deepen our knowledge on molecular pathways affected by long-term intake of an HP diet. We performed a transcriptome analysis on liver of rats chronically fed with a casein-rich HP diet and analyzed molecular parameters related to liver injury. Chronic increase in the dietary protein/carbohydrate ratio up-regulated processes related with amino acid uptake/metabolism and lipid synthesis, promoting a molecular environment indicative of hepatic triacylglycerol (TG) deposition. Moreover, changes in expression of genes involved in acid–base maintenance and oxidative stress indicate alterations in the pH balance due to the high acid load of the diet, which has been linked to liver/health damage. Up-regulation of immune-related genes was also observed. In concordance with changes at gene expression level, we observed increased liver TG content and increased serum markers of hepatic injury/inflammation (aspartate transaminase, C-reactive protein and TNF-alpha). Moreover, the HP diet strongly increased hepatic mRNA and protein levels of HSP90, a marker of liver injury. Thus, we show for the first time that long-term consumption of an HP diet, resulting in a high acid load, results in a hepatic transcriptome signature reflecting increased TG deposition and increased signs of health risk (increased inflammation, alterations in the acid–base equilibrium and oxidative stress). Persistence of this altered metabolic status could have unhealthy consequences.

overall_design: Wistar wildtype male rats, aged 8 weeks, received a low fat diet, high protein or high fat diet for 4 months. After sacrification, livers were dissected, and immediately snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 4x44K microarrays.

first: Ruben

last: Diaz

middle: M

first: Jaap

last: Keijer

first: Paula

last: Oliver

first: Andreu

last: Palou


title: Ontogenic gene expression profiling during pig hepatogenesis and effects of intrauterine growth retardation on liver development

status: Public on May 25 2017

city: Beltsville

first: Jakub

last: Kwintkiewicz

state: MD

address: 10300 Baltimore Ave. BARC-East

institute: USDA

summary: To better understand hepatogenesis, comprehensive ontogenic gene expression profiling was performed to determine baseline expression patterns associated with liver development. Liver was collected from the greatest weight fetus of four distinct unilaterally hysterectomized:ovariectimized gilts at prenatal day (PND) 37, 50, 70, and 110. In addition, liver from smallest weight fetuses (runts) were collected to investigate effects of intra-uterine growth retardation (IUGR) on liver development. Total RNA was isolated, mRNA amplified and subjected to microarray analysis (Agilent). Three comparisons were performed: PND50 vs. PND37, PND70 vs. PND50 and PND110 vs. PND70; only genes whose expression, between at least two time points, was ± 1.5 fold with P < 0.05 were characterized further. A total of 6061 annotated genes exhibited altered expression: 648 down- and 341 up-regulated at PND37 vs. PND50; 666 down- and 1399 up-regulated at PND70 vs. PND50; and 1564 down- and 1443 up-regulated at PND110 vs. PND70. Thirty-five transcripts were selected for validation by absolute quantitative PCR; they clustered into five functional categories: i) hematopoietic and early liver function, ii) extracellular matrix, iii) hepatocyte function, iv) biliary function, and v) transcription factors. Another four comparisons were made to elucidate effects of IUGR: greatest weight (control) vs. smallest weights (runt) on PND 37, 50, 70 and 110. A total of 412 were differentially exp[ressed. 29 down and 25 up-regulated at PND37, 72 down and 52 up-regulated at PND50, 20 down and 33 up-regulated at PND70 and 48 dwon and 45 up-regulated at PND110. 6 genes were further analyzed by qPCR. They all clustered into serum proteins category.

overall_design: Gene expression in pig fetal liver was analyzed on prenatal days: 37, 50, 70 and 110. Four liver samples from four independent pregnancies were collected at each time point.

first: C

last: Talbot Jr

first: LeAnn

last: Blomberg


title: FOXP3-mediated inhibition of a global gene regulator is required for maintaining Treg cell commitment

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Regulatory T (Treg) cells are characterized by the forkhead transcription factor FOXP3. Mutations in FOXP3 cause autoimmunity in mice and humans. Here, Treg cells as well as conventional T cells were isolated from B-CLL patients and analyzed by global gene expression analysis in order to identify biological differences in Treg cells of CLL patients.

overall_design: Freshly isolated peripheral CD4+ T cells of CLL patients, separated into CD25 negative and positive subpopulations.

first: S

last: Classen

first: J


title: Regulatory T-cell comittment is ensured by inhibition of the global gene regulator SATB1

summary: Regulatory T cells (Treg) are potent inhibitors of the activation of the immune system. Within these experiments we characterize the transcriptional profile of expanded Treg cells subjected to CD3CD28 short-time activation and subpopulations of CD4+ T cells.

overall_design: Freshly isolated CD4+ T cell subpopulations were compared to CD4+ T cells separated into CD25 negative and positive subpopulations activated under various conditions.

first: Marc

last: Beyer

last: Chemnitz

first: A

last: Gaarz


title: Human TNBC Cells 48h Treatment with OTSSP167 MELK Inhibitor vs. DMSO Control

first: Cecilia

last: Williams

summary: Microarray comparing TNBC cells treated for 48 hours with OTSSp167 MELK Inhibitor and control (DMSO)

overall_design: Two-condition arrays: MDA-MB-231 cells were treated with either 4.5nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 48h. Two biological replicates, one per array, with a dye swap (technical replicate).

first: Marisa

last: Simon

first: Fahmi

last: Mesmar


title: Human TNBC Cells 72h Treatment with 4.5nM OTSSP167 MELK Inhibitor vs. DMSO Control

overall_design: Two-condition arrays: MDA-MB-231 cells were treated with either 4.5nM OTSSP167 MELK Inhibitor or 0.045% DMSO for 72h. Two biological replicates, one per array, with a dye swap (technical replicate).


title: Effects of β-catenin knockdown on microRNAome in highly metastatic ovarian cancer cells

status: Public on Apr 18 2017

city: Hong Kong

first: Kit Yan

last: To

address: Pokfulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: We performed microRNA microarray to investigate the role of β-catenin in regulating microRNAs during ovarian cancer metastasis.

overall_design: Highly metastatic (HM) ovarian cancer cells derived form HEYA8 cell line were transiently transfected with non-specific (NS) or β-catenin-specific siRNA, followed by RNA extraction and analyses with the Affymetric miRNA 4.0 microarry.

first: Alice

last: Wong

first: Sally


title: DNA methylation profiling of prostate cancer

status: Public on Apr 30 2017

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

type: Methylation profiling by genome tiling array

summary: DNA methylation analysis of paired prostate tumor and noncancerous tissues was perform in order to identify potential DNA methylation biomarkers for prostate cancer diagnostics and prognosis. Based on comparison of tumors versus noncancerous tissues and cases with and without biochemical disease recurrence (BCR), several gene targets were selected for more detailed analysis. Differences in methylation were further confirmed by means of methylation-specific PCR and significantly correlated with gene expression. Survival analysis indicated various combinations of DNA methylation biomarkers as significant prognosticaters of time to BCR, therefore, showing their potential clinical significance.

overall_design: DNA methylation profile was analyzed in 9 pairs of tumor and noncancerous tissues of prostate cancer patients (18 samples in total). Biochemical disease progression was observed in 4 of 9 patients. No biolocigal replicates were performed.


title: miRNA expression profiles of estrogen-dependent and estrogen deprivation-resistant MCF-7 breast cancer cell lines

status: Public on Mar 01 2017

city: Stuttgart

first: Hiltrud

last: Brauch

address: Auerbachstr. 112

institute: Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology

summary: A series of MCF-7 variants were previously developed that are estrogen-dependent for growth (MCF-7:WS8 cells), or resistant to estrogen deprivation/vulnerable to fast (MCF-7:5C) and delayed (MCF-7:2A) E2-inducible apoptosis. To identify miRNAs associated with aromatase inhibitor (AI)-resistance and vulnerability to E2-induced apoptosis, estrogen deprivation-resistant 5C and 2A cells were compared to estrogen-dependent WS8 cells and among each other.

overall_design: Total RNA from MCF-7:WS8, MCF-7:2A and MCF-7:5C cells was extracted. Three biological replicates per cell line derivative were performed. The profiling series included a total of 12 samples, preprocessed data from 9 samples (triplicates for WS8, 2A and 5C) were extracted for this study. Hybridization of biotin-labelled RNA was performed on Affymetrix GeneChip miRNA_2.0 Arrays.

first: Reiner

last: Hoppe

first: Ping

last: Fan

first: Stefan

last: Winter

first: Virgil

last: Jordan


title: miRNAs in colorectal cancer metastasis

city: Madrid

first: Ignacio

last: Casal

state: Madrid

address: Ramiro de Maeztu 9

department: Department of Cellular and Molecular Medicine.

institute: Centro de Investigaciones Biológicas

summary: Metastasis is a complex process involving multiple steps. We were interested in the role of microRNAs (miRNAs) in the process of liver colonization by colorectal cancer cells. We hypothesized that the comparison between non-metastatic versus metastatic isogenic cell line should thus offer valuable insight to the molecular mechanisms involved in developing metastatic behavior. KM12C/KM12SM and SW480/SW620 are probably the best available models of isogenic cell lines differing in metastatic properties for colorectal cancer. Our first goal was to identify miRNAs that contribute to the metastatic traits of the isogenic colorectal cancer cell lines, KM12C/KM12SM and SW480/SW620. Total RNA was extracted from cells using the mirVana kit (Ambion). Total RNA (1 µg) from KM12C and SW480 (poorly metastatic) and KM12SM and SW620 (highly metastatic) cells was used to analyze the global miRNA expression profiling with TaqMan Megaplex human array A (v2.0) and B (v3.0) (Applied Biosystems).

overall_design: We compared miRNA expression profiles between colorectal cancer cell lines with different metastatic properties and then identified target proteins of the dysregulated miRNAs

first: I

last: Torres

last: García-Palmero


title: lncRNA-miRNA-mRNA expression profiles in esophageal squamous carcinoma tissues and adjacent normal tissues

status: Public on Mar 28 2017

city: Nanjing

first: chenyu

last: lin

address: Longmian Road No.639

department: Life science

institute: China Pharmaceutical University

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

platform_organism:
Homo sapiens
synthetic construct


title: Specific expression of microRNAs and snoRNAs characterize ERG-related B cell precursor acute lymphoblastic leukemia [microRNA]

status: Public on Mar 21 2017

city: Padova

first: Elena

last: Vendramini

address: Via Giustiniani, 3

department: Woman and Child's Health

institute: University of Padova

summary: ERG-related B cell precursor acute lymphoblastic leukemia (BCP ALL) is a recently described childhood ALL subtype characterized by aberrant ERG protein expression and highly recurrent ERG intragenic deletions. Several studies reported a remarkably favourable outcome for ERG-related BCP-ALL despite a high incidence of apparently inauspicious IKZF1 aberrations.  In this study we investigated by integrative genomic analysis the main features of the ERG-related group in a cohort of B-others BCP ALL patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a specific microRNA and snoRNA signature that characterizes ERG-related patients with up-regulation of the miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster.  Given the current lack of parameters for a comprehensive classification we suggest toexploit the noncoding RNAs signature for differential diagnosis of ERG-related patients.

overall_design: Noncoding RNA profiling by array. Class comparison between ERG-related and non-ERG-related patient groups.

first: Geertruy

last: te Kronnie


title: Comparative expression of bone metastasis clones and its parental cells on Chinese lung adenocarcinoma cell line SPC-A-1 and human larger cell lung cancer cell line NCI-H460 by cDNA array.

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

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

institute: GEORGE WASHINGTON UNIV

summary: Chinese lung adenocarcinoma cancer cells (SPC-A-1) and human larger cell lung cancer cells (NCI-H460) were injected into left cardiac ventricle of nude mice for bone metastases model, respectively. Bone metastatic lesions were detected by bone scintigraphy with 99mTc-methylene diphophonate, removed bone metastatic lesions for cell primary culture, chromosome analysis for determine the bone metastatic cells have a characterization of unchanged humanization, in the anesthesia death mice. Through eight in vivo ~ in vitro selections, the 4th, 8th generation cells of SPC-A-1, 8th generation cells of NCI-H460 and their parental cells were used for microarray analysis, respectively.

overall_design: Bone metastatic clones 4th and/or 8th generation SPC-A-1 vs. SPC-A-1, 8th generation NCI-H460 vs. NCI-H460, respectively. Biological replicates: one replicate for every group, independently grown and harvested. One replicate per array.

first: Shunfang

first: Jianzhong

last: Su

first: Meiping

last: Shi

first: Limin

first: Xiumu

last: Jin

first: Lanxiang

last: Zhao

first: Wenhui

last: Xie


title: lnc-mg is a long non-coding RNA that promotes myogenesis [miRNA Array]

city: guangzhou

first: jiafan

last: liu

address: No. 601 West Whampoa Road, Tianhe District, guangzhou

institute: Jinan University

summary: Recent studies have indicated important roles for long noncoding RNAs (lncRNAs) as potential essential regulators of myogenesis and adult skeletal muscle regeneration. However, in vivo, the role and mechanism of lncRNAs in myogenic differentiation of adult skeletal muscle stem cells (MuSCs) and myogenesis are still largely unknown. Here, we identified a skeletal muscle specific-enriched lncRNA (myogenesis-associated lncRNA, short for lnc-mg). In vivo, skeletal muscle conditional knockout of lnc-mg resulted in muscle atrophy and the loss of muscular endurance during exercise. Alternatively, skeletal muscle-specific overexpression of lnc-mg promoted muscle hypertrophy in mice. In vitro analyses of primary skeletal muscle cells isolated from mice showed that expression of lnc-mg was increased gradually during myogenic differentiation and overexpressed lnc-mg improved cell differentiation. Mechanistically, lnc-mg promoted myogenesis, by functioning as a competing endogenous RNA (ceRNA) for miR-125b to control protein abundance of Igf2. These findings identify lnc-mg as a novel and important noncoding regulator for muscle cell differentiation and skeletal muscle development. In order to test the hypothesis that lnc-mg may function as a ceRNA leading to the liberation of corresponding miRNA-targeted transcripts, microarrays were performed to detect miRNAs expression in lnc-mg overexpression and lnc-mg knockdown C2C12 cells.

overall_design:
Total RNAs was extracted from cells of lnc-mg overexpression or lnc-mg knockdown by TRIzol Reagent (Life Technologies). Then the RNA quality was assessed by formaldehyde agarose gel electrophoresis, quantified spectrophotometrically and Agilent 2200 Bioanalyzer (Agilent, USA). Then labelled on Cy5 using ULS.

The sequence of lnc-mg is available on GSE93276.

first: Jiafan

last: Liu


title: The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens

status: Public on Feb 28 2017

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: A first line of defense against pathogen infections is the recognition of pathogen-associated molecular patterns (PAMPs), leading to PAMP-triggered immunity (PTI). MicroRNAs (miRNAs) are primarily known as central regulators of plant development, but a few have also been connected to immunity. We have found that several fungal pathogens lead to a reduction in miR396 levels, suggesting that miR396 are negative regulators of downstream defense responses. In agreement with such as scenario, constitutive attenuation of miR396 activity enhances resistance to infection by fungal pathogens, while increased miR396 activity reduces pathogen resistance. We conclude that constitutive reduction of miR396 levels confer a primed state for enhanced defense reactions

overall_design: MIM396 Arabidopsis thaliana samples infected with Plectosphaerella cucumerina fungus and in control conditions. 3 biological replicates.

last: Baldrich

first: Mauricio

last: Soto-Suarez

first: Detlef

last: Weigle

last: Rubio-Somoza

first: Blanca

last: San Segundo


title: Transcriptome analysis of hopanoid biosynthetic mutant of Rhodopseudomonas palustris TIE-1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To understand the role of pentacyclic triterpenoids, we used whole genome microarray expression profiling of wild type and hopanoid deficient mutant. Hopanoid deficiency may leads to weakened structural integrity of cell membrane and may affect the other structures within or spanning cell envelope resulting in impaired lipid ordering which is linked to permeability, fluidity, permeability barrier, ion conductivity, cell potential, cell signalling and lateral segregation. Hopanoids are involved in antibiotic resistance and tolerance to stress, but the precise understanding is lacking. Understanding the role of hopanoids in shaping membrane properties would provide an important step towards bridging this gap.

overall_design: Organism : Rhodopseudomonas palustris, Agilent custom R palustris Gene Expression  8x15k Array (AMADID: 075878) designed by Genotypic Technology Private Limited

first: Tushar

last: Lodha

first: Venkata

last: Ramana


title: AMKL chimeric transcription factors are potent inducers of leukemia

status: Public on Feb 20 2017

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary: Acute megakaryoblastic leukemia in patients without Down syndrome is a rare malignancy with a poor prognosis. RNA sequencing of fourteen pediatric cases previously identified novel fusion transcripts that are predicted to be pathologic including CBFA2T3-GLIS2, GATA2-HOXA9, MN1-FLI, and NIPBL-HOXB9. In contrast to CBFA2T3-GLIS2 which is insufficient to induce leukemia, we demonstrate that the introduction of GATA2-HOXA9, MN1-FLI1 or NIPBL-HOXB9 into murine bone marrow induces overt disease in syngeneic transplant models. With the exception of MN1, full penetrance was not achieved through the introduction of fusion partner genes alone, suggesting that the chimeric transcripts possess a unique gain of function phenotype. Leukemias were found to exhibit elements of the megakaryocyte erythroid progenitor (MEP) gene expression program, as well as unique leukemia-specific signatures that contribute to transformation. Comprehensive genomic analyses of resultant murine tumors revealed few cooperating mutations confirming the strength of the fusion genes and their role as pathologic drivers. These models are critical for both the understanding of the biology of disease as well as providing a tool for the identification of effective therapeutic agents in preclinical studies.

overall_design: To gain insight into the genetic etiology of AMKL patients without Down syndrome, we previously performed transcriptome sequencing on diagnostic blasts from a discovery cohort of 14 pediatric cases and substantiated our findings in a recurrency/validation cohort. This analysis confirmed the unique biology of this disease as evidenced by novel fusion transcripts including CBFA2T3-GLIS2, GATA2-HOXA9, MN1-FLI1, and NIPBL-HOXB9.  To confirm their role in oncogenesis and gain insight into the mechanism whereby these novel fusions promote disease, we introduced each of them as well as their individual gene counterparts into murine hematopoietic progenitor cells that were assessed in murine syngeneic transplantation models. Accompanying histologic, immunophenotypic, and genome-wide molecular characterization of resultant tumors delineated common and unique modes of leukemogenesis.

first: Jinjun

last: Dang

first: Stephanie

last: Nance

first: Jing

last: Ma

last: Cheng

first: Michael

middle: P

last: Walsh

first: Peter

last: Vogel

first: John

last: Easton

first: Guangchun

last: Song

last: Rusch

first: James

last: Downing

first: Tanja

last: Gruber


title: Effect of addition of cysteine to isoniazid treatment of Mycobacterium tuberculosis

status: Public on Mar 27 2017

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv after 4 hours of combination isoniazid and cysteine treatment relative to treatment with isoniazid alone.

overall_design: Two condition experiment, 4 hour isoniazid/cysteine treated vs. isoniazid alone. Biological replicates: 3 of each condition, independently grown and harvested. One replicate per array, third array is a dye-flip.


title: microRNA expression profile of NPTr cells infected with swine H1N1/2009 influenza A virus

status: Public on Mar 24 2017

city: Wuhan

first: Shishuo

last: Zhang

address: Shizishan Street

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary:
In recent years, the roles of microRNAs playing in the regulation of influenza viruses replication caused researchers' much attenion. However, much work focused on the interactions between human, mice or chicken microRNAs with human or avian influenza viruses rather than the interactions of swine microRNAs and swine influenza viruses.
To investigate the roles of  swine microRNAs playing in the regulation of swine influenza A virus replication, the microRNA microarray was performed to identify which swine microRNAs were involved in swine H1N1/2009 influenza A virus infection.

overall_design: Two pools of total RNA were extracted from the swine H1N1/2009 influenza A virus infected or uninfected NPTr cells and hybrided on Affymetrix GeneChip miRNA 2.0 Array.

first: Hongbo

last: Zhou


title: MaHo002: Epstein-Barr virus miRNA BART16 suppresses type I interferon signaling

status: Public on Apr 05 2017

city: Utrecht

first: Marian

last: Groot Koerkamp

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: The prototypic gammaherpesvirus Epstein-Barr virus (EBV) is carried by over 90% of the adult human population. Although infection often proceeds asymptomatically, the virus is causally involved in infectious mononucleosis and various malignancies. Like all herpesviruses, EBV establishes a lifelong latent infection in its human host. To successfully establish a persistent infection and spread to new hosts, EBV needs to avoid clearance by the host immune system. In addition to ~100 proteins, some of which perform immunomodulatory functions, EBV encodes over 40 mature miRNAs. Cellular miRNAs regulate diverse cellular processes, but the functions of the EBV miRNAs remain poorly understood. In this study, we identify EBV-encoded miR-BART16 as a novel viral immune evasion factor that interferes with host type I IFN responses. miR-BART16-5p downregulates the cellular histone acetyltransferase CBP (CREBB-binding protein) by directly targeting the CBP-encoding mRNA. CBP plays an important role in the type I IFN signaling pathway. Inhibiting endogenously expressed miR-BART16 in EBV-transformed B cells and gastric carcinoma cells results in increased CBP levels. Consistent with the important role of CBP in type I IFN signaling, miR-BART16 expression interferes with ISRE-promoter activity and production of interferon-stimulated genes in response to IFN-α treatment. These combined data show that EBV employs miRNAs to modify IFN-induced gene transcription. Given the importance of the host IFN system in the antiviral defence, obstructing this response may provide a way for EBV to favour viral replication and could play an etiological role in EBV-associated malignancies.

overall_design: 293T-ISRE-mCherry cells were lentivirally transduced to coexpress miR-BART16 and the miR-BART19-14 helper cluster or the helper cluster alone as control. Sample versus common reference (cell line HK-1) hybridizations were performed on human whole genome gene expression microarrays V2 (Agilent, Belgium), in balanced dye-swap on 2 biological replicates per group.

first: Marjolein

last: Hooykaas

first: Michiel

last: van Gent

first: Ingrid

last: Boer

first: Elisabeth

last: Kruse

first: Dik

last: van Leenen

last: Koerkamp

first: Frank

last: Holstege

first: Maaike

middle: E

last: Ressing

first: Emmanuel

last: Wiertz

first: Robert

last: Lebbink


title: Temporal changes in the rainbow darter (Etheostome caeruleum) liver transcriptome associated with sewage treatment plant upgrades in the Grand River, Ontario

status: Public on Feb 21 2017

city: Waterloo

first: Patricija

last: Marjan

state: Ontario

address: 200 University Avenue  West

department: Department of Biology

country: Canada

institute: Univesity of Waterloo

summary: In this study, adult male rainbow darter were collected from three sites in the Grand River in the fall season for four consecutive years (2011-2014), from 3 sites: a reference site (US2) located in the non-urbanized area, and two exposure sites (DSW and DSK1) located dowstrem of two secondary wastewater treatment palnts (WWTP) (Waterloo and Kitchener). Kitchener WWTP has been undergone infrastructure upgrades that were initiated in the summer of 2012. The goal of this project was to see whether  the implemented upgrades can be reflected in the liver transcriptome response indicative of recovery.The RNA from male rainbow darter was exctracted from liver tissue and used for further gene expression analysis.

overall_design: There were 86 samples processed, 6-7 samples per site. Fish were collected in 2011, 2012, 2013 and 2014 dowstream of Waterloo WWTP (DSW) and  Kitchener WWTP (DSK1) representing exposure sites;  US2 males were used as controls and all the comparisons in gene expression were done using fish from this site, using a one way-ANOVA within each year. There was a total of 79 microarrays subjected to bioniformatics analysis (7 arrays did not pass the quality standards).

first: Christopher

middle: J

last: Martyniuk


title: miRNA Microarray analysis of TNFα induced senescence in Human umbilical vein endothelial cells

status: Public on Mar 10 2017

city: Barcelona

first: Renuka

last: Kadhaya Pillai

state: Barcelona

address: Passeig Vall d’Hebron

department: Aging Basic Research Group, Molecular Biology and Biochemistry Research Center for Nanomedicine

institute: CIBBIM-Nanomedicine

summary: Cellular senescence is a key cell-fate program that leads to an essentially irreversible proliferative arrest in potentially damaged cells. Cytokine production and signaling play a significant role in senescence. Tumor necrosis factor-alpha (TNFα), an important pro-inflammatory cytokine secreted by some senescent cells, can induce senescence in mouse and human cells. However, downstream signaling pathways and key regulatory genes linking inflammation to senescence are not fully characterized. Using human umbilical vein endothelial cells (HUVECs) as a model, we show TNFα induces permanent growth arrest and increased senescence markers such as p21, p16, and senescence-associated β-galactosidase (SA-β-gal), accompanied by persistent DNA damage and ROS. By gene expression profiling and pathway analysis, we identify the crucial involvement of inflammatory networks, an interferon signature, and persistent activation of the Janus kinase (JAK) /signal transducer and activator of transcription (STAT) pathway in TNFα-mediated senescence. TNFα initiates a STAT-dependent autocrine loop leading to sustained inflammation, DNA damage, and expression of interferon response genes to lock cells into senescence. Further, we show STAT1/3 activation is necessary for cytokine and ROS production during TNFα-induced senescence. However, inhibition of STAT1/3 did not rescue cells from TNFα-mediated senescence. Rather, blockade of STAT activation accelerated senescence, suppressed genes that control the cell cycle, and modulated TNFα-induced senescence. Our findings suggest a positive feedback mechanism via a STAT pathway that sustains cytokine production and reveal a reciprocal regulatory role of JAK/STAT in TNFα-mediated senescence.

overall_design: Human umbilical vein endothelial cells (HUVECs) were untreated or treated TNFα (5ng/ml) continuously for 26 days or (Passage 2 -Passage 8/ Passage 3- Passage9). Gene expression of TNFα treated/senescenced cells were compared to corresponding passaged untreated or control cells.

first: Francesc

last: Miro-Mur

first: Simo

last: Schwartz Jr


title: In search of genes necessary to induce cytoskeletal changes in B cells

city: Stockholm

first: Eva

last: Severinson

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

summary: We sought to identify genes necessary to induce cytoskeletal change in B cells. Using gene expression microarray, we compared B cells stimulated with Interleukin-4 (IL-4) and anti-CD40 antibodies that induce B cell spreading, cell motility, tight aggregates, and extensive microvilli with B cells stimulated with lipopolysaccharide (LPS) that lack these cytoskeletal changes.

overall_design:
3 animals per group were analysed in groups 1 and 3, 2 animals per group were analysed in group 2.
Group 1 = C57BL6 spleen B cells stimulated with anti-CD40+IL-4 for 2 days (alfa1, alfa2, alfa3), Group 2 = non-cultured C57BL6 spleen cells (B6-1, B6-4, B6-6) and Group 3 = C57BL6 spleen B cells stimulated with Lipopolysacharide (LPS) for 2 days (LPS1, LPS2, LPS3).

first: Lisa

last: Westerberg

first: Natalija

last: Gerasimcik


title: Genome-wide effects of the maternal embryonic leucine zipper kinase (MELK) in triple-negative breast cancer cells indicate context-dependent effects and p53 as a key determinant

status: Public on May 01 2017

city: Houston

first: Cecilia

last: Williams

address: 3605 Cullen Blvd

institute: The University of Houston

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

overall_design: Refer to individual Series


title: lnc-mg is a long non-coding RNA that promotes myogenesis [lncRNA]

first: jiafan

last: liu

summary: Recent studies have indicated important roles for long noncoding RNAs (lncRNAs) as potential essential regulators of myogenesis and adult skeletal muscle regeneration. However, in vivo, the role and mechanism of lncRNAs in myogenic differentiation of adult skeletal muscle stem cells (MuSCs) and myogenesis are still largely unknown. Here, we identified a skeletal muscle specific-enriched lncRNA (myogenesis-associated lncRNA, short for lnc-mg). In vivo, skeletal muscle conditional knockout of lnc-mg resulted in muscle atrophy and the loss of muscular endurance during exercise. Alternatively, skeletal muscle-specific overexpression of lnc-mg promoted muscle hypertrophy in mice. In vitro analyses of primary skeletal muscle cells isolated from mice showed that expression of lnc-mg was increased gradually during myogenic differentiation and overexpressed lnc-mg improved cell differentiation. Mechanistically, lnc-mg promoted myogenesis, by functioning as a competing endogenous RNA (ceRNA) for miR-125b to control protein abundance of Igf2. These findings identify lnc-mg as a novel and important noncoding regulator for muscle cell differentiation and skeletal muscle development. In order to identify functional lncRNAs correlating with myogenesis, microarrays were performed to detect the lncRNAs expression profile in undifferentiated  MuSCs (GM, growth media/GM) ) and differentiated MuSCs (DM, differentiation media/DM).

overall_design: Total RNAs was extracted from undifferentiated  MuSCs (GM, growth media/GM) ) and differentiated MuSCs (DM, differentiation media/DM) by TRIzol Reagent (Life Technologies). Then the RNA quality was assessed by formaldehyde agarose gel electrophoresis, quantified spectrophotometrically and Agilent 2200 Bioanalyzer (Agilent, USA). Then labelled on Cy5 using ULS.

first: Jiafan

last: Liu


title: Gene regulation network of drought escape, avoidance and tolerance strategies in black poplar

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

summary: Drought is one of the most important environmental fluctuations affecting tree growth and survival. Therefore, understanding of physiological and transcriptomic responses of trees to this stress factor will make important contributions to forest health and productivity. Here, we report comparative physiological and microarray based transcriptome analysis between drought resistant (N.62.191) and drought-sensitive (N.03.368.A) black poplar genotypes under well-watered (WWP), moderate drought (MD), severe drought (SD) and post drought re-watering (PDR) conditions. In the study, sensitive genotype exhibited a drought escape strategy with lower leaf water potential, higher reactive oxygen production, complete leaf abscission and subsequent terminal shoot necrosis under drought stress. On the other hand, resistant genotype had a dehydration tolerance indicating highly delayed leaf abscission under drought and fast growing capacity during re-watering conditions.  Gene ontology enrichment analysis attributed drought susceptibility of black poplar to significant up-regulation of genes functional in transcription regulation (AP2/ERF, NAC and WRKY), cell wall modification (Expansins), fatty acid metabolism (enoyl-ACP reductase, lipid transport protein particle), protein degradation (endopeptidases), ethylene synthesis (1-aminocyclopropane-1-carboxylate) and riboflavin synthesis (GTP cyclohydrolase II) under drought stress. Transcriptomic comparison indicated significant down-regulation of photosynthesis, electron transport and carbohydrate metabolism related genes under drought stress in sensitive genotype. Although, similar reduction in carbohydrate metabolism was also recorded for resistant genotype, genes related with photosynthesis and electron transport systems were not down regulated even under SD for this genotype. Resistant genotype specific up-regulation of small heat shock proteins (sHSP) and bark storage proteins revealed importance of protein protection and nitrogen remobilization under drought stress, respectively. This is the first study associating BSP production to delayed leaf abscission and drought tolerance in trees.

overall_design: Total RNA used in microarray experiment was isolated from the leaves of four seedlings for each drought escaped, avoided and tolerant genotype at well watered period, moderate drought, severe drought and post drought rewatering period. These four isolated RNA were assigned randomly to two biological replicates. In each replicate, two individuals contributed equally to the pool of total RNA and each replicate loaded onto one Affymetrix poplar Gene Chips for each genotype. Total 24 Affymetrix poplar GeneChips (3 genotypes × 4 water availability regimes × 2 biological replicates) were used for transcriptional analysis.

first: Kubilay

last: Yildirim

first: Zeki

last: Kaya


title: Spatail gradient approach application in assessing changes in the rainbow darter (Etheostome caeruleum) liver transcriptome in the Grand River, Ontario

summary: In this study, adult male rainbow darter (Etheostoma caeruleum) were collected from nine sites located at different distances from two wastewater treatment plants (WWTPs) in the Grand River, Ontario, Canada. The goal of this project was to see if the liver transcriptome of fish residing downstream of the two WWTPs  differs from the non-exposed fish. Further, this research was also addressing the affects of differnent reference site selection on gene expression patterns, and their subsequent interpretation.The RNA from male rainbow darter was exctracted from liver tissue and used for further gene expression analysis.

overall_design: Fish collections were conducted in the fall of 2013 (Oct-Nov). Experimental design included 9 sites: 3 reference sites (US1, US2 and US3), located upstream, in the non-urbanized area; an exposure site located downstream of Wateloo WWTP (DSW), an intermidiate site (INT), that was located in the urbanized area between the two WWTPs, a second exposure site, downstram of Kitchener WWTP (DSK1); there were also three downstream sites (DSK2, DSK3 and DSK4) whre revovery was possible. There were 63 samples analyzed, 7 samples per site. There was a total of 63 microarrays processed.


title: Cell Cycle-Targeting MicroRNAs as Therapeutic Tools  Against Refractory Cancers [dermatofibrosarcoma]

status: Public on Apr 10 2017

city: Beijing

first: Cheng

last: Li

address: No.5 Yiheyuan Road

country: China

institute: Peking University

summary: Cyclins and cyclin-dependent kinases (CDKs) are hyperactivated in nearly all human tumor types. To identify new approaches for interfering with cyclins/CDKs, we systematically searched for microRNAs (miRNAs) regulating these proteins. We uncovered a group of miRNAs that target nearly all cyclins and CDKs, and demonstrated that these miRNAs are very effective in shutting off cancer cell expansion. By profiling the response of over 120 human cancer cell lines representing 12 tumor types to these cell-cycle-targeting miRNAs, we identified miRNAs particularly effective against triple-negative breast cancers and KRAS-mutated cancers. We also derived expression-based algorithm that predicts response of primary tumors to cell-cycle-targeting miRNAs. Using systemic administration of nanoparticle-formulated miRNAs, we halted tumor progression in seven mouse xenograft models, including three highly aggressive and treatment-refractory patient-derived tumors, without affecting normal tissues. Our results highlight the utility of using cell-cycle-targeting miRNAs for treatment of refractory cancer types.

overall_design: Fresh dermatofibrosarcoma tumor was homogenized and total RNA isolated using Ambion mirVana miRNA isolation kit without enrichment for small RNAs. Total RNA was hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Per

last: Hydbring

first: Piotr

last: Sicinski


title: lnc-mg is a long non-coding RNA that promotes myogenesis


title: Long non-coding RNA in neurons: new players in early response to BDNF stimulation

status: Public on Feb 27 2017

city: Naples

first: Aldo

last: Donizetti

state: Naples

address: via Cinthia

department: Biology

institute: Federico II University

summary: Brain-derived neurotrophic factor (BDNF) is a neurotrophin family member that is highly expressed and widely distributed in the brain. BDNF is critical for neural survival and plasticity both during development and in adulthood, and dysfunction in its signaling may contribute to a number of neurodegenerative disorders. Deep understanding of the BDNF-activated molecular cascade may thus help to find new biomarkers and therapeutic targets. One interesting direction is related to the early phase of BDNF-dependent gene expression regulation, which is responsible for the activation of selective gene programs that lead to stable functional and structural remodeling of neurons. Immediate-early coding genes activated by BDNF are under investigation, but the involvement of the non-coding RNAs is largely unexplored, especially the long non-coding RNAs (lncRNAs). lncRNAs are emerging as key regulators that can orchestrate different aspects of nervous system development, homeostasis, and plasticity, making them attractive candidate markers and therapeutic targets for brain diseases. We used microarray technology to identify differentially expressed lncRNAs in the immediate response phase of BDNF stimulation in a neuronal cell model. Our observations on the putative functional role of lncRNA provide clues to their involvement as master regulators of gene expression cascade triggered by BDNF.

overall_design: We used the popular SHSY-5Y cell line as a neuronal cell model for BDNF stimulation. The SHSY-5Y line comprises at least two morphologically and biochemically distinct phenotypes: neuroblastic (N-type) and a low proportion of epithelial-like (S-type) phenotypes. For BDNF treatment on a more homogeneous neuronal cell population, we performed an enrichment procedure based on the different substrate adherence between the two cell phenotypes. The obtained N-enriched population of SHSY-5Y was differentiated  by decreasing FBS concentration from 15% to 1.5% and adding 10 μM of retinoic acid for 6 days (the medium was refreshed every 2 days). After 6 days of differentiation, the medium containing 1.5% FBS and RA was removed and substituted with a medium without FBS for two groups of cells. One of these groups was treated with 10 ng/mL of BDNF for 1 h, whereas the second group was not treated and used as a control for the gene expression analysis. Microarray experiments were performed on biological triplicate samples.

first: Vincenza

last: Aliperti

first: Matteo

last: Accetturo


title: Comprehensive analysis of differentially expressed  miRNAs  in aged mice presenting with postoperative cognitive dysfunction

first: changwei

last: wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

department: Department of Anesthesiology

institute: Beijing Chao-Yang Hospital, Capital Medical University

summary:
Postoperative cognitive dysfunction (POCD) is a common postoperative complication observed in elderly patients. However, the underlying mechanisms of POCD remain unclear. MicroRNAs (miRNAs) which are involved in the pathogenesis of neurodegenerative diseases, may also affect POCD. To identify the relevant potential mechanisms, in this study, we comprehensively compared the expression profiles of miRNAs in 5 hippocampal tissues from POCD mice and 5 hippocampal tissues from control mice by microarray. A total of 128 miRNAs, whose expression changed significantly, were identified. Four miRNAs were confirmed by quantitative real-time polymerase chain reaction (PCR) in 10 paired samples. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed to explore the principal functions of the deregulated genes.
We predicted the potential targets of miRNAs by using bioinformatics methods. In summary, novel miRNAs were identified as potential biomarkers and therapeutic targets for POCD treatment.

overall_design: In this study, we comprehensively compared the expression profiles of miRNAs in 5 hippocampal tissues from POCD mice and 5 hippocampal tissues from control mice by microarray. Mice from the POCD group were experienced tibia fracture surgery, mice from the control group did not receive any prior treatment or surgery.

first: Changwei

last: Wei

first: Suwei

last: Zhang


title: A Long Noncoding RNA TTN-AS1 Controls Esophageal Squamous Cell Carcinomas by Functioning as a Competing Endogenous RNA and Scaffolding mRNA Stabilizing Protein HuR [Affymetrix]

city: Nanjing

first: chenyu

last: lin

address: Longmian Road No.639

institute: China Pharmaceutical University

summary:
BACKGROUND & AIMS: Emerging long non-coding RNAs (lncRNAs) have been demonstrated to be associated with progression of various cancers. In the current study, we identified a novel lncRNA-TTN-AS1 and dissected the underlying mechanisms by which lncRNA-TTN-AS1 induced carcinogenesis of esophageal squamous cell carcinoma (ESCC).
METHODS: ESCC and adjacent non-malignant specimens from 7 ESCC patients were chosen to analyze the expression profiles of lncRNA-miRNA-mRNA using multiple microarrays. The novel lncRNA-TTN-AS1 was identified using multiple bioinformatics platforms. Levels of lncRNA-TTN-AS1 in tissues from 148 ESCC patients were verified by qRT-PCR and in situ hybridization. The biological function and mechanism of action of lncRNA-TTN-AS1 were performed both in vivo and in vitro using gain-of and loss-of function assays on TE-13 cells and KYSE-410 cells, luciferase reporter assays, RNA immunoprecipitation (RIP) assays and RNA pull-down assays.
RESULTS: lncRNA-TTN-AS1 levels were upregulated in ESCC tissues compared with adjacent non-malignant tissues, and correlated with poor prognosis. LncRNA-TTN-AS1, as an oncogene, promoted ESCC cell proliferation and prevented apoptosis. Additionally, lncRNA-TTN-AS1 increased snail1 levels by competitively binding to miR-133b, thereby facilitating epithelial-mesenchymal transition (EMT) cascades. Sharing miR-133b binding sites, lncRNA-TTN-AS1 as a ceRNA also derepressed FSCN1 mediated by miR-133b. Notably, lncRNA-TTN-AS1 stabilized FSCN1 mRNA by interacting directly with the mRNA stabilizing protein HuR, resulting in ESCC invasion-cascades and activation of FSCN1/β-catenin.
CONCLUSION: lncRNA-TTN-AS1 sponges miR-133b to govern the expression of snial1 and FSCN1, which promotes ESCC cell proliferation and metastasis. It also combines with HuR to modulate FSCN1 in ESCC cell lines. Our findings may provide a novel target for ESCC anti-metastatic therapies.

overall_design: Using microarrays to compare expression profiles of miRNAs in ESCC tissues and adjacent normal tissues.

first: Chenyu

last: Lin

first: Shengnan


title: MicroRNAs expression data from two different types of human breast cancer cells

city: shenyang

first: Xiujuan

last: Qu

address: No.155 North Nanjing Street

department: medical oncology

institute: China Medical University

summary:
Microarray analysis of microRNAs differences between MCF-7 and MCF-7/ADR cells.Sample 1- Human breast cancer cell MCF-7,which exibits ER and PR expression, belongs to non-triple negative breast cancer cell with epithelial morphology and character.Sample 2-human breast cancer cell MCF-7/ADR,derived from MCF-7 and cultured with 1 ug/ml adriamycin for at least one year and pocesses adriamycin-resistance with mesenchymal morphology and character.
We used microarrays to detail the global programme of microRNA expression between two distinct classes of breast cancer cells.

overall_design: Two types of breast cancer cells were selected at successive stages for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cells in order to normalize resolution of expression profiles.

first: Yunpeng


title: Expression data from Col-0 and hcr1 roots

status: Public on Feb 19 2017

city: Montpellier

first: Christophe

last: Maurel

state: Languedoc Rousillon

address: 2, Place Viala

department: Aquaporines

country: France

institute: CNRS

summary: Transcript profiling analysis of Hydraulic conductivity of Root 1 (HCR1) mutant compared to wild type (Col-0) using ARABIDOPSIS GENE1.1ST ARRAY STRIP (901793, Affymetrix, Santa Clara, USA).

overall_design: Arabidopsis Col-0 and hcr1 plants were grown under hypoxia (pO2 = 11.1 ± 1.1 % ) in hydroponic solution , and root samples of 21 d old plants were harvested. Each sample was a pool of five plants, and each type of sample was harvested in triplicate. Total RNAs were isolated using TRIzol reagent (Invitrogen) and purified using the RNeasy MinElute Cleanup Kit (74204, Qiagen) after DNase treatment (79254, Qiagen). RNA quantities were assessed with a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Wilmington, USA) and RNA qualities using RNA 6000 Nanochips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). For each sample, 100 ng of total RNA were amplified using the GeneChip® WT PLUS Reagent Kit (902280, Affymetrix, Santa Clara, USA) following the manufacturer’s instructions. 10 μg of the resulting biotin-labeled single stranded cDNA was used for hybridization to ARABIDOPSIS GENE1.1ST ARRAY STRIP (901793, Affymetrix, Santa Clara, USA).  Hybridization was carried out at 45 °C for 16 h, and the arrays were washed and stained according to the protocol described in the Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix). The arrays were scanned using GeneAtlas Imaging Station (Affymetrix). The microarray computaional analysis was performed on *.CEL and *.CHP data files.

first: Zaigham

last: Shahzad

first: Matthieu

last: Canut

first: Colette

last: Tournaire-Roux

first: Alexandre

last: Martinière

first: Yann

last: Boursiac

first: Olivier

last: Loudet


title: Liver miRNA Expression during the Rat Life Span in both Sexes

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

country: USA

institute: US FDA National Center for Toxicological Research

summary: Global miRNA expression was examined in liver tissues from male and female F344 rats over the life span for the purpose of evaluating their possible roles in susceptibility to liver toxicity and disease. Hepatic miRNA expression was characterized at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age in both sexes using Agilent 8x15k rat miRNA microarrays containing multiple probes for 677 unique miRNAs. Data processing, 75% normalization, and statistical analysis of microarray data were performed in SAS. Functional analysis (Ingenuity) was performed on select miRNAs exhibiting prominent age and sex expression differences. +

overall_design: Untreated male and female F344 rats from 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age (n=5) were sacrificed by CO2 asphyxiation, whole livers collected and homogenized, total RNA, including small RNA fraction, was used for miRNA expression arrays (Agilent).

first: James

last: Fuscoe