title: The effect of S1P on the gene expression in the bronchial epithelial cells

status: Public on Aug 23 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: As for asthma-related genes, in contrast to S1P-untreated epithelial cells, S1P-treated epithelial cells expressed ADRB2 and PTGER4.

overall_design: BEAS-2B and Calu-3 were stimulated with or without S1P (1 µM) for 3 h. Total RNA labeled with Cy3 or Cy5 was hybridized to a 3D-Gene Human Oligo chip 25 k (Toray Industries Inc., Tokyo, Japan). Genes with Cy3/Cy5 normalized ratios greater than 2.0 were identified.

first: Yuichiro

last: Yasuda

first: Tatsuya

last: Nagano

first: Masatsugu

last: Yamamoto

first: Asuka

last: Yoshizaki

first: Hiroshi

last: Kamiryo

first: Ryota

last: Dokuni

first: Kazuyuki

last: Kobayashi

first: Tomomi

last: Terashita

first: Yoshihiro

last: Nishimura


title: Intrathecal delivery of human ESC-derived mesenchymal stem cell spheres promotes recovery of a primate EAE model

status: Public on Aug 30 2018

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

country: China

institute: University of Macao

summary: Nonhuman primate experimental autoimmune encephalomyelitis (EAE) is a valuable model for multiple sclerosis an inflammatory demyelinating disease in the central nervous system (CNS). Human embryonic stem cell-derived mesenchymal stem cells (EMSC) are effective in treating murine EAE. Yet, it remains unknown whether the EMSC efficacy is translatable to humans. Here we induced a primate EAE model in cynomolgus monkeys and transported EMSC in spheres (EMSCsp) to preserve the cell viability under ambient conditions. First, single cells dissociated from EMSCsp were intravenously infused into normal and EAE monkeys. The cells reached various organs including CNS but diminished rapidly. To increase the number and viability of EMSC in the CNS, we injected EMSCsp intrathecally (i.t.) into the subarachnoid cavity of EAE monkeys multiple times post-onset and upon relapses during a 3-month observation. The clinical symptoms in these animals relieved rapidly following the injections and eventually disappeared. Whereas, symptoms in a vehicle control-injected EAE monkey remained and reduced slowly. Consistently, reduced lesions and active regeneration were found in the CNS of the EMSCsp-treated monkeys compared to the control. EMSC were found in the CNS long after the i.t. injections and some of the cells had differentiated into neurons and oligodendrocytes. Supporting evidence demonstrated that EMSCsp cultured in cerebrospinal fluid from the EAE monkeys largely converted to neural cells with elevated expression of genes for neuronal markers, neurotropic factors, and neuronal myelination. Together, this study suggests that i.t. injection of ambiently transported EMSCsp can treat EAE in nonhuman primates via remyelination and transdifferentiation, which shall expedite the clinical application of EMSC in patients.

overall_design: This study for the first time demonstrates that EMSCsp, following ambient transportation, can be delivered directly via i.t. injection into the subarachnoid cavity of the spinal cord, and promote recovery in a NHP model of EAE. Spheroidal formation and i.t. injection may both enhance the cell number and survival of EMSC in the CNS, compared to peripheral administration of dissociated EMSC. Transdifferentiation of EMSC into neurons and oligodendrocytes as well as neural trophic effects of the transplanted cells may contribute to the efficacy of the cells as schemed in Fig. 7. Ideally more monkeys and EMSC lines could have been used to further verify the conclusions if the costs had not been so high. Nevertheless, the present study has extended our understanding of EMSC efficacy in the EAE models from mice to primates, and shall facilitate the translation of this potential cell therapy to humans.

first: Li

last: Yan

first: Yuyu

last: Niu

first: Bin

last: Jiang

first: Wei

last: Si

first: Hongxuan

last: Wang

first: Enqin

last: Li

first: Yaping

first: Shaohui

last: Chang

first: Huiyan

last: Sun

first: Ying

last: Peng

first: Ren-He

first: Weizhi

last: Ji


title: The major patterns of changes in gene expression in mouse B cells in response to the latent membrane protein 1 (LMP1) of Epstein-Barr virus (EBV) in B cells gene expression

status: Public on Aug 24 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Analysis of gene expression profiling change by expression of Epstein-Barr virus latent membrane protein 1 (LMP1) in B cells

overall_design: Gene expression analysis of CD45.1 from GFP+CD45.1 (n=2), LMP1 from LMP1+CD45.1  (n=2) and CD45.1 from LMP1+CD45.1  (n=2) cells were performed using Agilent SurePrint G3 Mouse GE 8x60K Microarray as one color experiments.

first: Tsai

last: Chiau-Yuang


title: The IKKβ/FoxO3a axis regulates breast cancer tumorigenesis and bone metastasis

status: Public on Aug 29 2018

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: IKB Kinase beta (IKKB), a key component of the NFKB signalling pathway plays an important role in inflammation and cancer. Here we describe a previously unknown role of the IKKβ/FoxO3a axis in bone metastasis. We found that IKKβ was highly expressed in invasive human breast tumours and that levels of expression were elevated in bone metastasis. Overexpression of IKKβ in parental and bone-tropic human breast cancer cell-lines increased tumour volume, worsened cachexia, promoted osteolysis and increased mortality in adult mice whereas pharmacological inhibition and knockdown of IKKβ were inhibitory. Inhibition of IKKβ in breast cancer cell lines and bone cells stimulated bone formation and reduced tumour growth by a mechanism that was mediated in part, by cytoplasmic sequestering of FoxO3a independently of NFKB inhibition. We conclude that IKβ contributes significantly to the regulation of tumour growth and osteolysis in breast cancer by NFKB dependent and independent mechanisms.

overall_design: Human MDA-231 control (mock), IKKβ deficient (IKKB si) and p65NFKB deficient (p65 si) breast cancer cells were hybridised to HT-12 Beadarrays in triplicate

first: Silvia

last: Marino

first: John

middle: G

last: Logan

first: Mattia

last: Capulli

first: Antonia

last: Sophocleous

first: Patrick

last: Mollat

first: Barbara

last: Mognetti

first: Luca

last: Ventura

first: Nadia

last: Rucci

first: Stuart

last: Ralston

first: Aymen

middle: I

last: Idris


title: Differential Chemopreventive Activity of Sulindac and/or Atorvastatin in Apc+/Min-FCCC Mice With or Without Colorectal Adenomas

status: Public on Aug 31 2018

city: Philadelphia

first: Margie

last: Clapper

state: PA

address: 333 Cottman Ave

country: USA

institute: Fox Chase Cancer Center

summary: Emerging data suggest that some high-risk subjects benefit more than others from preventive intervention.  The goal of this study was to determine the efficacy of sulindac (Sul) and/or atorvastatin (Atorva) against spontaneous colorectal adenomas in Apc+/Min-FCCC mice in which the tumor-bearing status was known at the time of treatment initiation. Administration of Sul/Atorva to tumor-bearing mice led to a 43% reduction in the multiplicity of colorectal adenomas as compared to that of untreated tumor-bearing mice. Atorvastatin completely inhibited the formation of microadenomas in mice that were tumor-free at baseline, with associated decreases in the expression of inflammatory mediators observed.  Expression of Hoxb13 and Rprm was enhanced significantly following Sul/Atorva treatment, suggesting the importance of cell cycle regulation in colon tumor inhibition. The tumor status of animals at treatment initiation dictates response to atorvastatin, sulindac and Sul/Atorva. The tumor inhibition observed with Sul/Atorva in tumor-bearing mice was greater than that achieved with either agent alone.

overall_design: Male Apc+/Min-FCCC mice were subjected to colonscopy at 6-8 weeks of age.  Based on the results of the colonscopic exam, mice were categorized as tumor-free and tumor bearing.  Tumor-bearing mice were assigned to receive either meal form of Harlan Teklad 2018SX chow (Harlan Teklad Global Diets, Madison, WI, untreated control) or chow supplemented with sulindac 300 ppm plus atorvastatin 100 ppm.  Tumor-free mice were assigned to either the untreated control or the atorvastatin (100 ppm) group.  After 7 days of treatment, mice were euthanized and colons were collected and process for gene expression analyses.

first: Wen-Chi

middle: L

last: Chang

first: Christina

last: Ferrara

first: Stacy

last: Mosier

first: Harry

middle: S

last: Cooper

first: Karthik

last: Devarajan

first: Harvey

last: Hensley

first: Yan

last: Zhou

first: Lisa

last: Vanderveer

first: Minhhuyen

middle: T

last: Nguyen


title: Effect of Notch1 on inflammatory activation of human umbilical vein endothelial cells

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

summary: Inflammatory activation of endothelial cells enables leukocyte recruitment to tissues. We here investigate how Notch1 signaling affects the transcriptional profile of inflammatory activated human umbilical vein cells.

overall_design: Analysis of data from human umbilical vein endothelial cells (HUVECs) transfected with siRNA (scrambled or targeting NOTCH1), cultured for 48 hours and stimulated with IL-1b (5ng/ml) for 4 hours. RNA was submitted for hybridisation using the Illumina Human HT-12 v4.0 expressionbeadchip.

first: Tor

last: Espen Stav-Noraas

first: Lars

last: La Cour Poulssen

first: Johanna

last: Hol


title: CTCs vs. WBCs from a HNSCC patient

status: Public on Aug 25 2018

city: Taipei

first: Ching-Fei

last: Li

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: YM University

summary: For further validation that the circulating tumor cells (CTCs) from head and neck squamous cell carcinomas (HNSCC) patients were indeed cancer cells rather than non-specific contaminated cells such as white blood cells (WBCs), we examined the copy number alterations (CNAs) of the captured CTCs by aCGH (array comparative genomic hybridization).

overall_design: We sorted CTCs (panCK+/CD45- cells) and WBCs (panCK-/CD45+ cells) by flow cytometry. Whole genome amplification (WGA) was performed using REPLI-g Single Cell Kit (Qiagen, Hilden, Germany) and following the manufacturer's instructions following by aCGH. Healthy male genomic DNA was used as reference DNA.

first: Muh-Hwa

last: Yang

first: Ying-Chih

first: Yang-Hui

last: Ho

first: Jia-Yang

last: Chen

first: Liang-Chun

last: Wu


title: Genome-wide transcriptome analysis of Fusarium fujikuroi Δset1 and Δkdm5 mutants

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

summary:
We performed genome-wide transcriptome analyses of the Fusarium fujikuroi wild type (WT) in comparison to deletion mutants of the histone methyltransferase gene SET1 and the histone demethylase gene KDM5
The results show that Set1 and Kdm5 control large sets of genes involved in primary and secondary metabolism due to the modifications of the chromatin structure (methylation of histone 3 lysine 4)

overall_design: The WT and mutant strains were grown for 3 days in synthetic medium with low (6 mM glutamine) and high (60 mM glutamine) amounts of nitrogen. The RNA was isolated from two biological replicates each and used for microarray analysis.

last: Güldener

first: Martin

last: Münsterkötter

first: Slavica

last: Janevska

first: Bettina

last: Tudzynski


title: In vitro maturation of human pluripotent stem cell-derived intestinal organoids

status: Public on Aug 27 2018

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Human intestinal organoids (hIOs) derived from human pluripotent stem cells (hPSCs) have immense potential as a source of intestines. However, due to problems obtaining mature adult-like cells from hPSCs, effective strategies for the maturation of hIOs with improved functionalities must be developed. We established conditions that enable the in vitro maturation of hIOs derived from hPSCs, recapitulating the essential features of intestinal tissue. The maturity of the hPSC-derived hIOs was enhanced by the in vitro maturation in our co-culture system, evidenced by transcriptional changes observed in our microarray data. Global transcription of in vitro-matured hIOs is highly similar to that of adult human small intestine (hSI). Compared to control hIOs, in vitro-matured hIOs exhibited significant increases in the expression of intestinal maturation markers, major transporters, and key enzymes for drug absorption and first-pass metabolism.

overall_design: Changes in the gene expression profile of undifferentiated human pluripotent stem cells (hPSC), definitive endoderm cells (DE), hindgut cells (HG), hIOs (p0), hIOs (p2), in vitro matured hIOs and adult human small intestine (hSI). At least three independent experiments were performed for each condition.

first: Kwang

middle: B

last: Jung


title: Genes regulated/modulated by jagged1 in endothelial cells during inflammation

summary: Proinflammatory activation of endothelial cells leads to recruitment of leukocytes by upregulation of adhesion molecules and presentation of chemoattractants. In response to such activation there is also a strong shift in the endothelial expression of Notch ligands, with downregulation of Dll4 and a upregulation of JAG1. To assess whether Jagged1 would affect the endothelial activation profile, we suppressed JAG1 expression during IL-1β-induced activation by means of siRNA and performed a genome-wide transcriptome analysis. Our results show for the first time that Jagged1 modulates the transcription profile of activated endothelial cells and describe data that imply a role for Jagged1 in sharpening the inflammatory profile of the vasculature, giving it an edge towards leukocyte recruitment. These findings imply that Jagged1 might be a potential therapeutic target to attenuate inflammation and reduce tissue damage in inflammatory diseases.

overall_design: Genome-wide analysis of total RNA obtained from confluent human umbilival vein endothelial cells (pool of 7 individual donors) transfected with JAG1 siRNA or scrambled siRNA, and further subjected to proinflammatory activation by IL-1β 24 hours, compared to unstimulated controls (3 biological replicates in each group) (see below for the four resulting sample groups) .

first: Reidunn

middle: J

last: Edelmann

first: Eirik

last: Sundlisæter


title: Gene expression in SAS cell lines upon SNAI1 silencing

summary: Collective cell migration is one of the principal modes for cancer cell movements. However, the triggering event for collective migration and its clinical significance is unclear. Here, we found that Snail, a major inducer of epithelial-mesenchymal transition (EMT), is critical for orchestrating collective migration in squamous cell carcinoma (SCC). To invstigate how Snail contribute to collective migration and invasion, we used microarrays to identify the global gene alterations regulated by Snail in SCC cells.

overall_design: Control vs. Snail-depleted SAS cells were cultured on thick collagen (2.5D cultured system) for simulating virtual physiological environment. After 24 h, total RNA was harvested for microarray analysis.


title: Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [ChIP-seq]

status: Public on Aug 28 2018

city: Toyonaka

first: Koji

last: Nagao

address: 1-1 Machikaneyama

department: Graduate School of Science

institute: Osaka University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

overall_design: ChIP-seq analysis of mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1

first: Yuki

last: Sakakibara

first: Chikashi

last: Obuse

first: Takashi

last: Sado


title: PD-1 through asparaginyl endopeptidase regulates FoxP3 Stability in Induced Regulatory T cells

city: Hamilton

first: Eric

middle: W

last: Dahlstrom

state: MT

address: 903 S. 4th St

department: RTB

institute: NIAID, NIH

summary:
CD4+ T cell differentiation into multiple T helper lineages is critical for optimal adaptive immune responses. This report identified a novel intrinsic mechanism by which PD-1 signaling imparted regulatory phenotype to FoxP3+ Th1 cells  (denoted as Tbet+iTregPDL1 cells) and iTregs. Tbet+iTregPDL1 cells were capable of preventing inflammation in murine models of experimental colitis and experimental graft versus host disease. PDL-1 binding to PD-1 imparted regulatory function to Tbet+iTregPDL1 cells and iTregs by specifically downregulating an endolysosomal protease asparaginyl endopeptidase (AEP)
AEP regulated FoxP3 stability and blocking AEP imparted regulatory function in Tbet+iTregs cells. Also AEP-/- iTregs significantly inhibited GvHD and maintained FoxP3. Furthermore, PD-1 mediated FoxP3 maintenance in Tbet+Th1 cells occurred both in tumor infiltrating lymphocytes (TIL) and during chronic viral infection. Collectively, this report has identified a novel intrinsic function for PD-1 in converting Th1 cells into Tregs through an intrinsic proteolytic pathway

overall_design: Microarray of Tbet+iTregs expanded with or without PDL-1 stimulation

first: Chaido

last: Stathopouloou

first: Arunakumar

last: Gangaplara

first: Grace

last: Mallett

first: Francis

middle: A

last: Flomerfelt

first: Lukasz

middle: P

last: Liniany

first: David

last: Knight

first: Leigh

last: Samsel

first: Rolando

last: Berlinguer-Palmini

first: Joshua

last: Yim

first: Tania

middle: C

last: Felizardo

first: Michael

last: Eckhaus

first: Laura

last: Mitchell-Edgington

first: Jonathan

last: Martinez-Fabregas

first: Jinfang

last: Zhu

first: Daniel

last: Fowler

first: Sander

last: van-kasteren

first: Arian

last: Laurence

first: Mathew

last: Bogyo

first: Colin

last: Watts

first: Ethan

middle: M

last: Shevach

first: Shoba

last: Amarnath


title: Differential Genomic Effects of Six Different Nanomaterials on Human Liver HepG2 Cells

city: Durham

first: Carlton

last: Jones

address: 109 T.W. Alexander Drive

institute: U.S. Environmental Protection Agency

summary: Human Hepatocellular Carcinoma cells (HepG2) were exposed to six nanomaterials containing either Cerium oxide (CeO2) or Titanium oxide (TiO2) nanoparticles. Three different concentrations were tested: 0.3, 3, or 30 μg/mL) for 3 days. Microarray analysis was performed to identify genes differentially expressed following exposure to these chemicals.

overall_design: HepG2 cell cultures were maintained in a humidified incubator at 37°C and 95% air/5% CO2 during the study. Cells were plated at 40,000 cells/cm2 in vented T-25 flasks (Corning) for 48 h prior to nanomaterial exposure. Individual flasks were treated with 200 uL per cm2 of the appropriate nanomaterial dilution and incubated for 72 h. Six nano-TiO2 or nano-CeO2 formulations from different vendors were used in this study. The chemical purity was high (>98.8% for all cases and as high as 99.9% for five cases), the primary dry particle sizes ranged from 22 to 214 nm. The final concentrations for treatments were 0.3 (low dose), 3 (medium dose), and 30 (high dose) μg/mL. Each treatment was performed in multiple biological replicates. At the end of 72 h of cell exposure to the treatment, the media was vacuum aspirated and the flasks rinsed with warm Dulbecco’s phosphate-buffered saline. Total RNA was extracted from cells using a mirVanaTM RNA extraction kit (Life Technologies, Grand Island, NY) following the manufacturer’s protocol. The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol. The data processing was performed using Bioconductor’s beadarray package (version 2.4.1) for the R language (version 2.14.0).

first: Sheau-Fung

last: Thai

first: Kathleen

last: Wallace

first: Hongzu

last: Ren

first: Eric

last: Grulke

first: Benjamin

last: Castellon

first: James

last: Crooks

first: Kirk

last: Kitchin


title: Transcriptome analysis of flooded rice spikelets in response to high temperature at flowering

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

type: Expression profiling by high throughput sequencing

summary:
Purpose: understanding the complex genetic control of heat tolerance can be reached using whole transcriptome sequencing (RNA-seq) that is currently the most powerful tool to identify genes differentially regulated. Heat responses differ greatly between sensitive and tolerant genotypes, mainly in terms of the amount of genes and pathways involved in the response and differences in the expression level of constitutive genes in many pathways. The present study aims to compare the molecular response of Brazilian flooded rice cultivars with variable sensitivity to heat stress at anthesis stage and to discuss the possible processes involved in heat tolerance.
Methods: Panicle mRNA profiles of cultivars IRGA 428 (sensitive) and BR-IRGA 409 (tolerant) were generated by deep sequencing, in triplicate (each replicate is composed of two plants), under three days of heat stress and control condition at anthesis stage, using Illumina Hiseq 2500. The sequence reads from each sample that passed quality filters were mapped independently, generating contigs that were aligned with the reference genome sequences in rice (cv. MH63-indica). The transcripts were analyzed at the expression level with statistic test (EdgeR – Rstudio) to identify the significant changes in the expression level of the genes for each treatment condition and cultivar follow by identification of metabolic pathways (MapMan and Cytoscape) based on different programs.
Results: Using an optimized data analysis workflow, we identified 16,871 transcripts in the rice spikelet of sensitive and tolerant cultivars with HISAT workflow. Using filtered and aligned reads, transcript levels were used to find differentially expressed genes (DEGs) at different thermal condition and cultivars. We identified 2,064 genes for BR-IRGA 409 and 1,078 genes for IRGA 428 that showed a significant change in expression in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). When it was examined the multi-factor responsive genes, that is genes with an interaction between cultivar and heat stress (multi-factor analysis - cultivars vs control and high temperature), it was identified 65 DEGs in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). Comparison of our data set with other RNA-seq studies shows a significant overlap in heat responsive genes (hypergeometric enrichment test). This core set of genes common among RNA-seq studies indicates that it may be associated with basal response to heat. In the present study, genes related to light reaction pathway were induced in the panicle of the cultivar IRGA 428, while these genes in cultivar BR-IRGA 409 were already expressed highly in control conditions. The basal level of these genes in BR-IRGA 409 was as high as the heat-induced level in the sensitive IRGA 428. Photosynthesis is known to occur in rice panicles, but little has been reported about the photosynthetic characteristics of such panicles. To cope with heat stress, plants have developed a sophisticated mechanism to repair photosystem damage. Therefore, in IRGA 428 the induction of these genes suggests the activation of a repair mechanism to reverse damage on the photosynthetic apparatus caused by the heat stress. The difference in basal levels of the photosynthetic genes may be a contributing factor to the differences in spikelet fertility between the cultivars under heat stress.
Conclusion: This is the first study to evaluate the heat tolerance of Brazilian rice cultivars. In panicle tissue, most canonical heat responsive genes, such as HSF family, small HSP family and FKBP family, show a similar response in both Brazilian cultivars, despite the fact that these cultivars have not been specifically selected for heat tolerance. The response of photosynthetic genes to heat stress is a major difference between the cultivars BR-IRGA 409 and IRGA 428. This study indicates that the higher basal expression of photosynthetic genes in the panicle provides improved spikelet fertility under heat stress. This may provide potential markers that can be used to identify heat tolerant genotypes among rice breeding programs. This study emphasizes that the characterization of heat stress responses in individual cultivars provides insights into both the basic mechanisms of heat response and assists with understanding the complex phenomenon of responses to high temperature stress.

overall_design: Panicle mRNA profiles of cultivars IRGA 428 (sensitive) and BR-IRGA 409 (tolerant) were generated by deep sequencing, in triplicate (each replicate is composed of two plants), under three days of heat stress and control condition at anthesis stage, using Illumina Hiseq 2500 150bp single end reads.

first: Silmara

last: Correia

first: Paulo

middle: R

last: Silva

first: Carla

last: Delatorre

first: Colleen

last: Doherty


title: Analysis of the effect of cofactor knockdown on dexamethasone-induced gene expression in B-cell acute lymphoblastic leukemia

city: Iowa City

first: Miles

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

institute: University of Iowa

summary:
After identifying cofactors that affected the sensitivity of dex-induced cell death in B-ALL, we knocked down three cofactors, NCAO2, EHMT1, and EHMT2, using shRNAs in NALM6 cells
After measuring the effect of cofactor knockdown on dex-sensitivity of these cells, we looked at differences in gene expression after exposure to dexamethasone.

overall_design: NALM6 cells were treated with vehicle (0.1% ethanol) or dexamethasone (1µM) for four hours, then harvested.  The samples are unmodified NALM6 cells, NALM with a scrambled shRNA sequence, and the three cofactor knockdowns.

first: Mimi

last: Fang

first: Dawne

last: Shelton


title: Screening of differentially expressed microRNAs of essential hypertension in Uyghur Population

city: Urumqi

first: Yuanzheng

last: Ye

address: No.137 Liyushan South Road

institute: the First Affiliated Hospital of Xinjiang Medical University

summary: To know how microRNA works in hypertension and what kinds of microRNA can be used as specific biomarkers for hypertension are unknown, we screened 257 differentially expressed microRNAs between patients with essential hypertension and the healthy individuals.

overall_design: Eight subjects from Uygur aged between 30-60 years old were recruited. Four subjects were with essential hypertension and untreated (named as hypertension group) and the other four were healthy people (named as Control group). All subjects were fasted before sampling and sampled at the same time in the morning. They were asked to sit still for 10 minutes before blood collection. Totally, 3 ml of peripheral blood was collected from each subject.

first: Jianzhong

last: Yang


title: Establishment and characterization of a chemoresistant glioblastoma cell line from an Iraqi patient

city: Al-Qadysia

first: Ahmed

middle: Majeed

last: Al-Shammari

state: Baghdad

department: Experimental Therapy

country: Iraq

institute: Mustansiriyah University, Iraqi Center for Cancer and medical Genetic Research

summary:
Glioblastoma multiforme is a highly aggressive malignant primary brain tumor in humans, with poor prognosis. ANGM5 has been established from a cerebral glioblastoma multiforme in a 72-years-old Iraqi man who underwent surgery for an intracranial tumor in 2005. The morphology, growth kinetics, karyotype, immunocytochemistry and angiogenesis factors expression profile were studied. ANGM5 has been grown continuously for more than 200 serial passages in culture for the last 13 years. The cultured cells are elongated or multipolar in shape and the population doubling time is 28 hours. The karyotype is complex, and the chromosomal number varied between 39-114. ANGM5 is resistant to Temozolomide, cisplatin, vincristine and etoposide. This chemoresistance could be explained by the overexpression of the breast cancer resistance protein (BCRP) and MGMT. Immunocytochemistry analysis of glial markers demonstrated that cells are positive for glial fibrillary acidic protein (GFAP), and negative for nestin and calbindin. Protein microarray analysis showed high production of tissue inhibitor of metalloproteinase 2 (TIMP2) as well as other factors that are important for the invasiveness and aggressiveness of glioblastoma. ANGM5 is a useful addition to the cell lines currently available for study of the pathobiology and chemoresistance properties of glioblastoma multiforme and antitumor drug discovery.
Angiogenesis signaling is being evaluated in new human Iraqi glioblastoma multiforme cell line. Here, we measured angiogenesis factors released by cancer cells in vitro. We find that glioblastoma up-regulates many proteins and metabolites during the logarithmic phase, suggesting initiation of their endo-vesiculo-membrane system. Importantly, GM-CSF and G-CSF as they increase angiogenesis through promoting endothelial cell function. Also, b-FGF which promote tumor growth and proliferation.  Moreover, it showed up-regulation to inflammatory, and extracellular matrix proteins. These factors will help proliferating glioblastoma cells to overcome stress conditions, such as cytotoxic chemotherapy, serum deprivation, hypoxia in vitro and in vivo. These findings support other evidence of chemoresistance ability of this cell line named AMGN5 as it found to resist several types of conventional chemotherapies.

overall_design: Secreted Angiogenesis protein profile of ANGM5 glioblastoma multiforme cells during the logarithmic phase of cell proliferation was generated using antibody arrays. This is part of full characterization to the new established cell line.

last: Al-Jubory

first: Asmaa

last: Al-Mukhtar

first: Amal

last: Ali

first: Zaid

last: Alhili

first: Amer

last: Tawfeeq

first: Nahi

middle: Y

last: Yaseen


title: RocA has serotype-specific gene regulatory and pathogenesis activity in serotype M28 group A streptococcus

city: Houston

first: Paul

last: Bernard

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: RNA-seq experiments of a wild-type and isogenic rocA deletion mutant serotype M28 group A streptococcus strain at two time points

overall_design: RNA-seq data of 2 strains at 2 time points in triplicate

middle: E

first: Randall

last: Olsen


title: Gene expression data from endothelial cells isolated from DNFB-treated ears of mice with inducible endothelial-specific overexpression of constitutively active Notch1 intracellular domain

first: Guttorm

last: Haraldsen

summary: Notch1 is a key regulator of endothelial cell behaviour. This experiment was designed to identify genes regulated by Notch1 signaling in inflammatory activated mouse endothelial cells.

overall_design: NICD1-iEC-OE mice were treated with 5 daily tamoxifen injections to promote endothelial-specific overexpression of constitutively active Notch1 intracellular domain and used in the DNFB-induced contact hypersensitivity model. Endothelial cells (CD31+ CD45- Ter119-) were isolated from DNFB-treated ears by flow cytometry and submitted for transcriptional analysis.

first: Reidunn

last: Edelmann

first: Rodrigo

last: Diegues-Hurtado

first: Ralph

middle: H

last: Adams

first: Johanna

last: Hol


title: lncRNA and mRNA expression data in peripheral blood sampled from patients with Obsessive-Compulsive Disorder

city: Beijing

first: Yuqing

last: Song

address: No.51 Huayuan Beilu, Haidian District

institute: Institute of  Mental Health, Peking University

summary: The aim of the study is to identify the global messenger RNA (mRNA) and long noncoding RNA (lncRNA) expression profiling in peripheral blood from thirty patients with Obsessive Compulsive Disorders (OCD) and thirty paired normal controls.

overall_design: We quantified the gene transcripts in peripheral blood from thirty patients with OCD and thirty normal controls by the method of Microarray using Aglilent G3 lncRNA v4.04×180K.

first: Guoqiang

last: Wang

first: Fuquan

last: Zhang

first: Panpan

last: Wu


title: Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

city: Bologna

first: Roberta

last: Davoli

state: Bologna

address: Viale G. Fanin, 46

department: DISTAL

country: Italy

institute: Bologna University

type: Non-coding RNA profiling by high throughput sequencing

summary: The identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNA-seq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132 ,ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p, and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.

overall_design: Illumina RNAs sequencing for miRNAs and other short RNAs discovery, quantification, characterisation, and differential expression evaluation on 18 RNA samples collected from Italian Large White pigs.

first: Enrico

last: Gaffo

first: Martina

last: Zappaterra

first: Stefania

last: Bortoluzzi

first: Paolo

last: Zambonelli


title: Fecal transplants in zebrafish reveal effects of diet and microbiome on intestinal gene expression and enzyme activity.

city: Waterloo

last: Craig

state: ON

address: 200 University Ave West

department: Biology

country: Canada

institute: University of Waterloo

summary: This study examined the functional response of a host (zebrafish) to implantation of a conspecific or allospecific (goldfish) gastrointestinal (GIT) microbiome followed by diet manipulation and the repercussions of these manipulations on host GIT physiology. Implantation of a native zebrafish biome successfully reintroduced wildtype (WT) communities with the exception of several rare, phylogenetically distant species. Implantation of a foreign goldfish biome created communities that were distinct from WT, suggesting that the seeding community created substantial differences from the native host communities. A mismatched ?natural? diet and an implanted allospecific biome enriched for rarer and more phylogenetically diverse bacteria. Transcriptional changes within the GIT clustered in relationship to biome treatments, mirroring clustering of biome implants. Implantation of an allospecific biome along with an altered diet markedly down-regulated approximately 70% of the transcripts involved in cholesterol biosynthesis, while tissue content analysis revealed an increase in total tissue cholesterol. Furthermore, transcripts involved in lipogenesis pathways were significantly downregulated and correlated with a striking decrease in intestinal lipase activity driven by both biome and diet. Glucose-6P dehydrogenase (G6PD) activities increased during dietary manipulations regardless of biome, while the allospecific biome down-regulated transcripts involved in gluconeogenesis and altered glucokinase (GK) and hexokinase (HK) activities regardless of diet. However, growth rates did not reveal an impact of these responses. Adult zebrafish are unable to reform proportional representation within bacterial communities following transplantation of an allospecific biome resulting in transcriptional and enzymatic alterations for lipid and carbohydrate metabolism that did not affect overall animal homeostasis.

overall_design: The intestinal microbiome of zebrafish was manipulated either through removal and reintroduction or through removal and introduction of another specie's intestinal microbiome (goldfish). The diet was also manipulated, either maintaining the original zebrafish diet or switching to a goldfish diet.

first: Carol

last: Bucking

first: Christophe

last: LeMoine

first: Pranav

last: Dhakal

first: Thomas

last: Moon

first: Alexandre

last: Poulain


title: Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia

status: Public on Aug 21 2018

city: Cambrdige

first: Yunyu

state: MA

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

summary: Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia.

overall_design: Male Harlan SD rats (Harlan, Inc.) were obtained at 5, 11, 17, and 20 months of age and studied at 6, 12, 18, 21, 24, or 27 months of age. The gastrocnemius muscle was analyzed for age-related changes in RNA expression.

first: Chikwendu

last: Ibebunjo

first: David

last: Glass

first: John

middle: K

last: Eash

first: Tracee

last: Kendall


title: Gene expression profiling of pre-operative mTOR inhibitor everolimus treatment in breast cancer

city: Carrington Crescent

first: Andrew

last: Sims

address: Systems Medicine Building

institute: University of Edinburgh

summary: There is growing evidence that uncontrolled activation of the PI3K/Akt/mTOR pathway contributes to the development and progression of breast cancer. Inhibition of this pathway has antitumour effects in preclinical studies and efficacy in combination with other agents in breast cancer patients. The aim of this study is to characterise the effects of pre-operative everolimus treatment in primary breast cancer patients and to identify potential molecular predictors of response. Twenty-seven patients with oestrogen receptor (ER)-positive breast cancer completed 11–14 days of neoadjuvant treatment with 5-mg everolimus. Core biopsies were taken before and after treatment and analysed using Illumina HumanRef-8 v2 Expression BeadChips. Changes in proliferation (Ki67) and phospho-AKT were measured on diagnostic core biopsies/resection samples embedded in paraffin by immunohistochemistry to determine response to treatment. Patients that responded to everolimus treatment with significant reductions in proliferation (fall in % Ki67 positive cells) also had significant decreases in the expression of genes involved in cell cycle (P = 8.70E−09) and p53 signalling (P = 0.01) pathways. Highly proliferating tumours that have a poor prognosis exhibited dramatic reductions in the expression of cell cycle genes following everolimus treatment. The genes that most clearly separated responding from non-responding pre-treatment tumours were those involved with protein modification and dephosphorylation, including DYNLRB2, ERBB4, PTPN13, ULK2 and DUSP16. The majority of ER-positive breast tumours treated with everolimus showed a significant reduction in genes involved with proliferation, these may serve as markers of response and predict which patients will derive most benefit from mTOR inhibition.

overall_design: Primary biopsy and resection breast tumour samples, collected pre and post everolimus treatment for 2 weeks. Note that the are 21 pairs and 2 pre-treatment only samples.


title: Expression data from the cells of rat bronchoalveolar lavage fluid

city: ChongQing

first: Gang

last: Wu

address: 30 Gaotanyan, Shapingba, Chongqing

institute: Army Medical University

summary:
Acute lung injury (ALI) refers to a clinical syndrome characterized by bilateral lung injury, severe lung diffuse failure and hypoxemia caused by non-cardiogenic pulmonary edema.Sepsis is the leading etiology of ALI and a common admission to the intensive care unit, which induces pulmonary inflammation leading disruption of endothelial-epithelial barriers by surge release of pro-inflammatory cytokines that increases the permeability of the alveolar-capillary membrane, pulmonary infiltration, and edema.Ultimately, gas exchange across the alveolar-capillary membrane is severely impaired and acute respiratory failure and hypoxia occur. ALI patients may suffer from pulmonary inflammation and hypoxia simultaneously or sequentially, those two pathophysiological processes may interact mutually and contribute together to the development of ALI.
LPS is the most important biological mediator of sepsis induce secretion of inflammatory cytokines including TNF-α, IL-1, and IL-6 from many cell types in response to bacterial toxins. Thus LPS has been commonly used to establish inflammatory ALI models of rats and mice. Clinically, hypoxia commonly coexists with sepsis; however, the role of hypoxia on the development of inflammatory ALI is unclear. The understanding of interaction of hypoxia and inflammation in ALI is of the importance for the treatment of ALI.

overall_design: Briefly, 8-week-old male Sprague-Dawley (SD) rats, weighing 200 ± 20 g, were housed in microisolator cages with specific pathogen-free (SPF) condition and free access to water and food. Before experimentation, rats were housed for 3 days to adapt them to the environment. The rats were randomly divided into four experimental groups: (i) CTL group, naïve control rats with normoxia, (ii) LPS group, with LPS treatment with normoxia, (iii) HPO group, with exposure of acute hypobaric hypoxia, (iv) COMB group, with combined exposures of acute hypobaric hypoxia and LPS. For LPS administration, the animals were subjected to a tail vein injection of a 0.5 mg/kg LPS in saline at an injection volume of 0.2 ± 0.02 mL (LPS: 1 mg / ml). For exposure of hypobaric hypoxia, the animals were subjected to stay in the decompression chamber for 6 hours with an ambient air pressure of 405.35 mmHg (approx. 0.53atm, or equivalent of 5000 m altitude, or the equivalent of 11.2% O2). The animals in COMB groups who received double-stimulus were first subjected to LPS administration, then stay in the decompression chamber, the time used about twenty minutes when it achieved the ambient air pressure of 5000 m altitude from the plains. The rats in CTL group were subjected to a tail vein injection of 0.2 ± 0.02 mL of saline (0.9% NaCl water). All animals were fasted and banned water during the experiment. Per treatment received by the animal, the operation of collecting specimens were done in (normal or hypoxic) condition. Before specimen collection rats were subjected to anesthesia with a single dose of chloral hydrate (100 mg/kg, i.p.) and their lungs were removed. Bronchoalveolar lavage fluid (BALF)  was obtained from the right lung as follows. First, the left bronchus was ligated with sutures and the right bronchus was cannulated. Then a 3 ml saline was introduced into the right lungs, which were then gently manipulated, followed by the withdrawal of lavage fluid. This procedure was repeated 3 times for each rat. The collected BALF was centrifuged. The cells fraction was suspended in PBS for the evaluation of gene expression profiling. For microarray analysis, we pooled the total RNA from three animals in the same treatment group as a pooled RNA sample, and a total of 3 pooled RNA samples underwent microarray analysis in each group. We used cluster analysis to analyze the total 12 RNA samples to find the common genes identified by paired t-test. The gene expression profiles were determined using Gene Chip Rat Genome 230 2.0 Array (Affymetrix).

first: Yu-Qi

last: Gao


title: The differential gene expression in carcinoma-associated fibroblasts co-cultured with MCF7 cells before and after letrozole treatment

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

summary: We generated carcinoma-associated fibroblast (CAF) primary cultures from 6 patients with estrogen receptor positive invasive ductal breast carcinoma, co-cultured them with MCF7 cells in estrogen-deprived culture medium and compared their gene expression profiles before and after letrozole treatment.  We observed distinct changes in the gene expression profile of CAFs co-cultured with MCF7 cells after letrozole treatment.

overall_design: Total RNA obtained from carcinoma-associated fibroblasts.

first: Hua

last: Kang

first: Kaifu

last: Li


title: Differentially expressed genes after siRNA transfection in human cancer cell lines [TE8, 786-O, A498 and PANC1]

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (siRNAs and miRNAs) in human cancer, several cell lines (esophagus cancer, renal cell carcinoma and pancreatic cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (TE8, 786-O, A498 and PANC1) were treated with siRNAs (si-MYO1B, si-DHRS2 and si-EPS8) and miRNAs (miR-101-5p, miR-101-3p and miR-184).

first: Yasutaka

last: Yamada


title: Regulation of the human placental (pro)renin receptor-prorenin-angiotensin system by microRNAs

city: Newcastle

first: Kirsty

middle: G

last: Pringle

state: NSW

address: 1 Kookaburra Circuit

department: HMRI

country: Australia

institute: University of Newcastle

summary:
The placental renin-angiotensin system (RAS) is important for placentation. RAS expression is greatest in early gestation. This may be due (in part) to suppression of miRNAs that target the placental RAS, but this has never been explored.
In this study, human placental miRNAs were measured at 10–11 (early), 14–18 (mid), and 38–40 (term) weeks gestation, as well as in placentae from women with early- or late-onset preeclampsia (n=4/group), using an Agilent miRNA microarray (V19).  All miRNAs showed a gestational increase and could influence the transgestational profile of the human placental RAS. Additionally, on the array, three miRNAs predicted to target the RAS (miR-892c-3p, miR-378c and miR-514-3p ) were overexpressed in placentae of late-onset preeclamptic women.

overall_design:
We have identified placental miRNAs that are differentially expressed in early gestation and target RAS mRNAs. At least two suppress renin production by trophoblasts. Placental miRNAs could potentially regulate placental growth and development through actions on the placental RAS.
A total of 24 primary human placental samples were used in this study, from which we were able to compare the miRNA profiles across patients with and without preeclampsia, and all across gestation.  Gene expression microarray analysis was used to reveal which transcripts were differentially expressed between different gestational time points and patients with preeclampsia.

first: Yu

last: Wang

first: Eugenie

last: Lumbers

first: Anya

middle: L

last: Arthurs

first: Celine

last: Corbisier de Meaultsart

first: Andrea

last: Mathe

first: Kelly

last: Avery-Kjieda

first: Claire

last: Roberts

first: Fiona

last: Broughton Pipkin

first: Francine

middle: Z

last: Marques

first: Brian

last: Morris


title: affy_infection_medicago - Comparison of plant responses upon P. palmivora infection in wild type (A17) line and in the api mutant

city: CASTANET TOLOSAN

first: Thomas

last: Rey

address: 24 chemin de borde rouge, BP42617

country: France

institute: DE SANGOSSE

summary: affy_infection_medicago - api mutant has been shown to be more resistant to P. palmivora than the A17 wild type (WT) line. In this study, we want to compare both WT and mutant plant responses to the pathogen as well as their respective control transcriptomes in order to identify api-dependent gene networks. Following germination, A17 or api plants grown in vitro on Agar medium were inoculated (or not = controls) with a P. palmivora zoospores (10^5/ml) and harvested 16 hours after inoculation. Three independent repeats were performed.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 12 arrays - Medicago; normal vs. disease comparison, normal vs. ems mutant comparison, time course.

first: T

first: S

last: Schornack


title: Expression data from lung tissue of exsmokers

city: Córdoba

first: Sandra

last: Grumelli

state: Córdoba

address: Obispo Trejo

country: Argentina

institute: CIMeR

summary: Gene expression of lung tissue from ex-smokers

overall_design: Patients that had to go through surgery due to cancer or lung volume reduction were recruited and segregated by their lung function FEV1% and their GOLD classification.

first: Farrah

last: Kheradmand


title: Expression data from EBV-encoded latent membrane protein 2A (LMP2A) positive and negative nasopharyngeal carcinoma (NPC) cell lines

city: Stockholm

first: Ingemar

last: Ernberg

address: Solnavagen 9 C8

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

summary:
Latent infection with Epstein-Barr virus (EBV) is recognised as a factor in the pathogenesis of nasopharyngeal carcinoma (NPC). We found that EBV encoded Latent membrane protein 2A (LMP2A) enhances lipid accumulation significantly in NPC cells.
We used microarrays to identify differential genes regulated by LMP2A in NPC cell lines.

overall_design: Two pairs of NPC cell lines were included in the microarray analysis. LMP2A negative NPC cell line as control. There is one sample in each group.

first: Shixing

last: Zheng

first: Xiaoying

last: Zhou

first: Liudmila

last: Matskova

first: Zhe

last: Zhang


title: microRNA expression profile in colorectal adenoma and cancer

city: Nanjing

first: Shizhi

last: Wang

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Key Laboratory of Environmental Medicine Engineering, Ministry of Education

institute: Southeast University

summary: We evaluated the profile of miRNA expression in 6 colorectal adenoma (CRA), 6 colorectal adenocarcinoma (CRC) and 6 matched normal mucosa (NOR) using the Exiqon miRCURY LNA microRNA array,7th generation. We found that global dysregulated miRNAs between colorectal lesions and normal mucosa. Our findings implicates that dysregulation of miRNAs may play important role in the carcinogenesis and present therapeutic targets for CRC.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Examination of microRNA expression in CRA, CRC and NOR.

first: Rui

last: Chen


title: Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum (P.falciparum) parasites

status: Public on Aug 22 2018

first: Rickard

last: Sandberg

address: Solnavägen 9  Solna

department: Cell and Molecular Biology

summary: The malaria parasite has a complex lifecycle, including several events of differentiation and stage progression, while actively evading immunity in both its mosquito and human hosts. Important parasite gene expression and regulation during these events remain hidden in rare populations of cells. Here, we combine a capillary-based platform for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single infected red blood cells (sc.iRBCs) during the intra- erythrocyte developmental cycle (IDC). Unbiased analyses of single-cell data grouped the cells into eight transcriptional states during IDC. Interestingly, we uncovered a gene signature from the single iRBC analyses that can successfully discriminate between developing asexual and sexual stage parasites at cellular resolution, and we verify five, previously undefined, gametocyte stage specific genes. Moreover, we show the capacity of detecting expressed genes from the variable gene families in single parasites, despite the sparse nature of data. In total, the single parasite transcriptomics holds promise for molecular dissection of rare parasite phenotypes throughout the malaria lifecycle.

overall_design:
We combined fully automated CellSorter cell capture system for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single P. falciparum-infected red blood cells (sc.iRBCs) during the intra-erythrocyte developmental cycle (IDC). As a control, we generated 28 RNA-seq libraries from populations (population.iRBCs) containing approximately 5,000 iRBCs at each time point.

Please note that only 165 sc.iRBCs libraries which are of moderate to high quality (indicated in the 'library quality' sample characteristics) were used for the further processing (i.e. 15 samples of low quality have been excluded).

first: Mtakai

last: Ngara

first: Mia

last: Palmkvist

first: Sven

last: Sagasser

first: Daisy

last: Hjelmqvist

first: Åsa

last: Björklund

first: Mats

last: Wahlgren

first: Johan

last: Ankarklev


title: MODIFICATION OF BARLEY PLANT PRODUCTIVITY THROUGH REGULATION OF CYTOKININ CONTENT BY REVERSE-GENETICS APPROACHES

city: Olomouc

first: Petr

last: Vojta

address: Hnevotinska 5

department: Laboratory of experimental medicine

country: Czech Republic

institute: Palacky University

summary: Barley is one of the most important cereals, which is used for breweries, animal and human feeds. Genetic manipulation of plant hormone cytokinin (CK) levels may influence several physiological processes, besides others stress tolerance, root formation and crop yield. In planta, endogenous CK status is finely regulated by the enzyme cytokinin dehydrogenase (EC 1.5.99.12; CKX), that irreversibly cleaves the N6-side chain of adenine-derived CKs. Increasing grain yield by mean of manipulation of endogenous CK content was assayed by the silencing of the HvCKX1 gene. Moreover, to elucidate the putative role of HvCKX1 gene on grain production, knocked-out Hvckx1 mutant plants were generated using RNA-guided Cas9 system.

overall_design: Examination of 2 independent transgenic lines with silenced HvCKX1 gene and control line in 2 developmental stages of barley grains. Each sample was analysed in 3 biological replicates

first: Katarína

last: Holubová

first: Goetz

last: Hensel

last: Tarkowski

first: Veronique

last: Bergougnoux

last: Galuszka


title: Time series gene expression in critically ill patients: PREVAIL study

city: Kingston

first: David

last: Maslove

state: Ontario

address: 76 Stuart St.

department: Critical Care Medicine

institute: Queen's University

summary:
The PREVAIL study was a Phase II/III randomized controlled trial examining the use of lactoferrin to prevent nosocomial infections in critically ill patients undergoing mechanical ventilation.
Gene expression data was generated from a consecutive subset of patients at the lead study site. We used the Affymetrix PrimeView array to generate expression data at various time points during the ICU stay.

overall_design: Time series gene expression profiling of critically ill patients undergoing mechanical ventilation, who were enroled in the PREVAIL study

first: John

last: Muscedere


title: IL-1 receptor antagonist controls transcriptional signature of inflammation in patients with metastatic breast cancer

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

institute: Application Computational Scientist

summary: Inflammation affects tumor immune surveillance and resistance to therapy. Here we show that production of interleukin (IL)-1b in primary breast cancer (BC) tumors is linked with advanced disease. Patients with metastatic HER2-negative BC display a transcriptional signature of inflammation in the blood, which is attenuated after IL1 blockade.

overall_design:
Eleven female patients with HER2-negative metastatic BC received chemotherapy along with anakinra 100mg/day (FDA-approved dose for adults with rheumatoid arthritis) (Kineret®, Amgen Inc.) following 2-week treatment with anakinra only. The study was approved by Institutional Review Board (IRB 012-099), conducted in accordance with ethical guidelines (Declaration of Helsinki) and written informed consent was obtained from the patients. Blood was collected prior to anakinra treatment, then at 2 weeks, then monthly for 6 months (mos). 11 healthy controls were included (IRB 012-200). Whole blood mRNA was measured using the Nanostring nCounter Human Immunology V2 panel.

NOTE: Sample titles represent patient number and timepont.

first: Jacob

last: Turner

first: Xuan

last: Wang

first: Derek

last: Blankenship

first: Joyce

last: O’Shaughnessy


title: Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells

status: Public on Aug 20 2018

city: Boston

first: Chenxi

last: Qiu

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Arsenic trioxide (ATO) and all-trans retinoic acid (ATRA) combination safely cures fatal acute promyelocytic leukemia, but the mechanisms underlying their action and synergy remain elusive. ATRA inhibits APL, breast and liver cancers by targeting isomerase Pin1, a master regulator of oncogenic signaling. Here we show that ATO targets Pin1 and cooperates with ATRA to exert potent anticancer activity. ATO inhibits and degrades Pin1, and suppresses its oncogenic function by noncovalent binding to Pin1’s active site. ATRA increases cellular ATO uptake through upregulating aquaporin-9. ATO and ATRA, at clinically safe doses, cooperatively ablate Pin1 to block numerous cancer-driving pathways and inhibit the growth of triple-negative breast cancer cells and tumor-initiating cells in cell and animal models including patient-derived orthotopic xenografts, similar to Pin1 CRISPR knockout, which is substantiated by comprehensive protein and microRNA analyses. Thus, synergistic Pin1 inhibition by ATO and ATRA offers an attractive approach to combating breast and other cancers.

overall_design: 6 samples with biological duplicates (Control, ATRA, ATO, ATO+ATRA, Vector only control and Pin1 CRISPR KO)

first: Shingo

last: Kozono

first: Yu-Min

last: Lin


title: E5 human papillomavirus type 16 oncoprotein modify ST3GAL3 and ST6GAL1 gene expression

city: Atlixco

first: Verónica

last: Vallejo-Ruiz

state: Puebla

address: Km 4.5 Carretera Federal Atlixco-Metepec

department: Centro de Investigación Biomédica de Oriente

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: Human papillomavirus (HPV) is the etiological agent of cervical cancer. Three viral proteins, E5, E6 and E7 have been implicated in cell transformation. Increased expression of sialic acid and sialylated antigens have been reported during cervix transformation, these results agree with the increased mRNA levels of the sialyltransferases genes ST6GAL1 and ST3GAL3 reported in premalignant and malignant tissue of the cervix. E6 and E7 HPV oncoproteins modify the expression of some glycogenes. The role of E5 HPV oncoprotein in the glycogene expression changes in premalignant and malignant cervical tissue has not been reported. The objective of this work was to identify glycogenes that modify their expression by E5 HPV oncoprotein in HaCaT cell line. A gene expression microarray was performed on HaCaT cells that stably expressed the HPV16 E5 oncogene. Analysis revealed alteration in some glycogenes including upregulation of ST6GAL1 and ST3GAL3. The increased mRNA levels of both genes were confirmed by qRT-PCR. In addition, an in-silico analysis was performed to identify glycosylation networks altered in presence of E5 oncoprotein. The analysis showed that E5 could modify the sialic acid expression, keratan sulfate synthesis, N-glycosylation and biosynthesis of glycosaminoglycans. This is the first report of the role of HPV16 E5 oncoprotein on glycogenes expression changes. Moreover, our results suggest that the increase of the sialyltransferases genes reported in premalignant and malignant cervical tissue, could be the result of the expression of E5 oncoprotein. These results provide information of the possible role of HPV infection on the sialylation changes in the cervical epithelium identified in premalignant lesions and cancer.

overall_design:
Two-condition experiment, HaCat cell groups (HaCat-pMSG, and HaCat-E5) One replicate array. 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 (for HaCat-pMSG) or dUTP-Alexa647 (for HaCat-E5) employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.
Please note that [1] the experiment was performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but  the results was processed as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated) and that [2] In the microarray assay, each gene was evaluated as duplicate for the same condition, generating two values corresponding to each spot.

first: Denisse

middle: I

last: Cisneros-Ramírez


title: Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: BACKGROUND & AIMS: Sorafenib is the standard systemic therapy for advanced hepatocellular carcinoma (HCC). In early-stage HCC, survival benefits of resection/local ablation are compromised by high recurrence rates (70% at 5-years). In this setting, the phase-3 STORM-trial did not achieve its primary end-point of improving recurrence-free-survival (RFS) comparing sorafenib to placebo as adjuvant treatment. Herein we present results of the biomarker companion study BIOSTORM in which we define predictors of recurrence prevention with sorafenib and prognostic factors with B-level of evidence.  METHODS: Tumor tissue from 188 patients randomized to receive sorafenib (83) or placebo (105) in the STORM trial was collected. Analyses included gene-expression profiling, targeted exome sequencing (18 known onco-drivers), immunohistochemistry (pERK, pVEGFR2, Ki67), FISH (VEGFA) and immunome. A gene signature capturing improved RFS in sorafenib-treated patients was generated. All 70 RFS events were recurrences, thus time-to-recurrence equaled RFS. Predictive and prognostic value was assessed using Cox regression models and interaction test.  RESULTS: BIOSTORM recapitulates clinical and pathological characteristics of STORM patients. None of the biomarkers tested that are known to be related to angiogenesis and proliferation, or previously proposed gene-signatures, or mutations predicted sorafenib benefit. A newly generated 146-gene signature identifying 30% of patients captured benefit to sorafenib in terms of RFS (p-of-interaction=0.04). These sorafenib responders were significantly enriched in CD4+ T, B, and cytolytic Natural Killer cells, and showed absence of activated macrophages and other components of adaptive immunity. Hepatocytic pERK (HR=2.41; p=0.012) and microvascular invasion (HR=2.09; p=0.017) were independent prognostic factors.  CONCLUSIONS: In BIOSTORM, hepatocytic pERK and microvascular invasion predicted poor RFS. No mutation, gene amplification or previously proposed gene-signatures predicted sorafenib benefit. A newly generated multi-gene signature associated with improved RFS on sorafenib warrants further validation.  KEYWORDS: sorafenib; tyrosine-kinase inhibitor; trial enrichment; stratification.

overall_design: Formalin-fixed paraffin-embedded (FFPE) tissue blocks from 140 HCC patients resected between 2008 and 2010 and randomized into treatment in the STORM clinical trial (NCT00692770) were collected from the highest enrolling centers after ad-hoc IRB clearance.There are a total of 67 samples treated with Sorafenib (Sor) and 73 are Placebo(Plac).

first: R

last: Pinyol

last: Montal R

first: A

last: Moeini A

first: J

last: Llovet


title: Transcriptome change in response to citrinin stress in Cryptococcus podzolicus Y3

city: Zhenjiang

first: Xiangfeng

last: Zheng

address: 301, Xuefu Road

department: Food school

country: China

institute: Jiangsu university

summary: The yeast Cryptococcus podzolicus Y3 shown the capability to degrade citrinin by the intracellular enzymes. However, the enzymes which is responsible for the degradation process was unknown. Transcriptome change in response to mycotoxin citrinin was analyzed. The molecular mechanism of Cryptococcus podzolicus Y3 withstand  citrinin was revealed.

overall_design: Each one samples were analyzed , the yeast Cryptococcus podzolicus Y3 amending with citrinin and the control which was not amending with citrinin

first: Kaili

first: Zhen


title: Chromosomal aberrations associated with sequential steps of the metastatic cascade in colorectal cancer patients

city: Hamburg

first: Simon

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

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

summary:
Genomic profiling of primary colorectal carcinomas was performed in relation to the spread of CTCs in peripheral and hepatic venous blood,
liver metastases, and distant metastases beyond the liver, with the intent to identify specific patterns for the different stages of metastatic spread.

overall_design: DNA from primary colorectal tumors was processed according to manufacturers’ protocol (Infinium Assay, Illumina) and hybridized to Illumina Human 610-quad bead-chip, containing 610,000 probes covering the whole genome. Spot intensities were measured using the Illumina Bead Array Reader. Log transformed intensity measurements were processed by circular binary segmentation (CBS) algorithm (Matlab R2015a, The MathWorks) to identify chromosomal aberrations.


title: Expression profile of R. capsulatus by entering light after a dark period; and by high light intensity

status: Public on Aug 17 2018

city: Tekirdag

first: Muazzez

middle: Gürgan

last: Gürgan Eser

address: Degirmenaltı Kampusu Fen Edebiyat Fakultesi Biyoloji Bolumu Ofis 238

department: Department of Biology

country: Turkey

institute: Namık Kemal University

summary: The effects of low and high light intensities on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles of dark and low light intensity (2000 lux), and by comparing high light intensity (10,000 lux) with low light intensity (2000 lux).

overall_design: The bacteria were exposed to three light and dark periods (12 hours light/ 12 hours dark) where the light intensity was 2000 lux. in the middle of the third light period (6th hour) light intensity was increased to 10,000 lux. RNA samples from 1.5x10e9 cells were collected after at the end of the third dark period, 15 min and 1 hour after exposure to light period (2000 lux) and 15 min and 1 hour after exposure to 10,000 lux. A microarray chip for Rhodobacter capsulatus was not commercially available. For that reason, a GeneChip® array was custom designed and manufactured by Affymetrix, Santa Clara, California. The nucleotide sequence of the bacterium is available in GenBank with the accession numbers CP001312 for the chromosome and CP001313 for the plasmid pRCB133. The feature size of the antisense DNA array was 11 micron and the format was 100-3660. A total of 4,052 probe sets for open reading frames (ORFs) and 200 intergenic sequences with longer than 300bp were placed on the microarray. The cDNA synthesis, labeling, and hybridization protocols were performed according to the Affymetrix Expression Analysis Technical Manual given for prokaryotic samples.

first: M

last: Gurgan

first: N

last: Erkal

first: E

last: Ozgur

last: Yucel


title: Interferon tau-dependent and independent effects of the bovine conceptus on the endometrial transcriptome: effect of conceptus origin and sex

city: Dublin 4

first: PATRICK

last: LONERGAN

address: Belfield

country: Ireland

institute: University College Dublin

summary: This study aimed to identify bovine conceptus-induced modifications to the endometrial transcriptome both dependent and independent of interferon tau (IFNT), dependent on conceptus origin [in vitro fertilization (IVF) or artifical insemination (AI) derived blastocysts] and dependent on conceptus sex. Major findings include identification of genes differentially expressed in endometrium in response to the conceptus but independent of IFNT and genes differentially expressed in endometrium in response to AI vs. IVF and male vs. female conceptuses.

overall_design: Bovine uteri were collected during the mid luteal phase of the estrous cycle and utilized to produce endometrial explants. The explants were treated for 6 h with RPMI media only (Control, n=6), media containing 100ng/mL of ovine IFNT (IFNT, n=6) or with a Day in vitro (IVF, n=7) or Day 15 in vivo (AI, n=4) derived conceptus in media. Following treatment, conceptuses were identified as either male (Male, n=6) or female (Female, n=5). Total RNA was extracted from the treated endometrium and RNA samples (23) were submitted for RNA-seq analysis. Comparisons include Control vs. IFNT, Control vs. AI, Control vs. IVF, Control vs. Male, Control vs. Female, AI vs. IVF and Male vs. Female treatments.

first: Daniel

middle: J

last: Mathew

first: José

last: Sánchez

first: Claudia

last: Passaro

first: Gilles

last: Charpigny

first: Susanta

last: Behura

first: Thomas

last: Spencer

first: Patrick

last: Lonergan


title: microRNA profile of exosomes derived from acidic microenvironment culture in hepatocellular carcinoma cell line

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: microRNA profiling of acidic culture condition vs non-acidic culture condition

overall_design: exosomes centrifuged from HCC cell culture supernatant under acidic condition compared with non-acidic condition

first: X

first: D

last: Xie


title: ORY-1001/RG6016 effect on leukemia cell lines

status: Public on Aug 19 2018

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

institute: Oryzon Genomics S.A.

summary: The lysine-specific demethylase LSD1/KDM1A is a key regulator of stem cell potential in acute myeloid leukemia (AML). Inhibition of its expression or catalytic activity overcomes the differentiation block and reduces colony formation potential. We have developed ORY-1001 as highly potent and selective inhibitor of KDM1A. Treatment of AML cell lines with ORY-1001 induces accumulation of H3K4me2 marks at KDM1A target genes, compromises leukemic stem cell capacity, and provokes blast differentiation. ORY-1001 exhibits potent synergy with standard of care drugs and with inhibitors of other epigenetic targets; reduces tumor growth and extends survival in mouse xenograft models of acute leukemia. To develop tools for use in clinical trials, we selected a panel of surrogate biomarkers for pharmacodynamic analysis based on expression changes in a panel of 24 leukemia cell lines. ORY-1001/RG6016 was the first selective KDM1A inhibitor to enter the clinic and is currently being evaluated in leukemia and solid tumor clinical trials.

overall_design:
Compiled data of 4 two-colour experiments, 5 nM ORY-1001 treated and vehicle treated cells, after 24 and/or 96 h of treatment, for 24 leukemia cell lines. Three replicates per array for each gene probe.

Please note that the raw data files do not contain the identifiers represented in the sample or platform data table or Fold.txt.gz files (e.g. A_23_P100413). The correspondence (between raw data IDs and processed data IDs) is provided in the 'Agilent-Oryzon cross-reference' file (linked to GPL23032 records).


title: Genome-wide analysis of Lp(a) induced gene expression in human aortic valve interstitial cells

city: Montreal

first: Adel

last: Schwertani

state: Quebec

address: 1001 Decarie Blvd

department: Cardiology

institute: RI-MUHC

summary:
Lp(a)  induced human aortic valve interstitial cells calcification, this work intend to elucidate the undermined biological pathways by analysing Lp(a) induced gene expression.
Results provided important information of Lp(a) induced biological pathways, and showed that Lp(a) possibly exert its effects on osteogenesis, apoptosis, extracellular matrix remodeling, and vesicle biogenesis via 14-3-3 regulated biological pathways.

overall_design: Total RNAs were extracted from human aortic valve interstitial cells treated with or without 50µg/ml purified human Lp(a) for 3 days, 10 days and 20 days. Samples included: 3 days: HAVICs treated with/without Lp(a) in non-osteogenic medium (n=2 each group), and in osteogenic medium (n=2 each group); Day 10: HAVICs treated with or without  Lp(a) in osteogenic medium (n=1 each group);   Day 20: HAVICs treated with or without  Lp(a) in osteogenic medium (n=1 each group).

first: Bin

last: Yu


title: Real-time quantitative PCR analysis of expression profiles of dual-specificity phosphatase family members in mouse tissues

city: Beijing

first: Dan

last: Lu

address: 38# Xueyuan Rd

institute: Peking University Health Science Center

summary: Mouse tissues (including heart, skeletal muscle, brain, lung, stomach, small instestine, colon, liver, kidney, testis, uterus, bone marrow, thymus, lymph node, spleen and embryo) were isolated from three C57BL/6 mice (eight-week-old, uterus from female and other tissues from male). We used Applied Biosystems 7500/7500 Fast Real-Time PCR Systems to quantitate  expression levels of DUSP family members in the indicated mouse tissues.

overall_design: qPCR gene expression profiling.  Various tissues pooled from three C57BL/6 mice were used  as indicated in the summary. Equal amount total RNA from each tissue was pooled prior to gene expression analysis.

first: Yuxin

last: Yin


title: FVB mouse strain lung cells

status: Public on Aug 16 2018

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: We sacrificed 6 (3 males, 3 females) FVB mice 8 weeks old and harvested their lungs. The dissected lungs lungs were assayed to RNA extraction (via trizol) in order to identify their transcriptomic signature.

overall_design: Samples from FVB mice lung cells were analyzed using Genespring 12.5 GX to obtain the  data.

first: Nikolaos

last: Kanellakis


title: The nuclear Bile Acid Receptor FXR is a PKA- and FOXA2- sensitive Activator of Fasting Hepatic Gluconeogenesis [glucacon/GW4064]

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

institute: Inserm

summary: Identified genes deregulated in mouse primary hepatocytes after glucagon and /or GW4064 treatment

overall_design: We analyzed Mouse primary hepatocytes (MPH) using the Affymetrix MoGene 2,0ST chip. Array data was processed by Genespring software . Two technical replicates were pooled by sample. Each experiment was performed on pooled MPH providing from three mice

first: M

last: Ploton

first: C

last: Mazuy

last: Gheeraert

first: P

last: Lefebvre


title: The nuclear Bile Acid Receptor FXR is a PKA- and FOXA2- sensitive Activator of Fasting Hepatic Gluconeogenesis [modulated FOXA2/FXR]

summary: Identified genes deregulated in mouse primary hepatocytes after modulation of expression/activity of FOXA2 and FXR in glucagon or insulin state

overall_design: We analyzed Mouse primary hepatocytes (MPH) using the Affymetrix MoGene 2,0ST chip. Array data was processed by Genespring software . Three technical replicates were pooled by sample. Each experiment was performed on pooled MPH providing from three mice


title: The nuclear Bile Acid Receptor FXR is a PKA- and FOXA2- sensitive Activator of Fasting Hepatic Gluconeogenesis

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

overall_design: Refer to individual Series


title: Comparative genomic hybridization analysis in glycine max fast neutron mutants

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

country: USA

institute: University of Minnesota

summary: Soybean fast neutron mutant lines were maintained to an advanced generation (ranging between approximately M6 and M11) and compared to their wild-type parent (M92-220-Long) using CGH to identify sequence deletions and duplications in the mutant plants.

overall_design: 19 samples were analyzed, each identified as a soybean fast neutron lines from the appropriate genetic background. Each sample was compared to its wild type parent (M92-220-Long) using Agilent CGH arrays.

first: Adrian

last: Stec


title: Identificaion of long noncoding RNAs related to TGF-β signaling in human cultured tubular epithelial cells

status: Public on Aug 15 2018

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

summary: To identify differentially expressed long noncoding RNAs (lncRNAs) upon TGF-β stimulation in human cultured tubular epithelial cells HK2 and HKC8, we have employed long noncoding RNA microarray expression profiling as a discovery platform to find differentially expressed lncRNAs with TGF-β stimulation in these cells. Cultured human tubular epithelial cells HK2 and HKC8 were stimulated with PBS or TGF-β1. After incubation with TGF-β1 (10ng/ml) for 24 hours, 86 overlapping lncRNAs were upregulated and 47 overlapping lncRNAs were downregulated more than 2 fold vesus cells treated with PBS in these two epithelial cell lines. Expression of ENST00000429588 from this result was quantified in the same RNA samples by real-time PCR, confirming the upregulation upon TGF-β stimulation is repeatable.

overall_design: TGF-β1 (10ng/ml) or PBS induced lncRNAs expression in human cultured tubular epithelial cells HK2 or HKC8 for 24 hours was measured. No biologic repeat was conducted.

first: Peng

last: Wang


title: Gene expression data of organoids derived from human gastric tumor and normal stomach samples.

status: Public on Aug 14 2018

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

country: Japan

institute: Keio University

summary: Recent sequencing analyses have shed light on heterogeneous patterns of genomic aberrations in human gastric cancers (GCs). To explore how individual genetic events translate into cancer phenotypes, we established a biological library consisting of genetically engineered gastric organoids carrying various GC mutations and 37 patient-derived organoid lines, including rare genomically stable GCs. Phenotype analyses of GC organoids revealed divergent genetic and epigenetic routes to gain Wnt and R-spondin niche independency. An unbiased phenotype-based genetic screening identified a significant association between CDH1/TP53 compound mutations and the R-spondin independency that was functionally validated by CRISPR-based knockout. Xenografting of GC organoids further established the feasibility of Wnt-targeting therapy for Wnt-dependent GCs. Our results collectively demonstrate that multifaceted genetic abnormalities render human GCs independent of the stem cell niche and highlight the validity of the genotype-phenotype screening strategy in gaining deeper understanding of human cancers.

overall_design: We analyzed gene expression of 36 patient-derived gastric tumor, 9 normal-like, 1 IM, 8 normal stomach, 1 normal colon, 5 engineered normal stmomach and 1 engineered normal colon organoids. mRNA were extracted from organoids and hybridized to GeneChip PrimeView Human Gene Expression Array, and scanned using GeneChip Scanner 3000 7G.

first: Kosaku

last: Nanki

first: Kohta

last: Toshimitsu


title: CnAb1 knock down in R1 mESCs differentiated to mesoderm in Ebs

city: Madrid

first: Jesus

middle: Maria

last: Gómez-Salnero

address: Melchor Fernández Almagro, 3

institute: CNIC

summary:
R1 mESCs were trasnfected with siRNAs against CnAb1 or Control (Luciferase) using Lipofectamine. mRNA was extracted 48 hours using Qiagen RNeasy Mini kit using DNAse treatment
Microarray was performed after QPCR validation of the downregulation of CnAb1.

overall_design: Cells were transfected with siRNAs: Control, CnAb1 (1) and CnAb1 (2). For the MicroArray analysis we used 3 control, 3 CnAb1 (1), and 2 CnAb1 (2) samples.

first: Jesús

last: Gómez-Salinero

first: Enrique

last: Lara-Pezzi


title: Modulating plant growth-metabolism coordination for sustainable agriculture

first: Shan

last: Li

address: Lincui Road

institute: Insititute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Using ChIP-seq  experiment, find the downstream genes and binding motif of NGR2.

overall_design: ChIP-seq was carried out with anti-Flag antibodies using material from two weeks old seedlings of WYJ7-dep1-1/p35S::Flag-ngr2.

first: Yonghang

last: Tian

first: Kun

last: Wu

first: Yafeng

last: Ye

first: Jianping

last: Yu

first: Jianqing

last: Zhang

first: Qian

last: Liu

first: Mengyun

last: Hu

first: Hui

first: Yiping

last: Tong

first: Nicholas

middle: P

last: Harberd

first: Xiangdong

last: Fu


title: Type I IFN signaling blockade during ART-treated and untreated chronic SIV infection suppresses inflammation but does not increase virus replication

status: Public on Aug 10 2018

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Objective: Determine how admnistration of  type I IFN antagonist influences the expression levels of interferon stimulated genes (ISG) during ART-treated or untreated chronic SIV infection. Methods: SIVmac251 infectected animals on or off ART received 3.5mg/kg pasylated-IFN-Iant two or three times a week from week 16 to 24 post-infection. RNA was rextracted from PBMC collected at several timepoints around IFN-Iant trearment and analyzed by RNA sequencing to compare transcription between IFN-Iant or placebo animals. Results: ISG, which are involved in control of virus replication, were increased upon SIV challenge and reduced by ART. Administration of IFN-Iant to ART-treated animals resulted in further reduction of ISG expression. Blocking IFN-I signaling in ART-untreated animals resulted in the most prominent reduction of ISG expression. Conclusion: These findings indicate that administration of an antagonist during ART-treated and untreated chronic SIV infection significantly impact IFN-I signalling.

overall_design: 35 animals were infected with SIVmac251. At 8 weeks post infection (p.i.), 25 animals received ART. From week 16-24p.i., 6 ART-untreated animals received 3x weekly IFN-Iant as compared to 4 placebo. In the ART-treated arm, 11 animals received 2xweekly FN-Iant and 5 animals 3x weekly FN-Iant as compared to 9 placebo.

first: Krystelle

last: Nganou-Makamdop

last: O’Connor

first: Zachary

last: Yaffe

first: Gideon

last: Schreiber

first: Arne

last: Skerra

first: Martin

last: Schlapschy

first: Amy

last: Ransier

first: Farida

last: Labo

first: Jeffrey

last: Lifson

first: Martha

last: Nason

first: James

middle: M

last: Billingsley

first: Steven

last: Bosinger

first: Daniel

middle: C

last: Douek


title: Differential RNA-Seq (dRNA-seq) data from Sphingopyxis granuli strain TFA grown in two different carbon sources and RNA-seq from Hfq-coIP experiment.

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: We performed differential RNA-sequencing (dRNA-seq) experiments in both minimal medium (MM) plus β-hydroxybutyrate (β-HB) and MM plus tetralin (THN) of Sphingopyxis granuli strain TFA. The objective was mapping the Transcription Start Site (TSS) of each gene in the genome in both conditions, detecting non-coding RNAs (ncRNAs) and comparing the gene expression profile in a preferential carbon source (β-HB) versus tetralin (an aromatic pollutant). The dRNA-seq technique consists of using a termination exonuclease (TEX) to allow the discrimination of primary and processed transcripts. Furthermore, to detect Hfq-bound RNAs we co-immunoprecipitated RNA from the wild type strain (negative control) and a TFA strain with an Hfq-3xFlag tagged version (MPO501 strain) using an anti-3xFlag antibody and performed RNA-sequencing from the precipitated RNA.

overall_design: Comparison of gene expression and TSS detection in TFA cells growing exponentially on minimal medium plus β-hydroxybutyrate and minimal medium plus tetralin. Identification of Hfq-binding RNAs through a co-immunoprecipitation experiment.

first: Inmaculada

last: García-Romero

first: Cynthia

last: Sharma

last: Föstner

first: Eduardo

last: Santero

first: Belén

last: Floriano


title: Small RNA sequencing facilitates quantitative miRNA analysis of fetal and maternal placental tissue in IUGR bovine fetuses

city: Freising

first: Krzysztof

last: Flisikowski

address: Liesel-Beckmannstr. 1

department: Livestock Biotechnology

institute: Technical University of Munich

summary: Small RNA next generation sequencing and quantitative PCR revealed placental tissue-specific expression of the miR-4321, known to regulate many genes involved in early fetal development. This study also indicated that maternal and fetal components of the placenta respond differently to a deleterious fetal mutation.

overall_design: Maternal and fetal placenta samples were collected from cows gestating MIMT1Del/WT fetuses and cows gestating wild-type fetuses terminated on the 94th ± 12 day of pregnancy

first: Monika

last: Stachowiak


title: Training and validation of a novel 4-miRNA ratio model (MiCaP) for prediction of post-operative outcome in prostate cancer patients

city: Aarhus N

first: Karina

middle: Dalsgaard

last: Sørensen

state: Aarhus N

address: Palle Juul-Jensens Boulevard 99

department: Molecular Medicine

country: Denmark

institute: Aarhus University

summary: Background: New molecular biomarkers for prostate cancer (PC) prognosis are urgently needed. Ratio-based models are attractive, as they require no additional normalization. Here, we train and independently validate a novel 4-miRNA prognostic ratio model for PC. Patients and methods: By genome-wide miRNA expression profiling of PC tissue samples from 123 men who underwent radical prostatectomy (RP) (PCA123, training cohort), we identified six top candidate prognostic miRNAs and systematically tested their ability to predict post-operative biochemical recurrence (BCR). The best miRNA-based prognostic ratio model (MiCaP) was validated in two independent cohorts (PCA352 and PCA476) including >800 RP patients in total. Clinical endpoints were BCR and prostate cancer-specific survival (CSS). The prognostic potential of MiCaP was assessed by univariate and multivariate Cox-regression analyses and Kaplan-Meier analyses. Results: We identified a 4-miRNA ratio model, MiCaP (miR-23a-3p×miR-10b-5p)/(miR-133a×miR-374b-5p), that predicted time to BCR independently of routine clinicopathological variables in the training cohort (PCA123) and was successfully validated in two independent RP cohorts. In addition, MiCaP was a significant predictor of CSS in univariate analysis (HR 3·35 [95% CI 1·34 – 8·35], P=0·0096) and in multivariate analysis (HR 2·43 [95% CI 1·45 – 4·07], P=0·0210). Limitations include low mortality rates (CSS: 5.4%). Conclusions: We identified a novel 4-miRNA ratio model (MiCaP) with significant independent prognostic value in three RP cohorts, indicating promising potential to improve PC risk stratification.

overall_design: A total of 136 samples. 9 benign prostate samples and 127 samples from radical prostatectomies.

first: L

last: Schmidt

first: J

last: Fredsøe

first: H

last: Kristensen

first: S

last: Strand

first: A

last: Rasmussen

last: Høyer

first: M

last: Borre

first: P

last: Mouritzen

first: T

last: Ørntoft

first: K

last: Dalsgaard Sørensen


title: Gene expression profile of human lung epithelial cells with different culture methods.

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
The goal of our study is to establish a method to propagate human pneumocytes efficiently in a large scale. While human pneumectomy-derived lung epithelial cells (LECs) showed efficient long-term growth when co-cultured with irradiated NIH-3T3, they do not express molecular markers of mature pneumocytes or airway cells in this condition. Removal of feeders causes differentiation toward airway club cell-like phenotype, and an induction treatment with combination of small molecules and growth factors is required to differentiate them toward pneumocytes.
To elucidate the underlying mechanisms, we analyzed gene expression profile of LECs with or without induction treatment. We also included LECs under coculture and the original frozen lung tissue, as a reference.

overall_design: Microarray experiments were performed as single-color hybridizations. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Aki

last: Imai

first: Hilmar

last: Berger

first: Thomas

last: Meyer


title: Gene array of laser capture microdissectioned human diabetic vs non-diabetic plaque macrophages

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: The aim of this study was to understand if gene expression in atherosclerotic plaque macrophages is altered by diabetes. Laser capture microdissection (LCM) was used to specifically isolate macrophage enriched regions from human carotid atherosclerotic plaque samples. RNA isolated was then sent for sequencing using the Illumina bead array system. Gene expression data revealed that 106 genes from diabetic macrophages are differentially expressed (FDR<0.2) and provide mechanistic evidence for the involvement of Runt-related transcription factor 1 (RUNX1) in the development of diabetic atherosclerosis.

overall_design: Carotid plaques were defined as being either control (non-diabetic), diabetic, symptomatic (had experienced either a transient ischemic attack (TIA) or cerebrovascular accident(CVA)). Samples analysed totaled 16 non-diabetic (control) samples containing  6 asymptomatic, 10 symptomatic and 8 diabetic plaque samples - containing 6 asymptomatic and 2 symptomatic.

first: Joshua

last: Chai

first: Madeleine

middle: E

last: Lemieux

first: Robin

last: Choudhury


title: Repeated social defeat stress (R-SDS)-induced changes in gene expression profiles in the medial prefrontal cortex (mPFC)

status: Public on Aug 09 2018

city: Kobe

first: Tomoyuki

last: Furuyashiki

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

department: Pharmacology

institute: Kobe University Graduate School of Medicine

summary: To identify R-SDS-induced changes in gene expression profiles in the mPFC, we performed transcriptome analysis in the mPFC without or with R-SDS. We separately analyzed the data from susceptible mice, which showed social avoidance after R-SDS, and resilient mice, which did not, in addition to those from naïve mice.

overall_design: R-SDS induced gene expression in mPFC tissue was measured at 4 hours after the last session of R-SDS. Two independent experiments were performed using different mice for each experiment.

first: Shiho

last: Kitaoka

first: Xiang

last: Nie

first: Kohei

last: Tanaka

first: Eri

last: Segi-Nishida

first: Yuki

last: Imoto

first: Atsubumi

last: Ogawa

first: Fumitake

last: Nakano

first: Ayaka

last: Tomohiro

first: Kazuki

last: Nakayama

first: Masayuki

last: Taniguchi

first: Yuko

last: Mimori-Kiyosue

first: Akira

last: Kakizuka

first: Shuh

last: Narumiya


title: Gene plofiles of hepatic macrophages expressing mPGES-1.

status: Public on Aug 12 2018

city: Sagamihara

first: Nobuyuki

last: Nishizawa

address: 1-15-1 Kitasato Minami-ku

department: Surgery

institute: Kitasato University school of midicine

summary: The objectives of the present studies was examined to elucidate the role of hepatic macrophages in liver repair after acute liver injury.

overall_design: Hepatic macrophages at 48 h post-reperfusion were isolated from 10 WT and 10 mPGES-1-/- mice. We analyzed sorted macrophages using the GeneChip Mouse Gene 2.0 ST Array. Array data was processed by Affymetrix GeneChip Command Software and Affymetrix Expression Console.

first: Yoshiya

last: Ito

first: Koji

last: Eshima

first: Tomoyoshi

last: Inoue


title: Transcriptome analysis of microglia isolated from the mPFC or NAc without or with repeated social defeat stress (R-SDS)

first: Tomoyuki

last: Furuyashiki

summary: To identify R-SDS-induced changes in gene expression profiles in medial prefrontal cortex (mPFC) and nucleus accumbens (NAc) microglia, we performed transcriptome analysis in mPFC and NAc microglia without or with R-SDS. Based on our observation that TLR2/TLR4 mediate R-SDS-induced activation of mPFC microglia, we performed the analysis in wild-type (WT) mice and TLR2/TLR4-double knockout (TLR-DKO) mice.

overall_design: R-SDS induced gene expression in mPFC and NAc microglia was measured at 1.5 hours after the last session of R-SDS. Two independent experiments were performed using different mice for each experiment.

first: Shiho

last: Kitaoka


title: RNA-Seq analysis comparing transcriptome of transgenic and wild hybrid poplar under both greenhouse and sunlight exposed conditions

status: Public on Aug 11 2018

city: Victoria

first: C. Peter

last: Constabel

state: British Columbia

address: 3800 Finnerty Rd

department: Biology

institute: University of Victoria

summary: We compared the transcriptiome of MYB165-overexpressing and wild type hybrid poplars and try to identify the differentially expressed genes.

overall_design: Six wild type and six MYB165-overexpressing transgenic poplars were grown in greenhouse for two months. For sunlight treatment, three wild type and three MYB165-overexpressing transgenic poplars were moved outside of greenhouse and exposed to sunlight for a week in August 2014. Leaves number 7-10 (LPI7-10) were harvested and analyzed.

first: C

first: Dawei

last: Ma