title: De novo assembly and analysis of tartary buckwheat (Fagopyrum tataricum Garetn.) transcriptome discloses key regulators involved in salt-stress response

city: Chengdu

last: Wu

address: Shiling town, Longquanyi District,

institute: Chengdu University

summary: We conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an llumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs). Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs), ATP-binding cassette (ABC) transporters, Glutathione S-transferases (GSTs), abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into the salt tolerance mechanisms, and will serve as useful genetic information for tolerant elites breeding programs in future.

overall_design: mRNA profiles of 2-week old control and salt-treated  seedlings were generated by  deep sequencing, using Illumina Hiseq 2500.

first: Xue

last: Bai


title: Breaking the Atoh1 autoregulatory loop in hair cells: the repression of Atoh1 by Neurogenin1 during ear development

status: Public on Nov 09 2017

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The functional unit of the inner ear consists of hair cells (HCs) and neurons in the inner ear. Both genes are induced early in development, but Atoh1 expression is counteracted by Neurog1. As a result, HC development is prevented during neurogenesis. This work aimed at understanding the molecular basis of this interaction. Atoh1 regulation depends on a 3’Atoh1-enhancer that is the site for Atoh1 autoregulation. This enhancer recapitulates Atoh1 expression in the embryo and contains putative binding sites for several transcription factors, including basic helix-loop-helix (bHLH) factors like Atoh1, Neurog1 and Hes/Hey repressors. Reporter assays on chick embryos and P19 cells show that Neurog1 hampers the autoactivation of Atoh1, the effect being cell autonomous and independent on Notch activity. ATAC-seq analysis shows that the region B of the 3’Atoh1-enhancer is accessible during development and sufficient for both activation and repression. Neurog1 requires the regions flanking the class A E-box bound by Atoh1 to show its repressor effect. However, Neurog1 does not require binding to DNA for Atoh1 repression and prevention of HC formation, but the dimerization domains Helix-1 and Helix-2. The repression of Atoh1 by Neurog1 does not involve the direct interaction between Atoh1 and Neurog1, but rather an indirect effect on the levels of Atoh1 protein. The results suggest that Neurog1 induces the acceleration of  Atoh1 mRNA degradation and the consequent reduction of protein levels. Such a mechanism dissociates the prevention of Atoh1 expression in neuro-sensory progenitors from the unfolding of the neurogenic program.

overall_design: ATAC-seq in mouse otocysts in E10.5, E14 WT and E14 treated with LY411575

first: Héctor

last: Gálvez

middle: J

first: Fernando

last: Giráldez

first: Gina

last: Abelló


title: Role of  Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [expression_BCAT1-KD #2]

status: Public on Nov 08 2017

city: Heidelberg

first: Simon

last: Raffel

address: INF 280

country: Germany

institute: German Cancer Research Center

summary: The branched chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. By performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem cell (LSC) and non-LSC populations, we found the BCAA pathway enriched and BCAT1 overexpressed in LSCs. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Next to its role in the tricarboxylic acid (TCA) cycle αKG is an essential co-factor for αKG-dependent dioxygenases such as EGLN1 and the TET family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG leading to HIF1a protein degradation mediated by EGLN1. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. In contrast, overexpression (OE) of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation via altered TET activity. BCAT1high AMLs displayed a DNA hypermethylation phenotype similar to cases carrying mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate. High levels of BCAT1 strongly correlate with shorter overall survival in IDHwtTET2wt, but not IDHmut or TET2mut AMLs. Gene sets characteristic for IDHmut AMLs were enriched in IDHwtTETwtBCAT1high patient samples. BCAT1high AMLs showed robust enrichment for LSC signatures and paired sample analysis revealed a significant increase of BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1a stability and regulation of the epigenomic landscape. Our results suggest the BCAA-BCAT1-αKG pathway as a therapeutic target to compromise LSC function in IDHwtTET2wt AML patients.

overall_design: Primary AML samples were lentivirally transduced with shBCAT1-2 or shNT as control, transduced cells were FACS sorted 48 hrs after the transduction, cells were lysed and RNA was extracted

first: Mattia

last: Falcone


title: One year weight-loss intervention in healthy obese individuals at three time-points

city: Helsinki

first: Miina

last: Ollikainen

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Epigenome-wide analysis of healthy obese individuals during a one-year weightloss intervention

summary: Genome wide DNA methylation profiling of healthy obese individuals during a one-year weight loss intervention. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Adipose tissue biopsies were collected at three time points, baseline (T0), Fifth month (T1) and Twelfth month (T2).

overall_design: Bisulphite converted DNA from the adipose tissue biopsies of 19 healthy obese individuals at three time-points were hybridized to the Illumina Infinium HumanMethylation450 BeadChip

first: Kirsi

middle: H

last: Pietiläinen


title: The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation

status: Public on Nov 13 2017

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

country: USA

institute: Barnard College, Columbia University

type: Expression profiling by high throughput sequencing

sample_organism:
Homo sapiens
human gammaherpesvirus 4
human papillomavirus 31
Human gammaherpesvirus 8
Human papillomavirus 16


title: Expression data from adipose tissue of 19 healthy obese individuals at three time-points during one-year weightloss intervention

summary:
To understand the temporal changes occurring in adipose tissue gene expression during a one-year weightloss intervention, adipose tissue biopsies were collected from 19 healthy obese individuals at three time points.
We used microarrays to elucidate the gene expression changes occuring in adipose tissue during weightloss.

overall_design: Adipose tissue biopsies were collected from 19 obese healthy participants(Baseline (T0), fifth month (T1) and twelfth month (T2)) to understand the gene expression changes occurring in adipose tissue during weight loss.


title: Examining alterations in gene expression of LNCaP-Ctrl (PSMA +ve) vs LNCaP-KD (PSMA -ve) cells

status: Public on Nov 11 2017

city: Boston

first: Charalambos

last: Kaittanis

state: MA

address: 55 Fruit St, White 427

department: GCMI

institute: Massachusetts General Hospital

summary:
The biological role of PSMA, a biomarker expressed in prostate cancer and by the neovasculature of solid tumors, remains unknown. Although PSMA processes folates in our duodenum, and in the brain cleaves NAAG to control neuronal signaling, little is known about its role in cancer.
We used microarrays to detail the glonal perturbations in gene expression in the absence of PSMA, in order to identify disease-specific driving pathways that may lead to new therapies for cancer.

overall_design: LNCaP-Ctrl (PSMA +ve) cells grown on Petri dishes and in complete media where compared with LNCaP cells lacking PSMA (Platinum Select retroviral shRNA-mir platform DU53991)

first: Haley

last: Hieronymus


title: Comparison of Transcriptomic Platform for Analysis of Whole Blood from Ebola-Infected Cynomolgus Macaques

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

summary: Ebola virus disease (EVD) is a serious illness associated with 20-90% fatalities. EVD is characterized by robust virus replication and strong host inflammatory immune response. Analyzing the host immune response has increasingly involved multimodal approaches including transcriptomics to profile gene expression.  We studied cynomolgus macaques exposed to Ebola virus (EBOV) Makona via different routes with the intent of comparing RNA-Seq to a NanoString nCounter codeset targeting 769 non-human primate (NHP) genes. RNA-Seq analysis of serial blood samples showed different routes led to the same overall transcriptional response seen in previously reported EBOV-exposed NHP studies. Similar profiles were observed using the NanoString codeset. Both platforms displayed a strong correlation in gene expression patterns, thus cross-validating the two methods. This included a strong induction of innate immune response genes at early time points post-infection, and neutrophil-associated genes at later time points. Using data generated from either platform, we could deploy a 41-gene classifier to cluster samples by EBOV infection status. Finally, NanoString and RNA-Seq identified changes in circulating immune cell populations that matched traditional hematology. Together, these results show the complementarity of RNA-Seq and NanoString for gene expression analysis, verifying host biomarkers of infection, and predicting changes in cell types.

overall_design: Whole blood total RNA-seq analysis of 5 Cynomolgus macaques infected with Ebola variant Makona at three different doses and three different routes of infection.

first: Louis

middle: A

last: Altamura

first: Kirsten

last: Kulcsar

first: Sandra

middle: L

last: Bixler

first: Cynthia

last: Rossi

first: Randall

last: Scheopp

first: Elyse

last: Nagle

first: William

last: Aguilar

first: Christina

middle: E

last: Douglas

first: Korey

last: Delp

first: Timothy

middle: D

last: Minogue

first: Gustavo

last: Palacios

first: Arthur

last: Goff

first: John

last: Connor


title: Genome-wide RNA deep sequencing of CAL-101 or AKTi primed human T cells in comparison to traditionally expanded T cells

city: Charleston

first: Chrystal

middle: M

last: Paulos

address: 173 Ashley Avenue

institute: Medical University of South Carolina

summary: Differential expression patterns of total mRNA in traditionally expanded T cells (vehicle) compared to T cells expanded under drugs (AKT inhibitor and CAL-101)

overall_design: Comparison of transcriptional effects of two different drugs

first: Jacob

middle: S

last: Bowers

first: Bulent

last: Arman Aksoy

first: Jeff

last: Hammerbacher


title: Gene expression analysis of Drosophila WT and dDP-/- mutant larvae.

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

summary:
WT and dDP-/- mutant larvae RNAs were analyzed on Drosophila 12 x 135 Nimbelgen gene expression microarrays. dDP-/- mutants are described in Frolov et al., 2001. Genes Dev. Aug 15;15(16):2146-60. PMID: 11511545
The complete elimination of E2F/DP function in Drosophila results in upregulation of DNA damage responses. The net effect of E2F regulation in larval tissues is that all classes of E2F target genes are reppressed by E2F/DP complexes.

overall_design: Drosophila 12 x 135 Nimbelgen gene expression microarrays were prepared with triplicates of larval RNA from WT and dDP-/- mutant larvae.

first: Ana

last: Guarner

first: Michael

last: Korenjak

first: Myriam

last: Boukhali

first: Maria

last: Zappia

first: Capucine

last: Van Rechem

first: Johnathan

middle: R

last: Whetstine

first: Sridhar

last: Ramaswamy

first: Lee

last: Zou

first: Maxim

middle: V

last: Frolov

first: Wilhelm

last: Haas

first: Nicholas

last: Dyson


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [methylation_MOLM13_BCAT1-OE_20weeks]

first: Simon

last: Raffel

overall_design: MOLM13 cell lines were lentivirally transduced with an inducible BCAT1 overexpression construct and selected for transduced cells. Overexpression was induced with Doxycyclin for 20 weeks and cells were lysed and RNA was extracted.

first: Mattia

last: Falcone


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [methylation_HL60_BCAT1-OE_10weeks]

overall_design: HL-60 cell lines were lentivirally transduced with an inducible BCAT1 overexpression construct and selected for transduced cells. Overexpression was induced with Doxycyclin for 10 weeks and cells were lysed and RNA was extracted.


title: Profiling of microRNA expression in canine mammary cancer

city: Warsaw

first: Malgorzata

last: Bulkowska

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: MicroRNAs may act as oncogenes or tumour suppressor genes, which make these small molecules potential diagnostic/prognostic factors and targets for anticancer therapies. On account of this, we performed large-scale profiling of microRNA expression in canine mammary cancer.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Expression profiles of 317 microRNAs in 146 canine mammary tumours of different histological type, malignancy grade and clinical history (presence/absence of metastases) and in 25 control samples were evaluated.

first: Agata

last: Rybicka

first: Kerem

last: Senses

first: Katarzyna

last: Ulewicz

last: Witt

first: Joanna

last: Szymanska

first: Barlomiej

last: Taciak

last: Klopfleisch

first: Eva

last: Hellmén

first: Izabella

last: Dolka

first: Ali

middle: O

last: Gure

last: Mucha

first: Mariusz

last: Mikow

first: Slawomir

last: Gizinski

first: Magdalena

last: Krol


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [methylation_MOLM13_BCAT1-OE_10weeks]

last: Raffel

overall_design: MOLM13 cell lines were lentivirally transduced with an inducible BCAT1 overexpression construct and selected for transduced cells. Overexpression was induced with Doxycyclin for 10 weeks and cells were lysed and RNA was extracted.


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [methylation_HL60_BCAT1-OE_20weeks]

overall_design: HL-60 cell lines were lentivirally transduced with an inducible BCAT1 overexpression construct and selected for transduced cells. Overexpression was induced with Doxycyclin for 20 weeks and cells were lysed and RNA was extracted.

last: Falcone


title: Ileum Microarray Data from Transcriptomics Driven Lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism Study

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary:
Microbiome regulation of lipid metabolism
Germfree male C57BL/6J mice were purchased at 8 weeks of age from Charles River Laboratories (L'Arbresle, France). Mice were treated with 10^8 CFU/mL E. coli M8 strain (isolated from the feces of an ob/ob mouse) in drinking water for 14 days. At the end of the treatment, mice were subjected to an oral lipid tolerance test (OLTT) (with 6ml/kg of corn oil) after overnight fasting (14h). All mice were sacrificed 6 hours after the lipid tolerance test and ileum samples were collected for further analysis.

overall_design: In order to identify key pathways involved in microbiome regulation of lipid metabolism we took advantage of gnotobiotic preclinical models and an E. coli strain isolated from an obesity mouse model (Ob/Ob).

first: Anirikh

last: Chakrabarti

first: Mathieu

last: Membrez

first: Delphine

last: Morin-Rivron

first: Jay

last: Siddharth

first: Chieh

last: Chou

first: Hugues

last: Henry

first: Stephen

last: Bruce

first: Sylviane

last: Metairon

first: Bertrand

last: Betrisey

first: Carole

last: Loyer

first: Scott

last: Parkinson

first: Mojgan

last: Masoodi


title: RNA-seq analysis of in vivo differentiated and dedifferentiated mouse Schwann cells

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Schwann cells were acultely purified from intact nerves and the bridge and distal regions of transected nerves at different time-points following transection and sequenced to determine gene expression profiles of the differentiated and dedifferentiated state and its regulation by the wound microenvironment

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: The design comprises three independent packages: 1) Schwann cells sorted from 3 pooled nerves collected at day 6 post-injury for Intact, Distal and Bridge nerve regions (n=4 each). 2) 35 samples of Schwann cells sorted from single nerves for Intact nerves (n=5), Distal nerve regions (n=3 each ) at days 1, 2, 4, 6, 8, 10 post-injury, Bridge nerve regions (n=3 each) at days 4, 6, 8, 10 post-injury. 3) Rat Schwann cells in culture untreated (n=3) or treated with Tfgβ (n=3).

first: Simona

last: Parrinello

first: Samuel

last: Marguerat


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [expression_BCAT1-KD]

first: Simon

last: Raffel

overall_design: HL-60, SKM1 and MOLM13 cell lines were lentivirally transduced with shBCAT1 or shNT as control, transduced cells were FACS sorted 48 hrs after the transduction, cells were lysed and RNA was extracted

first: Mattia

last: Falcone


title: UTX guided neural crest function underlies craniofacial features of Kabuki Syndrome

status: Public on Nov 07 2017

city: Chapel Hill

first: Karl

middle: B.

last: Shpargel

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

summary: We report RNA-seq and ChIP-seq from flow-sorted E12.5 primary mouse neural crest from WT and UTX knockout embryos

overall_design: RNA-seq as well as H3K27me3, H3K4me3, and UTX ChIP-seq in WT and UTX knockout neural crest

middle: B

first: Terry

last: Magnuson


title: MicroRNA microarray of Haemonchus contortus lifecycle stages and gut tissue

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

summary:
Examined expression of microRNAs in different life-cycle stages and gut tissue of the pathogenic nematode Haemonchus contortus and identified differentially expressed miRNAs.
Custom array contained probes to 609 Haemonchus contortus miRNA sequence (all mature and start miRNAs identified by Winter et al., 2012, BMC Genomics13:4;  DOI: 10.1186/1471-2164-13-4)  and all C. elegans sequences in miRBase release 16

platform_organism:
Caenorhabditis elegans
Haemonchus contortus

overall_design: Three biological replicates were used for all stages and gut, except for L4 stage, where two were used. Parasites were Haemonchus contortus ISE(MHco3) strain

first: Collette

last: Britton

first: Neil

last: Marks

first: Alan

last: Winter

first: Henry

middle: Y

last: Gu

first: Kirsty

last: Maitland

first: Victoria

last: Gillan

first: Eileen

last: Devaney


title: Trigger-happy resident memory CD4+ T cells inhabit the human lungs.

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: Resident memory T-cells (TRM) reside in the lung epithelium and mediate protective immunity against respiratory pathogens. While lung CD8+ TRM have been extensively characterized, the properties of CD4+ TRM remain unclear. Here we determined the transcriptional signature of CD4+ TRM, identified by the expression of CD103, retrieved from human lung resection material. Various tissue homing molecules were specifically upregulated on CD4+ TRM, while expression of tissue egress and lymph node homing molecules were low. CD103+ TRM expressed low levels of T-bet, only a small portion expressed Eomes, and while the mRNA levels for Hobit were increased, protein expression was absent. On the other hand, the CD103+ TRM showed a Notch signature.  CD4+CD103+ TRM constitutively expressed high transcript levels of numerous cytotoxic mediators, which was functionally reflected by a fast recall response, magnitude of cytokine production, and a high degree of polyfunctionality. Interestingly, the superior cytokine production appears to be due to an accessible IFNγ locus and was partially due to rapid translation of preformed mRNA. Our studies provide a molecular understanding of the maintenance and potential function of CD4+ TRM in the human lung. Understanding the specific properties of CD4+ TRM is required to rationally improve vaccine design.

overall_design: Lung material was collected from non-cancerous lobectomy tissue of six patients with non-small cell lung carcinoma. Lung mononuclear cells where isolated after digestion of the partial or complete human lung resection material. Peripheral blood mononuclear cells were isolated from five healthy donors. Three populations were sorted from the lung, CD3+CD4+CD45RO+CD27-CD103+, CD3+CD4+CD45RO+CD27-CD103-, and CD3+CD4+CD45RO+CD27+CD103-. For the blood three populations were also sorted, CD3+CD4+CD45RA+CD45RO-CD27+ (memory), CD3+CD4+CD45RO+CD27+ (naive), CD3+CD4+CD45RO+CD27- (effector memory). RNA was isolated from the sorted cell samples. For the blood T cell naive, memory and effector memory subsets, RNA from five individually sorted samples was pooled. RNA from 24 samples (n=6 for the three lung T cell subsets; n=1 for the three blood T cell subsets, in duplicate) was hybridised on Illumina HumanHT-12 V4.0 microarrays. Four microarray samples were excluded after hybridization since their average signal was too low and one microarray was excluded after quality control using the arrayQualityMetrics R package.

first: Pleun

last: Hombrink

first: Anna

last: Oja

first: René

last: van Lier


title: Transcriptional profiling of Bacillus subtilis WT (ABS2005) and ydcH mutant (ASEC56)

status: Public on Nov 06 2017

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

summary: With these experiments we investigate the impact of the deletion of the ydcH gene on the transcriptomes of Bacillus subtilis strains ABS2005.

overall_design: Mutant and parental background of the strain were subjected to stranded RNA-Seq profiling in both exponential and stationary phase. A total of 12 biological samples were examined with triplicates for each condition.

first: Alba

last: De San Eustaquio-Campillo

first: Arnaud

last: Chastanet

last: Guérn


title: Role of Branched Chain Amino Acid Transaminase 1 (BCAT1) in Acute Myeloid Leukemia [hydroxymethylation_HL60_BCAT1-OE_12weeks]

first: Simon

last: Raffel

overall_design: HL-60 cell lines were lentivirally transduced with an inducible BCAT1 overexpression construct and selected for transduced cells. Overexpression was induced with Doxycyclin for 12 weeks and cells were lysed and RNA was extracted.

first: Mattia

last: Falcone


title: Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [ChIP-Seq]

city: Salt Lake City

first: Jay

last: Gertz

address: 2000 Circle of Hope Dr.

institute: University of Utah

summary: Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to impact gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that can prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor a binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine tune the expression of target genes.

overall_design: ChIP-seq was performed on Enhancer-I and control gRNA treated cells as well as parental Ishikawa lines

first: Julia

last: Carleton

first: Jason


title: Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

summary: Misincorporation of ribonucleotides into DNA during genome replication has recently become recognized as a significant source of genomic instability. The frequency of ribonucleotides in the genome is determined by dNTP/rNTP ratios, the ability of the DNA polymerases to discriminate against ribonucleotides, and by the capacity of repair mechanisms to remove misincorporated ribonucleotides. To simultaneously compare how the nuclear and mitochondrial genomes incorporate and remove ribonucleotides, we challenged these processes by imbalancing cellular dNTP pools. Using a collection of yeast strains with altered dNTP pools, we discovered an inverse relationship between the concentration of individual dNTPs and the amount of the corresponding ribonucleotides incorporated in mitochondrial DNA, while in nuclear DNA the ribonucleotide pattern was only altered in the absence of ribonucleotide excision repair. Our analysis uncovers major differences in ribonucleotide repair between the two genomes and provides concrete evidence that yeast mitochondria lack mechanisms for repair of misincorporated ribonucleotides.

overall_design: Mapping ribonucleotides in DNA from yeast that have unbalanced dNTP pools with HydEn-seq (5´end sequencing of genomic fragments generated by alkaline hydrolysis). The genomic DNA of these cells were also digested with the ristriction enzyme PmeI to allow for an estimation of the abosulte number of mitochondrial ribonucleotides in these lines.

first: Paulina

last: Wanrooij

first: Martin

middle: K

last: Engqvist

first: Josefin

last: Forslund

first: Clara

last: Navarrete

last: Karin Nilsson

first: Juhan

last: Sedman

first: Sjoerd

first: Anders

first: Andrei

last: Chabes


title: Expression profiling of MDA-MB-231 and MDA-MB-468 after ALDH1A3 manipulation, all-trans retinoic acid treatment, decitabine treatment

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

country: Canada

institute: Dalhousie University

summary: Retinoids, derivatives of vitamin A, are key physiological molecules with regulatory effects on cell differentiation, proliferation and apoptosis. As a result, they are of interest for cancer therapy. Specifically, models of breast cancer have varied responses to manipulations of the retinoid signaling cascade. This study characterizes the transcriptional response of MDA-MB-231 and MDA-MB-468 breast cancer cells to retinaldehyde dehydrogenase 1A3 (ALDH1A3) and to all-trans retinoic acid (atRA). We demonstrate limited overlap between ALDH1A3-induced gene expression and atRA-induced gene expression in both cell lines, suggesting that the function of ALDH1A3 in breast cancer progression extends beyond its role as a retinaldehyde dehydrogenase. Our data reveals divergent transcriptional responses to atRA, which are largely independent of genomic retinoic acid response elements (RAREs) and consistent with the opposing responses of MDA-MB-231 and MDA-MB-468 to in vivo atRA treatment. We identify transcription factors associated with each gene set. Manipulation of one of the transcription factors (i.e. interferon regulatory factor 1; IRF1) demonstrates that it is the level of atRA-inducible and epigenetically regulated transcription factors that determine expression of target genes (e.g. CTSS, cathepsin S). This study provides a paradigm for complex, combinatorial responses of breast cancer models to atRA treatment, and illustrates the need to characterize RARE-independent responses to atRA in a variety of models.

overall_design: Samples run in triplicate: MDA-MB-231 and MDA-MB-468 with or without ALDH1A3 expression; with or without atRA treatment; with or without decitabine treatment.

first: Krysta

last: Coyle

first: Selena

last: Maxwell

first: Margaret

last: Thomas


title: Profiling of the transcriptional response to all-trans retinoic acid in breast cancer cells reveals RARE-independent mechanisms of gene expression

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

overall_design: Refer to individual Series


title: Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers


title: DNA methylation profiling of MDA-MB-231 and MDA-MB-468 after ALDH1A3 manipulation, all-trans retinoic acid treatment, decitabine treatment


title: DNA hypermethylation enhanced telomerase reverse transcriptase expression in human induced pluripotent stem cells

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

summary: During reprogramming into human induced pluripotent stem cell (iPSCs), several stem cell marker genes are induced, such as OCT-4, NANOG, SALL4, and TERT. OCT-4, NANOG, and SALL4 gene expression can be regulated by DNA methylation. Their promoters become hypomethylated in iPSCs during reprogramming, leading to their induced expression. However, epigenetic regulation of the TERT gene remains unclear. In this study, we focused on epigenetic regulation of the human TERT gene and identified a differentially methylated region (DMR) at a distal region in the TERT promoter between human iPSCs and their parental somatic cells. Interestingly, the TERT-DMR was highly methylated in iPSCs, but low-level methylation was observed in their parental somatic cells. Region-specific, methylated-promoter assays showed that the methylated TERT-DMR up-regulated the promoter activity in iPSCs. In addition, Lamin B1 accumulated at the TERT-DMR in iPSCs, but not in their parent somatic cells. These results suggested that the TERT transcription was enhanced by DNA methylation at the TERT-DMR via binding to nuclear lamina during reprogramming. Our findings shed light on a new functional aspect of DNA methylation in gene expression.

overall_design: Bisulphite converted DNA from the samples were hybridized to the Illumina Infinium Human Methylation450K Beadchip

first: Ken

last: Takasawa

first: Yoshikazu

last: Arai

first: Mayu

last: Inoue-Yamazaki

first: Masashi

last: Toyoda

first: Hidenori

last: Akutsu

first: Koichiro

last: Nishino


title: The transcriptional response to unilateral nephrectomy with and without ischemia-reperfusion injury

status: Public on Nov 04 2017

city: Aarhus N

first: Casper

middle: Kierulf

last: Lassen

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University

summary:
Transcriptome analysis was done after warm renal ischemia-reperfusion injury (IRI) in a rat model. Earlier studies have shown a protective effect of prior unilateral nephrectomy (UNx) against IRI in the remaining, contralateral kidney compared to a non-neprectomized control group. We aimed at identifying the underlying molecular mechanisms. We used the Affymetrix Clariom D array (formerly known as RTA 1.0 st.)
Array data was processed in the Affymetrix Console Software.

overall_design: We analysed kidney tissue (left) from male Wistar rats. Number of animals from each group, n = 3. Wistar rats were randomized to either UNx or sham UNx immediately prior to 37 minutes of unilateral renal artery clamping or sham operation under sevoflurane anesthesia. Groups: sham (2 normal kidneys), UNx (1 remaining kidney), IR (1 ischemic kidney, 1 normal kidney), IR+UNx (1 ischemic kidney). MRI was performed 24 hours after reperfusion. Blood and renal tissue were harvested. RNA was isolated for microarray analysis.

last: Kierulf-Lassen

first: Per

last: Nielsen

first: Haiyun

last: Qi

first: Mads

last: Damgaard

first: Christoffer

last: Laustsen

first: Michael

last: Pedersen

first: Henrik

last: Birn

first: Rikke

last: Nørregaard

first: Bente

last: Jespersen


title: Whole larvae and nociceptive neuron RNA-Seq samples

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

summary: The goal of this study was to identify ion channels, specifically transient receptor potential cation channel A (trpA1) channels, that were highly expressed and enriched in nociceptive sensory neurons of Drosophila larvae. In class IV da sensory neurons, we find that TrpA1 is the most highly expressed trpA1 channel of the 14 trpA1 channels in Drosophila, and that its expression is highly enriched when compared to the whole animal transcriptome.

overall_design: Four biological replicates of 100 Drosophila melanogaster larval class IV dendritic arborization sensory neurons and five biological replicates of whole Drosophila melanogaster larvae were profiled by mRNA-Seq

first: Claire

last: Williams

middle: Z

first: Charles

middle: C

last: Kim


title: Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [RNA-Seq]

last: Gertz

overall_design: The effects of Enhancer interference (Enhancer-i) and control guide RNA treatment on the transcriptome before and after estrogen treatment, with 2 replicates per condition.

first: Julia

last: Carleton

first: Jason


title: PolyA RNA-seq from HCT116 (WT and CDK8as/as) cells in normoxia or hypoxia and treated with DMSO or 3MB-PP1

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: To determine the impact of CDK8 kinase activity on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (CDK8wt/wt and CDK8as/as) in the presence of absence of 3MB-PP1 to specifically inhibit analog senstitive (as) CDK8.

overall_design: PolyA RNA for two independent biological replicates was purified  from HCT116 cells (CDK8wt/wt and CDK8as/as) incubated in normoxic (ambient oxygen) or hypoxic (1% oxygen) conditions for 24 hrs and treated with DMSO or the ATP-analog 3MB-PP1, and was sequenced on the Ion Torrent Proton platform. Reads were aligned (GSNAP) to the human genome (hg19) and gene-level counts (HTseq-count) were used for differential expression analysis (DESeq2).

first: Ahwan

last: Pandey

first: Joaquín

last: Espinosa


title: ATAC-seq profiling of open chromatin in Arabidopsis thaliana shoot apical meristem stem cells and leaf mesophyll cells.

status: Public on Nov 03 2017

city: Atlanta

first: Roger

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: Cell differentiation is driven by changes in transcription factor (TF) activity and subsequent alterations in transcription. To study this processes, differences in TF binding between cell types can be deduced by methods that probe chromatin accessibility. Here we use cell type-specific nuclei purification followed by the Assay for Transposase Accessible Chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF-to-TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells of Arabidopsis thaliana. We found thousands of quantitative differences in chromatin accessibility between SAM stem cells and leaf mesophyll cells. Analysis of the genomic regions that were preferentially accessible in each cell type identified hundreds of overrepresented TF binding motifs, providing a list of TFs that may be important for each cell type. By focusing on TFs with evidence for differential expression between the cell types and physical interactions among themselves, we found evidence for extensive co-regulation of target genes by multiple TFs exclusively in each cell type. For example, a set of zinc-finger TFs appear to control a suite of growth- and development-related genes specifically in stem cells, while another TF set co-regulates genes involved in light responses and photosynthesis in mesophyll cells. Our analysis of chromatin accessibility differences between stem cells and differentiated mesophyll cells allowed us to identify TF-to-TF regulatory networks that are likely important in each cell type. This work further demonstrates the utility of of cell type-specific chromatin accessibility profiling to develop testable models of regulatory control during cell differentiation.

overall_design: ATAC-seq was performed on nuclei purified by INTACT affinity purification from Arabidopsis thaliana shoot apical meristem stem cells and leaf mesophyll cells. INTACT transgenics were CLV3p:NTF/ACT2p:BirA for labeling of stem cell nuclei and RbCSp:NTF/ACT2p:BirA for labeling of mesophyll nuclei. All ATAC-seq experiments were performed in three biological replicates.


title: Structural basis for the recognition of GC-motifs by Smad4 transcription factor

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

summary: ChIP-Seq analysis of Smad4 in differentiated embryonic stem cells revealed the enrichment of a GC-rich motif.

overall_design: In this dataset, results of Smad4 ChIP-Seq performed with two different antibodies are presented.

first: Qiaoran

last: Xi

first: Joan

last: Massagué


title: Blood-brain barrier transport and neuroprotective potential of blackberry-digested polyphenols: an in vitro study

city: Oeiras

first: Claudia

middle: Nunes

last: Santos

address: Av Republica, EAN

country: Portugal

institute: ITQB/IBET

summary:
Purpose: Epidemiological and intervention studies have attempted to link the health effects of a diet rich in fruits and vegetables with the consumption of polyphenols and their impact in neurodegenerative diseases. Studies have shown that polyphenols can cross the intestinal barrier and reach concentrations in the bloodstream able to exert effects in vivo. However, the effective uptake of polyphenols in the brain is still regarded with some reservations. Here we describe a combination of approaches to examine the putative transport of blackberry-digested polyphenols (BDP) across the blood-brain barrier (BBB) and ultimate evaluation of their beneficial effects.
Methods: BDP was obtained by in vitro digestion of blackberry extract and BDP major aglycones (hBDP) were obtained by enzymatic hydrolysis. Chemical characterization and BBB permeability of extracts were evaluated by LC-Orbitrap MS. BBB permeability and cytoprotection of both extracts was assessed in HBMEC monolayers. Neuroprotective potential of BDP was assessed in NT2-derived 3D co-cultures of neurons and astrocytes and in mouse cerebellar granule cells. Microarray analysis of BDP-modulated genes was evaluated in SK-N-MC cells.
Results: Components from BDP and hBDP proven to be BBB permeable. Physiologically-relevant concentrations of both extracts were cytoprotective at endothelial level and BDP revealed to be neuroprotective in advanced cell models. The major canonical pathways involved in the neuroprotective effect of BDP were unveiled, comprising mTOR signaling and the unfolded protein response pathway. Genes like ASNS and ATF5 emerged as novel BDP modulated targets.
Conclusions: BBB permeability of BDP and hBDP components reinforce the health benefits of a diet rich in polyphenols in neurodegerative disorders context. Our results suggest some novel pathways and genes that may be involved in the neuroprotective mechanism of the BDP polyphenol components.

overall_design: Microarray analysis was performed on SK-N-MC cells incubated with in vitro digested extracts of commercial blackberry (BB) or of wild blackberry - Rubus vagabundus (RV) for 24h, with or without post-incubation with a stress inducer - hydrogen peroxide (S) . Control SK-N-MC cells were also analyzed (C). This experiment was performed three times, so three independent biological replicates per treatment were included in the microarray analysis.

first: Inês

last: Figueira

first: Lucélia

last: Tavares

first: Carolina

last: Jardim

last: Costa

first: Ana

middle: P

last: Terrasso

first: Andreia

middle: F

last: Almeida

first: Coen

last: Govers

first: Jurrian

middle: J

last: Mês

first: Rui

last: Gardner

first: Jörg

last: Becker

first: Gordon

last: McDougall

first: Derek

last: Stewart

first: Augusto

last: Filipe

first: Kwang

first: Dora

last: Brites

first: Catarina

last: Brito

first: M

middle: A

first: Cláudia

middle: N


title: Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: Plasmacytoid dendritic cells (pDC) specialize in type I interferon production to coordinate innate and adaptive immunity. We identify two pDC subsets in vivo, evaluate their genome-wide expression, and demonstrate a developmental requirement for Bcl11a to provide insight into this enigmatic cell type.

overall_design: ChIP sequenicng was performed for a transcription factor of BCL11A in the Nalm6 B cell line and the Raji B cell line. Input was sequenced and used as a control.

first: Joseph

last: Dekker

first: Haley

last: Tucker

first: Vishy

last: Iyer


title: Estrogen signaling through Estrogen Receptor ⍺ alters lipid metabolism and promotes glomerulonephritis

city: Philadelphia

first: Roberto

last: Caricchio

state: PA

address: 3322 N. Broad Street

department: Medicine/Rheumatology

institute: Lewis Katz School of Medicine

summary:
Transcriptome analysis of RNA samples from glomeruli with and without functional ER⍺ duringnNephrotoxic serum-induced nephritis.
There is sex bias in SLE and lupus nephritis with a 9:1 women to men ratio. Timecourse microarray analysis of glomeruli isolated from kidneys during nephrotoxic serum-induced nephritis (NTN) reveled altered expression of genes related to lipid metabolism in WT females compared to ER⍺KO females.

overall_design: We analyzed glomerular extracts from the kidney cortices of 16 female mice (8 C57Bl/6 (B6), 8 B6.ER⍺KO) from 4 time-points after NTS injection: untreated, 18 hours, 6 days, 2 weeks.(2 mice per time point per strain)

first: Chelsea

last: Corradetti

first: Neelakshi

middle: R

last: Jog

first: Matteo

last: Cesaroni

first: Michael

last: Madaio


title: Fibrinogen activates BMP signaling in oligodendrocyte progenitor cells (OPCs) and inhibits remyelination after vascular damage [Rat_OPC_48h_Fibrinogen]

status: Public on Nov 02 2017

city: San Francisco

first: Mark

last: Petersen

address: 1650 Owens Street

institute: Gladstone Institutes

summary:
Determination of the mechanism by which fibrinogen, a central blood coagulation protein, regulates OPC functions and remyelination in the CNS.
We used microarrays to determine the genes involved in OPC responses to fibrinogen, which is deposited in the CNS after blood-brain barrier disruption.

overall_design: Primary rat OPCs were stimulated with fibrinogen for 48 hr and subjected to RNA extraction and hybridization on Affymatrix microarrays. Three unstimulated and three fibrinogen-stimulated samples were generated.

first: Katerina

last: Akassoglou


title: Fibrinogen activates BMP signaling in oligodendrocyte progenitor cells (OPCs) and inhibits remyelination after vascular damage [Rat_OPC_12h_Fibrinogen]

overall_design: Primary rat OPCs were stimulated with fibrinogen for 12 hr and subjected to RNA extraction and hybridization on Affymatrix microarrays. Three unstimulated and three fibrinogen-stimulated samples were generated.


title: Fibrinogen activates BMP signaling in oligodendrocyte progenitor cells (OPCs) and inhibits remyelination after vascular damage


title: Cold adaptation of tRNA nucleotidyltransferases: a tradeoff in activity, stability and fidelity

city: Leipzig

first: Felix

middle: Georg Maria

last: Ernst

address: Bruederstrasse 34

department: Faculty of Bioscience

institute: University of Leipzig

summary: CCA-adding enzymes are highly specific RNA polymerases that synthesize and maintain the sequence CCA at the tRNA 3‘-end. Here, we investigated the impact of cold adaptation on the reactivity and specificity of CCA-adding enzymes from psychrophilic bacteria. A comparative study of the corresponding enzymes from closely related psychro-, meso-, and thermophilic Bacillales indicates that the cold-adapted enzymes show a considerable error rate during CCA synthesis, resulting in additional incorporations of C and A residues. It seems that the activity of psychrophilic CCA-adding enzymes is not only achieved at the expense of structural stability, reaction velocity and substrate affinity, but also results in a reduced polymerization fidelity.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: in vivo tRNA from four Bacillales species was isolated from exponential and stationary growth phase each in triplicates resulting in a total of 24 samples. Sequencing libraries were created for small RNA species and sequenced on 3 runs of a MiSeq using 8 indices. Reads were analyzed regarding 3'-ends of tRNA and results summed up as a mean for the 8 conditions investigated. Results from B. subtilis were regarded as reference sample for a mesophilic Bacillales species. Differences towards psychophilic Planococcus halocryophilus and Exiguobacterium sibiricum and thermophilic Geobacills stearothermophilus were investigated.

middle: G

first: Frank

last: Juehling

first: Mario

last: Moerl


title: Long-term exposure of Mytilus galloprovincialis to Diclofenac, Ibuprofen and Ketoprofen: insights into bioavailbility, biomarkers and transcriptomic changes

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: Pharmaceutical compounds are emerging contaminants in aquatic environment due to their massive use (human and veterinary medicines, agriculture and aquaculture) and a limited removal by waste water treatment plants (WWTPs).  In this work, a representative determination of ecotoxicological potential of Ketoprofen s was studied in the sensitive bioindicator marine organism M. Galloprovincialis. Mussels were exposed, under regulated laboratory conditions, to Ketoprofen (KET) a, dosed alone at the realistic environmental concentration of 2.5µg/L for 14, 30 and 60 days. Gene expression analyses of Mytilus galloprovincialis exposed to KET have been performed trough a DNA microarray platform.

overall_design: Mussels Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater, at 18  ± 1 °C, 37 ? salinity, pH 7.5 ± 0.5 and oxygen saturation >94%. Mussels were distributed into three 17 L aquarium and exposed at 2.5µg/L to ketoprofen (KET) for 14, 30 and 60 days . All treatments were compared to control (CTRL) containing 0.00001% of methanol. Water was changed every other day and concentration of molecules were restored. Gene transcription analyses of 4 digestive glands pools (four pools for each treatment composed by 3 digestive glands; CTRL,  KET) were performed using a 8X60K Agilent oligo-DNA microarray platform GPL18667. Microarrays were synthesized in situ using the Agilent non-contact ink-jet technology including default positive and negative controls. Total RNA was isolated using Extract-all (Eurobio) procedure. RNA quality and integrity was controlled on the Agilent bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use. Gene expression profiling was performed using an Mytilus galloprovincialis oligo-DNA microarray of 59,971 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Marica

last: Mezzelani

first: Francesco

last: Regoli


title: Expression data from IMR90 cells expressing either E7-ca-STAT5A-shNTC vs E7-ca-STAT5a-shSOCS1 at 7 days post infection

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

summary: SOCS1 plays a role in cellular senescence. Knocking down SOCS1 in senescence induced by the STAT5 oncogene results in senescence bypass by preventing p53 activation

overall_design: IMR90 cells were infected with retroviral constructs of either E7 oncoprotein with pWZL ca-STAT5A and pLKO shNTC or E7 with pWZL ca-STAT5A and pLKO shSOCS1

first: Emmanuelle

last: Saint-Germain

first: Lian

last: Mignaca

first: Véronique

last: Bourdeau

first: Gerardo

last: Ferbeyre


title: Genome-wide maps of methylations in experimental lingual carcinogenesis

city: Kunming

first: XiaoMing

last: Dai

state: Yunnan

address: 293#,Xichang road

department: The maxillofacial service of the department of plastic surgery,

institute: The first affiliated hospital of Kunming Medical University

type: Methylation profiling by high throughput sequencing

summary: To identification of genome wide DNA methylation profiling during lingual tumorigenesis, tongue cancer was induced by oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L for 16weeks in C57BL/6J female mice. Nine samples of lingual mucosa from 0 (encoded as C in experiment), 12 (encoded as M in experiment) and 28 (encoded as E in experiment) week, which were supposed as normality, early and advanced stage during lingual tumorigenesis, were harvested for methylated DNA Immunoprecipitation sequencing. Illumina HiSeq 2000 was used to obtain DNA methylation profiles across 16023 CpG Islands including 26600 promoters and 21625 genebodies in murine tongue samples. Samples included 3 normal lingual mucosa,3 lingual mucosa with hyperplasia, mild and moderate dysplasia, 3 lingual mucosa with carcinoma in situ and invasive cancer.

overall_design: DNA from the 9 samples were fragmented and methylated DNA were  immunoprecipitated by anti-5-methylcytosine antibody. The samples were sequenced by Illumina HiSeq 2000.

first: Xiaoming

first: Hua

last: Liu


title: Chromatin interaction profiles at bivalent genes by multiplexed splinkerette 4C sequencing

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

institute: Kyoto University

summary: To examine chromatin interaction profiles around bivalent gene loci, we developed a multiplexed splinkerette Chromosome Conformation Capture Combined with high-throughput sequencing (ms4C-seq). By using ms4C-seq, we showed that bivalent gene loci tend to be colocalized in hiPSCs and that the colocalization requires PRC1, PRC2 and TrxG complexes that are the essential regulatory factors for maintenance of developmental genes in the transcriptionally poised state.

overall_design: Examination of chromatin interaction profiles for 89 bait loci on human iPSCs, and for 42 bait loci out of 89 bait loci on their original HFs, and those at 8 gene loci for hiPSC treated with shRNA against EED, WDR5 and RING1B. All experiments were performed in biological replicates.

first: H

last: Ikeda

first: T


title: A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR–Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single Drosophila homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: ChIP-seq/RNA-seq of various cell lines depleted for BRWD2 or COMPASS components

first: Marc

last: Morgan

first: Clayton

last: Collings


title: High-Throughput Drug Screening identifies Pazopanib and Clofilium tosylate as effective treatments for malignant rhabdoid tumors

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary: We used microarrays to compared gene re-expression of SMARCB1 in I2A SMARCB1-deficient rhabdoid tumor cell line.

overall_design: [human mRNA] 3 I2A SMARCB1-def cell line samples, 12 I2A SMARCB1-reexpressed cell line samples at 4 different times (3 at day2, 3 at day4, 3 at day7 and 3 at day14 after re-expression of SMARCB1)

first: Franck

last: Bourdeaut

first: Celine

last: Chauvin

first: Marie-Ming

last: Aynaud


title: Variations in diet type and temperature significantly affect the transcriptional profile of C. elegans

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

summary: The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20ºC on an Escherichia coli diet. Temperatures ranging from 15ºC to 25ºC or feeding with other species of bacteria are considered physiological lab conditions, but the effect of these conditions on the worm transcriptome have not been well characterized. Here, we compare the global patterns of gene expression for the reference Caenorhabditis elegans strain (N2) grown at 15oC, 20oC, and 25oC on two different diets, Escherichia coli and Bacillus subtilis. When C. elegans were fed E. coli and the growth temperature was increased, we observed an enhancement of defense response pathways and down-regulation of genes associated with metabolic functions. However, when C. elegans were fed B. subtilis and the growth temperature was increased, the nematodes exhibited a decrease in defense response pathways and an enhancement of expression of genes associated with metabolic functions. Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiologically accepted experimental range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome.

overall_design: C. elegans mRNA profiles at different temperatures and feeding in six samples, three replicates per sample. Deep sequencing in Illumina HiSeq2500.

first: Eva

last: Gomez-Orte

first: Eric

last: Cornes

first: Angelina

last: Zheleva

first: Beatriz

last: Saenz-Narciso

first: Maria

last: Iñiguez

first: Rosario

last: Lopez

first: Juan-Felix

last: San-Juan

first: Begoña

last: Ezcurra

last: Sacristan

first: Adolfo

last: Sanchez-Blanco

first: Julian

last: Ceron

first: Juan

last: Cabello


title: Non-canonical thyroid hormone signaling mediates cardiometabolic effects in vivo

status: Public on Nov 01 2017

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: Thyroid hormone (TH) and TH receptors (TRs) α and β act by binding to TH response elements (TREs) in regulatory regions of target genes. This nuclear signaling is established as the canonical pathway for TH action. In addition, however, TRs can activate intra-cellular second messenger signaling pathways. Whether such non-canonical TR signaling is physiologically relevant in vivo is unknown. Here we generated knock-in mice with a mutation in the TR DNA-binding domain that abrogates binding to DNA and TREs and leads to a complete loss of canonical TH action. We show that several important physiological TH effects are preserved despite disrupted DNA-binding, most notably heart rate, body temperature, blood glucose and triglyceride concentration, all of which were regulated by non-canonical TR signaling. Additionally, we confirm that TRE-binding defective TRβ leads to disruption of the hypothalamic-pituitary-thyroid axis with resistance to TH, while mutation of TRα causes a severe delay in skeletal development, showing TRE-mediated and tissue-specific canonical signaling. Our findings provide first in vivo evidence that non-canonical TR signaling exerts important cardiometabolic effects, which are clearly separated from canonical actions. Consequently, these data challenge the current paradigm that TH action is exclusively mediated through regulation of gene transcription at the nuclear level.

overall_design: Global H3K27ac ChIP-seq in livers of WT TR mice or mice with different TR mutations treated with T3 or control (PBS).

first: Majken

middle: S

last: Siersbæk

last: Moeller


title: Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Avenue

department: Center for Pediatric Biomedical Research

institute: University of Rochester

summary: Erythropoietin (EPO) and its receptor are highly expressed in the developing nervous system, and is exogenous EPO therapy is potentially neuroprotective, however the epigenetic and transcriptional changes downstream of EPO signaling in neural cells are not well understood. To delineate epigenetic changes associated with EPO signaling, we compared histone H3 lysine 4 dimethylation (H3K4me2) in EPO treated and control fetal neural progenitor cells, identifying 1,150 differentially bound regions. These regions were highly enriched near protein coding genes and had significant overlap with H4Acetylation, a mark of active regulatory elements.  Motif analyses and co-occupancy studies revealed a complex regulatory network underlying the differentially bound regions, including previously identified mediators of EPO signaling (STAT5, STAT3), and novel factors such as REST, an epigenetic modifier central to neural differentiation and plasticity, and NRF1, a key regulator of antioxidant response and mitochondrial biogenesis.  Global transcriptome analyses on neural tubes isolated from E9.0 EpoR-null and littermate control embryos validated our in vitro findings, further suggesting a role for REST and NRF1 downstream of EPO signaling. These data support a role for EPO in regulating the survival, proliferation, and differentiation of neural progenitor cells, and suggest a basis for its function in neural development and neuroprotection. The human sequencing data is not shared publicly due to privacy concerns, but is available from the investigators on request

overall_design: RNA-seq on Epo wildtype, heterozygotes and null neural tubes from E8.5 mouse embryos.

first: Jeffrey

last: Malik

first: Christina

last: Sollinger

first: Jacquelyn

last: Lillis


title: NRF2 Controls Endothelial Plasticity with miR-93

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

institute: University of Eastern Finland

summary: Here we studied the role of oxidized phospholipids in mediating phenotype switching of endothelial cells between quiescent and angiogenic states. Two oxPAPC datasets, a microRNA array and global run-on sequencing (GRO-seq), was combined with Nuclear factor erythroid 2-Related Factor 2 (NRF2) binding model to select candidate miRNAs for further studies. The pre-screening resulted in a selection of miR-106b~25 cluster for further studies. The cluster was shown to be both oxPAPC-responsive and NRF2-regulated, and its diagnostic and prognostic potential was investigated in pericardial fluid samples of heart failure and atherosclerosis patients. As the most abundant member of the cluster in both endothelial cells and pericardial fluid of atherosclerosis patients, miR-93-5p was selected for more detailed studies. RNA-seq from miR-93 overexpressing cells revealed significant changes in pathways related to angiogenesis. Together with NRF2, miR-93 was shown to control endothelial plasticity through regulation of the key players, namely Krüppel-like factor 2 (KLF2) for quiescence, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) for glycolysis, and Vascular Endothelial Growth Factor A (VEGFA), Forkhead box protein O1 (FOXO1) and MYC proto-oncogene protein (MYC) for growth and proliferation.The findings show that NRF2 and miR-93 control the activity of endothelial cells and mediate the effects of oxPAPC on endothelial activation, collectively providing novel mechanisms for the control of endothelial plasticity and oxPAPC response.

overall_design: Two samples. Human umbilical vein endothelial cells, control vs oxPAPC 6h

first: Suvi

middle: M

last: Kuosmanen

first: Anna-Liisa

last: Levonen


title: Biological Research in Canisters-16 (BRIC-16): Investigations of the plant cytoskeleton in microgravity with gene profiling and cytochemistry

city: Mountain View

first: NASA

last: GeneLab

address: Mail Stop N211

institute: NASA Ames Research Center

summary: These investigations studied the fundamentals of how plants perceive gravity and develop in microgravity. It informs how gene regulation is altered by spaceflight conditions.

overall_design:
transcription profiling by array
Microgravity/Weightlessness

first: John

last: Kiss

last: Johnson


title: Stress response of a marine ammonia-oxidizing archaeon N. maritimus SCM1 to copper

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

summary: We used transcription analyses to explore the whole cellular response of Nitrosopumilus maritimus strain SCM1 to varying  copper concentrations, and relate those patterns to its global proteome.

overall_design: RNA-seq was used to profile transcriptomics responses of N. maritimus induced by copper limitation and toxicity. Two replicates for Cu-limited and Cu-replete experiments and three replicates for Cu-toxic experiments were sequenced.

first: Wei

last: Qin

first: Shady

last: Amin

first: Willm

last: Marterns-Habbena

first: Neeraja

last: Vajrala

first: Daniel

last: Arp

first: Luis

last: Sayavedra-Soto

first: Nitin

last: Baliga

first: David

last: Stahl


title: ILC1 confer early host protection at initial sites of viral infection [ATAC-Seq]

city: New York

last: Leslie

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: We show that tissue-resident ILC1 serve a non-redundant early role in host immunity through rapid production of interferon (IFN)-γ following mouse cytomegalovirus (MCMV) infection.

overall_design: Comparative ATAC-seq analysis of innate and adaptive lymphocytes in the liver and spleen

first: Orr-El

last: Weizman

first: Tim

last: O'Sullivan

first: Colleen

last: Lau


title: Response of an alga-associated marine flavobacteria to polysaccharide degradation

city: Roscoff

first: Francois

last: Thomas

address: Place George Teissier

department: UMR8227, CNRS-UPMC

institute: Station Biologique de Roscoff

summary: Transcriptome analysis of Zobellia galactanivorans DsijT growing on algal polysaccharides or glucose as a sole carbon source.

overall_design: A total of 21 samples were analyzed, for 7 growth conditions in independent triplicates. Z. galactanivorans DsijT cells were grown in a marine minimum medium containing either alginate, laminarin, agar, porphyran, kappa-carrageenan or iota-carrageenan as a sole carbon source. Cultures with glucose as a sole carbon source were used as a reference.

first: François

first: Gurvan

last: Michel


title: Nitrosopumilus maritimus SCM1: exponential phase control vs. 24 hours starvation vs. 24 hours recovery after starvation

summary: Transcriptional profiling of marine ammonia oxidizing archaea Nitrosopumilus maritimus cells comparing exponential phase control cells with cells under 24 hours starvation and with cells under recovery after 24 hours starvation.  Goal was to determine the effects of global transcriptional responses of N. maritimus cells under ammonia starvation and recovery conditions.

overall_design: three-condition experiment, AS24 vs. ML cells & AR 24 vs. AS24. Biological replicates: 3 exponential control replicates, 3 AS24 replicates and 2 AR24 replicates.


title: Human umbilical vein endothelial cells (HUVECs): VEGF vs. ctrl, oxPAPC vs. ctrl

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

summary: MicroRNA profiling of human endothelial cells comparing VEGF and oxPAPC treated cells with their respective control-treated cells

overall_design:
HUVECs: VEGF vs. ctrl, oxPAPC vs. ctrl
Number of biological replicates: 3 per samples group

first: Kati

last: Pulkkinen

first: Anna-Liisa

last: Levonen


title: Sex-biased miRNA expression in mouse, opossum and chicken

city: Heidelberg

first: Maria

last: Warnefors

address: Center for Molecular Biology of Heidelberg University (ZMBH)

institute: University of Heidelberg

type: Non-coding RNA profiling by high throughput sequencing

summary: Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing dataset to analyse male and female miRNA expression profiles in mouse, opossum and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, especially in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalise male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.

sample_organism:
Gallus gallus
Mus musculus
Monodelphis domestica

overall_design: Small RNA sequencing of 72 tissue samples from mouse, opossum and chicken. Libraries were prepared with the NEXTflex Small RNA-Seq Kit (NF). For two of the samples, libraries were also prepared with the lllumina TruSeq Small RNA Library Prep Kit (IL) and the HD protocol (HD) developed by Sorefan et al, 2012 (DOI: 10.1186/1758-907X-3-4).

first: Katharina

last: Mössinger

first: Jean

last: Halbert

first: Tania

last: Studer

first: John

middle: L

last: VandeBerg

first: Isa

last: Lindgren

first: Amir

last: Fallahshahroudi

first: Per

last: Jensen

first: Henrik

last: Kaessmann


title: Comparison of gene expression between Hep3B tumors treated with sorafenib plus mouse-IFN treatment and those treated with sorafenib alone

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary:
In our experiments with a xenograft model, mouse-IFN (mIFN) treatment was suggested to exaggerate the antitumor effects of sorafenib on hepatocellular carcinoma in vivo.
We explored how mIFN enhances the in vivo antitumor effects of sorafenib.

overall_design: The gene expression profiles in developed Hep3B tumors receiving sorafenib plus mIFN treatment were compared with those noted in Hep3B tumors receiving sorafenib treatment alone in the mouse xenograft model.

first: H

last: Enomoto

first: L

last: Tao

first: R

last: Eguchi

first: A

last: Sato

first: M

first: S

last: Kaneko

first: Y

last: Iwata

last: Nishikawa

last: Imanishi

last: Iijima

first: T

last: Tsujimura

last: Nishiguchi


title: Transcriptomic analysis reveals mechanisms of leaf coloration between the leaf color mutant and normal green leaves in Ginkgo biloba

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We sequenced mRNA from the leaves of mutant and normal green leaves of Ginkgo biloba using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for leaf color variation of the mutant in Ginkgo biloba.

overall_design: Transcriptome sequencing in leaf color mutant and normal green leaves of Ginkgo biloba

first: Shunbo

last: Yang


title: The BET bromodomain inhibitor CPI203 overcomes resistance to ABT-199 (venetoclax) by downregulation of BFL-1/A1 in in vitro and in vivo models of MYC+/BCL2+ double hit lymphoma

city: Barcelona

first: Juan

middle: Garcia

last: Valero

state: Barcelona

address: Rosselló, 153

department: Oncology and haematology

institute: IDIBAPS

summary:
Double Hit Lymphoma (DHL) were treated with the BRD4 inhibitor 100 nM CPI203 for 6h
We used microarrays to uncover the mechanisms underlying CPI203 activity in Double Hit Lymphoma (DHL)

overall_design: Global RNA expression was done in three DHL cell lines and two DHL patients treated in vitro with CPI203 for 6h

first: Anna

middle: E

last: Arenys

first: Gaël

last: Roué


title: Enhancing the Potency of Mouse Embryonic Stem Cells [RNA-Seq]

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Mouse naïve pluripotent stem cells (ESC) can contribute to all embryonic tissues and the germline, but rarely to the extra-embryonic tissues in chimeric embryos. Here we describe a novel advanced pluripotent stem cell (ASC) with higher potency, since a single ASC contributes very efficiently to the fetus, germline, yolk sac and the placental labyrinth in chimeras. ASCs were derived from blastocysts in two steps in a chemically defined medium with Activin A (ActA) and basic fibroblast growth factor (bFGF), followed by Wnt and BMP. Notably, ASCs exhibit a distinct transcriptome with the expression of both naïve pluripotent genes, as well as mesodermal somatic genes; Eomes, Eras, Tdgf1, Evx1, hand1, Wnt5a, and distinct repetitive elements. Established ESCs can also be readily and directly to ASCs. Importantly, ASCs exhibit a stable hypermethylated epigenome unlike the hypomethylated epiblast in blastocysts and naïve ESCs, indicating that ASCs might represent a state in between the naïve and primed states of pluripotency.

overall_design: The RNA-seq libraries for this paper were constructed by using NEBNext Ultra Directional RNA Library Prep Kit from Illumina. After isolation of total RNA from bulk amount of mouse stem cells using RNeasy Micro Kit (QIAGEN), approximately 500ng total RNA was used to enrich mRNA with polyA tails by using NEBNext Magnetic Oligo d(T)25 beads. After RNA fragmentation and random priming, the first strand cDNAs and second strand cDNAs were synthesized, which was followed by end repair, dA-tailing, adapter ligation and PCR enrichment. The RNA-seq libraries were sequenced on HiSeq4000 platform.

first: Fuchou

last: Tang

first: Walfred

middle: W

first: Jingyun

last: Li

first: Lin


title: Enhancing the Potency of Mouse Embryonic Stem Cells

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

overall_design: Refer to individual Series


title: ILC1 confer early host protection at initial sites of viral infection

first: Christina

last: Leslie


title: Ovaries of PNA mice and controls

city: Nanjing

first: LEI

last: LEI

address: changle road 68#

department: Department of Obstetrics and Gynecology

institute: Nanjing First Hospital, Nanjing Medical University

summary: To investigate the etiology of the hyperandrogenic phenotype of polycystic ovary syndrome (PCOS), a prenatally androgenized (PNA) mouse model was validated and used for microarray analysis.

overall_design: 2 groups of samples were tested, with each group containing 5 mouse ovaries. Over 39,000 transcripts were analyzed with the GeneChip® Mouse Genome 430 2.0 Array by using the selection criteria of fold change ≥1.5. Transcripts whose fold change <1.5 are listed in the 'Normalized_Data' sheet of the 'DifferentialData.xlsx' file.

first: Lei

last: Lei

first: Lijun

last: Ding

first: Jing

last: Su

first: Mengyuan

last: Liu

first: Qingqing

last: Shi

first: Jianjun

last: Zhou

first: Haixiang

last: Sun

first: Guijun

last: Yan


title: GPR56/ADGRG1 inhibits Mesenchymal Differentiation and Radioresistance in Glioblastoma [GIC7]

status: Public on Oct 31 2017

first: Nuria

last: de la Iglesia

address: Rossello 153

summary: A mesenchymal transition occurs both during natural evolution of glioblastoma (GBM) and in response to therapy. However, the molecular mechanisms underlying mesenchymal differentiation are not well understood. We have found that the adhesion G protein-coupled receptor GPR56/ADGRG1 inhibits mesenchymal differentiation and radioresistance in glioblastoma stem-like initiating cells (GICs). Here, we have performed microarray analysis of parental- versus GPR56 knockout-GICs to identify gene expression changes upon GPR56 knockout

overall_design: To interrogate the effect of GPR56 loss on the transcriptome of glioma initiating cells (GICs) we compared the gene expression profile of parental- and GPR56 knockout-GICs by genome-wide microarray analysis. Patient-derived GICs (parental and KO5) were cultured under adherent conditions on laminin in serum-free neural stem cell medium (in the presence of bFGF and EGF) at 37°C, 5% CO2 and 5% oxygen. Total RNA was extracted, labeled and hybridized in a SurePrint G3 Human GE 8x60k array (Agilent Technologies). Four paired biological replicates of each parental- and GPR56 knockout-GICs were used

first: Núria


title: Expression data from human CD8+ T cell subsets, defined using CD27 and CD45RA

city: London

first: Sian

last: Henson

address: Charterhouse Square

institute: QMUL

summary:
CD27 and CD45RA can be used to split T cells into 4 subsets, naïve cells, CD27+CD45RA+, central memory cells CD27+CD45RA-, effector memory cells CD27-CD45RA-, effector memory CD45RA re-expressing cell, CD27-CD45RA+. It is with in this final EMRA subset that it is belived the senenscent T cells reside. Cellular senescence is accompanied by a senescence-associated secretory phenotype (SASP), to date a SASP has not been demonstrated in T cells.
We used microarray analysis to show primary human senescent CD8+ T cells also display a SASP comprising of chemokines, cytokines and extracellular matrix remodelling proteases. We also wanted to investigate whether p38MAPK regulated the SASP seen in EMRA T cells.

overall_design: Heparinised peripheral blood samples were taken from healthy volunteers (age range: 32-55 n = 6). Healthy was taken as individuals who had not had an infection or immunisation within the last month, no known immunodeficiency or any history of chemotherapy or radiotherapy, and were not receiving systemic steroids within the last month or any other immunosuppressive medications within the last 6 months.

first: Arne

last: Akbar


title: Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma

first: Sean

last: Maden

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

summary: Our analysis reveals an extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes. Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE and EAC progression.

overall_design: Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA).

first: Georg

last: Luebeck

first: Kit

last: Curtius

first: William

last: Hazelton

first: Ming

last: Yu

first: Prashanthi

last: Thota

first: Deepa

last: Patil

first: Amitabh

last: Chak

first: Joseph

last: Willis

last: Grady


title: Analysis of gene expression in control, Hic1 KO and p53 KO mouse embrynoic fibroblast (MEF) cell lines II

city: Clayton

first: Jason

last: Cain

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: We hypothesised that genetic inactivation of the transcriptional repressor Hic1, would lead to changes in gene expression that may lead to transformation. We assessed changes in gene expression in immortal MEF cell lines in which Hic1 or p53 was inactivated.

overall_design: Total RNA from was collected from immortal Hic1 KO and p53 KO MEF cell lines. A minimum number of 3 cell lines for all genotypes was collected.

first: Anette

last: Szczepny

first: Kirstyn

last: Carey

first: Lisa

last: McKenzie

first: W

last: Jayasekara

first: Fernando

last: Rosello

first: Alvaro

last: Gonzalez-Rajal

first: Andrew

last: McCaw

first: Dean

last: Popovski

first: Die

last: Wang

first: Anthony

last: Sadler

first: Annabelle

last: Mahar

first: Prudence

last: Russell

first: Gavin

last: Wright

first: Rachael

last: McCloy

first: Daniel

last: Garama

last: Gough

first: Stephen

middle: B

last: Baylin

last: Burgess

first: D

last: Watkins


title: Haploid embryonic stem cells

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Mammalian haploid embryonic stem cells (haESCs) provide new possibilities for large-scale genetic screens because they bear only one copy of each chromosome. However, haESCs are prone to spontaneous diploidization through unknown mechanisms. Here, we report that a small molecule combination could restrain mouse haESCs from diploidization by impeding exit from naïve pluripotency and by shortening the S-G2/M phases. Combined with 2i and PD166285, our chemical cocktail could maintain haESCs in the haploid state for at least five weeks without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Taken together, we established an effective chemical approach for long-term maintenance of haESCs, and highlighted that proper cell cycle progression was critical for the maintenance of haploid state.

overall_design: RDF cocktail vs. DMSO control

first: Haisen

last: Li

first: Ao

last: Guo

first: Zhenfei

last: Xie

first: Wanzhi

last: Tu

first: Jiali

last: Yu

first: Huihan

first: Jian

last: Zhao

first: Cuiqing

last: Zhong

first: Jiuhong

last: Kang

first: Jinsong

first: Shichao

last: Huang


title: A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs


title: Müller glial microRNAs are required for the maintenance of glial homeostasis and retinal architecture

first: Stefanie

last: Wohl

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

summary:
In order to identify the miRNAs in adult Dicer1-CKO Müller glia of the neural retina, we isolated the Müller glia from Rlbp-CreER: Stopf/f-tdTomato/Dicerf/f mice by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies®.
miRNA expression of Dicer1-CKO Müller glia was compared to wild type Müller glia (a re-analyzed sample from GSE94759). We found that all highly expressed miRNAs declined in the Dicer-CKO leading to a disruption in retinal architecture over time.

overall_design:
Fluorescence activated cell sorting (FACS) was used to purify adult Müller glia (pooled from 26 retinas, > postnatal day 21), using an Müller glia specific cre-lox labeling strategy by crossing Rlbp1-CreER:tdTomato mice with Dicer1f/f mice. The RNA was extracted from purified Müller glia (tdTomato+) and miRNA expression was analysed using NanoString and nCounter Technologies ®.

This work was funded by these additional grants:

Grant Number: Wo 2010/1-1
Source: DFG scholarship for S.G. Wohl, German Research Foundation (DFG)

Grant Number: TA-RM-0614-0650
Source: for  T.A. Reh, Foundation Fighting Blindness (FFB)

Grant Number: P30EY01730
Source: Vision Core Grant for the use of imaging facilities

first: Nikolas

last: Jorstad

first: Edward

last: Levine

first: Thomas

last: Reh


title: LMO2 Is Required for TAL1 DNA Binding Activity and Initiation of Definitive Haematopoiesis at the Haemangioblast Stage

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: We differentiated  WT, LMO2KO or TAL1 KO mouse ES cell lines into Flk-1+ haemangioblasts and/or Tie2+;Kit+;CD41- haemogenic endothelium 1 (HE1). We performed RNAseq, ChIPseq and/or DHS seq on these cells and compared the samples. Our study showed that Lmo2-/- embryonic stem cells differentiated less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. LMO2 was required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, TAL1 protein levels were low and the target site recognition of TAL1 was impaired.

overall_design: RNAseq (paired end) of WT, LMO2KO or TAL1KO Flk-1+ haemangioblasts in triplicates and  WT, LMO2KO Tie2+;Kit+;CD41- haemogenic endothelium 1 (HE1) in duplicate. ChIPseq, using aLMO2, aTAL1, aLDB1 antibodies, of WT, LMO2KO Flk-1+ haemangioblasts in duplicates. DHSseq on WT, LMO2KO Flk-1+ haemangioblasts.

first: Vesna

last: Stanulovic


title: Analysis of gene expression in control, Hic1 KO and p53 KO mouse embrynoic fibroblast (MEF) cell lines I

first: Jason

last: Cain

summary: We hypothesised that genetic inactivation of the transcriptional repressor Hic1, would lead to changes in gene expression that may lead to transformation. We assessed changes in gene expression in pre-immortal MEF cell lines in which Hic1 was inactivated compared to controls.

overall_design: Total RNA from pre-immortal ESRCre;Hic1lox/lox and control MEF lines at P2 cultured with (or without out) 500nM tamoxifen for 24 hours was collected following a further 48 hour incubation period. A minimum number of 3 cell lines for all genotypes was collected.

first: Anette

last: Szczepny

first: Kirstyn

last: Carey

first: Lisa

last: McKenzie

first: W

last: Jayasekara

first: Fernando

last: Rosello

first: Alvaro

last: Gonzalez-Rajal

first: Andrew

last: McCaw

first: Dean

last: Popovski

first: Die

last: Wang

first: Anthony

last: Sadler

first: Annabelle

last: Mahar

first: Prudence

last: Russell

first: Gavin

last: Wright

first: Rachael

last: McCloy

first: Daniel

last: Garama

last: Gough

first: Stephen

last: Baylin

last: Burgess

first: D

last: Watkins


title: The Tumor Suppressor Hic1 Maintains Chromosomal Stability Independent of Tp53

first: Jason

last: Cain


title: MiR-471-5p–Dependent Regulation of Phagocytosis/Autophagy-Associated Proteins

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Phagocytic clearance of apoptotic germ cells by Sertoli cells is vital for germ cell development and differentiation. Using a tissue-specific miRNA transgenic mouse model, we show that interaction between miR-471-5p and autophagy member proteins regulates clearance of apoptotic germ cells via LC3-associated phagocytosis (LAP).

overall_design: Ago2 immuno-precipitation profiles of miR-471-5p–transfected Sertoli cells compared to those of scramble-transfected Sertoli cells

first: Subbarayalu

last: Panneerdoss

first: Majeet

last: Rao


title: Transcriptomic analysis of the role of the RasGEF1B circular RNA in the TLR4/LPS pathway

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Circular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. However, the detailed functional significance of the vast majority of them remains to be elucidated. Most functional characterization studies targeting circRNAs have been limited to resting cells, leaving their role in dynamic cellular responses to stimuli largely unexplored. In this study, we focus on the LPS-induced cytoplasmic circRNA, mcircRasGEF1B, and combine targeted mcircRasGEF1B depletion with high-throughput transcriptomic analysis to gain insights into its function during the cellular response to LPS stimulation. We show that knockdown of mcircRasGEF1B results in altered expression of a wide array of genes. Pathway analysis revealed an overall enrichment of genes involved in cell cycle progression, mitotic division, active metabolism, and of particular interest, NF-?B, LPS signaling pathways and macrophage activation. These findings expand the set of functionally characterized circRNAs and support the regulatory role of mcircRasGEF1B in immune response during macrophage activation and protection against microbial infections.

overall_design: RNA-seq of wild-type and mcircRasGEF1B knock-down macrophages with and without LPS stimulation

first: Wei

last: Ng

middle: K

first: Chee-Kwee

last: Ea


title: Impact of TLR7 on Salmonella enterica serovar Typhimurium (STM) infection of bone marrow-derived macrophages (BMDMs)

first: Michael

middle: Paul

last: Gantier

state: VIC

address: Hudson Institute of Medical Research

department: Centre for Innate Immunity and Infectious Diseases

summary: BMDMs from congenic TLR7 KO mice and WT mice were infected with STM and analysed for gene expression at 24 h post infection.

overall_design:
Each sample is from one mouse. Samples 1-2 originate from a different infection experiment from samples 3-7.
Each sample was analysed on Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray.

middle: P

first: Di

last: Wu


title: ASXL3 is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

summary: In order to investigate epigenetic mechanisms contributing to stemness/pluripotency in lung cancers and potentially identify novel therapeutic targets in these malignancies, induced pluripotent stem cells (iPSCs) were generated from normal human small airway epithelial cells (SAEC) by lentiviral transduction of Oct4, SOX2, KLF4, and MYC (Yamanaka factors). The lung iPSC (Lu-iPSC) exhibited hallmarks of pluripotency including morphology, surface antigen and stem cell gene expression, in-vitro proliferation, and teratoma formation. Additionally, Lu-iPSC exhibited no chromosomal aberrations, complete silencing of reprogramming transgenes, genomic hypermethylation, up-regulation of genes encoding components of polycomb repressive complex 2 (PRC2), hypermethylation of stem cell polycomb targets, and modulation of more than 15,000 other genes relative to parental SAEC. Additional Sex Combs Like-3 (ASXL3), encoding a PRC2 associated protein not previously described in reprogrammed cells, was markedly up-regulated in Lu-iPSC as well as human small cell lung cancer (SCLC) lines and specimens. ASXL3 over-expression correlated with increased genomic copy number in SCLC lines. Knock-down of ASXL3 inhibited proliferation, clonogenicity, and teratoma formation by Lu-iPSC, and significantly diminished in-vitro clonogenicity and growth of SCLC cells in-vivo. Collectively, these studies highlight the potential utility of this Lu-iPSC model for elucidating epigenetic mechanisms contributing to pulmonary carcinogenesis, and suggest that ASXL3 is a novel target for SCLC therapy.

overall_design: DNA methylation experiment on Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA. USA) was performed as described previously. Briefly, DNA was isolated using QIAamp DNA Mini Kit (Qiagen #51304) and treated with bisulfite using EpiTect Bisulfite Kit (Qiagen). Efficiency of methylation level was measured by Illumina Infinium methylation assays (Illumina).  The raw data file “FinalReport.txt” generated from Illumina “GenomeStudio” (Illumina) was normalized with “Simple Scaling Normalization” (SSN) method implemented in the “lumi” R package following the color-bias adjustment. Two files were produced, one with beta value for individual target and another one with corresponding “M” values for the beta values. The file with “M” values was used for statistical analysis with FDR<0.05 (adjusted based on Benjamini-Hochberg procedure) as significant cutoff unless otherwise indicated, and also the absolute beta value difference greater than 0.2 from the same contrast comparison was applied. Partek Genomics Suite (Partek Inc.), R packages of lumi, methlumi and also other related R packages were used for data processing, analyzing and data presentation.

first: Vivek

last: Shukla

first: Yonghong

last: Wang


title: Characteristics and localization of prospective fibroblast subpopulations isolated from the mouse lung

city: Hamamatsu city

first: Toshihide

last: Iwashita

state: Shizuoka

address: 1-20-1 Handayama, Higashi-ku

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

summary: By fluorescence-activated cell sorting, we classified lung fibroblasts highly expressing Pdgfra into three subpopulations, Sca-1highThy-1low (A-type), Sca-1highThy-1high (B-type), and Sca-1lowThy-1low (C-type). We then performed microarray analysis to identify specific genes for each subpopulation.

overall_design: To obtain fibroblast subpopulations, pulmonary single cells (Pu) were incubated with antibodies against lineage-specific cell surface markers (CD31, CD45, CD146, Lyve-1, TER119, and E-Cadherin), Pdgfra, Sca-1, and Thy-1. 50,000 cells of subpopulations (A-, B-, and C-type fibroblasts) in addition to Pu were isolated, and then RNA was extracted from each population and amplified for the gene expression comparison.

first: Sayomi

last: Matsushima