title: Gene expression profile in tongue squamous carcinoma cells with stably transduced with LINC01011 shRNA under cisplatin treatment

first: Guokai

last: Pan

summary: chemoresistance frequently leads to therapeutic failure in oral squamous cell carcinoma (OSCC). Recently, studies have reported that lncRNAs play active regulatory roles in gene transcription and further regulate biological properties of cancer in this way. In this study, to further expore lncRNAs downstream target gene in regulating mitochondrial fission and cisplatin sensitivity in TSCC, we profiled the expression of gene in two TSCC cell lines(CAL-27 and SCC-9) after  LINC01011 knockdown and treated with cisplatin treatment for 24h.

overall_design: We investigated the differential gene expression profiles in tongue squamous carcinoma cells between 6 groups: the CAL27 control group, the CAL27 stably transduced with shRNA2 targeted LINC01011  (CAL27 shRNA2 group), the CAL27 stably transduced with shRNA5 targeted LINC01011  (CAL27 shRNA5 group), the SCC9 control group and the SCC9 stably transduced with shRNA2 targeted  LINC01011  (SCC9 shRNA2 group), the SCC9 stably transduced with shRNA5 targeted LINC01011  (SCC9 shRNA5 group). Sample labeling and array hybridization were performed by Human Gene expression 4×44K v2 microarrays according to the Agilent Whole Genome Oligo Microarrays protocol (Arraystar, Inc., Rockville, MD, USA). After quantile normalization of the raw data, the genes detected were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through P value/FDR filtering.


title: Exosomal microRNA (miRNA) expression in Blonchoalveolar lavage fluid (BALF) collected from mice infected with influenza virus and inoculated with poly(I:C).

status: Public on Jun 08 2018

city: Madison

first: Tadashi

last: Maemura

state: Wisconsin

address: 575 Science Drive

country: USA

institute: Influenza Research Institute

summary: To clarify the profile of in BALF exosome collected from mice infected with influenza virus, we infected 100000 pfu of A/Puerto Rico/8/1934 (PR8) strain. BALF was collected at 24, 48, and 72 hour post infection (hpi). For comparison of the profile of the miRNA in BALF exosome induced by innate immune response, we also intranasally inoculated mice with 50 μg of poly(I:C) and collected BALF at 72 hour post inoculation. We found that some miRNAs were common to both influenza virus infectiona and poly(I:C) inoculation, suggesting that exosomal miRNAs in BALF may function in the innate immune response to virus infection.

overall_design: Each group had three biological replication. Exosome was isolated by using filteration and ultracentrifugation. BALF exosome isolated from naive mice was used as control. After isolation of total RNA, miRNA microarray was performed.

first: Satoshi

last: Fukuyama

first: Tiago

middle: J

last: Lopes

first: Yoshihiro

last: Kawaoka


title: RNA sequencing-based analysis of the visceral tissue transcriptome of chicken embryo infected with F48E9 or La Sota

status: Public on Jun 06 2018

city: Yangling

first: Yanqing

last: Jia

state: Shaanxi

address: Xinong Road 22#

country: China

institute: Northwest A&F University

type: Expression profiling by high throughput sequencing

summary: We attempted to characterize the transcriptome of the chicken embryo during Newcastle disease virus (NDV) infection using RNA-sequencing analysis. The cDNAs derived from Total RNA of the pooled visceral tissues infected with F48E9 or La Sota were sequenced and analysed. The collected clean reads covered about 4.02% (2,341,868 reads) of the entire F48E8 reference sequence, while only 0.02% reads (13,886) were mapped to the La Sota genome. RNA-Seq datasets from groups La Sota, F48E9 and control, were respectively mapped to 71.76%, 68.55% and 70.05% of the reference genome Galgal 4.73. Compared with the control, 2,035 and 1,604 differentially expressed genes of hosts were found responding to F48E9 and La Sota infection, respectively. GO and KEGG pathway enriched various signalling pathways with elements playing roles in enhancing or preventing viral infection, like IFP35, NMI, Mx, OAS*A, IFITM5, STAT1 and IFNβ. So far, we know that velogenic NDV made far more transcripts during infection and caused significant impact on the host, showing a large number of genes in various pathways at high levels of expression.

overall_design: Using high-throughput sequencing, revealed differences of SPF chick embryos after infected different virulence NDVs.

first: Xinglong

last: Wang

first: Zengqi

last: Yang


title: miRNA expression profiles of chicken embryonic visceral tissue infected with F48E9 or La Sota

type: Non-coding RNA profiling by high throughput sequencing

summary: Three cDNA libraries of mixed visceral tissues from F48E9, La Sota, or uninfected chicken embryos were constructed, and small-RNA deep sequencing was conducted to detect the expression levels of small-RNAs. Intergroup comparisons were used to identify changes in miRNA expression caused by NDV infection. La Sota affected the expression of 61 miRNAs (36 upregulated and 25 downregulated) at 36 hpi, and F48E9 infection altered the expression levels of 66 miRNAs (33 upregulated and 31 downregulated).

overall_design: Using high-throughput sequencing, revealed miRNA expression differences of SPF chick embryos infected different virulence NDVs.


title: Chicken embryonic visceral tissue with F48E9 or La Sota

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

overall_design: Refer to individual Series


title: The EBV-Encoded Oncoprotein, LMP1, Induces an Epithelial-to-Mesenchymal Transition (EMT) via its CTAR1 Domain Through Integrin-Mediated ERK-MAPK Signalling

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: The Epstein-Barr virus (EBV)-encoded LMP1 oncogene can induce profound effects on epithelial growth and differentiation including many of the features of the epithelial-to-mesenchymal transition (EMT). To better characterise these effects, we used the well-defined MDCK cell model and found that LMP1 expression in these cells induces EMT as defined by characteristic morphological changes accompanied by loss of E-cadherin, desmosomal cadherin and tight junction protein expression. The induction of the EMT phenotype required a functional CTAR1 domain of LMP1 and studies using pharmacological inhibitors revealed contributions from signalling pathways commonly induced by integrin-ligand interactions: ERK-MAPK, PI3-Kinase and tyrosine kinases, but not TGFbeta. More detailed analysis confirmed the role of integrin and ERK-MAPK signalling in the LMP1-induced EMT and implicated the CTAR1-mediated induction of Slug and Twist in these effects. A key role for beta1 integrin signalling in LMP1-mediated ERK-MAPK and FAK phosphorylation was observed and beta1 integrin activation was found to enhance LMP1-induced cell viability and survival. These findings support an important role for LMP1 in the early stages of NPC pathogenesis through transcriptional reprogramming that enhances tumour cell survival and leads to a more invasive, metastatic phenotype.

overall_design: Gene expression was measured in MDCK cells expressing the neomycin resistance gene (neoR), wildtype LMP1, CTAR1+/2-, CTAR1-/2+ and the CTAR1-/2- double mutant derivatives, each in triplicates

first: Mhairi

middle: A

last: Morris

first: Louise

last: Laverick

first: Alexandra

middle: M

last: Davis

first: Samantha

last: O’Neill

first: Liam

last: Wood

first: Jack

last: Wright

first: Christopher

middle: W

last: Dawson

first: Lawrence

middle: S

last: Young


title: ZNF281 inhibits neuronal differentiation

status: Public on Jun 05 2018

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

country: Italy

institute: University of Rome "Tor Vergata"

summary: Derangement of cellular differentiation due to mutation or inappropriate expression of specific genes is a common feature in tumours. Here, we show that depletion of ZNF281 induces neuronal differentiation of neuroblastoma cells.

overall_design: To investigate the effect of ZNF281 depletion on neuronal differentiation, we used microarray expression profiling to identify the genes with altered expression. Human neuroblastoma cells BE2(M17) were transiently knocked-down by RNA interference.

first: Consuelo

last: Pitolli

first: Sara

last: Nicolai


title: Characteristics of differentiated newly identified adipose precursor cells

city: Gifu city

first: Shigeo

last: Takashima

state: Gifu

address: 1-1 Yanagido

department: Life Science Research Center

country: Japan

institute: Gifu University

summary: We have identified proliferative cells in adipose tissue expressing adipocyte specific genes, which were named small proliferative adipocytes (SPA). Comparison of gene expression among stromal vascular cells (SVC), SPA and mature adipocyte (MA) revealed that adipocyte specific genes and several neuronal genes were increased in the order of SVC < SPA < MWA. However, proliferin 2 (PLF) was detected only in SPA. We found that SPA changed to lipid laden cells by incubation with differentiation medium containing insulin/dexamethasone/IBMX. In this study, we investigated the gene expression of differentiated SPA (SPAD) comparing with differentiated SVC (SVCD). Microarrays and real time PCR revealed that uncoupling protein 1 (UCP1) and PLF were strongly expressed in D-SPA. These data suggested that SPA might be able to differentiate into beige cells.

overall_design: Microarray was performed to investigate the characteristics of differentiated SPA (SPAD). The results were confirmed with real time PCR and immunocytochemical study.

first: Kazuo

last: Kajita

first: Koichiro

last: Taguchi


title: Overexpression of KLF genes in retinal ganglion cells

city: Palo Alto

first: Jeffrey

middle: L

last: Goldberg

address: 2452 Watson Ct

institute: Stanford University

summary: Adult mammalian CNS neurons undergo a developmental switch in intrinsic axon growth ability associated with their failure to regenerate axons after injury. Krüppel-like transcription factors (KLF) regulate intrinsic axon growth ability, but signaling regulation upstream and downstream is poorly understood. Here we find that suppressing expression of KLF9, an axon growth suppressor normally upregulated 250-fold in retinal ganglion cell (RGC) development, promotes long-distance optic nerve regeneration in vivo. We identify a novel binding partner, MAPK10/JNK3, critical for KLF9’s axon growth suppressive activity. Additionally, by screening genes regulated by KLFs in RGCs, we identify dual-specificity phosphatase 14 (Dusp14) as key to limiting axon growth and regenerative ability downstream of KLF9, associated with its dephosphorylation of MAPKs critical to neurotrophic signaling of RGC axon elongation. These results now link intrinsic and extrinsic regulation of axon growth and suggest new therapeutic strategies to promote axon regeneration in the adult CNS.

overall_design: RGCs from early postnatal rats were purified and KLF9, -16, -7, and -11 genes and control, FLAG-tagged mCherry gene were transduced using lentivirus.  RNA was then extracted using RNEasy (Qiagen) and processed for hybridization onto Affymetrix Rat Genome 230 2.0 Arrays.

first: Akintomide

last: Apara

first: Joana

last: Galvao

first: Keiichiro

last: Iwao

first: Yan

last: Wang

first: Allison

last: Trillo

first: Dale

middle: P

last: Brown Jr

first: Kimberly

last: Fernandes

first: Masoumeh

last: Ashouri

first: Tu

last: Nguyen

first: Tejas

middle: N

last: Shah

first: Abigail

last: Huang

first: Xiong

last: Zhang

first: Noelia

last: Kunzevitzky

first: Peter

middle: X

last: Shaw

first: Muray

last: Blackmore

first: Darcie

last: Moore

first: Richard

middle: T

last: Libby


title: DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin

city: Wuhan

first: Feng

last: Tan

state: Hubei

address: No.1 Shizishan street

institute: National Key Lab of Crop Genetic Improvement

type: Methylation profiling by high throughput sequencing

summary: In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). The ddm1a/1b mutation resulted in increases of heterochromatic sRNA but decreases of euchromatic sRNA production,induced expression of a set of developmentally regulated heterochromatic lncRNA , and increased nucleosome occupancy of TE-related or silent genes including heterochromatic lncRNA loci. In particular,DDM1-mediated repression ofCentromericRetrotransposons of Rice1 (CRR1) was essential for centromere function.

overall_design: BS-seq of ddm1a/1b/drm2 triple mutant; two replicates for smRNA-seq of wt and ddm1a/1b double mutant.

first: Yue

last: Lu


title: Gene expression signatures during differentiation of mouse hippocampal neurons in primary culture

status: Public on Jun 03 2018

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: To investigate the possible roles on mitotic/microtubule-related genes during hippocampal neuron differentiation, we dissected E18.5 mouse embryonic hippocampi, cultured neurons in vitro  and collected total RNA samples from  different timepoints of differentiation.

overall_design: Total RNA samples were collected at 0 Days in vitro (DIV), 1DIV, 3DIV, 6DIV, 12DIV and 15DIV of neuron culture.

last: Stephan-Otto Attolini

first: F

last: Freixo

first: C

last: Lacasa

first: J

last: Luders


title: Transcriptome analysis of LRP5- and LRP6-depleted HCC38 cells.

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

country: France

institute: Institut Curie

summary: In order to characterize the differences between the co-receptors LRP5 and LRP6, we have analyzed the transcriptome of  HCC38 cells - a triple negative breast cancer cell line - 24, 48 and 72 hours following the depletion of LRP5 or LRP6 using siRNAs.

overall_design: Cells were transfected with control siRNA, 2 different siRNA targeting LRP5 (#2, #4), or 2 different siRNA targeting LRP6  (#7, #8).Total RNA was extracted and hybridized onto Gene 2.1 Affymetrix chips. Duplicates for each condition were included in the experiment.

first: Sylvie

last: Maubant

first: Bruno

last: Tesson

first: Mengliang

last: Ye

first: David

last: Gentien


title: Rhodococcus EP4 Aromatic Transcriptomics

status: Public on Jun 01 2018

city: Vancouver

last: Levy-Booth

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Transcriptomics of Rhodococcus EP4 on ethylphenol, propylguiacol and succiate

overall_design: rRNA-depleted mRNA from mid-log Rhodococcus EP4 on 1.0 mM ethylphenol, propylguiacol and succiate on 1 lane HiSeq4000 100bp-PE

first: William

last: Mohn


title: Effects of microbiota on intestinal macrophages

status: Public on Jun 02 2018

city: Berlin

first: Franziska

last: Schmidt

address: Hindenburgdamm 30

department: Medizinische Klinik für Gastroenterologie, Infektiologie and Rheumatology

country: Germany

institute: Charité-Universitätsmedizin Berlin

summary: Analysis of gene expression of colon or ileum tissue of germfree, germfree mice colonized with SPF microbiota at 5 weeks of age, and SPF mice at 6 or 10 weeks of age under health and DSS colitis

overall_design: total RNA was extracted from colon or ileum tissue of germfree, germfree mice colonized at 5 weeks of age with SPF microbiota or SPF mice at 6 or 10 weeks of age; some mice were treated with DSS; triplicates were analyzed


title: The lack of α1,3-fucosyltransferase (Osfuct) affects in anther and pollen development in rice (Oryza sativa)

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary:
The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp).
We have identified and characterized a T-DNA insert rice mutant (Osfuct) with loss of α1,3-fucosyltransferase function. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycan revealed the lack of α1,3-fucose in the N-glycan structure of rice Osfuct mutant. The mutant displayed the pleiotropic developmental defects such as diminished growth, shorter plant height, less number of tillers, shorter panicle lengths and internode, impaired anther and pollen development. In addition, the anther was curved, pollen grains shapes were shriveled, pollen viability and pollen number per anther was dramatically decreased in Osfuct mutant. The complementation test of Osfuct mutant clearly exhibited that the phenotype is caused by the loss of α1,3-fucosyltransferase function bescause complementation line is rescued. Transcriptome profiling data revealed that several genes essential in plant developmental processes were significantly altered in Osfuct mutant including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis and hypothetical proteins. Moreover, Osfuct mutant exhibited the enhanced salt insensitivity. Taken together, these findings demonstrated that Osfuct plays a critical role in growth, anther, pollen development and salt stress response.

overall_design: Experimental group :  alpha1,3-fucosyltransferase gene knock-out rice (three biological replicates)   Control group : Dongjin (three biological replicates)

first: Bum-Soo

last: Hahn

first: Joon-Soo

last: Sim

first: Mahipal

last: Singh Kesawat

first: Chang-Muk

last: Lee

first: Soyoung

last: Park


title: The in vitro influence of orexin A on the porcine endometrium on days 15 to 16 of gestation.

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

summary: Orexin A belongs to the group of hypothalamic-derived peptides that are involved in a number of processes, such as regulation of energy metabolism, control of food intake and regulation of the reproductive system. Orexin A is also expressed in the endometrium, myometrium and placenta, which suggests that it may act as an important local regulator of the reproductive functions. The aim of this study was to explore the influence of orexin A on global gene expression in the porcine endometrium during early gestation, on days 15 to 16 of pregnancy (implantation period).

overall_design: We analyzed samples obtained from 4 individuals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and orexin A treated grous. The concentration of orexin A in the culture medium was 10 µM. In vitro tissue cultures were cultivated with treatments for 24 hours.

first: Karol

last: Szeszko

first: Marta

last: Kiezun

first: Edyta

last: Rytelewska

first: Katarzyna

last: Kisielewska

first: Marlena

last: Gudelska

first: Tadeusz

last: Kaminski

first: Nina

last: Smolinska


title: Vitis Myb14 confer cold and drought tolerance by mediated nsLTP genes expression and ABA signaling passway in arabidopsis

first: Lingye

last: Su

address: Lumo Road, Moshan

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: The growth and fruit quality of grapevine are widely affected by abnormal climatic conditions such as extreme temperature. But how grapevine responds to cold stress is still largely unknown. Here we found that VaMyb14, a member of R2R3 Myb transcription factor family, was up-regulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardiness wild Vitis species. Overexpression VaMyb14 in Arabidopsis increased antioxidant enzyme activity, especially POD activity, than that of the wild type and decreased the MDA content. A series of ABA metabolism and signal transduction genes in transgenic Arabidopsiswere were up-regulated in microarry results, including several nsLTPs, PP2Cs, RD29B, COR78 and other structural genes, suggesting that VaMyb14 not only affect the ABA signaling pathways, but also activates the CBF-COR independent nsLTP genes. Collectively, these results illustrate that Vitis Myb14 could represent a node of convergence regulating grapevine stress responses, including improve defence induced phytoalexin resveratrol against necrotrophic as well as drought and/or cold stress tolerance, highlighting Myb14 as a potential gene resource in future grapevine breeding.

overall_design: Leaves from wild-type and three transgenic lines were collected before and after 8 h cold stress. An equal amount of leaves from three independent transgenic lines that were harvested in same day was pooled as OE lines for RNA isolation. Four samples were collected, which including WT 0d, OE 0d, WT 8h and OE 8h and each sample were represented by two replicates.

first: Linchuan

last: Fang

first: Nian

last: Wang

first: Xiaoming

last: Sun

first: Shaohua

last: Li

first: Haiping

last: Xin


title: Gene expression profiling of leiomyoma and myometrium specimens collected at distinct phases of the menstrual cycle

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Despite progesterone’s key role in uterine smooth muscle tumorigenesis, the mechanisms by which it promotes the growth of uterine leiomyomas remain poorly understood.  The aim of this study was to identify novel gene products mediating progesterone’s effects in uterine leiomyomas. Gene expression profiling was used to identify putative progesterone-regulated genes differentially expressed in uterine leiomyomas, which were then studied in vitro. Our analyses identified secreted frizzled-related protein 4 (sFRP4) as a key gene product functionally linked to PR activation whose expression was a) 2.6-fold higher in leiomyomas than myometrium (n=26, p<0.01) and b) 2.5-fold higher during the proliferative phase of the menstrual cycle (n=26, p<0.01).

overall_design: We comprehensively profiled and compared patterns of gene expression in matched specimens of leiomyoma and myometrium collected at distinct phases of the menstrual cycle. Gene expression was comprehensively profiled using the Illumina WG Bead Chip (v2.6).

first: Matthew

last: Anderson

first: Yiqun

last: Zhang


title: Skin gene expression is prognostic for the trajectory of skin disease in patients with diffuse cutaneous systemic sclerosis

status: Public on Jun 04 2018

city: South San Francisco

first: Janina

last: Reeder

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

summary: Currently, there are no clinical or laboratory measures that accurately predict progression of skin fibrosis and organ involvement in patients with systemic sclerosis (SSc). The goal of this study is to identify skin biomarkers in early diffuse cutaneous SSc patients, to prognosticate the progression of skin fibrosis. We found that skin gene expression of biomarkers associated with macrophages (CD14, IL13RA1) and TGFβ activation (SERPINE1, CTGF, OSMR) are prognostic for progressive skin disease. These biomarkers might help to guide decisions about which patients should be considered for aggressive therapies and/or for clinical trials.

overall_design: We analyzed clinical data and skin biopsy gene expression from 42 placebo patients, part of the Roche faSScinate phase 2 study of tocilizumab in SSc. RNA samples were analyzed using nCounter technology. A trajectory model, based on the modified Rodnan skin score was used to describe three skin disease trajectories over time. We examined the association of skin gene expression with trajectory groups of skin score using the Chi-square test. We used logistic regression to examine the prognostic power of each gene identified.

first: Giuseppina

last: Stifano

first: Thierry

last: Sornasse

first: Lisa

last: Rice

last: Lu

first: Haiyin

last: Chen-Harris

first: Dinesh

last: Khanna

first: Angelika

last: Jahreis

first: Yuqing

first: Jeffrey

last: Siegel

first: Robert

last: Lafayatis


title: Expression data from wildtype and islet2a mutant and morphant embryos

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: Modifications of gene expression were compared between wildtype control, and islet2a mutants and morphants. We used microarrays to detect modifications in gene expression in mutant vs. control, morphant vs. control, and mutant vs. morphant.

overall_design: To identify potential changes in gene expression underlying different motor neuron phenotypes of islet2a mutants vs. morphants, RNA was extracted from 2 day post fertilization (dpf) embryos of four different treatments: 1) uninjected wild type (WT_control; n=2); (2) wildtype injected with translation blocking morpholino (Morphant, n=3); (3 and 4) sibling homozygous wildtype (mock_control, n=2) and islet2a mutants (Mutant, n=3).  For comparisons, the WT_Control and mock_control were pooled, resulting in a final control group with n=4.

first: Angeles

middle: B

last: Ribera


title: HDAC genes play distinct and redundant roles in Cryptococcus neoformans virulence

first: Shannon

last: Esher

state: NC

address: 337 Sands Building, 303 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

summary: The human fungal pathogen Cryptococcus neoformans undergoes many phenotypic changes to promote its survival in specific ecological niches and inside the host. To explore the role of chromatin remodeling on the expression of virulence-related traits, we identified and deleted seven genes encoding predicted class I/II histone deacetylases (HDACs) in the C. neoformans genome. Our results identified the HDA1 HDAC gene as a central mediator controlling several cellular processes, including mating and virulence. A global gene expression profile comparing the hda1Δ mutant versus wild-type revealed altered transcription of specific genes associated with the most prominent virulence attributes in this fungal pathogen. This study directly correlates the effects of Class I/II HDAC-mediated chromatin remodeling on the marked phenotypic plasticity and virulence potential of this microorganism. Furthermore, our results provide insights into regulatory mechanisms involved in virulence gene expression that are likely shared with other microbial pathogens.

overall_design: Gene expression analysis of WT and hda1∆ mutant cells generated in triplicate by RNA-Sequencing

first: Fabiana

last: Brandão

middle: K

first: J

last: Alspaugh


title: screen and quantify human muscle miRNAs

city: Johnson City

first: Charles

middle: Albert

last: Stuart

state: TN

address: ETSU Quillen, PO 70622

department: Internal Medicine

institute: Quillen College of Medicine

summary:
observational: quantify muscle miRNAs and compare obese and lean men and women
using Qiagen array miRNome performed by Qiagen in their laboratory

overall_design:
isolate RNA from percutaneous muscle biopsies previously flash frozen and stored at -85 C
miRNA profiling


title: Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms [Forsythia viridissima var. koreana]

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

institute: Chiba University

summary: Here, de novo transcriptome assemblies for leaf and flower tissues of Forsythias were performed, resulting in 81913 unigenes of F. suspensa, 88491 unigenes of F. viridissima and 69458 unigenes of F. koreana (F. viridissima var. koreana). Classification of the annotated unigenes by gene ontology terms and KEGG pathways was used to explore transcriptomic differences among the Forsythias. Orthogroup was introduced to compare expression levels of unigenes in tissues from different species, which unveiled that three leaf tissues of Fosythias were closely correlated based on expression values of orthologous unigenes. Showing high expression mainly in leaves of F. viridissima and F. koreana, candidate homologs for genes involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were determined in these transcriptome assemblies.

overall_design: Examination of flower and leaf tissues of Forsythia suspensa, F. viridissima and F. viridissima var. koreana

first: Kazuki

last: Saito

first: Nobuo

last: Kawahara

first: Hideyuki

last: Suzuki

first: Kayo

last: Yoshimatsu

first: Noriaki

last: Kawano

first: Michimi

last: Nakamura

first: Megha

last: Rai

first: Amit

first: Luchao

last: Sun


title: Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms [Forsythia suspensa]


title: Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms

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

sample_organism:
Forsythia suspensa
Forsythia viridissima
Forsythia koreana

overall_design: Refer to individual Series


title: Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms [Forsythia viridissima]


title: PRKCI promotes immune suppression in ovarian tumors through YAP1

first: Sharmistha

last: Sarkar

state: Texas

address: 1515 Holcombe Boulevard

department: Genomic Medicine

institute: The University of Texas MD Anderson Cancer Center

summary: A key feature of ovarian high-grade serous carcinoma is frequent amplification of the 3q26 locus. Here we show that PRKCI, located on the 3q26 locus is not only amplified and overexpressed in 78% of HGSC patient samples but is also expressed in early fallopian tube lesions, called Serous Tubal Intraepithelial Carcinoma. In vivo studies in a transgenic mouse model establish PRKCI as an ovarian cancer oncogene and identify YAP1 as a downstream regulator. Together, PRKCI and YAP1 regulate TNFα to promote an immune suppressive microenvironment and inhibit cytotoxic T-cell infiltration in tumors. High PRKCI expressing human ovarian tumors show decreased cytotoxic T-cell infiltration. Taken together, we identify PRKCI and YAP1 as key mediators of a tumor-promoting immune microenvironment in ovarian cancer.

overall_design: Transcriptional characterization of iPrkci tumors and normal fallopian tubes.

first: Christopher

last: Bristow

first: Lynda

last: Chin


title: PRKCI promotes immune suppression in ovarian cancer through YAP1

summary:
A key feature of high-grade serous ovarian carcinoma (HGSOC) is frequent amplification of the 3q26 locus harboring PRKC-iota (PRKCI). Here, we show that PRKCI is also expressed in early fallopian tube lesions, called Serous Tubal Intraepithelial Carcinoma. Transgenic mouse studies establish PRKCI as an ovarian cancer specific oncogene and system level and functional analyses identify YAP1 as a downstream effector in tumor progression. Mechanistically, the oncogenic activity of the PRKCI-YAP1 axis relates in part to the upregulation of TNFα to promote an immune suppressive tumor microenvironment characterized by an abundance of myeloid-derived suppressor cells and inhibition of cytotoxic T cell infiltration. In human ovarian cancers, high PRKCI expression also correlates with high expression of YAP1 and low infiltration of cytotoxic T-cell. The PRKCI-YAP1 regulation of the tumor immunity provides a therapeutic strategy for highly lethal ovarian cancer.
Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package

overall_design: Charterization of transcriptional alterations of tumors from a genetically engineered mouse model (GEMM) compared with fallopian tube of wild type mice.


title: microRNA data in human EGFR positive versus  EGFR negative colorectal cancer tissues

status: Public on May 31 2018

city: ChengDu

first: Yong

last: Lv

state: SiChuan

department: Department of pediatric surgery

institute: West China hospital of Sichuan university

summary: This study was to identify microRNAs responsible for colorectal cancer

overall_design: Total RNAs were extracted from human EGFR positive versus EGFR nagative colorectal cancer tissues and paired adjacent normal tissue, and then subjected to microRNA array analysis (Agilent Human miRNA).

first: Zhu

last: Yufeng


title: The miRNA expression patterns in WSN-infected A549 cells at various time points post-infection.

city: Taoyuan

first: Sheng-Yu

last: Huang

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan (R.O.C.)

country: Taiwan

institute: chang gung university

summary: To identify miRNAs that are affected by IAV infection, we adopted a systematic approach, and performed a miRNA microarray analysis using a human alveolar adenocarcinoma cell line, A549, which was infected with a common laboratory strain of influenza A/WSN/33(H1N1) virus (WSN). We compared miRNA expression profiles in A549 cells infected with WSN for 2, 6, and 10 hours at a multiplicity of infection (MOI) of 2. Among 955 miRNAs on the microarray, 209 miRNAs were detected in all three infected A549 samples, but when compared with analysis results from mock-infected A549 cells, most expression changes were less than 1.5-fold , which was consistent with a previous report (Buggele et al., 2013). Therefore, we established 1.5-fold expression change as a threshold to select for miRNAs potentially affected by WSN infection. Further screening revealed 116 miRNAs that underwent 1.5-fold or greater expression changes at any timepoint following WSN infection.

overall_design: The A549 cells were infected with WSN at an MOI of 2 in serum-free MEM medium for 2, 6 and 10 hours.

first: Chi-Jene

last: Chen

first: Ting-Wen

first: Shin-Ru

last: Shih


title: Bovine Glycomacropeptide promotes the growth of Bifidobacterium longum subsp. infantis and modulates its gene expression

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

summary: Microarray analysis of gene transcription in B. infantis following exposure to Glycomacropeptide (GMP) revealed a substantial transcriptional response to GMP relative to untreated bacteria or bacteria treated with periodate denatured GMP-P, with a greater number of differentially expressed transcripts and larger fold changes versus the control. The pool of differentially expressed transcripts included two glycoside hydrolase (family 25) genes, which were substantially up-regulated following exposure to GMP but not GMP-P.

overall_design: 9 samples were analysed comprising 3 biological replicates for each of 3 treatment conditions

first: Noelle

last: O'Riordan

first: John

last: O'Callaghan

first: Ludovica

middle: F

last: Butto

first: Michelle

last: Kilcoyne

first: Marian

last: Kane

first: Lokesh

last: Joshi


title: Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed single-cell transcriptome analysis (using MARS-seq) in the cnidarian Nematostella vectensis. Additionally we performed bulk ATAC-seq experiments on wild-type specimens, as well as ELAV::mOrange reporter transgenic lines (separating ELAV+ and ELAV- cell populations, representing neurons and non-neurons, respectively).

overall_design: Multiple animals (20-25) were dissociated and pooled before sorting single-cells for scRNAseq. 200,000 cells were used in bulk ATAC-seq experiments.

first: Amos

last: Tanay


title: Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [ATAC-Seq]

status: Public on May 30 2018

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: Nucleus was isolated from flash frozen from tunicamycin treated (0,6 and 12 hours) maize root samples, purified, then transposition reaction and and purification steps were carried out following the standard ATAC-seq protocol

overall_design: Each sample was collected in three biological replicates

first: Renu

last: Srivastava

first: Zhaoxia

last: Li

first: Giulia

last: Russo

first: Jie

last: Tang

first: Ran

last: Bi

first: Usha

last: Muppirala

first: Sivanandan

last: Chudalayandi

first: Mingze

last: He

first: Sam

last: Vaitkevicius

first: Carolyn

last: Lawrence-Dill

first: Peng

last: Liu

first: Ann

last: Stapleton

first: Diane

last: Bassham

first: Federica

last: Brandizzi

first: Stephen

last: Howell


title: Impact of rex delation on the transcriptome of Streptococcus pneumoniae D39

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary:
The objective of this comparison was to identify the impact of rex deletion on the transcriptome of Streptococcus pneumoniae D39. This comparison showed that the transcriptional regulator, Rex acts as a transcriptional repressor of a number of genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in niacin uptake and biosynthesis in the presence of NADH.
In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to NADH. Transcriptome comparison of the D39 wild-type grown in chemically-defined medium (CDM) with 0 mg/ml NADH to 0.5 mg/ml NADH revealed elevated expression of various genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in the transport and biosynthesis of niacin. Microarray results were further confirmed by β-galactosidase assays. Promoter-lacZ fusions assays and microarray studies showed that the transcriptional regulator, Rex acts as a transcriptional repressor of a number of genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in niacin uptake and biosynthesis in the presence of NADH. The putative operator site of Rex in the promoter regions of Rex-regulated genes is predicted and confirmed by promoter mutational experiments.

overall_design: One condition design comparision of two strains including a dye swap

first: Muhammad

last: Afzal

first: Oscar

last: Kuipers


title: Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death

first: Andrew

last: Severin


title: Transcriptome response of the Streptococcus pneumoniae D39 wild-type to NADH

summary:
The objective of this comparison was to identify the impact of NADH on the transcriptome of Streptococcus pneumoniae D39. Transcriptome comparison of the D39 wild-type grown in chemically-defined medium (CDM) with 0 mg/ml NADH to 0.5 mg/ml NADH revealed elevated expression of various genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in the transport and biosynthesis of niacin.
In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to NADH. Transcriptome comparison of the D39 wild-type grown in chemically-defined medium (CDM) with 0 mg/ml NADH to 0.5 mg/ml NADH revealed elevated expression of various genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in the transport and biosynthesis of niacin. Microarray results were further confirmed by β-galactosidase assays. Promoter-lacZ fusions assays and microarray studies showed that the transcriptional regulator, Rex acts as a transcriptional repressor of a number of genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in niacin uptake and biosynthesis in the presence of NADH. The putative operator site of Rex in the promoter regions of Rex-regulated genes is predicted and confirmed by promoter mutational experiments.

overall_design: Two conditions design comparison of one strain including a dye swap.


title: Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii. [ChIP-chip]

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

institute: CNRS

type: Genome binding/occupancy profiling by genome tiling array

summary:
Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TFs, TgAP2X-5. The purpose of the study is to determine the impact of the absence of TgAP2X-5 on the binding of TgAP2XI-5 on its targets.
Chromatin immunoprecipitation (ChIP) of TgAP2XI-5 together with chromatin in absence of TgAP2X-5 profiling by ChIP-on-chip analysis demonstrated that TgAP2X-5 co-acts with TgAP2XI-5 for its binding to DNA of certain promoter targets.

overall_design: comparison of the binding of TgAP2XI-5 in presence of TgAP2X-5 (WT) or absence of TgAP2X-5 (iKD TgAP2X-5 / KI TgAP2XI-5)

first: Kevin

last: Lesage

first: Ludovic

last: Huot


title: Impact of NADH on gene expression of Streptococcus pneumoniae and role of Rex as a transcriptional repressor of the Rex regulon


title: Replacing C189 in the bZIP domain of Zta to S, T, V, and A changes DNA binding specificity to four types of double-stranded DNA (mC)

status: Public on May 14 2018

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: Zta is a bZIP transcription factor (TF) in the Epstein-Barr virus that binds unmethylated and methylated DNA sequences.  Substitution of cysteine 189 of Zta to serine (Zta(C189S)) results in a virus that is unable to execute the lytic cycle which was attributed to a change in binding to methylated DNA sequences.  To learn more about the role of this position in defining sequence-specific DNA binding, we mutated cysteine 189 to four other amino acids producing Zta(C189S), Zta(C189T), Zta(C189A), and Zta(C189V) mutants.  Zta and mutants were used in protein binding microarray (PBM) experiments to evaluate sequence-specific DNA binding to four types of double-stranded DNA (dsDNA):  1) with cytosine in both strands (DNA(C|C)), 2) with 5-methylcytosine (5mC) in one strand and cytosine in the second strand (DNA(5mC|C)), 3) with 5-hydroxymethylcytosine (5hmC) in one strand and cytosine in the second strand (DNA(5hmC|C)), and 4) with both cytosines in all CG dinucleotides containing 5mC (DNA(5mCG)).  Zta(C189S) and Zta(C189T) bound the TRE (AP-1) motif (TGAG/CTCA) more strongly than wild-type Zta, while binding to other sequences, including the C/EBP half site GCAA was reduced.  Binding of Zta(C189S) and Zta(C189T) to DNA containing modified cytosines (DNA(5mC|C), DNA(5hmC|C), and DNA(5mCG)) was reduced compared to Zta.  Zta(C189A) and Zta(C189V) had higher non-specific binding to all four types of DNA.  Our data suggests that position C189 in Zta impacts sequence-specific binding to DNA containing modified and unmodified cytosine.

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of the Epstein Barr Virus Zta protein and for 4 mutant constructs of Zta in which the cysteine at position 189 of wild type Zta was changed to serine (C189S), threonine (C189T), alanine (C189A) or valine (C189V).  Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines.  We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine.  Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.


title: Replacing C189 in the bZIP domain of Zta to S, T, V, and A changes DNA binding specificity to four types of double-stranded DNA (mCG)

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of the Epstein Barr Virus Zta protein and for 4 mutant constructs of Zta in which the cysteine at position 189 of wild type Zta was changed to serine (C189S), threonine (C189T), alanine (C189A) or valine (C189V).   Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded and methylated or unmethylated 44K Agilent microarrays, containing a DeBruijn sequence design, in order to determine their sequence preferences. Details of the methylated PBM protocol are described in Mann et al., Genome Research, 2013


title: Expression data from human T24 cells transfected with siNC or siNF90

city: Nanjing

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

institute: Institute of Urology, Drum Tower hospital

summary:
NF90 is a double-stranded RNA binding protein that takes part in microRNA biogenesis, as a competitor for the association of the microprocessor complex with pri-miRNAs, leading to a decrease in miRNA production. We want to know which miRNAs changed in human bladder cancer cell T24 when we downregulated NF90.
We used microarrays to detail the mature miRNA expression and identified distinct classes of 2-fold changed miRNAs during this process.

overall_design: T24 cells were transfected with control siRNA (siNC) and NF90 siRNA (siNF90). After verifying the knockdown efficiency, cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

last: Yan


title: Temporal expression of small RNAs during rice anther development

status: Public on May 09 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Sequencing of sRNA and PARE libraries was performed for tissues collected from developmentally staged young panicles and anthers in rice variety Nongken 58

overall_design: We generated small RNA data during seven stages of panicle or anther development (3 reps per stage) in rice, and PARE data for selected stages of the same material.

middle: C

first: Saleh

last: Tamim

first: Zhaoxia

last: Cai


title: Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

status: Public on May 08 2018

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

summary: In this study, we reported the updated chromosome and plasmid sequence of ZM4, and its two engineered xylose-utilizing strains derivatives (strains 2032 and 8b). The majority of plasmid genes have either homologs from other organisms or some conserved domains.  Our bioinformatics analysis suggested that several plasmid genes may be essential genes of ZM4. To further validate the function of these plasmid genes, an RNA-Seq pipeline was developed for Z. mobilis and used to compare the gene expression under various conditions, including anaerobic and aerobic conditions, and in different biomass hydrolysates.  Overall, these plasmids genes are more responsive to different concentrated hydrolysates than the different oxygen concentrations tested (such as anaerobic vs. aerobic conditions). Moreover, our results also indicate that the plasmid copy number is affected by growth conditions and foreign gene insertion while the chromosomal gene expression is relatively stable across different conditions in different strain backgrounds.

overall_design: We combined and cross-compared the genome resequencing and RNA-Seq results of four independent research laboratories from three countries: USA, Greece, and China. This GEO submission contains 17 paired-end RNA-seq samples for Zymomonas mobilis subsp. mobilis strain 2032 with a minimum of two biological replicates per test condition. Cell samples were collected at different timepoints during batch fermentation culture.

first: Shihui

last: Yang

first: Jessica

last: Vera

first: Jeff

last: Grass

first: Giannis

last: Savvakis

first: Oleg

last: Moskvin

first: Yongfu

first: Sean

last: McIlwain

first: Yucai

last: Lyu

first: Irene

last: Zinonos

first: Alexaner

last: Hebert

first: Joshua

last: Coon

first: Donna

last: Bates

first: Trey

last: Sato

first: Steven

middle: D

last: Brown

first: Michael

middle: E

last: Himmel

first: Min

last: Zhang

first: Katherine

last: Pappas

first: Yaoping


title: Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes [aCGH]

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

summary: Purpose: Tamoxifen is the most commonly used antiestrogen drug for breast cancer treatment, however, acquired resistance is a considerable challenge in clinic. Complexity and redundancy in biological system implies tamoxifen resistance is associated with complex biological processes. The aim of this study is to attempt to reveal the mechanism of tamoxifen resistance using high-throughput sequencing technique. Methods: We applied digital gene expression (DGE), RNA-seq, Small RNA-seq, bisulifte-seq (reduced representation bisuflite sequencing (RRBS)) with Illumina sequencing platforms, and Array CGH to analyze two well-established tamoxifen resistant cell line models: one is the LCC cell line model that was derived from MCF-7 breast cancer cell line and developed tamoxifen resistance following a step-wise strategy. This cell line model includes LCC0 (estrogen-dependent and tamoxifen sensitive), LCC1 (estrogen-independent and tamoxifen sensitive), LCC2 (derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant), and LCC9 (derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to both fluvestrant and tamoxifen). The other is the TAMR cell line model that was derived from MCF-7 breast cancer cell line and developed four tamoxifen-resistant sublines following the strategy of high-dosage of tamoxifen treatment. Each subline was developed from the survived single cell after the tamoxifen treatment. Results: The DGE and RNA-seq results showed characteristic expression features for the both cell line models, for instance, high expression of SOX2 and alterations of other SOX gene family members, decreased expression of PGR, PTEN, TP53, EZH2, SMAD3, TGF-β1, DNMT1, APOBEC3B, FOXO3 and FOXO4, and increased expression of CDH1, APOBEC3H, FOXA1, TET2, TET3, TDG, MBD4, DNMT3a and DNMT3b between the tamoxifen-resistant cell lines with their matched parental cell lines. Small RNA seq showed the decreased expressions of miR-1, miR-196-3p, miR-18a-5p, miR-125b-5p, and the increased expression of miR-23a-3p, miR-26b-5p, miR-320d, miR-141-3p, miR-23a-3p, miR-30a-5p, miR-9-5p, miR-200c, miR-129-5p, miR-125b-5p, miR-1285-3p and miR-30b-5p between the tamoxifen-resistant cell lines and their matched parental cell lines. Additionally, let-7a and let-7c have been found to present high expression levels in the tamoxifen resistant cells in the both cell line models, even it showed significantly decreased in some TAMR cells compared with their parental cell line. The RRBS showed similar DNA methylation levels between the LCC cell lines. Array CGH showed a small number of copy number variants between the LCC cell lines. Conclusion:  Our present study suggests the development of tamoxifen resistance is associated with a dynamic process of cell fate changing. Therefore, new therapeutic method that targets whole cell system and cell fate dynamics, will be a promising strategy.

overall_design:
Integrative analysis of genomic, transcriptomic and epigenomic profiles of the two well-established tamoxifen-resistant cell line models.
Array CGH was used to analyze the LCC cell line model only.

first: Xue

last: Lin

first: Shida

last: Zhu

first: Fei

last: Teng

last: Huang

first: Ning

first: Jihua

last: Sun

first: Boxin

last: Wu

first: Anne

last: Lykkesfeldt

first: Jun

last: Wang

first: Henrik

middle: J

last: Ditzel

first: Nils

last: Brünner

first: Huanming

first: Lars

last: Bolund


title: Cardiac-specific developmental and epigenetic functions of Jarid2 during embryonic development

status: Public on May 02 2018

first: Youngsook

last: Lee

address: 1111 Highland Ave

department: CRB

institute: University of Wisconsin-Madison

summary:
Jarid2 cooperates with PRC2 for H3K27me3 accumulation on a subset of Jarid2 target genes in the developing heart, which contributes to repress differentiation of other lineages such as neural differentiation, and to guide normal myocardial development.
Jarid2 forms a functional complex with PRC2 to increase or maintain H3K27me3 levels on the specific promoters in the developing heart.

overall_design: Sonicated chromatin from 20 pooled E17.5 fixed hearts was immunoprecipitated using H3K27me3 antibody, followed by the reversal of cross-linking and DNA purification. Immuno-enriched DNA targets were amplified by whole genome amplification and fluorescently labeled, which were then hybridized onto the Roche NimbleGen 3X720K RefSeq promoter arrays and scanned with an Axon 4000B.

first: Eunjin

last: Cho


title: Estrogens and selective estrogen receptor modulators differentially antagonize Runx2 in ST2 mesenchymal progenitor cells

status: Public on Apr 27 2018

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

summary:
This study investigates how 17ß-estradiol (E2) both stimulates and inhibits Runx2 in a locus-specific manner. We compare the effects of E2 to those of the Selective Estrogen Receptor Modulators (SERMs) raloxifene (ral) and lasofoxifen (las) and the phytoestrogen peurarin
15-week old C57BL/6 female mice, either wild type or mice with deletion of ERα-AF1, were ovariectomized and injected subcutaneously one week later with either E2 (115 µg/kg body weight) or olive oil vehicle (Apoteksbolaget, Göteborg, Sweden).  Mice were sacrificed after 18 hours of treatment and RNA was isolated from either long bone shafts (flushed femora and tibiae) or vertebral bodies (L5+L6) using an RNAlater reagent (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.  Gene expression was profiled at the Southern California Genotyping Consortium (SCGC) using MouseRef-8 v2.0 Illumina BeadChips (n=5 mice per group).

overall_design: Microarray analysis of RNA extracted from certebral bodies or long bone shafts of ovariectomized mice, wild type or Era-AF1 deletion


title: Multi-omics Profiling of Younger Asian Breast Cancers Reveals Distinctive Molecular Signatures

status: Public on Apr 17 2018

city: San Diego

first: YING

last: DING

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

summary: We observed higher proportions of HER2+ and Luminal B but lower proportions of ER+ and Luminal A subtypes along with lower estrogen receptor (ER) expression in SMC compared to TCGA. Germline pathogenic mutations affecting BRCA1 or BRCA2 were found in 11% of SMC but only 5% of TCGA. TP53 was also more frequently mutated in SMC (48%) than in TCGA (32%).

overall_design: 178 samples (168 tumors, 10 normals) from whole transcriptome sequencing

first: Ying

last: Ding

first: Jinho

last: Kim


title: Global transcriptional response of wild type and transcription factor deletion strains of Saccharomyces cerevisiae to the environmental stress of cold shock and subsequent recovery

status: Public on Jun 22 2018

first: Kam

middle: D.

last: Dahlquist

address: 1 LMU Drive, MS8220

department: Biology

institute: Loyola Marymount University

summary: Previous studies on the global transcriptional response of budding yeast, Saccharomyces cerevisiae, to cold shock have revealed that the response can be divided into a set of early response genes (after 15 minutes to 2 hours of cold temperatures) and late response genes (after 12 to 60 hours of cold temperatures). The late response genes include the ESR genes induced by many environmental stresses and are regulated by the Msn2 and Msn4 transcription factors, as they are during other environmental stresses (Kandror et al. 2004 PMID:15053871; Schade et al. 2004 PMID:15483057). However, the transcription factors responsible for the induction of the early response genes, the overall regulatory mechanism governing this early response, and the transcriptional response to recovery after cold shock remain largely unknown. Thus, we measured the early transcriptional response of S. cerevisiae to cold shock and subsequent recovery using DNA microarrays. To determine which transcription factors were responsible for these changes in expression, the same cold shock and recovery microarray experiments were then performed on six strains individually deleted for the transcription factors Cin5, Gln3, Hap4, Hmo1, Swi4, and Zap1.

overall_design: Yeast cells were grown to early log phase at 30°C, then shifted to 13°C for 60 minutes (cold shock), and then shifted back to 30°C for another 60 minutes (recovery). Samples from independently grown replicate cultures (flasks) were collected before cold shock (t0), after 15 (t15), 30 (t30), and 60 minutes (t60) of cold shock, and after 60 minutes of cold shock followed by 30 (t90) and 60 minutes (t120) of recovery at 30°C. Data was collected for the following strains: wild type (BY4741 or BY4739), BY4741 Δcin5, BY4741 Δgln3, BY4741 Δhap4, BY4741 Δhmo1, BY4741 Δswi4, and BY4741 Δzap1. Generally, 4 independent biological replicates were performed for each strain (independent culture flasks), although for some timepoints and strains there are 3 or 5 replicates instead. Note that the t15 sample was not collected for the BY4741 Δswi4 strain. The sample from each experimental timepoint (t15, t30, t60, t90, and t120) was labeled with Cy5, and the t0 sample (before cold shock control) was labeled with Cy3. Experimental and control samples from the same flask were co-hybridized onto the same microarray slide. The dye orientation was swapped for two of the biological replicates per timepoint per strain (experimental sample labeled with Cy3 and control sample labeled with Cy5), except in one instance when there was only one dye swap performed for a particular strain and timepoint. Technical replicates were not performed. There were a total of 137 microarrays hybridized in this study.

first: Hassan

last: Abdulla

first: Ashley

last: Arnell

first: Cybele

last: Arsan

first: Jessa

middle: M

last: Baker

first: Ross

last: Carson

first: Wesley

last: Citti

first: Steven

last: De Las Casas

first: Lauren

middle: G

last: Ellis

first: Kevin

last: Entzminger

first: Stephanie

first: Ben

last: Fitzpatrick

first: Samantha

last: Flores

first: Nicolette

last: Harmon

first: Kathleen

last: Hennessy

first: Andrew

last: Herman

first: Monica

middle: V

last: Hong

first: Heather

last: King

last: Kubeck

first: Okensama

last: La-Anyane

first: Douglas

last: Land

first: Michael

last: Leon Guerrero

first: Elizabeth

last: Liu

first: Minh

last: Luu

last: McGee

first: Matthew

middle: R

last: Mejia

first: Sheila

last: Melone

first: Nicole

last: Pepe

first: Kenny

last: Rodriguez

first: Nicholas

middle: A

last: Rohacz

first: Robert


title: Exosomal miRNAs released by neural stem/progenitor cells versus astrocytes

status: Public on Apr 20 2018

city: Bronx

first: Dongsheng

last: Cai

state: NY

address: 1300 Morris Park Avenue, 1300 MORRIS PARK AVENUE

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

summary: An Affymetrix microRNA (miRNA) Array was used to compare exosomal miRNAs released by hypothalamic stem/progenitor cells (htNSC), hippocampal NSC (hippoNSC) and astrocytes in primary culture. This assay is to provide preliminary information on the general profile of exosomal miRNAs released by these cells, while to study any particular miRNA species should require further quantitative analyses such as qPCR based on enough sample sizes.

overall_design: Exosomal RNAs were obtained from the culture media of htNSC, hippoNSC and astrocytes, adjusted to the same amount  and run through an Affymetrix miRNA Array chip.

first: Baosen

last: Jia

first: Yalin

last: Zhang


title: Electromagnetic field-mediated direct lineage reprogramming into induced dopamine neurons in vivo for Parkinson’s disease therapy [microarray2]

status: Public on Apr 10 2018

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

institute: Dongguk Uvi.

summary: Electromagnetic fields (EMF) are physical energy generated by electrically charged objects that can influence numerous biologic processes, including control of cell fate and plasticity. In this study, we show that magnetic gold nanoparticles in the presence of EMF can facilitate efficient direct lineage reprogramming to induced dopamine neurons both in vitro and in vivo. Remarkably, electromagnetic stimulation leads to the specific activation of the histone acetyl transferase Brd2, resulting in H3K27 acetylation and robust activation of neuronal-specific gene expression. In vivo reprogramming in conjunction with EMF stimulation efficiently alleviated symptoms in a mouse model of Parkinson’s disease (PD) in a noninvasive and controllable manner. These studies provide a proof of principle that EMF-based approaches may represent a viable and safe therapeutic strategy facilitating in vivo lineage conversion for neurodegenerative disorders.

overall_design: Total RNA obtained from control fibroblasts, APNL, APNL+AuEMF and primary neuron

first: Junsnag

last: Yoo

first: Wonhee

last: Jang

first: Jongpil

last: Kim


title: Tumor infiltrating lymphocytes in patients receiving trastuzumab/pertuzumab-based chemotherapy: A TRYPHAENA substudy

status: Public on Apr 01 2018

city: Brussel

first: Yacine

last: Bareche

address: Rue Héger-Bordetstraat 1

country: Belgium

institute: Jules Bordet Institute

summary:
Background: It is critical to identify biomarkers for treatment tailoring in HER2-amplified early breast cancer treated with trastuzumab/pertuzumab-based chemotherapy.
Patients and methods: Among the 225 patients randomized to trastuzumab/pertuzumab concurrently or sequentially with an anthracycline-containing regimen or concurrently with an anthracycline-free regimen in the Tryphaena trial, we evaluated TILs at baseline in 213 patients of whom 126 with pathological complete response, pCR (ypT0/is ypN0)  and 28 with Event Free Survival, EFS events. We computed associations between baseline TILs and either pCR or EFS after adjusting for clinicopathological characteristics using logistic and Cox regression models, respectively. To understand TILs biology, we evaluated associations between baseline TILs and baseline tumor gene expression data (800 gene set by NanoString) in a subset of 173 patients.
Results: Among the 213 patients with evaluable TILs at baseline, the median level of TILs was 14% (interquartile range, IQR, 7-32%). After adjusting for clinicopathological characteristics, baseline TILs were not associated with pCR (adjusted odds ratio for every 10% increase in TILs aOR 1.12, 95%CI 0.95-1.31, p=0.17). At a median follow-up of 4.7 years, for every increase in baseline TILs of 10 percentage units there was a 25% reduction in the hazard of the EFS event (adjusted hazard ratio 0.75, 95%CI 0.56-1.00, p=0.05) after adjusting for baseline clinicopathological characteristics and pCR. Genes associated with Epithelial-Mesenchymal Transition (EMT) such as SNAIL1, TWIST1, ZEB1, B7-H3 and NOTCH3 were significantly anti-correlated with TILs.
Conclusions: Baseline TILs provide independent prognostic information in patients treated with trastuzumab/pertuzumab-based neoadjuvant chemotherapy. Further validation is needed.

overall_design: Gene expression data were generated from frozen tumor samples of patients with HER2 Breast Cancer from the TRYPHAENA study.

first: M

last: Ignatiadis

first: G

last: Van den Eynden

first: S

last: Salgado

last: Fornili

first: Y

first: C

last: Desmedt

first: F

last: Rothé

last: Maetens

first: D

last: Venet

first: E

last: Holgado

first: V

last: McNally

first: A

last: Kiermaier

first: H

last: Savage

first: T

last: Wilson

first: J

last: Cortes

last: Schneeweiss

first: K

last: Willard-Gallo

last: Biganzoli

last: Sotiriou


title: Electromagnetic field-mediated direct lineage reprogramming into induced dopamine neurons in vivo for Parkinson’s disease therapy [microarray1]

first: Junghyun

last: Jung

overall_design: Total RNA obtained from control fibroblasts and fibroblasts on AuNPs exposed to EMF condition

first: Junsnag

last: Yoo

first: Wonhee

last: Jang

last: Kim


title: A Retinoic Acid-dependent Stroma-Leukemia Crosstalk Promotes Chronic Lymphocytic Leukemia Progression [microarray]

city: Milan

first: Linda

last: Pattini

address: piazza Leonardo da Vinci, 32

department: Department of Electronics, Information and Bioengineering

institute: Politecnico di Milano

summary:
In B-cell chronic lymphocytic leukemia (CLL), the non-hematopoietic stromal microenvironment plays a critical role in promoting tumor cell recruitment, activation, survival and expansion.
Using the Eμ-TCL1 mouse model, we demonstrate that leukemic cells induce the activation of retinoid acid synthesis and signaling in stromal cells of the lymphoid microenvironment.

overall_design: Four stromal samples cocultured with  Eμ-TCL1 leukemic cells and four stromal samples cocultured with control (splenic) B cells

first: Diego

last: Farinello

first: Andrea

last: Brendolan


title: Transcriptomic comparison of Botrytis cinerea wild type and VELVET mutants

status: Public on Apr 02 2018

city: Kaiserslautern

first: Matthias

last: Hahn

address: Paul-Ehrlich-Str. 22

institute: University of Kaiserslautern

summary: An RNAseq-based transcriptomic comparison of Botrytis cinerea wild type and the three VELVET mutants was performed, to  correlate common virulence defects of the mutants with changes in gene expression. A large number of genes encoding infection-related and secreted proteins was strongly underexpressed in the mutants, in particular genes encoding proteases and carbohydrate active enzymes. Many VELVET-regulated genes were found to be upregulated in the wild type during host plant infection (Müller et al.: Investigations on VELVET regulatory mutants confirm the role of host tissue acidification and secretion of proteins in pathogenesis of Botrytis cinerea; New Phytologist, 2018)

overall_design: RNA was obtained from  tomato leaves 24-28 h.p.i. with B. cinerea wild type B05.10 (3 repl.), and  the VELVET mutants vel1* (4 repl.), lae1 (3 repl.s) and vel1 (3 replicates). For transcriptome comparison of in vitro and in planta growth, RNA was also isolated from liquid culture (32 h.p.i.).

first: Nathalie

last: Müller


title: Anopheles gambiae midgut tissue: Oral exposure to Chromobacterium sp. Panama filtered cell-free biofilm supernatant vs. Oral exposure to LB.

status: Public on Mar 31 2018

city: Baltimore

first: George

last: Dimopoulos

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: Transcriptome analysis to determine the impact of oral exposure (in a sugar meal) to the liquid supernatant (i.e. LB culture media) of Chromobacterium sp. Panama biofilm culture. The biofilm supernatant (i.e. media) was first filtered with a 0.2uM filter to remove all live bacterial cells. It was then mixed with 10% sucrose, and a control sucrose meal was mixed with filtered LB. Mosquitoes were exposed to each sugar meal for 24 hours and then midguts were dissected from 20 adult females per treatment. The entire experiment was performed 4 independent times.

overall_design: Two condition experiment, Chromobacterium sp. Panama (C.sp_P) vs. LB control, dye swap design, 4 replicates per treatment.

first: Sarah

last: Short

last: van Tol

first: Brendan

last: Smith

first: Yuemei

last: Dong


title: Targeting Sphingosine Kinase Isoforms Effectively Reduces Growth and Survival of Neoplastic Mast Cells with D816V-KIT

status: Public on Mar 30 2018

first: Ana

last: Olivera

address: 10 Center Dr, Bldg 10

institute: NIAID (National Institutes of Health)

summary: Mastocytosis is a disorder resulting from an abnormal mast cell (MC) accumulation in tissues that is often associated with the D816V mutation in KIT, the tyrosine kinase receptor for stem cell factor. Therapies available to treat aggressive presentations of mastocytosis are limited, thus exploration of novel pharmacological targets that reduce MC burden is desirable. Since increased generation of the lipid mediator sphingosine-1-phosphate (S1P) by sphingosine kinase (SPHK) has been linked to oncogenesis, we studied the involvement of the two SPHK isoforms (SPHK1 and SPHK2) in the regulation of neoplastic human MC growth.  While SPHK2 inhibition prevented entry into the cell cycle in normal and neoplastic human MCs with minimal effect on cell survival, SPHK1 inhibition caused cell cycle arrest in G2/M and apoptosis, particularly in D816V-KIT MCs. This was mediated via activation of the DNA damage response cascade, including phosphorylation of the checkpoint kinase 2 (CHK2), CHK2-mediated CDC25c depletion and p53 activation. Combination treatment of SPHK inhibitors with KIT inhibitors showed greater growth inhibition of D816V-KIT MCs than either inhibitor alone.  Furthermore, inhibition of SPHK reduced the number of malignant bone marrow MCs from patients with mastocytosis and the growth of D816V-KIT MCs in a xenograft mouse model. Our results reveal a role for SPHK isoforms in the regulation of growth and survival in normal and neoplastic MCs and suggest a regulatory function for SPHK1 in the DNA damage response in MCs with KIT mutations.  The findings also suggest that targeting the SPHK/S1P axis may provide an alternative to tyrosine kinase inhibitors, alone or in combination, for treatment of aggressive mastocytosis and other hematological malignancies associated with the D816V-KIT mutation.

overall_design: HMC-1.2 cells cultured with vehicle, SPHK1 inhibitor (SPHK1-I) or SPHK2 inhibitor (SPHK2-I) for 24 h.  Each treatment was done in duplicate for a tottal number of 6 samples

first: Geethani

last: Bandara

first: Rosa

last: Muñoz-Cano

first: Araceli

last: Tobío

first: Yuzhi

last: Yin

first: Hirsh

last: Komarow

first: Avanti

last: Desai

first: Dean

last: Metcalfe


title: Gene expression profiling of human cardiac macrophages sorted from failing human hearts

status: Public on Apr 04 2018

city: St Louis

first: Kory

last: Lavine

address: 660 South Euclid, Campus Box 8086

institute: Washington University

overall_design: Human macropages were sorted from tissue explants obtained from patients with dilated and ischemic cardiomyopathy using flow cytometry. Cells were sorted directly into lysis buffer. Sunstes examined included CCR2+ monocytes, CCR2+ macrophages, and CCR2- macrophages.


title: RNAseq profiliing of Xenopus laevis animal caps expressing Xnr2 at st14

status: Public on Mar 28 2018

city: La Jolla

first: Chris

last: Kintner

address: 10010 N Torrey Pines Rd

department: Molecular Neurobiology Lab

institute: Salk Institute for Biological Studies

summary: To determine if Xnr2 induces mesodermal genes expression in ectodermal tissues

overall_design: We force the ectodermal tissues to express xnr2 by injecting xnr2 RNA at the 2-4cell stage. The animal caps were excised at st10, the blastula stage. Tissues are cultured at DFA and harvested at stage 14 for RNA extraction.

first: Yuan-Hung

last: Chien


title: Transcriptome analysis of gene expression of PAK-AR2 and 1-9

status: Public on Mar 27 2018

city: Tianjin

first: jia

middle: jia

last: You

address: 29 13th Street, TEDA

department: College of Biotechnology

institute: Tianjin             University of Science & Technology

summary: RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) ≤ 0.001, fold change |log2Ratio|≥1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic.

overall_design: Gene expression of PAK-AR2 and 1-9 were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.

first: Jiajia

first: Hongjiang

last: Yang


title: Placental miR-340 mediates vulnerability to activity based anorexia in mice

city: Munich

first: Mira

middle: Alexandra

last: Jakovcevski

state: Bavaria

address: Kraepelin Str. 2-10

department: Stress Neurobiology and Neurogentics

institute: Max Planck Institute of Psychiatry

summary: Anorexia nervosa (AN) is a devastating eating disorder characterized by self-starvation that mainly affects women. Its etiology is unknown, which impedes successful treatment options leading to a limited chance of full recovery. Here, we show that gestation is a vulnerable window that can influence the predisposition to AN. By screening placental microRNA expression of naive and prenatally stressed (PNS) fetuses and assessing vulnerability to activity-based anorexia (ABA) in early adulthood, we identify miR-340 as a sexually dimorphic regulator involved in prenatal programming of ABA. PNS caused gene-body hypermethylation of placental miR-340, which is associated with reduced miR-340 expression and increased protein levels of several target transcripts; Gr, Cry2 and H3F3b. MiR-340 is linked to the expression of several nutrient transporters both in mice and human placentas. Using placenta-specific lentiviral transgenes and embryo transfer, we demonstrate the key role miR-340 plays in the mechanism involved in early life programming of ABA.

overall_design: Placenta RNA from female ICR/CD1 offspring of stressed and control mothers

first: Mariana

last: Schroeder

first: Alon

last: Chen


title: Impact of conditional uterine deletion of Esr1, Foxa2 or Foxo1 on DES-induced gene expression

city: RTP

first: Wendy

last: Jefferson

address: 105 T. W. Alexander Drive

institute: NIEHS

summary: Neonatal exposure to diethylstilbestrol (DES) results in abnormal reproductive tract morphology, female infertility and uterine cancer in mice.  This exposure also causes altered gene expression in the female reproductive tract that persists into adulthood. To further explore on a genome-wide basis how neonatal estrogen exposure results in permanent epigenetic changes, we performed RNA-seq and ChIP-seq analyses of DES-treated and control mice.  CD-1 mice were treated on postnatal days (PND) 1-5 with DES (2 µg/pup/day) or corn oil as a control; uterine tissues were collected on PND5. RNA-seq analysis resulted in 4,498 differentially expressed genes (>1.5 fold difference; RPKM >1; FDR <0.05).  ChIP-seq was performed on uterine samples using H3K4me3, H3K27me3, H3K27acetyl and H3K4me1 as the precipitating antibodies. The most significant findings at the TSS were increased H3K4me3 at up-regulated genes (22%), increased H3K27ac at up-regulated genes (55%) and differential H3K27ac at down-regulated genes (33%). The most striking finding was differential association of H3K27ac at presumed enhancer regions; 3,012 out of 4498 altered genes (67%) had a differential H3K27ac peak associated with them and 2,962 out of 4,498 (66%) had differential H3K4me1.  These differences were generally coordinated with gene expression with increased gene expression having more H3K27ac associated although a small subset of genes showed the opposite. To further investigate the mechanism of differential H3K27ac binding in enhancer regions near estrogen regulated genes, we overlapped these enhancers to Esr1 ChIP seq data; a large percentage of them overlap with Esr1 peaks (39%). We also performed motif analysis where ERE was enriched in the differential H3K27ac peaks. We further investigated Esr1’s role in differential H3K27ac enhancer binding by using a conditional uterine deletion of Esr1 by crossing Esr1 floxed mice with PgR-cre and then treating with vehicle or DES and collecting uteri on day 5.  We performed a microarray and pattern analysis and determined there were 4,073 out of 4,617 altered genes (88%) protected by conditional uterine deletion of Esr1. We also performed H3K27ac ChIP seq on these samples and found a large number of these protected genes have a differential H3K27ac enhancer. Several Fox genes were up-regulated following DES treatment and Fox binding motifs were found to be enriched in both H3K27ac and H3K4me1 differential enhancer peaks. To further study the impact of Foxa2 or Foxo1, we conditionally deleted each of these using PgR-cre.  There were far fewer genes impacted by deletion of either Foxa2 or Foxo1 suggesting these Fox genes are not responsible for DES induced gene expression and these two lines were not followed further. Taken together, these data suggest estrogen regulates gene expression in the neonatal mouse uterus by H3K27ac association at Esr1 binding sites near estrogen regulated genes.  Changes in the epigenome during the time of treatment may contribute to the permanent alterations in gene expression observed in aged DES treated mice.

overall_design: Each group has 4 biological replicates - day 5 control Esr1 WT, day5 control Esr1 cKO, day 5 DES Esr1 WT, day 5 DES Esr1 cKO, day 5 Foxa2 WT, day 5 Foxa2 cKO, day 5 Foxo1 WT, day 5 Foxo1 cKO

middle: N

first: Tianyuan

last: Wang

first: Harriet

last: Kinyamu

first: Elizabeth

last: Padilla-Banks

first: Alisa

last: Suen

first: Carmen

last: Williams


title: Altered MicroRNA Profile in Osteoporosis Caused by Impaired WNT signaling

status: Public on Mar 29 2018

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: WNT signaling is fundamental to bone health and its aberrant activation leads to skeletal pathologies. A heterozygous missense mutation p.C218G in WNT1, a key WNT pathway ligand, leads to severe early-onset osteoporosis with multiple peripheral and spinal fractures. Despite the severe skeletal manifestations, conventional bone markers are normal in mutation-positive patients. The objective of this study was to find novel biomarkers that differentiate between WNT1 mutation-positive and -negative subjects. We evaluated serum levels of 192 miRNAs in 12 mutation-positive (median age 39 years, range 11-76 years) and 12 mutation-negative (35 years, range 9-59 years) subjects from two Finnish families. The results indicate significant differences in circulating miRNA profiles with 2 upregulated (miR-18a-3p, miR-223-3p) and 6 downregulated miRNAs (miR-22-3p, miR-31-5p, miR-34a-5p, miR-143-5p miR-423-5p, miR 423-3p) in the mutation-positive subjects. Three of these (miR-22-3p, miR-34a-5p, and miR-31-5p) are known inhibitors of WNT signaling: miR-22-3p and miR-34a-5p target WNT1 mRNA and miR-31-5p is predicted to bind to the WNT1 3’UTR. Our results suggest that the WNT1 mutation disrupts a feed-back regulation between these miRNAs and WNT1, providing new insights into the pathogenesis of WNT-related bone disorders. Future studies are warranted to explore the potential diagnostic and therapeutic applications of these findings in osteoporosis.

overall_design: Cross-sectional design comparing serum microRNA profiles of 12 subjects with heterozygous missense mutation p.C218G in WNT1 to a control group with wildtype WNT1.

first: Riikka

last: Mäkitie

first: Riitta

last: Niinimäki

first: Sakari

last: Kakko

first: Johannes

last: Grillari

first: Outi


title: Gene expression profiling in the seminal vesicles (SVs) from neonatal DES-treated mice [array]

first: Yin

last: Li

address: 111 TW alexander Drive

country: USA

summary:
DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER-dependent pathways in mediating the effects of neonatal DES exposure in female and male reproductive tract tissues.
The objective of this study is to compare gene expression profiles between the WT-veh and -DES groups or αERKO-veh and -DES from the adult male mice (week 10) of the SV tissues to identify differential genes.

overall_design: Mice were neonatally exposed to DES. RNA was isolated from week 10 SVs and then hybridized on Affymetrix microarray.

first: Liwen

last: Liu

first: Kevin

last: Gerrish

first: Kenneth

last: Korach


title: Glycyrrhetinic acid antagonizes pressure-induced venous remodeling in mice

status: Public on Mar 23 2018

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Development of spider veins is caused by the remodeling of veins located in the upper dermis and promoted by risk factors such as obesity or pregnancy that chronically increase  venous pressure. We have repeatedly shown that the pressure-induced increase in biomechanical wall stress is sufficient to evoke the formation of enlarged corkscrew-like superficial veins in mice. Subsequent experimental approaches revealed that interference with endothelial- and/or smooth muscle cell activation counteracts this remodeling process. Here, we investigate whether the herbal agent glycyrrhetinic acid (GA) is a suitable candidate for that purpose given its anti-proliferative as well as anti-oxidative properties.
While basic abilities of cultured venous smooth muscle cells (SMCs) such as migration and proliferation were not influenced by GA, it inhibited proliferation but not angiogenic sprouting of human venous endothelial cells (ECs). Further analyses of biomechanically stimulated ECs revealed that GA inhibits the DNA binding capacity of the mechanosensitive transcription factor activator protein-1 (AP-1) which, however, had only a minor impact on the endothelial transcriptome. Nevertheless, by decreasing gelatinase activity in ECs or mouse veins exposed to biomechanical stress, GA diminished a crucial cellular response in the context of venous remodeling. In line with the observed inhibitory effects, local transdermal application of GA attenuated pressure-mediated enlargement of veins in the mouse auricle. In summary, our data identifies GA as an inhibitor of EC proliferation, gelatinase activity and venous remodeling. It may thus have the capacity to attenuate spider vein formation and remodeling in humans.

overall_design: Comparison of biomechanically stretched HUVEC treated with DMSO or Glycyrrhetinic acid

first: Thomas

last: Korff


title: Late cornified envelope 1C (LCE1C) gene is a transcriptional target of TAp63.

status: Public on Mar 22 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: As a member of the p53/p63/p73 family, p63 is a transcriptional regulator that induces apoptosis, cell cycle arrest, or senescence. TAp63 protein, a p53-like master transcriptional regulator, plays an essential role in epithelial development because p63-null mice are born alive but die shortly after birth due to developmental defects. However, its molecular mechanism remains elusive.  We identified these phosphorylation sites during a search for the targets of Cyclin G-associated kinase (GAK) in vitro. LCE1C was drastically upregulated by doxycycline-dependent expression of Myc-TAp63 wild-type (WT) proteins, but not non-phosphorylatable Myc-TAp63-T46A/T281A (AA) proteins.

overall_design: Gene expression analysis of Tet-ON inducible Myc-TAp63-WT or Myc-TAp63-T46A/T281A (AA) U2OS cells with (+) or without (-) doxycycline (Dox) was performed using Agilent Human Gene Expression 4x44K v2 Microarray as one color experiments.

first: Hiroshi

last: Nojima


title: Transcriptome analysis of Sulfolobus islandicus E233S1 and ∆tfb3 upon NQO treatment

status: Public on Mar 20 2018

city: Copenhagen N

first: Xu

last: Feng

address: Ole Maaløes Vej 5

institute: University of Copenhagen

summary: Transcriptome sequencing was carried out with an Illumina HiSeq platform to investigate the differently expressed genes in wide type strain E233S1 and tfb3 gene deletion mutant ∆tfb3 with or without 2 µM NQO treatment for 6 hours.

overall_design: Examination of  different gene expression in E233S1 and ∆tfb3  with or without NQO treatment

first: Qunxin

last: She


title: Inhibition of NF-κB signaling by a novel siRNA sequence induces apoptosis and suppresses tumor growth in KRAS mutant colorectal cancer.

status: Public on Mar 17 2018

summary: KRAS mutation is one of the major genetic alterations in colorectal cancer (CRC). Treating patients with KRAS mutant CRC remains one of the biggest challenges in oncology. In this study, we aimed to discover an effective therapeutic microRNA (miRNA) that could target KRAS mutant CRC. For this purpose, we investigated the functional relevance of dysregulated miRNAs in KRAS mutant cancers. We transfected exogenous KRASG12V into human embryonic kidney 293 (HEK293) cells and human lung fibroblasts (MRC5) cells, and performed comprehensive microRNA expression profiling by microarray analysis. The results showed that 6 miRNAs are significantly upregulated in KRAS-transfected HEK293 and MRC5 cells. Among 6 miRNAs, we identified mature miRNA-29b-1-5p as potent growth inhibitor in CRC cell proliferation. However, miRNA-29b-1-5p was found to be a passenger strand with a star form (miRNA-29b-1-5p*), and did not function in CRC cells. Proliferation assay revealed that completely opposite complementary strand to miRNA-29b-1-5p possessed a potent anti-tumor effect. We named this novel anti-tumor siRNA sequence “MIRTX”. MIRTX induced apoptosis and significantly inhibited cell proliferation in KRAS mutant CRC in vitro. In addition, MIRTX suppressed NF-κB signaling pathway, which is downstream effector of KRAS in CRC. Furthermore, MIRTX directly targeted 3'-UTR of PIK3R1 and CXCR2 mRNA, and indirectly suppressed KRAS itself. In vivo xenograft mouse models, systemic administration of MIRTX significantly inhibited the tumor growth with no particular toxicity, using carbonate apatite as a vehicle. These findings indicate that inhibition of NF-κB signaling by siRNA-based therapeutic could be a promising strategy against KRAS mutant CRC.

overall_design: Gene expression analysis using Whole Human Genome Microarray Kit, 4x44K v2 (G4845A) (Agilent) was performed as one color experiments.

first: Akira

last: Inoue

first: Hirofumi

last: Yamamoto


title: The DYRK1A kinase positively regulates angiogenic responses in endothelial cells

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: CRG

summary: Angiogenesis is a highly regulated process essential for organ development and maintenance, and its deregulation contributes to inflammation, cardiac disorders and cancer. The Ca2+/Nuclear Factor of Activated T-cells (NFAT) signaling pathway is central to endothelial cell angiogenic responses, and it is activated by stimuli like the vascular endothelial growth factor A (VEGF). NFAT phosphorylation by dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) is thought to be an inactivating event. Contrary to expectations, we show that the DYRK family member DYRK1A positively regulates VEGF-dependent NFAT transcriptional responses in primary endothelial cells. DYRK1A silencing reduces intracellular Ca2+ influx in response to VEGF, which dampens NFAT activation. The effect is exerted at the level of VEGFR2 accumulation leading to impairment in PLCg1 activation. Notably, Dyrk1a heterozygous mice show defects in developmental retinal vascularization. Our data establish a regulatory circuit, DYRK1A/ Ca2+/NFAT, to fine-tune endothelial cell proliferation and angiogenesis.

overall_design:
RNA microarray analysis using VEGF-stimulated HUVECs infected with lentivirus expressing a control shRNA or a shRNA targeting DYRK1A.
To discriminate the NFAT-dependent group of genes, VEGF-stimulated cells in the presence of the CN/NFAT inhibitor cyclosporin A (CsA) were analyzed.

first: Esteban

last: Rozen

first: Julia

last: Roewenstrunk

first: María

last: Barallobre

first: Susana

last: De La Luna


title: BP180 dysfunction triggers spontaneous skin inflammation in mice

city: Chapel Hill

first: Zhi

address: 4157 Genome Sciences Building, CB#2360

department: Dermatology

institute: University of North Carolina at Chapel Hill

summary: BP180, also known as collagen XVII, is a hemidesmosomal component and plays a key role in 2 maintaining skin dermal/epidermal adhesion. Dysfunction of BP180, either through genetic 3 mutations in Junctional Epidermolysis Bullosa (JEB) or autoantibody insult in Bullous Pemphigoid 4 (BP), leads to subepidermal blistering accompanied by skin inflammation. However, whether BP180 5 is involved in skin inflammation remains unknown. To address this question, we generated a BP180-6 dysfunctional mouse strain and found that mice lacking functional BP180 (termed ΔNC16A) 7 developed spontaneous skin inflammatory disease, characterized by severe itch, defective skin 8 barrier, infiltrating immune cells, elevated serum IgE levels and increased expression of thymic 9 stromal lymphopoietin (TSLP). Severe itch is independent of adaptive immunity and histamine, but 10 dependent on increased expression of TSLP by keratinocytes. Our data provide the first direct 11 evidence showing that BP180 regulates skin inflammation independently of adaptive immunity, and 12 BP180 dysfunction leads to a TSLP mediated itch.

overall_design: Total six samples, three controls (WT) and three test (KO). All of the sample are the RNA extracted from fresh mouse skin tissue; from three WT mice and three KO mice. Age and sex are matched.

first: Bin-Jin

last: Hwang


title: Gene expression profiling of spheres from primary ovarian cancer cells and from primary fallopian tube epithelial cells

status: Public on Mar 15 2018

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary:
The biological features of ovarian cancer stem cells (OCSC) remain elusive, mainly because 1) most studies so far have focused on cell lines that recapitulate the human disease only to a limited extend; and 2) because the identification of OCSC has relied on markers inferred from different and unrelated tumor types. Our study has harnessed the intrinsic, stemness-related properties of OCSC to identify and isolate this cell subpopulation from primary cultures freshly established from high-grade serous ovarian cancer (HGSOC), the most common and aggressive from of the disease. In addition, OCSC were compared to stem cell-enriched cultures from fallopian tube epithelium, which is the most accredited tissue of origin for HGSOC. The transcriptomes of the two cell types were compared to infer genes differentially regulated in OCSC.
We used affymetrix expression microarray to analyze the transcriptional profile of spheres deriving from high-grade serous ovarian cancer or from normal ovarian fimbria.

overall_design: Total RNA was extracted from primary cells derived from either 7 HGSOC ascites samples or 9 normal ovarian fimbriae samples. Samples were pooled together (3-5 samples/pool; Ascites, N=2; Fimbria, N=2) and analyzed using the Affymetrix Human Gene 2.1-st, following manufacturer's standard protocols. Raw affymetrix data were analyzed ausing the Expression Consol suite (Affymetrix)  and normalized by RMA_sketch.

first: Ugo

last: Cavallaro

first: Michela

last: Lupia


title: Heart expression data after short ischemia/reperfusion in WT, Reverb alpha KO and Reverb alpha antagonist-treated mice

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

institute: Inserm

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

overall_design: Refer to individual Series


title: Heart expression data from WT and reverb alpha KO mice after short ischemia/reperfusion at ZT0, ZT12

summary:
Nuclear receptor Reverb alpha is a component of circadian rythm which could be evolved in cardioprotection strategy. We test if pharmacological modulation of these target could be suitable for cardioprotection after ischemia reperfusion injury
We used microarrays to detail the global programme of gene expression

overall_design: Heart ischemia reperfusion were performed using Langendorff isolated heart model and twenty minutes stop flow ishemia with twenty minutes reperfusion.

first: Xavier

last: Marechal

first: David

last: Montaigne

first: Celine

last: Gheeraert

first: Philippe

last: Lefebvre


title: Gene expression profiles in RAW264.7 cells with CpG and Gf

city: Cleveland

first: Manoj

last: Veleeparambil

state: OH

address: 9500 Euclid Avenue

department: Immunology

institute: Lerner Research Institute Cleveland Clinic

summary: RAW264.7 cells were untreated or treated with CpG+/-Gf for 6 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. CpG‐induced genes and their regulation by Gf were examined.

overall_design: Total RNA from RAW cells treated or untreated with CpG or Gf or both CpG and Gf were analyzed. Gene expression was compared between CpG and CpG+Gf samples.

first: G

last: Sen


title: Rosa Chinensis epigenome

city: Orsay

first: Maria Victoria

last: Gomez-Roldan

address: bat 630

institute: CNRS

summary: Genome-wide studies in plants have provided evidence for the role of H3K9ac and H3K27me3 in gene activation and repression, respectively. The roles of these histone modifications in rose remain unknown and represent a represent a limitation to the full understanding of how thousands of bioprocesses are regulated. To determine the genomic landscape of these marks, we performed a ChIP-seq analysis using H3K9ac and H3K27me3 antibodies on petals from a heterozygous plant.

overall_design: Provide the first insight into Rose epigenome.

first: Marion

last: Verdenaud

last: Latrasse

first: Moussa

last: Benhamed

first: Mohammed

last: Bendahmane


title: Ventral prostate in male F344 rats: Control vs. PhIP treatment

city: Nagoya

first: Shugo

last: Suzuki

state: Aichi

address: 1 Kawasumi, Mizuho-Cho, Mizuho-Ku

department: Experimental Pathology and Tumor Biology

institute: Nagoya City University Graduate School of Medical Sciences

summary: The gene expression profling between Control and 300 mg/kg PhIP treatment  in ventral prostate lobe of male F344 rats

overall_design: Two-condition experiment, Control vs. PhIP treatment. Biological replicates: 4 control rats, 4 PhIP-treated rats. Mixed 2 samples from each group on one array


title: Follistatin dysregulates systemic glucose homeostasis during hepatic insulin resistance

status: Public on Mar 14 2018

city: boston

first: rongya

last: tao

state: MA

address: 300 Longwood Ave

institute: boston children's hospital