title: MiRNA expression profile in relation to oocyte developmental competence

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The objective of this study was to identify the expression profile of miRNAs in porcine oocytes derived from follicles of different sizes using RNA high throughput sequencing technology. Oocytes were aspirated from large (3-6 mm) or small (<2 mm) ovarian follicles and tested for developmental competence and chromatin configurations. Small RNA libraries were constructed from both groups and then sequenced on an Illumina NextSeq500. Oocytes from large follicles showed higher developmental competence and different chromatin configuration compared to small oocyte group. In total, 167 and 162 known miRNAs were detected in large and small oocyte groups, respectively with 153 miRNAs were commonly expressed in both groups. In addition, 155 predicted novel miRNAs were detected and quantified. MiR-205, miR-16, miR-148a-3p, miR-125b, and let-7 family were among the top 10 highly abundantly expressed miRNAs in both oocyte groups. Further analysis showed that 8 miRNAs were differentially expressed (DE) between both groups (>2 fold change) with 4 up- and 4 down-regulated miRNAs in large compared to small oocyte group. Target gene prediction followed by KEGG pathway analysis revealed 46 pathways that were enriched with miRNA-target genes. Oocyte meiosis pathway and signaling pathways including FoxO, PI3K-Akt, TGFβ, and cAMP were predictably targeted by DE miRNAs. These results give more insights into the potential role of miRNAs in controlling oocyte developmental competence.

overall_design: Six small RNA libraries were constructed from two oocytes groups (From large and small follicles, 3 biological replicates each) and then sequenced on an Illumina NextSeq500

first: Lucie

last: Nemcova

first: Matej

last: Murin

first: Jiri

last: Kanka

first: Jozef

last: Laurincik

first: Michal

last: Benc

first: Lazo

last: Pendovskie

first: Radek

last: Prochazka


title: Affymetrix GeneChip miRNA 4.0 Array for meningioma recurrence profilling

status: Public on Feb 15 2019

city: Olomouc

first: Josef

last: Srovnal

address: Hnevotinska 5

department: IMTM

country: Czech Republic

institute: Palacky University

summary: Variability of meningioma growth, even within benign subgroup, makes some remain unaltered, while others grow fast despite an appended radiotherapy. Biomarkers that differentiate between less and more aggressive meningiomas would therefore have a significant clinical benefit in prediction of their biological behaviour. The aim of the study was to identify new candidate miRNAs enabling better and proper prediction of meningioma recurrence.  We used miRNA 4.0 array (Applied Biosystems, Foster City, CA, USA) to detect miRNA profiles in 44 primary meningioma patients (19 with subsequent recurrence) and 5 healthy controls. Moreover, miRNA profiles were analyzed in 15 secondary meningiomas.

overall_design:
Affymetrix GeneChip miRNA 4.0 Arrays were performed according to the manufacturer's directions on total RNA extracted from macrodisected FFPE meningioma samples.
MiRNA expression analysis of Affymetrix GeneChip miRNA 4.0 Arrays was performed at 45 meningioma patients and 5 healthy controls.  Healthy control samples were not included in the final analysis.

first: Vladimir

last: Balik


title: Gut hepcidin: a key regulator of inflammation

status: Public on Feb 14 2019

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: Hepcidin is demonstrated to be the key iron regulatory hormone, produced by the liver. Here we show an unexpected role of hepcidin as a master initiator of the local and systemic inflammatory response. We found that hepcidin was highly expressed in the colon of two major idiopathic inflammatory bowel diseases : Crohn's disease (CD) and ulcerative colitis (UC). Thanks to the generation of intestinal specific hepcidin KO mice (Hepc{delta}int), we found in a DSS-induced colitis model that hepcidin mediated the induction of key inflammatory cytokines and was protective against intestinal injury. In a model of LPS-induced acute inflammation, intestinal hepcidin expression was increased through a TLR4 dependent pathway andwas required for intestinal neutrophil infiltration and inflammation. Strikingly, intestinal hepcidin was absolutely required for the systemic production of key inflammatory cytokines  (IL-6, CXCL1, TNF-alpha ...) as well as for the setting of the hypoferremia of inflammation. In a sepsis model, Hepc{delta}int mice were protected against LPS-induced mortality. Mechanistically, we showed that hepcidin was a direct neutrophil chemoattractant and a proinflammatory molecule in macrophages through a Myd88 dependent pathway. Altogether, we demonstrated that Hepcidin is a key new essential component of the immune system and may be a promising target in many inflammatory diseases.

overall_design: We used microarrays to detail the global program of gene expression of BMDM treat with hepcidin for 1 hour.

first: Sara

last: Zumerle

first: Jacques

middle: R

last: Mathieu


title: Bathymodiolus azoricus caging experiment

status: Public on Feb 13 2019

city: Roscoff

first: Arnaud

last: TANGUY

address: Place Georges Teissier

department: Station Biologique

institute: Sorbonne University

summary: Colonization of deep-sea hydrothermal vents by invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers of these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts on the deep-sea mussel Bathymodiolus azoricus’ molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels

overall_design: an in situ depletion of symbionts has been performed through a translocation of 30-40 individuals, divided in two wire steel cages, a dozen meters away from the hydrothermal fluid, capitalizing on a natural gradient in concentration of reduced ,compounds (H2S, CH4) between the mussel bed and the translocated site. The recovery of these cages was performed after 7 and 27 days (respectively T1 and T2) after the start of the translocation. Two pool of individual were used in each Basalt condition and 4 pools were used for the T0 (natural population).

first: Camille

last: Détrée

first: Iman

last: Haddad

first: Emmanuelle

last: Demey-Thomas

first: Joelle

last: Vinh

first: François

middle: H

last: Lallier

last: Tanguy

first: Jean

last: Mary


title: This study examined gene expression in zebrafish embryos exposed to 0 (0.01% DMSO), 16 µM, or 32 µM perfluorobutane sulfonate.

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

country: USA

institute: Michigan State University

type: Expression profiling by high throughput sequencing

summary: The objective of this study is to compare the toxicity of the emerging replacement surfactant PFBS to the legacy chemical PFOS in the developing pancreas. Because of its chemical properties, it is hypothesized that PFBS would result in fewer or more mild aberrant pancreas phenotypes and ameliorated pancreas gene expression compared to PFOS. Herein, we use transgenic zebrafish models to visualize these processes in vivo throughout the developmental process, and use RNA-Seq to examine major pathways affected by these embryonic exposures.

overall_design: Each sample contained 15 pooled zebrafish embryos at 96 hours post fertilization. Three samples were analyzed per exposure group (n=3 samples for each exposure). Three experimental replicates were performed, each yielding one sample per exposure group. Embryos were exposed in 100 mm polystyrene plates containing 30 ml of exposure media, prepared in 0.3x Danieau's medium. Prior to collection, embryos were thoroughly washed 3 times to remove excess PFBS.

first: Paul

middle: P

last: Sinno

first: Olivia

middle: L

last: Venezia

first: Alicia

last: Timme-Laragy


title: Gene expression data from bioprinted liver tissues treated with 0.1% DMSO (dimethyl sulfoxide: vehicle), 10 ng/mL transforming growth factor beta 1 (TGF-β1) or 0.209 µM methotrexate (MTX) for either 14 or 28 days.

city: RTP

first: Leah

middle: M.

last: Norona

state: NC

address: 6 Davis Drive

department: Institute for Drug Safety Sciences

institute: University of North Carolina at Chapel Hill

summary:
Gene expression data from bioprinted liver tissues comprising primary human hepatocytes (HCs), hepatic stellate cells (HSCs), and human umbilical vein endothelial cells (HUVECs) with and without Kupffer cells (KCs) treated with 0.1% DMSO (dimethyl sulfoxide: vehicle), 10 ng/mL transforming growth factor beta 1 (TGF-β1) or 0.209 µM methotrexate (MTX) for either 14 or 28 days.
Agents known to cause fibrotic injury were modeled over an extended period of time in this model system in the standard (-KCs) and modified (+KCs) tissue model to elucidate the role of Kupffer cells in modulating the injury/fibrogenic response over time.
Samples are from studies corresponding to 4 independent tissue prints 1-4r

overall_design: 33 samples were analyzed representing n=3 per treatment group for each time point and tissue composition except 3 samples (3_P3, 1_P3, 20_P1 and 14_P3) that clustered together and were > 3 SD away from the mean on a PCA plot suggesting that these samples may also be aberrant and were therefore omitted from analysis.

middle: M


title: EGR1 and the MAPKinase pathway provide a focus for signal integration in antibody secreting cells (STC data set)

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

summary: Antibody secreting cells (ASCs) survive in niche microenvironments as mature plasma cells, but how niche signals are integrated is poorly understood. Here we dissect such a response in human ASCs using an in vitro model, time course expression data, and a parsimonious gene correlation networking approach (PGCNA), we map expression changes that occur during the maturation to quiescent PCs. We demonstrate that TGF-beta, a niche factor, drives a focused effect on gene expression, including up-regulation of CXCR4, while progression to secretory optimization is completed. Heightened expression of CXCR4 in the presence of TGF-beta is in turn associated with enhanced ERK activation in response to SDF1.  Mapping expression changes following SDF1/TGF-beta signaling we identify a module of immediate early genes including EGR1 as a primary nexus, upstream of subsequent waves of gene expression including genes encoding membrane proteins, such as solute channels and surface receptors.  We conclude that niche signals delivered from SDF1 and TGFB integrate at the level of MAPkinase pathway and link downstream to changes in potential capacity for further niche sensing.proteases (MBTPS2/S2P) and release of the cytoplasmic domain as an active transcription factor. Such regulation is shared with a family of CREB3-related transcription factors and sterol regulatory element-binding proteins (SREBPs). Of these, we identify that the CREB3 family member CREB3L2 is strongly induced and activated during the transition from B-cell to plasma cell state. Inhibition of site-1 protease leads to a profound reduction in plasmablast number linked to induction of autophagy. Plasmablasts generated in the presence of site-1 protease inhibitor segregated into CD38high and CD38low populations, the latter characterized by a marked reduction in the capacity to secrete IgG. Site-1 protease inhibition is accompanied by a distinctive change in gene expression associated with amino acid synthesis, steroid and fatty acid synthesis pathways. These result demonstrate that transcriptional control of metabolic programs necessary for secretory activity can be targeted via site-1 protease inhibition during ASC differentiation.

overall_design: B-cells were isolated from the peripheral blood of 3 adult donors and differentiated in vitro until day 7 (see individual samples for culture conditions)

middle: A

first: Reuben

last: Tooze

first: Sophie

last: Stephenson


title: EGR1 and the MAPKinase pathway provide a focus for signal integration in antibody secreting cells (LTC data set)

overall_design: B-cells were isolated from the peripheral blood of 4 adult donors and differentiated in vitro until day 20 (see individual samples for culture conditions)


title: DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RNA-seq]

city: Milwaukee

first: Pengyuan

last: Liu

state: Wisconsin

address: 8701 Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

summary: Numerous adult diseases involving tissues that consist primarily of non-dividing cells are associated with changes in DNA methylation.  It suggests a role for de novo methylation or demethylation of DNA, which is catalyzed by DNA methyltransferase 3 (Dnmt3) and ten-eleven translocases (Tet).  However, the contribution of DNA de novo (de)methylation to these diseases remains nearly completely unproven.  Broad changes in DNA methylation occurred within days in the renal outer medulla of Dahl SS rats fed a high-salt diet, a classic model of hypertension.  Intra-renal administration of anti-Dnmt3a/Tet3 GapmeR’s attenuated high salt-induced hypertension in SS rats.  The high salt diet induced differential expression of 1,712 genes in the renal outer medulla.  Remarkably, the differential expression of 76% of these genes were prevented by anti-Dnmt3a/Tet3 GapmeR’s.  The genes differentially expressed in response to the GapmeR’s were involved in the regulation of metabolism and inflammation and were significantly enriched for genes showing differential methylation in response to the GapmeR’s.  These data indicate DNA de novo (de)methylation in the kidney contributes to the development of hypertension in SS rats.  The findings should help to shift the paradigm of DNA methylation research in diseases involving non-dividing cells from correlative analysis to functional and mechanistic studies.

overall_design: Transcriptome analysis was performed in renal outer medulla tissues from individual rats (3 groups, n=3 per group).

first: Mingyu

last: Liang


title: Regulatory non-coding sRNA in response to cyanide in Pseudomonas pseudoalcaligenes CECT5344

city: Córdoba

first: Alfonso

last: Olaya Abril

state: Córdoba

address: Campus de Rabanales, edificio c6, primera planta, ala norte

department: Biochemistry and molecular biology

country: Spain

institute: University of Córdoba

summary: Biological treatments to degrade cyanide are a powerful technology for cyanide removal from industrial wastewaters. It has been previously demonstrated that the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to use free cyanide and several metal-cyanide complexes as the sole nitrogen source. In this work, the strain CECT5344 has been used for detoxification of the different chemical forms of cyanide that are present in alkaline wastewaters from the jewelry industry. This liquid residue also contains large concentrations of metals like iron, copper and zinc, making this wastewater even more toxic. To elucidate the molecular mechanisms involved in the bioremediation process, a quantitative sRNA sequencing analysis has been carried out in P. pseudoalcaligenes CECT5344 cells grown with the jewelry residue, free cyanide and ammonium as sole nitrogen sources.

overall_design: Examination of 2 different nitrogen sources, ammonium and cyanide (both free as salt and in jewelry wastewater).

first: A

last: Olaya-Abril

first: V

last: Luque-Almagro

first: L

last: Sáez

first: C

last: Moreno-Vivián

first: M

middle: D

last: Roldán-Ruiz


title: Th1 and T17 activation with and without CB839 treatment

city: NASHVILLE

first: Aguirre

last: de Cubas

state: TN

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

summary: Activated T cells differentiate into functional subsets which require distinct metabolic programs. Glutaminase (GLS) converts glutamine to glutamate to provide substrate for the tricarboxylic acid cycle and epigenetic reactions and here we identify a key role for GLS in T cell activation and specification. Though GLS-deficiency diminished T cell activation, proliferation and impaired differentiation of Th17 cells, loss of GLS also increased Tbet and Interferon-γ expression and CD4 Th1 and CD8 CTL effector cell differentiation. These changes were mediated by differentially altered gene expression and chromatin accessibility, leading to increased sensitivity of Th1 cells to IL-2 mediated mTORC1 signaling. In vivo, GLS-null T cells failed to drive a Th17-mediated Graft-vs-Host Disease model. Transient inhibition of GLS, however, increased Th1 and CTL T cell numbers in viral and chimeric antigen receptor models. Glutamine metabolism thus has distinct roles to promote Th17 but constrain Th1 and CTL effector cell differentiation.

overall_design: Cells were treated with glutaminase1 inhibitor or vehicle

first: Marc

last: Johnson

first: Jeffrey

last: Rathmell


title: The placental transcriptome in late gestational hypoxia resulting in murine intrauterine growth restriction predicts adult cardiometabolic disease

city: Los Angeles

first: David

last: Casero

state: CA

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

institute: UCLA

summary: Intrauterine growth restriction (IUGR) affects up to 10% of pregnancies and often results in short- and long- term sequelae for offspring, including risk for adult cardiovascular disease (CVD). The mechanisms underlying IUGR are poorly understood, though poor blood flow and oxygen/nutrient provision to the IUGR fetus are thought to be the common endpoints of disease. Though several animal models of IUGR exist, few demonstrate later phenotypes of CVD despite a large body of evidence in humans linking IUGR and adult CVD onset. We thus hypothesized that in murine pregnancy, maternal late gestational hypoxia (LG-H) exposure resulting in IUGR would result in (1) adult phenotypes of CVD in hypoxia-exposed offspring, and (2) the placental transcriptome will demonstrate alterations that can be linked to risk of later disease. After subjecting pregnant mice to hypoxia (10.5% oxygen) from gestational day (GD) 14.5 to 18.5, we collected placentas at GD19. We examined RNA isolated from these placentas to perform RNA sequencing and analysis. Functional gene and cluster-based analysis suggest multiple changes in structural and functional genes important for placental health, with the top dysregulation involving vascular and metabolic pathways. Concordantly, a ~ 10% decrease in birthweights and ~30% decrease in litter size after LG-H (p<0.05) was observed, suggesting an environment of placental insufficiency. We also found that offspring exposed in-utero to LG-H exhibit CVD at 4 months of age, with males being worse than females, supporting developmental programming. Specifically, males exhibit increased body weight and an enlarged heart size, whereas both males and females develop hypertension, elevated abdominal fat, elevated leptin and elevated total cholesterol levels with aging. In summary, LG-H exposure in the pregnant mouse mimics human placental insufficiency related IUGR. The placentas of these exposed fetuses demonstrate a transcriptional response to the stressor of gestational hypoxia and predicts cardiovascular and metabolic effects that culminate into hypertension and adiposity with dyslipidemia.

overall_design: Pregnant female mice were randomly assigned to two groups: 1) late gestation-room air (LG-RA) pregnant mice which were house in standard conditions, and 2) late gestation-hypoxia (LG-H) pregnant mice were exposed to hypoxia for 4 days (days 14.5 to 18.5 of gestation).

first: Alison

last: Chu

first: Shanthie

last: Thamotharan

first: Amy

last: Cosi

first: Madhuri

last: Wadehra

first: Sherin

middle: U

last: Devaskar


title: DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RRBS-seq]

first: Pengyuan

last: Liu

type: Methylation profiling by high throughput sequencing

overall_design: DNA methylation profile analysis was performed in renal outer medulla tissues from individual rats (7 groups, n=3-4 per group) using multiplexed RRBS protocols


title: DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension

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

overall_design: Refer to individual Series


title: Methylglyoxal Down-Regulates the Expression of Cell Cycle Associated Genes and Activates the P53 Pathway in Human Endothelial Cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Although methylglyoxal (MGO) has emerged as key mediator of diabetic microvascular complications, the influence of MGO on the vascular transcriptome has not thoroughly been assessed. This study addressed 1) to what extent MGO changes the endothelial transcriptome when endothelial cells are exposed to an inflammatory milieu, 2) what are the dominant pathways by which these changes occur and 3) to what extent is this normalized by carnosine, a putative scavenger of MGO. Using gene expression profiling analysis, we demonstrated that MGO initiates distinct transcriptional changes in cell cycle/apoptosis gene, which may explain MGO toxicity at high concentrations. MGO did not augment TNF-α induced inflammation.

overall_design: For microarray analysis, six groups were employed as defined by a 24-hour incubation with the following substances:  HUVECs in pro-inflammatory media (12,5 ng/ml TNF-α) with  1-2) no MGO ± 20 mM CN  3-4) 400 µM MGO ± 20 mM CN  5-6) 800 µM MGO ± 20 mM CN.   HUVECs incubated with only TNF-α (without MGO and CN) served as control. Total RNA was isolated from all groups followed by gene expression profiling using Affymetrix microarrays.

first: Benito

last: Yard

first: Carste

last: n Sticht


title: RNA sequencing reveals RNA binding protein HuR/ELAVL1 regulates extracellular matrix gene expression in nucleus pulposus cells of the intervertebral disc

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary: We used RNA sequencing to identify transcripts that were controlled by the RNA binding factor HuR/ELAVL1 in nucleus pulposus cells of the intervertebral disc.

overall_design: Nucleus pulposus cells were isolated from rat intervertebral discs and cultured under hypoxic conditions. Cells were transduced with either control (MISSION PLKO.1 non-target ShRNA) or HuR-specific shRNA (ShHuR). mRNA was isolated using Rneasy mini columns (Qiagen), treated with DNase I, and RNA sequencing was performed. n=4 for each experimental group.

middle: V

first: Hehai

last: Pan

first: Zariel

middle: I


title: EGR1 and the MAPKinase pathway provide a focus for signal integration in antibody secreting cells

first: Matthew

last: Care


title: Real-time quantitative PCR analysis of mouse colon samples [12 weeks]

status: Public on Feb 12 2019

city: Ribeirao Preto

first: Vinicius

last: Kannen

state: SP

address: Av Café, s/ N°

department: DACTB

country: Brazil

institute: Universidade de São Paulo

summary: Tph1WT (n = 3) and Tph1KO (n = 3) mice were exposed to 6 azoxymethane (AOM) injections and euthanatized after 12 weeks from the first carcinogenic exposure.

overall_design: qPCR gene expression profiling.  Mouse colon samples were used following the experiment described in the summary. Equal amount total RNA from each sample was pooled prior to gene expression analysis.


title: miRNA profile  in human cardiac progenitor cells and iPS cells

city: Augusta

first: Wanling

last: Xuan

state: Georgia

address: 1460 laney walker blvd, CB-3712

department: Vascular Biology Center

institute: Augusta University

summary: We investigated the enriched miRNAs in exosomes from cardiac progenitor cells (CPCs) which were induced by a small molecule-ISX-9 compared with exosomes from human iPSC, embryoid bodies and commerical cardiac progenitor cells.

overall_design: Examination of global miRNA expression profile in exosomes from human iPSCs, cardiac progenitor cells and Embryoid bodies (n=3).

first: Muhammad

last: Ashraf


title: Real-time quantitative PCR analysis of mouse colon samples [72 h]

summary: Tph1WT (n = 2) and Tph1KO (n = 2) mice were exposed to ionizing radiation (IR; single dose, 700 cGy) and euthanatized after 72 h.


title: Ascites-derived circulating microRNAs as potential diagnostic biomarkers of gastric cancer-associated malignant ascites

city: Cheongju

first: Hye Sook

last: Han

address: Chungdae-ro 1, Seowon-gu

country: South Korea

institute: College of Medicine, Chungbuk National University

summary: Peritoneal carcinomatosis with malignant ascites is associated with dismal prognosis in gastric cancer. Malignant ascites is the most relevant body fluid in which to seek diagnostic biomarkers for peritoneal carcinomatosis. We aimed to identify and validate ascites-derived circulating microRNAs (miRNAs) that are differentially expressed between liver cirrhosis-associated benign ascites (LC-ascites) and gastric cancer-associated malignant ascites (GC-ascites). MiRNA expression levels were investigated in three independent cohorts. Overall, 165 ascites samples (73 LC-ascites and 92 GC-ascites) were obtained from the National Biobank of Korea. Initially, microarrays were used to screen the expression levels of 2,006 miRNAs in the discovery cohort (n = 22). Subsequently, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analyses were used to validate the expression levels of selected miRNAs in the training (n = 70) and validation (n= 73) cohorts. In addition, the levels of carcinoembryonic antigen (CEA), a commonly used tumor marker, were determined in the ascites samples. Expression levels of miR-574-3p, miR-181b-5p, miR-4481, and miR-181d were significantly lower in the GC-ascites samples than in the LC-ascites samples, and miR-181b-5p showed the best diagnostic performance for GC-ascites (area under the curve [AUC] = 0.798 and 0.846 for the training and validation cohorts, respectively). The diagnostic performance of CEA for GC-ascites was improved if CEA and miR-181b-5p were analyzed together (AUC = 0.981 and 0.946 for the training and validation cohorts, respectively). Overall, we identified ascites-derived circulating miRNAs capable of differentiating non-malignant ascites and GC-ascites, and demonstrated that the combined use of miR-181b-5p and CEA produces the optimal diagnostic yield.

overall_design: All ascites samples were transported to the National Biobank of Korea within 1 hour of collection and then centrifuged at 3,134 g for 10 min to remove large cell particles and cell debris. The supernatant from each sample was aliquoted into microcentrifuge tubes and stored at -80°C prior to miRNA measurements. Exosomal RNA was extracted from the 22 ascites samples in the discovery cohort (10 liver cirrhosis [LC]-ascites and 12 gastric cancer [GC]-ascites). The exosomes in each ascites sample (500 μL of supernatant) were precipitated using the miRCURY Exosome Isolation Kit (Exiqon, Woburn, MA, USA). Exosomal RNA was isolated using Trizol LS Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions, and then quantified by measuring absorbance at 260 nm. RNA integrity was confirmed using a Bioanalyzer 2100 instrument (Agilent Technologies, San Carlos, CA, USA). MiRNA profiling was performed using the Agilent Human miRNA Microarray Release 19.0 platform.

first: Hy-Sook

first: Jieun

last: Yun


title: Fine tuning of Sox17 and canonical Wnt coordinates the permeability properties of the blood-brain barrier

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary:
Rationale. The microvasculature of the central nervous system includes the blood-brain barrier (BBB),  which regulates the permeability to nutrients and restricts the passage of toxic agents and inflammatory  cells. Canonical Wnt/b-catenin signaling is responsible for the early phases of brain vascularization and  blood-brain barrier differentiation. However, this signal declines after birth and other signaling pathways  able to maintain barrier integrity at postnatal stage are still unknown.
Objective. Sox17 constitutes a major downstream target of Wnt/b-catenin in endothelial cells and  regulates arterial differentiation. In the present paper, we asked whether Sox17 may act downstream of  Wnt/b-catenin in inducing BBB differentiation and maintenance.
Methods and Results. Using reporter mice and nuclear staining of Sox17 and b-catenin, we report that  while b-catenin signaling declines after birth, Sox17 activation increases and remains high in the adult.  Endothelial-specific inactivation of Sox17 leads to increase of permeability of the brain microcirculation.  The severity of this effect depends on the degree of BBB maturation: it is strong in the embryo, and  progressively declines after birth. In search of Sox17 mechanism of action, RNA-Seq analysis of gene  expression of brain endothelial cells has identified members of the Wnt/b-catenin signaling pathway as  downstream targets of Sox17. Consistently, we found that Sox17 is a positive inducer of Wnt/b-catenin  signaling and it acts in concert with this pathway to induce and maintain BBB properties. In vivo,  inhibition of the b-catenin destruction complex or expression of a degradation-resistant b-catenin mutant,  prevent the increase in permeability and retina vascular malformations observed in the absence of Sox17.
Conclusions. Our data highlight a novel role for Sox17 in the induction and maintenance of the BBB and  they underline the strict reciprocal tuning of this transcription factor and Wnt/b-catenin pathway.  Modulation of Sox17 activity may be relevant to control BBB permeability in pathological conditions.

overall_design: Brain endothelial cells (ECs) mRNA profiles over 4 developmental stages (from embryos to adult) of wt and Sox17iECKO mice generated, in triplicate.

first: Monica

last: Corada

first: Fabrizio

last: Orsenigo

first: Ganesh

last: Bhat

first: Lei

last: Conze

first: Ferruccio

last: Breviario

first: Sara

last: Cunha

first: Lena

last: Classeon-Welsh

first: Galina

last: Beznoussenko

first: Alexander

last: Mironov

first: Marco

last: Bacigaluppi

first: Gianvito

last: Martino

first: Mara

last: Pitulescu

first: Ralf

last: Adams

first: Peetra

last: Magnusson


title: The role of mirna-146b-tbc1d14 in the autophagy of RAW264.7 cells mediated by B. melitensis m5-90 [mRNA]

status: Public on Feb 11 2019

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

country: China

institute: LC sciences

summary: We used B. melitensis M5-90 wild type to construct gene-deleted strains of B. melitensis ∆per, RAW264.7 cells infected with B. melitensis M5-90 and B. melitensis M5-90 ∆per for 4h, respectively. miRNA microarray and mRNA array experiments were performed, qRT-PCR validation for miRNAs and mRNAs. We performed a joint analysis of differentially expressed miRNAs and mRNAs, and proved that the target gene of miRNA-146b is Tbc1d14. It further confirmed that miR-146b targeting tbc1d14 regulates brucella-mediated autophagy of RAW264.7 cells. Finally, the molecular mechanism of tbc1d14 influencing brucella-mediated autophagy of RAW264.7 cells was preliminarily revealed by DGE sequencing.

overall_design: In this study，We used B. melitensis M5-90 wild type to construct gene-deleted strains of B. melitensis ∆per, RAW264.7 cells infected with B. melitensis M5-90 and B. melitensis M5-90 ∆per for 4h, respectively. Three samples from each of the two groups were selected for the mRNA microarray.

first: Hanwei

last: Jiao


title: Hepatic mRNA expression in three zebrafish strains exposed to PCB-126 or vehicle control

city: Portland

first: Kim

last: Brown

state: OR

address: 1719 SW 10th Ave

institute: Portland State University

summary: Adult zebrafish hepatic mRNA expression following 24 hour static exposure to 130 ng/L PCB-126 or 20 ppm (v/v) acetone vehicle control.

overall_design: Hepatic mRNA expression following 24 hour static exposure to 130 ng/L PCB-126 or 20 ppm (v/v) acetone vehicle control in three wild-type zebrafish strains (AB, Tuebingen, WIK). n=3 sex/treatment/strain; n=36 total

first: Lindsay

last: Holden


title: Strain-specific CNV in zebrafish treated with PCB-126, vehicle control, or untreated

summary: Strain-specific CNV in zebrafish as determined by competitevly hybridizeing AB, Tuebingen, or WIK individuals exposed to PCB-126, vehicle control, or naïve versus pooled Casper strain

overall_design: AB, Tuebingen, or WIK individuals exposed to PCB-126 (130 ng/L PCB-126 for 24 hours), vehicle control (20 ppm (v/v) acetone for 24 hours), or naïve (untreated) competitvely hybridized against pooled untreated Casper; n=3/treatment/sex/strain; n=54 total


title: The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [ncRNA-Seq]

status: Public on Feb 08 2019

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Protein phosphatase 4 (PP4) is a highly conserved serine/threonine protein phosphatase in yeast, plants, and animals. The composition and functions of the plant PP4 are poorly understood. Here, we uncovered previously unsuspected complexity of Arabidopsis PP4 and identified the composition of one form of PP4 containing the regulatory subunit PP4R3A. We showed that PP4R3A, together with one of two redundant catalytic subunit genes PPX1 and PPX2, promotes the biogenesis of microRNAs. PP4R3A is a chromatin-associated protein, interacts with RNA polymerase II (Pol II), and recruits Pol II to the promoters of MIR genes to promote their transcription. PP4R3A probably also promotes the cotranscriptional processing of miRNA precursors as it recruits the microprocessor component HYPONASTIC LEAVES1 (HYL1) to MIR genes and nuclear dicing bodies. Moreover, we showed that hundreds of introns exhibit splicing defects in pp4r3a mutants. Together, this study revealed a role of Arabidopsis PP4 in transcription and nuclear RNA metabolism.

overall_design: Small RNAs from total RNA extracted from 12-day-old seedlings of Col-0, pp4r3a-1, pp4r3a-2 with 3 biological replicates.

first: Suikang

last: Wang

first: Xuemei

last: Chen


title: The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis


title: PDGFRα and αSMA mark two distinct mesenchymal cell populations involved in parenchymal and vascular remodeling in pulmonary fibrosis

city: Graz

first: Leigh

last: Marsh

address: Neue Stiftingtalstraße 6/VI

country: Austria

institute: Ludwig Boltzmann Institute  for Lung Vascular Research

summary: We utilized a fate-mapping approach to investigate alpha-smooth muscle actin (αSMA)+ and platelet derived growth factor-alpha (PDGFRα)+ cells in two lung fibrosis models, complemented by cell-type specific next-generation sequencing and investigations on human lungs. Our data revealed that αSMA+ and PDGFRα+ cells mark two distinct mesenchymal lineages with minimal transdifferention potential during lung fibrotic remodeling. Parenchymal and perivascular fibrotic regions were populated predominantly with PDGFRα+ cells expressing collagen, while αSMA+ cells in the parenchyma and vessel wall showed  variable expression of collagen and the contractile protein desmin. The distinct gene expression profiles found in normal conditions was retained during pathologic remodeling. Cumulatively, our findings identify αSMA+ and PDGFRα+ cells as two separate lineages with distinct gene expression profile in adult lungs.

overall_design: Pdgfra- or Acta2-CreERT2; tdTomatoflox  reporte mice were treated with saline or bleomycin (n=4/group). A single cell suspension was made from the lung and tdTomato-positive cells were sorted directly into RNA lysis buffer (Qiagen, Venlo, Netherlands) using a FACSAria II cell sorter (BD Biosciences, San Jose, CA, USA). RNA was isolated with the RNeasy micro kit (Qiagen). Library preparation using the SmartSeq2 protocol and sequencing on the Illumina HiSeq 3000 platform was done by the Biomedical Sequencing Facility, CeMM, Vienna. NGS reads were aligned with the TopHat2 (v2.1.1) (Kim et al., 2013) splice junction mapper using the Bowtie2 short read aligner (v2.2.9) (Langmead and Salzberg, 2012). Transcriptome assembly and differential expressing calling was performed with Cufflinks (v2.1.1) (Trapnell et al., 2013).  cells fromt he lungs were enzymatically isolated.

first: Grazyna

last: Kwapisewska

first: Valentina

last: Biasin

first: Anna

last: Gungl

first: Slaven

last: Crnkovic

first: Chritoph

last: Bock


title: K13 580Y allele not linked to increased P. falciparum recrudescences in artesunate-treated Aotus

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Concerns about impending failure of artemisinin compounds (ART) have grown with global use of ART-based combination therapy (ACT) against malaria. WHO has defined Plasmodium falciparum resistance to ART as prolonged parasite clearance half-life in vivo (t1/2) plus the presence of certain K13 Kelch-propeller substitutions, e.g. C580Y. Recrudescences and fever clearance times after ART monotherapy, however, have not correlated well with these criteria. We have crossed K13 C580 wild-type and 580Y-mutant parasites for ART studies in Aotus. Artesunate treated C580- but not 580Y-infections recrudesced requiring retreatment, and K13 type had little or no effect on t1/2. These results challenge K13 and t1/2 variations as markers of increased resistance to ART per se and emphasize the need for effective partner drugs in ACTs.

overall_design: 57 samples, no replicates, Plasmodium falciparum various clones.

first: Juliana

last: Sá

first: Sarah

last: Kaslow

first: Michael

last: Krause

first: Viviana

last: Melendez-Muniz

first: Rebecca

last: Salzman

first: Whitney

last: Kite

first: Min

last: Zhang

first: Roberto

last: Moraes Barros

first: Jianbing

last: Mu

first: Paul

middle: K

last: Han

first: J

last: Mershon

first: Christine

last: Figan

first: Ramoncito

last: Caleon

first: Tyler

middle: J

last: Gibson

first: Chanaki

last: Amaratunga

first: Theresa

last: Engels

first: Soundarapandian

last: Velmurugan

first: Stacy

last: Ricklefs

first: Judith

last: Straimer

first: Nina

last: Gnädig

first: Bingbing

last: Deng

last: Liu

first: Ababacar

last: Diouf

first: Kazutoyo

last: Miura

first: Gregory

middle: S

last: Tullo

first: Richard

middle: T

last: Eastman

first: Sumana

last: Chakravarty

first: Eric

last: James

first: Kenneth

last: Udenze

first: Suzanne

last: Li

first: Daniel

first: Robert

middle: W

last: Gwadz

first: Stephen

middle: F

last: Porcella

first: Carole

last: Long

first: David

last: Fidock

first: Marvin


title: The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [RNA-Seq]

first: Chenjiang

last: You

overall_design: Polyadenylated RNA was isolated from total RNA extracted from 12-day-old seedlings of Col-0, pp4r3a-1 and pp4r3a-2 with 3 biological replicates

first: Suikang

last: Wang

first: Xuemei

last: Chen


title: Whole-genome gene expression profiling of  UGT2B15 Knockdown/Negative Control MHCC-97H  Cell Line

city: Guangzhou

first: Shuqiang

state: Guangdong

address: Outer ring road No. 232

institute: Guangzhou University of Chinese Medicine

summary: Whole-genome gene expression profiling of MHCC-97H cells, to further dissect the possible molecular mechanisms mediated by UGT2B15 downregulation.

overall_design: Microarray was utilized to identify differently expressed genes in UGT2B15 shRNA group and negative group.

first: Liyan

last: Ji


title: The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with  Mycobacterium bovis

city: Dublin

first: Thomas

last: Hall

state: Select One

address: 2, Taney Grove

department: Vet sciences

country: Ireland

institute: UCD

summary: Whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome (5-methylcytosine). The methylomes of bAM infected with M. bovis (n = 8) were compared to those of non-infected control bAM (n = 8) at 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed between control and infected bAM. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation = 33–66%). Gene ontology (GO) analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of two non-imprinted genes in the IM category, C1QB and IL2RA, confirmed the WGBS observation. This study is the first in cattle to examine genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model and provides evidence for intermediate promoter methylation in bAM.

overall_design: Examination of CpG methylation in control and Mycobacterium bovis infected bovine macrophages, 24 hours post infection

first: Alan

last: O'Doherty

first: Kevin

middle: C

last: Rue-Albrecht

last: Magee

first: Simone

last: Ahting

first: Rachelle

middle: E

last: Irwin

first: John

last: Browne

first: Nicolas

last: Nalpas

first: Colum

last: Walsh

last: Gordon

first: Marcin

last: Wojewodzic

last: MacHugh


title: Transcriptome analysis of hospital-acquired and community-acquired Pseudomonas aeruginosa, PAO1 and B136-33, respectively

city: Hsinchu

first: Hwan-You

last: Chang

address: No. 101, Section 2, Kuang-Fu Road

country: Taiwan

institute: National Tsing Hua University

summary: In this study, we report the genome-wide expression profiles of hospital-acquired and community-acquired P. aeruignosa. The analysis of that provides crucial implications concerning the virulence determinants associated with the community-acquired diarrheagenic strain of P. aeruginosa

overall_design: The transcriptome profiles of P. aeruginosa PAO1 and B136-33 were generated by next-generation sequencing, HiSeq 4000 system (Illumina Inc.), 2 x 150 paired-end. The coverage rate of RNA samples of B136-33 and PAO1 were 943.49× and 969.71×, respectively.

first: Yi-Ling

last: Lo


title: RpoS regulates genes associated with development of the small cell variant developmental form of Coxiella burnetii

first: Dan

last: Sturdevant

summary: Coxiella burnetii, the etiological agent of Q fever, undergoes a unique biphasic developmental cycle where bacteria transition from replicating (exponential phase) large cell variant (LCV) forms to a non-replicating, (stationary phase) small cell variant (SCV) forms. The alternative sigma factor RpoS is an essential regulator of stress responses and stationary phase growth in several bacterial species, including Legionella pneumophila, which has a developmental cycle superficially similar to C. burnetii. To characterize RpoS function during C. burnetii growth and developmental, we constructed a C. burnetii ∆rpoS mutant to define the effects on intracellular and axenic growth, as well as, gene regulation during SCV development. C. burnetii ∆rpoS exhibited intracellular growth defects in J774 mouse macrophage-like cells, but not in Vero epithelial cells. RNA sequencing of C. burnetii ∆rpoS revealed that a substantial portion of the C. burnetii genome is regulated by RpoS during SCV development. Genes previously shown to have increased expression during SCV generation, including the expression of the SCV-specific protein ScvA and pathways involved in oxidative stress, arginine transport, and peptidoglycan remodeling pathways, were dysregulated in the rpoS mutant. These genes were enriched for a predicted RpoS-binding site. These data were corroborated with independent assays demonstrating that the C. burnetii rpoS mutant had increased sensitivity to hydrogen peroxide and carbenicillin. Collectively, these results demonstrate that RpoS is essential for the regulation of genes involved in SCV development and growth inside macrophage-like cells.

overall_design:
Wild type vs. rpoS mutant
At days 5 and 14, RNA was extracted using a hot trizol extraction

first: Derek

last: Moormeier

first: Kelsi

last: Sandoz

first: Paul

last: Beare

first: Daniel

first: Robert

last: Heinzen


title: RNA-sequencing after sevoflurane exposion in Rhesus macaque

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: RNA-sequencing of 4 Rhesus macaque Samples

overall_design: examing 2 conditions, each with 2 replicates

first: Lei

last: Zhang


title: LncRNA expression  in ectopic APC overexpressed CRC cell lines and control cells

status: Public on Feb 07 2019

first: Fengwei

last: Wang

address: No.651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

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

summary: To determine the lncRNA expression profile in ectopic APC overexpressed CRC cell lines and control cells, we uesed lncRNA microArray analysis form Arraystar to examine lncRNA expression profile in ectopic APC overexpressed CRC cell lines and control cells.

overall_design: Colorectal cancer cell line SW480 and DLD-1 cells were transfected with wild-type APC full-length coding sequence or control vector and the total RNA was extracted, then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar)

first: Chenhui

last: Cao

first: Kai

last: Han


title: Reversible Histone H2B Monoubiquitination Fine-tunes Abscisic Acid Signaling and Drought Response in Rice

status: Public on Feb 09 2019

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

institute: Huazhong Agricultural Uinveristy

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone H2B monoubiquitination (H2Bub1) has been implicated in several important physiological and developmental processes, but its role in the regulation of stress responses remains elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found the rice (Oryza sativa) HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, interacted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, induced by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were increased in the promoters of OsbZIP46 target genes under the drought stress and ABA treatments, and the increased H2Bub1 levels were positively correlated to the increased expression levels of the target genes. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance through mediation of OsbZIP46 deactivation and degradation, can repress the H2Bub1 level in the promoters of OsbZIP46 target genes by recruiting a putative deubiquitinase OsOTLD1. Suppression of OsOTLD1 in vivo resulted in increased H2Bub1 levels and expression of drought-responsive genes targeted by OsbZIP46. These findings established an elaborate mechanism of histone monoubiquitination in the fine-turning of ABA signaling and drought response via balancing H2Bub1 deposition and removal.

overall_design:
H2Bub1 modifcation and gene expression levels in Zhonghua11 wild type lines under normal conditions, moderate drought conditions and severe drought conditions.
H2Bub1 modifcation levels in wild type lines and osbzip46 mutant lines under normal conditions drought  treatment conditions.

first: Siqi

last: Ma

first: Lizhong

last: Xiong


title: Expression of neural crest markers GLDC and ERRFI1 is correlated with melanoma prognosis

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

institute: DKFZ

summary: Regulation of particular genes during the formation of neural crest (NC) cells is also described during progression of malignant melanoma. In this context it is of paramount importance to develop neural crest models allowing the identification of candidate genes, which could be used as biomarkers for melanoma prognosis. Here, we used a human iPSC-based approach to present novel NC-associated genes, expression of which was upregulated in melanoma. A list of 8 candidate genes, based on highest upregulation, was tested for prognostic value in a tissue microarray analysis containing samples from advanced melanoma (good versus bad prognosis) as well as from high-risk primary melanomas (early metastasizing versus non or late-metastasizing). CD271, GLDC and ERRFI1 showed significantly higher expression in metastatic patients who died early than the one who survived at least 30 months. In addition, GLDC and TWIST showed a significant higher IHC score in primary melanomas from patients who developed metastases within 12 months versus those who did not develop metastases in 30 months. In conclusion, our iPSC-based study reveals a significant association of NC marker GLDC protein expression with melanoma prognosis.

overall_design: mRNA isolated from NHM, NC, melanoma lines HT144, C32, Skmel173.

last: Larribère


title: TCR repertoire analysis revealed the mobilization of novel CD8+ T cell clones into Cancer-Immunity Cycle following anti-CD4 antibody administration

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

summary: Depletion of CD4+ cells by anti-CD4 monoclonal antibody (anti-CD4 mAb) induces expansion of tumor-reactive CD8+ T cells and exhibits strong antitumor effects in several murine tumor models. However, whether the anti-CD4 mAb treatment activates particular or a broad variety of tumor-reactive CD8+ T cell clones is not answered. To investigate the changes of TCR repertoire induced by the anti-CD4 mAb treatment, we performed unbiased high throughput TCR sequencing in a B16F10 mouse subcutaneous melanoma model.

overall_design: In the B16F10 subcutaneous tumor model, CD8+ T cells in tumor, peripheral blood (PBL) and draining lymph node (dLN), and CD8+ CD44hi T cells in dLN were purified by cell sorting at day 14 post-tumor inoculation. Then, we prepared libraries from these CD8+ T cell sample and performed unbiased high throughput TCR sequencing using an IonProton next generation sequencer.

first: Satoshi

last: Ueha

first: Shigeyuki

last: Shichino

first: Haru

last: Ogiwara

first: Shin-ichi

last: Hashimoto

first: Kazuhiro

last: Kakimi

first: Satoru

last: Ito

first: Kouji

last: Matsushima


title: Neuropathologic Basis of WNV Infection: Mechanisms and Treatment

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

summary: Since live West Nile Virus (WNV) has rarely been detected in the autopsy brain tissue, plasma or CSF of WNV patients,  our objective is study the early repsonses of astrocytes, which could get primed by viral particles. The long-term goal of this project is to determine the neuropathologic basis of WNV infection with a hope to develop specific treatments, treatments that will have a broader impact, and help design innovative strategies to treat WNV as well as other forms of neuroinvasive viral infections

overall_design: Cerebellar tissue treated with mock or west nile virus in mice.

first: Parminder

last: Vig


title: MicroRNA expression profile of porcine alveolar macrophages infected with Toxoplasma gondii

city: WuHan

first: Li

last: Ssenyang

state: HuBei

address: shizishan road

institute: State Key Laboratory of Agricultural Microbiology

summary:
Purpose: Porcine alveolar macrophage was infected by T. gondii including Rh strain and Me49 strain. We want to explore the change of miRNAs after infected with T. gondii in porcine alveolar macrophages.
Results: Our study generated six mi RNA expression profiles from macrophages which infect with Rh strain and Me49 and control group in different time. Compare with T. gondii-infected and uninfected with T. gondii, 81 differentially expressed mi RNAs were identified, including 36 novel mi RNAs and 45 mature mi RNAs.

overall_design: The sample were harvested at 12h and 24h after porcine alveolar macrophages (3D4-21) infected with Rh strain (Type I) and Me49 strain (Type II). MiRNA libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) and miRNA expression levels were estimate by Transcript per million (TPM).

first: Senyang

last: Li

first: Jing

last: Yang

first: Luyao

last: Wang

first: Fen

last: Du


title: mRNA expression of HUVEC cells treated by exosomes derived from colorectal cancer cell line HCT116 transfected with lncRNA-APC1 silenced or control vector

first: Fengwei

summary: To determine the mRNA expression profile of HUVEC cells treated by exosomes derived from colorectal cancer cell line HCT116 transfected with lncRNA-APC1 silenced or control vector, we performedd gene expression microArray analysis form Arraystar to examine the expression of mRNAs.

overall_design: Gene expression profiles of the HUVEC cells incubated with lncRNA-APC1 silenced or control HCT116 cancer cell derived exosomes were determined using Phalanx human OneArray microarrays (HOA 6.1) following the manufacturer's instructions.

first: Chenhui

last: Cao

first: Kai

last: Han


title: Negative regulation of lymphoid specification by the transcription factor Tal1

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary:
Lymphoid primed multipotent progenitors are a subset of MPPs that are undergoing specification to the lymphoid and myeloid cell fates. The transcription factors Lyl1 and E2A are both essential for the development LMPPs and can form a heterodimeric complex. We examined the consequences of E2A- or Lyl1-deficiency on development of LMPPs and on their gene expression program in comparison with wild-type LMPPs
We used microarray data to examine the differences in gene expression between control, E2A-/- and Lyl1-/- CD138+ LSK cells.

overall_design: RNA was extracted from Lineage-CD117+SCA-1+CD135+ cells purified by flow cytometric cell sorting from the bone marrow of control, E2A-/- and Lyl1-/- mice. Thre independent samples were created from each genotype. The RNA was hybridized to Affymetrix microarrays.

first: Renee

last: dePooter

first: Sheila

last: Dias

first: Elizabeth

last: Bartom

last: Okoreeh

first: Mikael

last: Sigvardsson


title: DUSP4 regulates input to the suprachiasmatic circadian network via VIP-induced activation of the ERK1/2 pathway

city: Stanford

first: Ryan

last: Hamnett

state: California

address: James H. Clark Center, 318 Campus Drive

department: Neurosurgery

institute: Stanford University

summary: Analysis of the genes and cellular signalling cascades mediating the response of SCN slices to vasoactive intestinal peptide (VIP). Primary goal was to find novel genes that may be involved in circadian phase shifting for further study. Promoter analysis of significantly regulated genes and gene ontology analysis would provide information into pathways VIP acts through in the SCN.

overall_design: Organotypic SCN slices from pups treated at circadian time (CT)10 with 1 µM vasoactive intestinal peptide (VIP) or vehicle, where CT12 is defined as the peak of PER2::LUC expression. 4 groups with 4 slices per group analysed: 1) T0: untreated, harvested at CT10. 2) T2 Veh: Treated with vehicle at CT10, harvested 2 h later at CT12. 3) T2 VIP: Treated with 1 µM VIP at CT10, harvested 2 h later. 4) T6 VIP: Treated with VIP at CT10, harvested 6 h later at CT12. T0 group acts as a baseline, T2 Veh acts as negative control. T2 VIP is main experimental/treatment group. T6 VIP provides longer term information on VIP treatment, and also acts as phase control for T2 Veh group.

first: Johanna

last: Chesham

middle: H

last: Hastings


title: Global transcriptome profiling was performed for keratinocytes transfected with either miR-146a mimics (Pre-146a) or negative control (Pre-NC).

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

institute: hinese Academy of Medical Sciences and Peking Union Medical College

summary: To find out potiential target gene of miR-146a,we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to target miR-146a. Human keratinocytes was transfected with either miR-146a mimics (Pre-146a) or negative control (Pre-NC) for 48h, then RNA was extracted for whole genome microarray expression profiling.

overall_design: Three independent experiments were performed at 48 hours using keratinocytes treated with either miR-146a mimics (Pre-146a) or negative control (Pre-NC) for each experiment.

first: Du

last: Leilei

last: Min


title: Gene expression analysis of JAGGED-1 treated human periodontal ligament stem cells using microarray technique

city: BANGKOK

first: KANOKPORN

last: HANSAMUIT

address: HENRY DUNANT

country: Thailand

institute: CHULALONGKORN UNIVERSITY

summary:
The present study aimed to evaluate mRNA expression profiling of Jagged1 treated human periodontal ligament cells (hPDLs) using microarray technique.
Jagged1 regulates various biological pathway in hPDLs.

overall_design: Notch ligands, Jagged1, were indirectly immobilized on tissue culture surface. Subsequently, hPDLs were seeded on Jagged1 immobilized surface and maintained in growth medium for 48 h. Total RNA was collected and processed. Gene expression profiling was examined using microarray technique.

first: Kanokporn

last: Hansamuit

first: Jaijam

last: Suwanwela


title: Assessing the role of the heterologous expression of the bacterial arsenic efflux pump ACR3 in plant roots: implications for transcriptomics and As accumulation

city: Seville

first: Patricia

last: Pérez Palacios

address: Dr. Fedriani

institute: Hospital Virgen Macarena

summary:
Transgenic tobacco hairy roots (HR) were developed by expressing the bacterial arsenite efflux pump ACR3, either at the plasma membrane or at the tonoplast of root cells. The aim of the present work was assessing the effect of the heterologous expression of Acr3 on the transcriptome of transgenic HR, in presence (0) or abscence of arsenite, in order to understand the accumulation properties of the roots developed.
Our results reveal that transgenic HR expressing ACR3 at the plasma membrane displayed a completely different gene expression profile as compared to control HR (transformed with the empty vector). On the other hand, HR expressing ACR3 at the tonoplast, made through the fusion of the ACR3 protein to the tonoplast integral protein TIP1.1, showed a gene expression profile much more similar to that of control HR.

overall_design: HR clones obtained were named as: Control HR (HR-2, HR-6 and HR-7), ACR3 (ACR3-5, ACR3-7, ACR3-12 and ACR3-14) and TIP-ACR3 (TIP-ACR3-4 and TIP-ACR3-6). Data obtained from RNA extraction and hybridization on Affymetrix microarrays were organized in six different hybridizations: Hybridizations 1, 2 and 3 that compare the different HR, i.e., control HR, ACR3 and TIP-ACR3 in the presence of 0.1 mM As(III) (E0.1) with regard to the same roots exposed to water (E0). On the other side, hybridizations 4 and 5 compare, respectively, the ACR3 and TIP-ACR transgenic roots with control HR, all of them exposed to As(III), whereas hybridization 6 compares ACR3 vs. TIP-ACR3 both exposed to As(III).

last: Pérez-Palacios

first: Kieron

last: Edwards

first: Ignacio

last: Rodríguez-Llorente

first: Miguel

last: Caviedes

first: Eloísa

last: Pajuelo


title: DNA:cytoplasm ratio defines an upper limit to cell size [RNA-seq]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important is not understood. Here we show that growing beyond a certain size has wide-ranging effects on cell physiology. Large cells are defective in gene induction, cell cycle progression and cell signaling. We further show that these defects are caused by the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. Finally, we determine why nucleic acid and protein biosynthesis do not scale with cell volume beyond a certain critical size. DNA becomes limiting. We conclude that the correct DNA to cytoplasm ratio is vital for many perhaps all cellular functions and that the range where this ratio supports optimal cell function is remarkably narrow.

sample_organism:
Saccharomyces cerevisiae
Candida albicans

overall_design: Total RNA sequenced from fixed numbers of S. cerevisiae cells of varying size mixed with a fixed number exponentially growing C. albicans cells. The S. cerevisiae counts were normalized to total number of C.albicans reads in each sample.

first: Gabriel

last: Neurohr

first: Rachel

last: Terry

first: Fabien

last: Moretto

first: Teemu

last: Miettinen

first: Laura

last: Pontano Vaites

first: Luis

middle: M

last: Soares

first: Joao

last: Paulo

first: Wade

last: Harper

first: Stephen

last: Buratowski

first: Scott

last: Manalis

first: Folkert

last: van Werven

first: Bela

last: Novak

first: John

last: Tyson

first: Angelika

last: Amon


title: Systemically administered extremely low HMGN1 with anti-CD4 depleting antibody exerts synergistic anti-tumor effects

city: Boston

first: Alex Chang-Yu

last: Chen

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

summary: Recently there has been growing interest in the immunomodulatory effects of endogenous danger signals known as alarmins.  In this study, we explore a new combination therapy of anti-CD4 depleting antibody with an alarmin, high mobility group nucleosome binding protein 1 (HMGN1). Extremely low dose of HMGN1 with anti-CD4 depleting antibody exerted robust anti-tumor effects in Colon26 subtaneous murine model. To understand transcriptomic differences of CD8+ T cells in the tumor-bearing mice after treated with anti-CD4 depleting antibody or combination therapy of HMGN1 with anti-CD4 depleting antibody, we performed CD8 T cell transcriptome analysis using 3'SAGE-seq and Ion Proton sequencer.

overall_design: CD8+ T cells were purified from single cell suspension of each implanted mouse tumor by lineage sorting (CD45-CD11b-B220-CD49b-Ter119-CD4-CD8+) through FACSAria. CD8 T cell transcriptome analysis were generated by 3'SAGE-seq using Ion Proton sequencer.

first: Chang-Yu

first: Satoshi

last: Ueha

first: Yoshiro

last: Ishiwata

first: Shoji

last: Yokochi

first: De

last: Yang

first: Joost

last: Oppenheim

first: Haru

last: Ogiwara

first: Shigeyuki

last: Shichino

first: Shungo

last: Deshimaru

first: Francis

last: Shand

first: Shiro

last: Shibayama

first: Kouji

last: Matsushima


title: Gene expression profiling of diffuse malignant peritoneal mesothelioma

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

summary: Diffuse malignant peritoneal mesothelioma (DMPM) is a rapidly lethal malignancy. The comprehension of the molecular features of DMPM is of utmost importance for the fruitful management of the disease, especially in patients who fail standard treatments and have a poor prognosis due to the lack of effective alternative therapeutic options.

overall_design: Gene expression profiling was carried out on a series of 45 frozen surgical specimens of diffuse malignant peritoneal mesothelioma (DMPM), 3 normal peritoneum samples and 2 patient-derived cell lines.

first: Stefano

last: Percio


title: Development of gene expression signatures for the A549 cells that overexpressed of FOSB

city: Yilan

first: Chen-Hung

last: Ting

state: Taiwan

address: 23-10 Dawen Rd., Jiaoxi

department: Marine research station, Institute of Cellular and Organismic Biology

institute: Academia Sinica

summary: Strongly induction of FOSB was observed in a cationic anticancer peptide TP4 treated human A549 lung cancer cell-line, causing obvious cell death. This work aims to address the gene expression profiling upon FOSB overexpression in A549 cell.

overall_design: A549 cells were transfected with either FOSB-GFP or GFP vector  for 40hr. Duplicated total RNA samples (i.e. two GFP and two FOSB-GFP transfected groupse) were collected for further microarray study.

first: Yi-Chun

first: Jyh-Yih


title: The genomic tandem quadruplication is associated with ketoconazole resistance of Malassezia pachydermatis

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary:
Purpose: Understanding the ketoconazole resistance mechanism in Malassezia pachydermatis
Methods: The transcriptome profile of the ketoconazole resistant M. pachydermatis KCTC 27587 cells compared to that of ketoconazole sensitive M. pachydermatis CBS 1879 cells were generated by RNA-Seq using Illumina HiSeq.
Results: The expressions of genes in the region of quadruplicated chromosome 4 were up-regulated.

overall_design: Transcriptome of M. pachydermatis KCTC 27587 (resistant to ketoconazole) vs. M. pachydermatis CBS 1879 (sensitive to ketoconazole)

first: Won

last: Jung

first: Mnchul

last: Kim

first: Minji

last: Park

first: Sun

middle: Y

last: Hwang


title: EGCG-treated non-small cell lung cancer associated signature miRNA expression analysis: NGS approach for novel miRNA sequence detection

city: VELLORE

first: Abul

middle: Kalam Azad

last: Mandal

state: Tamil Nadu

address: VELLORE

department: BIOTECHNOLOGY, SCHOOL OF BIOSCIENCES AND TECHNOLOGY

country: India

institute: VELLORE INSTITUTE OF TECHNOLOGY

summary: In the current study, we investigated the modulatory effect of epigallocatechin gallate (EGCG, an active derivative of green tea) on cellular miRNA expression and cell cycle proliferation in NSCLCs (A549). As the IC50 value of EGCG is approximately 304 μM, our studies support the resistance of A549 lung cancer cell by EGCG. In addition, it was interesting to observe its G0/G1 cell cycle arrest activity at 40μM EGCG treatment. So, in the present study, next-generation sequencing (NGS) was used to study the miRNA expression between the cancer control and EGCG-treated samples. A549 cells were treated with 40 μM and 100 μM EGCG. NGS was employed to study the differential expression of novel and known miRNAs. The data generated was analysed with computational approach to study and correlate the expression profiles of both known and novel miRNAs. Differential expression of known miRNAs was observed between control and EGCG-treated samples. Some putative novel miRNA sequences were also observed in the current study. The differential expression levels of putative novel miRNA sequences were estimated by counting the number of reads in the given dataset. Together the analysis of these miRNA profiles revealed log2-fold modulation in the expression levels. We detected 344, 337, and 346 number of known mature miRNAs in control, 40 μM EGCG treated, and 100 μM EGCG treated samples, respectively. We also reported 119, 126, and 125 number of putative novel mature miRNA sequences in control, 40 μM EGCG treated, and 100 μM EGCG treated samples, respectively. In conclusion, the analysis demonstrates that EGCG is actively involved in miRNA modulation in NSCLCs, which further attests to its chemoprotective role and could play a major role in therapeutic applications.

overall_design: A549 cells were treated with 40 micromolar or 100 micromolar concentration of EGCG for 24h. Total RNA was extracted from the samples. Small RNA sequencing was done by MiSeq, to study the differential miRNA expression profiles of known and putative novel miRNA sequences.

first: Vaishali

last: Bhardwaj


title: Heme and GATA1 coordinately regulate erythroid differentiation [expression]

city: Osaka

first: Shinya

last: Tanaka

state: Osaka

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

department: Immunology Frontier Research Center

institute: Osaka University

summary: In mice lacking the heme exporter, FLVCR, differentiation fails at the CFU-E/proerythroblast stage from excessive heme and reactive oxygen species. We show that Flvcr1-deleted CFU-E/proerythroblasts have low GATA1 mRNA and GATA1-target gene mRNAs along with increased ribosomal protein mRNAs as a direct result of increased heme. Thus heme increases ribosomal protein transcription when globin production needs to be increased, and when heme is excessive, GATA1 is reduced allowing for normal termination of erythroid differentiation. This demonstrates that heme and GATA1 are co-master regulators of erythroid differentiation.

overall_design: Total RNA obtained from erythroid cells of mice with Flvcr deleted compared to those of wild-type mice.

first: Raymond

last: Doty


title: Transcriptional profiling of intestinal epithelial cells in response to Enterococcus gallinarum MRx0518

status: Public on Feb 06 2019

city: Aberdeen

first: Imke

last: Mulder

address: Cornhill Road

institute: 4D Pharma Research Ltd

summary:
In this study we describe the immunostimulatory properties of Enterococcus gallinarum MRx0518, a candidate live biotherapeutic agent with anti-tumorigenic properties. Here we demonstrate that strain MRx0518 elicits a strong pro-inflammatory response in intestinal epithelial cells. Treatments with metabolically active cells, inactivated cells  or culture supernatants were found to induce distinct host responses.
Microarray analysis was used to investigate and compare changes in the gene expression of intestinal epithelial cells in response to live MRx0518, heat-killed MRx0518 and MRx0518 culture supernatant.

overall_design: Confluent monolayers of HT29-MTX cells (ten days post seeding) were incubated with treatments of live MRx0518 and heat-killed MRx0518 at a multiplicity of infection (MOI) of 100 bacterial cells to 1 human cell, and an equivalent dilution of MRx0518 cell-free culture supernatant for 3 h at 37 °C in anaerobic conditions. Untreated cells and cells treated with bacterial culture medium (YCFA) were used as assay controls. Following incubation, RNA was isolated and hybridised to Affymetrix Human Transcriptome Array 2.0 GeneChips (GEO Accession Number GPL17586). Three independent biological replicates of each condition were carried out.

first: Delphine

last: Lauté-Caly

first: Emma

last: Raftis

first: Philip

last: Cowie

last: Hennessy

first: Amy

last: Holt

first: D

middle: A

last: Panzica

first: Christina

last: Sparre

first: Beverley

last: Minter

first: Eline

last: Stroobach


title: Microarray expression profile of micro RNAs in serum for Esophageal Squamous Cell Carcinoma

city: Beijing

first: Fen

last: Liu

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

institute: Capital Medical University

summary: The purpose of this study is to explore the miRNAs expression profiles in the serum from esophageal squamous cell carcinoma (ESCC) patients.

overall_design: We have completed the Arraystar Human miRNA Array analysis of the 104 serum samples from preoperative ESCC patients (n=52) and healthy controls (n=52).

first: Yuanjie

last: Ding

first: Yi

last: Shen

first: Xudong

last: Guo

first: Wenqiang

last: Wei

first: Xinqing

last: Li


title: Molecular specification of cell types underlying central and peripheral vision in primates (macaque peripheral single cell RNA-seq)

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Among mammals, only primates including human possess a small central retinal region called the fovea, which mediates high acuity vision. As other mammals lack a fovea, molecular bases of its specialized function and dysfunction in retinal diseases remain poorly understood. By analyzing >165,000 single-cell transcriptomes from macaque fovea and peripheral retina, we identified and molecularly characterized >60 major cell types in each region. A few cell types are unique to each region, and there are also substantial differences in proportions and gene expression between corresponding types in the two areas, some of which can be related to functional differences. Comparison of macaque and mouse retinal taxonomies reveals both similarities and differences between species. Many molecular features of macaque retinal cell types are conserved in two other primates, marmosets and humans, and key human retinal disease-associated genes are expressed in specific macaque cell types

overall_design: Peripheral samples from four crab-eating macaque are included.

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: M

last: Do

first: Aviv

last: Regev

first: Joshua

last: Sanes


title: Whole-genome transcriptomic analysis of Notch1-expressing cells in mouse intestinal tumours

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: To define and compare the genome-wide transcriptional signatures of Notch1+ cells in intestinal tumors and in normal ISCs we performed Affymetrix analyses of these two populations.

overall_design: Three replicates from a pool of 5-7 mice (tumors) and 2 mice (normal ISCs) were used for the analysis. GFPpos and GFPneg tumor and normal ISCs were sorted from the same replicate. A total of 12 samples were analyzed (6 per condition).

first: Larissa

last: Mourao

first: Silvia

last: Fre


title: Self-renewal capability of hepatocytic parental progenitor cells derived from an adult rat  liver is maintained for a long term in the chemically defined medium cultured on lamini111

status: Public on Feb 05 2019

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

summary: We analyzed gene expression of hepatocytic parental progenitor cells cultured on laminin (LN) 111, LN511 and Matrigel (Mat) in a population of small hepatocytes.

overall_design: Primary rat small hepatocytes were isolated from fresh livers by using collagenase perfusion method and cultured in serum-free medium. Nine days after plating, colonies were treated with a separation solution and CD44+ cells were isolated by using MACS methods.The sorted CD44+ cells were cultured in Matrigel(Mat)-coated dishes. Second passage cells were cultured on laminin (LN)111, LN511 and Mat for 3 hours.  As a control, mature heptocytes (MH) were isolated from fresh livers.

first: N

first: T

last: Mitaka


title: Microarray profiling peripheral blood mononuclear cells

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

summary: We performed RNA-Seq transcriptome profiling on 29 immune cell types consituting peripheral blood mononuclear cells (PBMCs) sorted from 4 Singaporean-Chinese individuals (S4 cohort). We also performed RNA-Seq and microarray transcriptome profiling of PBMCs from an extended cohort of 13 individuals (S13 cohort). The data was used first to characterize the transcriptomic signatures and relationships among the 29 immune cell types. Then we explored the difference in mRNA composition in terms of transcripts proportions and abundance. Lastly, we performed deep deconvolution for both microarray and RNA-Seq technologies.

overall_design:
Total RNA of 29 immune cell types (from 4 individuals) and peripheral blood mononuclear cells (PBMCs, from 13 individuals) was extracted for gene expression profiling. The 13 PBMCs samples were processed with both microarray and RNA-Seq platforms.

This submission represents microarray data.

first: Bernett

last: Lee

first: Weili

last: Xu

first: You

last: Hwang

first: Michael

last: Poidinger

first: João

middle: P

last: de Magalhães

first: Anis

last: Larbi


title: Expression data from freshly isolated mouse mammary luminal cells

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
The mammary luminal cell compartment is heterogeneous. In adult virgin mice, it contains clonogenic luminal progenitors and non-clonogenic luminal cells expressing estrogen and progesterone receptors that can be
discrimated by their cell surface expression of ICAM-1. We have separated ICAM1+ luminal progenitors  and ICAM-  non-clonogenic luminal cells and analyzed their transcriptomic profiles. After showing that the luminal progenitor population overexpressed Met,  Trp53 and numerous p53 target genes, we analyzed how the p53 and Met signaling pathways cooperate to control the function and plasticity of luminal progenitors.

overall_design: Single cells were prepared from seven distinct pools of at least 12 mammary glands and sorted by flow cytometry according to their CD24 and ICAM-1 expression. Seven paired samples of CD24+ ICAM1+ (LuPos) and CD24+ ICAM1- (LuNeg) cells were collected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Amandine

last: Di-Cicco

first: Laura

last: Bresson

first: Audrey

last: Rapinat

first: David

last: Gentien

first: Marisa

last: Faraldo

first: Marie-Ange

last: Deugnier


title: LncRNA HAND2-AS1 controls liver cancer stem cell functions and serves as a potential therapy target (RNA microarray)

first: Runsheng

last: Chen

address: 15 Datun Road, Chaoyang District

department: CAS Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinsese Academy of Sciences

summary:
Investigation the RNA profiling in Huh7 cells upon knock-out lncRNA HAND2-AS1 or knock-down INO80 via gene expression microarray analysis
Hepatocellular carcinoma (HCC) is the most prevalent liver cancer, characterized by a high rate of recurrence and heterogeneity. Liver cancer stem cells (CSCs) may well contribute to both of these pathological properties, but the mechanism underlying their self-renewal and maintenance are poorly understood. Here we identified a long noncoding RNA (lncRNA) termed HAND2-AS1 that is highly expressed in liver CSCs. Human HAND2-AS1 is highly conserved to its mouse ortholog lncHand2. HAND2-AS1 is required for the self-renewal maintenance of liver CSCs to initiate HCC development. Mechanically, HAND2-AS1 recruits the INO80 complex onto BMPR1A promoter to trigger its expression, leading to the activation of BMP signaling. Importantly, targeting HAND2-AS1 by antisense oligonucleotides (ASOs) and BMPR1A by siRNAs have synergistic anti-tumor effects on humanized HCC models. Moreover, knockout of lncHand2 or Bmpr1a in mouse hepatocytes impairs BMP signaling and suppresses the initiation of liver cancer. Our findings reveal that HAND2-AS1 promotes the self-renewal of liver CSCs and drives liver oncogenesis, which may be a potential target for HCC therapy.

overall_design: Two-color expression assay for HAND2-AS1 KO vs scr and INO80 KD vs scr.

first: Yanying

last: Wang

first: Pingping

last: Zhu

first: Jianjun

last: Luo

first: Jing

first: Zhiwei

last: Liu

first: Ying

last: Du

first: Wei

last: Wu

first: Lei

last: He

first: Chen

last: Runsheng

first: Yong

last: Tian

first: Zusen

last: Fan


title: circRNAs microarray analysis of ischemic postconditioning (IPO) to attenuate hepatic ischemia-reperfusion injury in mice

city: Changsha

first: Pengpeng

last: Zhang

state: Hunan

address: No.138 Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

summary: this is the first study to investigate circRNA expression profiling in regard to hepatic I/R and IPO by microarray analysis. Our results may provide an experimental basis for elucidating the underlying mechanism of IPO and reveal candidate biomarkers with which to assess hepatic I/R injury

overall_design: liver circRNAs expression  profiles of sham, I/R and IPO mice were generated by microarray analysis in triplicate.

first: Qifa

last: Ye


title: Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Metabolically versatile bacteria use catabolite repression control to select their preferred carbon sources, thus optimizing carbon metabolism. In pseudomonads, this occurs through the combined action of the proteins Hfq and Crc, which form stable tripartite complexes at target mRNAs, inhibiting their translation. The activity of Hfq/Crc is antagonised by small RNAs of the CrcZ family, the amounts of which vary according to carbon availability. The present work examines the role of Pseudomonas putida Hfq protein under conditions of low-level catabolite repression, in which Crc protein would have a minor role since it is sequestered by CrcZ/CrcY. The results suggest that, under these conditions, Hfq remains operative and plays an important role in iron homeostasis. In this scenario, Crc appears to participate indirectly by helping CrcZ/CrcY to control the amount of free Hfq in the cell. Iron homeostasis in pseudomonads relies on regulatory elements such as the Fur protein, the PrrF1-2 sRNAs, and several extracytoplasmic sigma factors. Our results show that the absence of Hfq is paralleled by a reduction in PrrF1-2 small RNAs. Hfq thus provides a regulatory link between iron and carbon metabolism, coordinating the iron supply to meet the needs of the enzymes operational under particular nutritional regimes.

overall_design: Total RNA from wild-ype and three mutants of P. putida KT2440 was deep-sequenced and gene expressions were quantified. Differential expression of bacterial genes for each mutant against wild type was determined.

first: Dione

last: Sánchez-Hevia

first: Luis

last: Yuste

first: Renata

last: Moreno

first: Fernando

last: Rojo


title: Transcriptome analysis of lung epithelial cells and lung fibroblasts from various developmental stages (E18.5, P0.5, P2, P7, P28, and P56)

city: Noda, Chiba

first: Kazushige

last: Shiraishi

address: Yamasaki 2669

institute: Tokyo University of Science

summary: In the alveoli, lung fibroblasts are in close contact with alveolar epithelial cells type 2, and are considered to support alveolar epithelial cells, forming an alveolar stem cell niche. However, what fibroblast-to-epithelial cell interactions occur during the alveolar maturation stage remains unclear. To understand the lung fibroblast-to-epithelial cell interactions, we performed time-course 3´SAGE-seq analysis of lung epithelial cells and fibroblasts.

overall_design: Lung epithelial cells and lung fibroblasts from various developmental stages (E18.5, P0.5, P2, P7, P28, and P56) were purified by cell sorting. The time series transcriptome of the epithelial cells and fibroblasts was generated by 3'SAGE-seq using Ion Proton sequencer.

first: Shigeyuki

last: Shichino


title: Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary: To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations.

overall_design: Median per feature was used to summarize data when two or three technical replicates were available. Median of normal human colon tissues are used as reference for further analysis.

first: Jordi

last: Camps

first: Quang

last: Nguyen

first: Hesed

last: Padilla-Nash

first: Turid

last: Knutsen

first: Nicole

last: McNeil

first: Danny

last: Wangsa

first: Amanda

middle: B

last: Hummon

first: Marian

last: Grade

first: Thomas

last: Ried

first: Michael

middle: J

last: Difilippantonio


title: Transcriptomic analysis of human tumor cell lines

city: Tokyo

first: Masatoshi

last: Wakui

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Laboratory Medicine

institute: Keio University School of Medicine

summary: To investigate tumor heterogeneity based on information theory applied to transcriptomics, we analyzed gene expression profiles of human tumor cell lines cultured under normoxia or hypoxia.

overall_design: Gene expression profiles of human tumor cell lines cultured under normoxia or hypoxia.


title: Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius [RNA-seq]

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

summary: We test the hypothesis that intraspecific genomic divergence is linked to regulatory variation between Heliconius butterfly populations. We show that population-level divergence in chromatin accessibility and regulatory activity during wing development is abundant, and that differences in regulatory activity between populations are strongly associated with developmental stage. Genomic regions with high Fst are highly enriched for regulatory variants, and enrichment patterns vary significantly across development. Regulatory variants are associated with most differential gene expression between populations, and our data point to two roles for histone modifications in the evolution of gene expression.

sample_organism:
Heliconius himera
Heliconius erato petiverana
Heliconius erato lativitta

overall_design: Examination of mRNA abundance in day 3 pupal wings.

first: Robert

middle: D

last: Reed


title: Exon expression profiling of de novo diffuse large B-cell lymphoma samples

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary:
Exon expression profiling was performed on 37 clinical DLBCL samples and subsequently analyzed using alternative splice analysis of vairance (asANOVA) implemented in Partek Genomics Suite in order to identify alternative spliced genes.
Diffuse large B-cell lymphoma (DLBCL) is a very heterogeneous malignant disease with diverse clinical presentation, outcome, and pathogenic mechanism. In order to better risk stratify patients there is a current need to find and validate new biomarkers of the disease.  An alternatively spliced transcript of NOTCH3 missing exon 16 was identified and displayed prognostic and predictive biomarker potential.

overall_design: In this study 37 DLBCL patients were analyzed using HuEx. 1.0 array

first: Ditte

middle: S

last: Jespersen

first: Anna

last: Schönherz

first: Hanne

last: Due

first: Hans

last: Johnsen

first: Martin

last: Bøgsted

first: Karen

last: Dybkær


title: Real-time quantitative PCR analysis of RNA extracted from whole blood from dengue infected patients

status: Public on Feb 04 2019

city: Stanford

first: Purvesh

last: Khatri

state: CA

address: 279 Campus Dr., Beckman B235A

department: Medicine

institute: Stanford University

summary: Human RNA extracted from whole blood was evaluated for a panel of genes to identify uncomplicated from severe dengue patients

overall_design: qPCR gene expresion profiling. RNA from whole blood from dengue infected patients or healthy controls was used. Equal amount of total RNA from each donor was used.

first: Einav

last: Shirit

first: Khatri

last: Purvesh


title: Cortisol acting through the glucocorticoid receptor is not responsible for exercise-enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish (Danio rerio)

city: Leiden

first: Ron

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

summary: Forced sustained swimming exercise at optimal speed enhances growth in many fish species, particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism, we first subjected wild-type zebrafish to an exercise protocol validated for exercise-enhanced growth, and showed that exercised zebrafish, which indeed showed enhanced growth, had higher cortisol levels than the non-exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor (Gr). Second, we subjected wild-type zebrafish and zebrafish with a mutant Gr to exercise at optimal, suboptimal and super-optimal speeds and compared them with non-exercised controls. Exercised zebrafish showed growth enhancement at all speeds, with highest growth at optimal speeds. In the Gr mutant fish, exercise resulted in growth enhancement similar to wild-type zebrafish, indicating that cortisol cannot be considered as a main determinant of exercise-enhanced growth. Finally, the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild-type fish (183 versus 351). A cluster of 36 genes was regulated by exercise in both wild-type and mutant fish. In this cluster, genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild-type fish and mutants, these processes may play an important role in exercise-enhanced growth.

overall_design: Deep-sequencing transcriptome analysis of white muscle samples derived from wild-type (++) or glucocorticoid receptor (Gr) mutant (--) Danio rerio specimens that were exposed to either a resting (REST) or a swimming (UOPT) regimen: wild-type resting (REST++; n=3), Gr mutant resting (REST--;  n=3), wild-type swimming (UOPT++; n=3), Gr mutant swimming (UOPT--; n=3).

first: Arjan

last: Palstra


title: Identification of Novel Regulatory Genes in APAP Induced Hepatocyte Toxicity by a Genome-Wide CRISPR-Cas9 Screen

city: Kansas City

first: Shui

middle: Q

last: Ye

state: MO

address: 2411 Holmes Street

department: Departmetn of Biomedical and Health Informatics

country: USA

institute: University of Missouri Kansas City School of Medicine

summary: Acetaminophen (APAP) is a commonly used analgesic responsible for more than half of acute liver failure cases. Identification of previously unknown genetic risk factors would provide mechanistic insights and novel therapeutic targets for APAP-induced liver injury. This study used a genome-wide CRISPR-Cas9 screen to evaluate genes that are protective against, or cause susceptibility to, APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR-Cas9 gene knockouts were treated with 15mM APAP for 30 minutes to 4 days.  A gene expression profile was developed based on the 1) top screening hits, 2) overlap of expression data from APAP overdose studies, and 3) predicted affected biological pathways. We further demonstrated the implementation of intermediate time points for the identification of early and late response genes. This study illustrated the power of a genome-wide CRISPR-Cas9 screen to systematically identify novel genes involved in APAP-induced hepatotoxicity and to provide potential targets to develop novel therapeutic modalities.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Single-read DNA amplicon sequencing of a CRISPR/Cas9 genome-wide knockout screen of acetaminophen-induced hepatotoxicity in the HuH7 human hepatocarcinoma cell line. sgRNA library transfer plasmid isolated from E. coli was sequenced alongside the screen to assess library representation. For each sample there are 4 technical replicates.

first: Katherine

last: Shortt

first: Daniel

last: Heruth

first: NiNi

last: Zhang

first: Weibin

last: Wu

first: Shipra

last: Singh

first: Ding-You

last: Li

first: Li

first: Gerald

last: Wyckoff

first: Lei

last: Qi


title: Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB)

status: Public on Feb 03 2019

city: Brisbane

first: Renato

last: de Souza Pinto Lemgruber

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd

country: Australia

institute: University of Queensland

summary: Gas fermentation is emerging as an economically attractive option for the sustainable production of fuels and chemicals from gaseous waste feedstocks. Clostridium autoethanogenum can use CO and/or CO2 + H2 as its sole carbon and energy sources. Fermentation of C. autoethanogenum is currently being deployed on a commercial scale for ethanol production. Expanding the product spectrum of acetogens will enhance the economics of gas fermentation. To achieve efficient heterologous product synthesis, limitations in redox and energy metabolism must be overcome. Here, we engineered and characterised at a systems-level, a recombinant poly-3-hydroxybutyrate (PHB)-producing strain of C. autoethanogenum. Cells were grown in CO-limited steady-state chemostats on two gas mixtures, one resembling syngas (20% H2) and the other steel mill off-gas (2% H2). Results were characterised using metabolomics and transcriptomics, and then integrated using a genome-scale metabolic model reconstruction. PHB-producing cells had an increased expression of the Rnf complex, suggesting energy limitations for heterologous production. Subsequent optimisation of the bioprocess led to a 12-fold increase in the cellular PHB content. The data suggest that the cellular redox state, rather than the acetyl-CoA pool, was limiting PHB production. Integration of the data into the genome-scale metabolic model showed that ATP availability limits PHB production. Altogether, the data presented here advances the fundamental understanding of heterologous product synthesis in gas-fermenting acetogens.

overall_design: RNA sequencing of steel mill off gas- and syngas-grown Clostridium autoethanogenum (PHB-type and Empty plasmid-type); 8 samples in total (2 biological replicates for each type and gas mixture used)

middle: d

last: Lemgruber

first: Kaspar

last: Valgepea

first: Ryan

last: Tappel

first: James

last: Behrendorff

first: Robin

middle: W

last: Palfreyman

first: Manuel

last: Plan

first: Mark

last: Hodson

first: Sean

last: Simpson

first: Lars

middle: K

last: Nielsen

first: Michael

last: Köpke

first: Esteban

last: Marcellin


title: Genotype study of celiac disease and control individuals

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: This collection of samples were genotyped to use altogether with other data to gain insight into the mechanism behind celiac disease.

overall_design: 48 samples, controls and celiac, were analyzed using the Illumina HumanImmuno BeadChip array.