title: Expression profile comparison of African American and American Caucasian esophageal squamous epithelium from subjects with and without Barrett's Esophagus

city: Ann Arbor

first: Derek

middle: John

last: Nancarrow

state: MI

address: 1500 E. Medical Center Dr.

department: Department of Surgery

institute: University of Michigan

summary: Histologically normal biopsies of the esophageal squamous epithelium were collected from consented individuals of either African American (AA) or American Caucasion (Cau) ethnicity. Total RNA was extracted and used to generate Affymetrix expression array profiles. For each racial group collected samples were either controls (no history of BE or EAC) or those with a history of BE (Barrett's Esophagus) and/or EAC (esophageal adenocarcinoma). This allowed us to identify gene with tissue specific expression differences between the two racial groups, as well as those that differed between control and disease groups.

overall_design: RNA was extracted from histologically normal squamous mucosa arising within the tubular esophagus above the gastrointestinal junction. Specimens were either collected as biopsies during upper GI endoscopy or as material collected at the time of tumor resection. Samples were processed for hybridization to Affymetrix Human Gene 2.1 ST arrays. Samples were collected from individuals self-identified as either AA or Cau, who had no history of BE or EAC (controls), or those diagnosed with BE and/or EAC. The array data includes 12 AA and 12 Cau controls, as well as 8 AA and 8 Cau diagnosed with BE/EAC.

first: Daysha

last: Ferrer-Torres

middle: J

first: Marcia

last: Canto

first: Joel

middle: H

last: Rubenstein

first: Amitabh

last: Chak

first: Andrew

last: Chang

first: David

last: Beer


title: Transcriptomic analysis of in vitro cultured horizontal basal cells of the murine olfactory epithelium

status: Public on Feb 01 2019

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

country: USA

institute: Tufts University

type: Expression profiling by high throughput sequencing

summary: We report bulk RNAseq of in vitro cultured horizontal basal cells, and in vivo isoalted respiratory basal cells of the murine olfactory epithelium, and compared their profiles with pre-existing bulk RNAseq of in vivo isolated HBCs and single cell RNAseq of in vivo HBCs.

overall_design: RNAseq of in vitro horizontal basal cells (HBCs) in triplicate under control conditions, and FACS isolated in vivo respiratory basal cells in singlet

first: Jesse

middle: N

last: Peterson

first: James

middle: E

last: Schwob


title: Gene expression data from human bronchial epithelial cell lines: comparison between normal and CFTR-deficient cells

status: Public on Jan 31 2019

city: Kumamoto

first: Tsuyoshi

last: Shuto

state: Kumamoto

address: 5-1 Oe-honmachi, Chuo-Ku

department: Molecular Medicine

country: Japan

institute: Graduate School of Pharmaceutical Sciences, Kumamoto University

summary:
Whole transcriptional analysis of normal 16HBE14o- cells, cystic fibrosis (CF) patients-derived CFBE41o- cells, and WT-CFTR-rescued CFBE41o- cells.
We utilized the gene expression data to understand the transcriptional regulation underlying the loss of CFTR function.

overall_design: The human bronchial epithelial cell lines were used for RNA extraction and hybridization on Affymetrix HTA2.0 microarray. One replicate per array.

first: Shunsuke

last: Kamei


title: Long intergenic non-coding RNA linc-SUMF1-2 mediates CFTR-associated transcriptional regulation in human airway epithelia

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

overall_design: Refer to individual Series


title: The Anaphase Promoting Complex/Cyclosome degrades DMS3 to maintain RNA-directed DNA Methylation in Arabidopsis

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing


title: Gene expression data in linc-SUMF1-2 knockdown human bronchial epithelial cells

summary:
Whole transcriptional analysis of cystic fibrosis (CF) patients-derived CFBE41o- cells under the linc-SUMF1-2 knockdown condition.
We utilized the gene expression data to understand the linc-SUMF1-2 function in CF bronchial epithelial cells.

overall_design: The linc-SUMF1-2 antisense oligonucleotide (ASO)-treated CFBE41o- cells were used for RNA extraction and hybridization on Affymetrix HTA2.0 microarray. One replicate per array.


title: The Anaphase Promoting Complex/Cyclosome degrades DMS3 to maintain RNA-directed DNA Methylation in Arabidopsis [small RNA-seq]

summary: RNA-directed DNA methylation (RdDM) plays an essential role in transposable element (TE) silencing in plants. In the Arabidopsis RdDM pathway, the DDR complex containing DRD1, DMS3, and RDM1, is necessary for recruiting Pol V to transcribe scaffold RNA. Although the role of DDR is known, the mechanism by which the DDR complex is regulated remains unexplored. Here, we demonstrate that the Anaphase Promoting Complex/Cyclosome (APC/C) monitors the assembly of the DDR complex by targeting DMS3 for degradation. We show that a subset of Pol V-dependent RdDM loci are de-repressed in apc/c mutants, accompanied by defective recruitment and transcription of Pol V. APC/C targets DMS3 for ubiquitination and degradation in a D box-dependent manner, and the D-box-mutated DMS3 fails to complement the dms3 mutant. Competitive binding assays shows that the dosage of DMS3 is critical for the assembly of the DDR complex, and in vivo gel filtration analysis shows that the assembly of both DDR and Pol V is compromised in the apc8 mutant. These findings uncover a safeguard role of APC/C-mediated DMS3 degradation in the assembly of the DDR complex, and provide a direct link between selective protein degradation and RdDM.

overall_design: Illumina sequencing of duplicate small RNA libraries from inflorescences

first: Binglian


title: Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming I

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: We collected single or duplicate samples at the various time points, generated single cell suspensions and performed scRNA-Seq. We also collected samples from established iPSC lines reprogrammed from the same MEFs, maintained in either 2i or serum conditions. Overall, we profiled 68,339 cells to an average depth of 38,462 reads per cell. After discarding cells with less than 1,000 genes detected, we retained a total of 65,781 cells, with a median of 2,398 genes and 7,387 unique transcripts per cell.

overall_design: We collected scRNA-seq profiles of 65,781 cells across a 16-day time course of iPSC induction, under two conditions

first: Jian

last: Shu


title: The Anaphase Promoting Complex/Cyclosome degrades DMS3 to maintain RNA-directed DNA Methylation in Arabidopsis [lncRNA-seq]

overall_design: Illumina sequencing of duplicate lncRNA libraries from 14-day-old seedlings


title: A microRNA profile of saliva and role of miR-375 in Haemaphysalis longicornis (Ixodida: Ixodidae)

city: Shanghai

first: Muhammad

middle: Irfan

last: Malik

state: China

address: 518 Ziyue Rd,

department: Shanghai Veterinary Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: Tick saliva contains many bioactive molecules that are involved in attachment to the host, blood feeding and transmission of pathogens. MicroRNAs (miRNAs) are a class of short non-coding RNAs with a length of 19-24 nucleotides. They act as regulators of gene expression by binding to their target mRNA at the post-transcriptional level and control a variety of cellular functions, including regulation of growth, metabolism, and development. The detection and characterizations of miRNAs from tick saliva may help explain the molecular mechanisms involved in the interaction between ticks, pathogens, and hosts. They may also contribute to the discovery of vaccines, which can control ticks and the pathogens they transmit. An RNA library was generated from the saliva of fed adult Haemaphysalis longicornis ticks, and it contained 17.4 million clean reads of 18-30 nucleotides. Overall, 319 known miRNAs and 1 novel miRNA were found. The 10 most abundantly expressed miRNAs present in tick saliva were miR-100_2, miR-315, miR-184_1, miR-100-5p_2, miR-5307, miR-184-3p_3, Let-7-5p_6, miR-71_5, miR-1-3p_6, and miR-10-5p_2. The miR-375, one of the abundantly expressed, was subjected to Quantitative Real-Time PCR analysis (qRT-PCR) in various tick developmental stages, as well as in different tissues isolated from adult ticks. The expression of miR-375 in different tick development stages was highest in unfed nymphs and lowest in the egg stage. In the tissues of adult ticks, miR-375 was most highly expressed in the salivary gland. To investigate the possible role of miR-375, Ant-375 was used to inhibit the miR-375. Treated group (Ant-375) had a reduced number of eggs (t(10)= 2.652, P=0.0242), eggs that were partially desiccated, and reduced egg hatchability (t(10)=2.272, P=0.044) compared to Ms-Ant and the non-injected control. This is the first study to investigate the miRNAs profile in tick saliva and the role of miR-375 in H. longicornis. The identification and characterization of miRNA in tick saliva may help to reveal the molecular mechanisms of interactions among ticks, pathogens, and hosts and suggest new vaccine strategies to control tick borne diseases.

overall_design: Construction of the small RNA (sRNA) library from the saliva of fed adult H. longicornis, using Hiseq technology and their role in H. longicornis

middle: I

first: Mohsin

last: Nawaz

first: Ibrahim

middle: A

last: Hassan

first: Houshuang

last: Zhang

first: Haiyan

last: Gong

first: Jie

last: Cao

first: Yongzhi

last: Zhou

first: Jinlin


title: Analysis of Transcript Abundance in white, intermediate, and opaque cell states from WT and EFG1 heterozygotes in Candida albicans

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

summary: The ability to undergo heritable switching between cell states is well recognized in microbial species.  In the human fungal pathogen Candida albicans, cells can stably exist in several alternative states that show differential interactions with the mammalian host.  Here, we demonstrate that gene dosage of the master transcription factor, Efg1, controls access to distinct cell states in diploid C. albicans cells.  Thus, cells that are hemizygous for EFG1 can stably differentiate into a cell state that is not available to cells with two functional copies of the EFG1 gene.  Strikingly, we reveal that a number of clinical isolates of C. albicans encode polymorphisms that produce a hemizygous EFG1 genotype and that this enables access to the novel cell state.  Furthermore, we show that C. albicans cells in different cell states each exhibit unique interactions with the mammalian host, with consequences for both commensalism and pathogenesis.

overall_design: Three biological replicates were performed for each strain-condition.  Controls were included for WT cells in the white and opaque states from an MTL matched a/a strain (matched to strains 7021-7023 and 7057-7059).  SN78 serves as a white control set for 7064 and 7065.

first: Shen-Huan

last: Liang

first: Matthew

middle: Z

last: Anderson

first: Joshua

middle: M

last: Wang


title: Mechanistic insights into allele-specific properties of inter-chromosomal contacts

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: The eukaryotic nucleus not only encloses meters of DNA, but also requires DNA to be differentially packaged in a cell-specific manner. Advances in chromosome-capture techniques have made great progress in understanding intra-chromosomal interactions. Yet, the mechanistic identities of homologous or non-homologous inter-chromosomal contacts (HCCs or NHCCs) remain elusive. Recently, two long non-coding RNA loci, CISTR-ACT and FIRRE, have been observed at NHCCs and implicated in human disease. Based on single nucleotide polymorphisms (SNPs), we developed an allele-specific CRISPR live-cell DNA imaging technique, named SNP-CLING, to describe primary locus characteristics across space and time. We observed allele-specific gene positioning, frequencies of HCCs or NHCCs, their motility and stability, and their positioning at the distinct sub-nuclear compartment of the nucleolus. Collectively, we define allele-specific locus properties and dynamics, and uncover an important new layer of genome organization in live cells.

overall_design: Allele-specific Hi-C in 129xCast mouse embryonic fibroblasts

first: Philipp

middle: G

last: Maass

first: A

middle: R

first: David

last: Shechner

first: Catherine

middle: L

last: Weiner

first: Marta

last: Melé

first: John

last: Rinn


title: SCD – Stem Cell Differentiation on board the International Space Station [miRNA-seq on miRNAs from exosomes]

city: Milan

first: Silvia

last: Bradamante

address: Via Golgi 19

country: Italy

institute: CNR-ISTM, Institute of Molecular Science and Technology

summary: The bone loss observed in astronauts and animal models after spaceflight is attributable to alterations in the bone tissue formation that depends from the continuous remodeling through the activities of bone-resorbing osteoclasts of hematopoietic lineage and bone-forming osteoblasts of mesenchymal origin. This disease is frequent in aged people, but develops much more rapidly in space. Our experiment, selected by ESA (European Space Agency), aimed to determine how human bone marrow mesenchymal stem cells (hBMSCs) react and differentiate in real microgravity, on board the International Space Station, in approx. 2 weeks time.

overall_design: Increased formation of exosomes/macrovescicle was observed in samples on board the ISS. To further investigate cell-cell communication through miRNAs secreted into the medium, exosomes were purified from spent growth media

first: Damariz

last: Rivero

first: Livia

last: Barenghi

first: Michele

last: Balsamo

first: Simone

last: Minardi

first: Francesco

last: Vitali

first: Duccio

last: Cavalieri


title: SCD – Stem Cell Differentiation on board the International Space Station [RNA-seq]

summary:
The bone loss observed in astronauts and animal models after spaceflight is attributable to alterations in the bone tissue formation that depends from the continuous remodeling through the activities of bone-resorbing osteoclasts of hematopoietic lineage and bone-forming osteoblasts of mesenchymal origin.
This disease is frequent in aged people, but develops much more rapidly in space. Our experiment, selected by ESA (European Space Agency), aimed to determine how human bone marrow mesenchymal stem cells (hBMSCs) react and differentiate in real microgravity, on board the International Space Station, in approx. 2 weeks time.

overall_design:
The SCD experiment consisted of 24 experimental hardware modules (EH) (12 flight modules and 12 ground modules), each of which had one experiment unit (EU) integrated into the KUBIC interface container single level (KIC-SL).
Each EU consisting of a brick containing 5 cylinders (for the medium and chemicals), a cell culture chamber (CC), and connecting channels. Five small valves were placed to separate the different fluids and the CC. Each cylinder had a piston to inject a new fluid into the CC; the waste medium was collected in the previously emptied cylinder and suitably preserved.
EH were trasferred on board the ISS by the Soyuz-TMA-16M (ISS 42S, launched on March 27, 2015); 27°C was the temperature recorded for the samples in the Soyouz vehicle before docking and installation in the KUBIK incubator on board the ISS
The experimental proifile consisted of: 1) installation in KUBIK (T0); 2) Start with the first medium exchange (T0+7h); 3) Second medium exchange (T0+7d); 4)Third medium exchange with PBS (T0+14d); 5) Stop by means of two subsequent exchanges with RNAlater
Here, the effect of microgravity on hBMSCs were investigated by means of mRNA sequencing using Ion Proton. Four spaceflight samples were considered; three samples were cultured in standard medium (SM) while one sample was cultured in osteogenic medium (OM).


title: Roles of Structural maintenance of chromosome flexible domain containing 1 (Smchd1) in early lineage formation and development in mice

city: East Lansing

first: Uros

last: Midic

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

summary: The function of Structural maintenance of chromosome flexible domain containing 1 (Smchd1) was examined during mouse preimplantation development using an siRNA knockdown approach.  Transient SMCHD1 deficiency during the period between fertilization and morula/early blastocyst stage compromised embryo viability and resulted in reduced cell number, reduced embryo diameter, and reduced nuclear volumes at the morula stage. RNAseq analysis of Smchd1 knockdown morulae revealed aberrant increases in expression of mRNAs related to the trophoblast lineage, indicating SMCHD1 inhibits trophoblast lineage gene expression and promotes inner cell mass formation.  siRNA knockdown also reduced expression of cell proliferation genes, including S-phase kinase-associated protein 2 (Skp2). Smchd1 expression was elevated in Caudal type homeobox transcription factor 2 (Cdx2)-/- blastocysts, indicating enriched expression, and further indicating a role in inner cell mass development.  These results indicate that Smchd1 plays dual roles in the preimplantation embryo, promoting a lineage-appropriate pattern of gene expression supporting inner cell mass formation, whilst controlling lineage formation and gene expression in the trophectoderm.

overall_design: Effects of SMCHD1 siRNA knockdown were tested in mouse embryos

first: Kailey

last: Vincent

first: Kai

first: Alyson

last: Lokken

first: Ashley

last: Severance

first: Amy

last: Ralston

first: Jason

last: Knott

first: Keith

last: Latham


title: Leucegene: bone marrow sequencing from human normal tissue

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Normal human  Bone marrow RNAseq

overall_design: RNA-Seq of normal bone marrow from human

first: Josée

last: Hébert


title: Gene profiles in inguinal white adipose tissue in Hsp20 knockout mice

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: To investigate the function of HSP20 in adipogenesis and thermogenesis of white adipose tissue.

overall_design: Total RNA were extracted from inguinal white adipose tissue of 6 mice (12 weeks old, 3 Hsp20 knockout, 3 wild type in C57BL/6 background as control).

first: Jiangton

last: Peng

first: Yutian

last: Li

first: Guo

middle: C

last: Fan


title: Circulating microRNAs combined with PSA for an accurate and non-invasive prostate cancer detection

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Background: Early detection of prostate cancer (PCa) is limited by the lack of accurate non-invasive biomarkers easily evaluable in men within a screening context. Prostate-specific antigene (PSA) measurement leads to high percentages of both false positives and false negatives. In the era of liquid biopsies, we propose to combine PSA dosage with the evaluation of circulating microRNAs (miRs), to discriminate between men harbouring or not PCa.  Methods: miR profiling of plasma samples from 60 men with PCa, 51 with benign prostatic hyperplasia (BPH) and 27 healthy donors (HD) was performed using microarrays. Univariate analysis (linear models with an empirical Bayes approach) and multivariate penalized logistic regression models were applied to highlight miRs and clinical variables associated with the presence of malignant disease, and were combined in a classification score. Finally, the developed score was tested on an independent dataset of 242 plasma samples (68 PCa, 8 premalignant lesions, 93 BPH, 73 HD), where miR expression was evaluated by RT-qPCR.  Results: Out of 2006 miRs analyzed, a linear combination of miR-103a-3p and let-7a-5p with PSA defined our score. A classification rule based on this score allowed reclassification of samples with accuracy (0.61), sensitivity (0.87), specificity (0.35) and AUC (0.68) higher than those obtained by PSA alone. On the validation set, the same classification rule still performed better than PSA alone in terms of specificity (0.57 versus 0.55) and AUC (0.76 versus 0.74), allowing correct reclassification of all but one tumors not detected by PSA and 33% of BPH with PSA in the 4-16 ng/ml range.  Conclusion: The combination of two circulating miRs with PSA could be an interesting biomarker to detect the presence of PCa (even when PSA levels are below the standard cut-off of 4 ng/ml) and the absence of PCa in an important fraction of men with high PSA, who may avoid unnecessary biopsies.

first: Maurizia

last: Mello-Grand

first: Ilaria

last: Gregnanin

first: Lidia

last: Sacchetto

first: Andrea

last: Zitella

first: Giulia

last: Bottoni

first: Marco

last: Oderda

first: Giancarlo

last: Marra

first: Stefania

last: Munegato

first: Barbara

last: Pardini

first: Alessio

last: Naccarati

first: Mauro

last: Gasparini

first: Paolo

last: Gontero

first: Giovanna

last: Chiorino


title: SQSTM1/p62-directed metabolic reprogramming is essential for normal neurodifferentiation

city: Solna

first: Florian

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

country: Sweden

institute: Karolinska Institutet

summary: Neurodegenerative disorders are an increasingly common and irreversible burden on society, often affecting the ageing population, but their aetiology and disease mechanisms are poorly understood. Studying monogenic neurodegenerative diseases, with known genetic cause, provides an opportunity to understand cellular mechanisms also affected in more complex disorders. We recently reported that loss-of-function mutations in the autophagy adaptor protein, SQSTM1/p62, lead to a slowly progressive neurodegenerative disease presenting in childhood. To further elucidate the neuronal involvement, we studied the cellular consequences of loss of p62 in a neuroepithelial stem (NES) cell model and differentiated neurones, derived from reprogrammed p62 patient cells, or by CRISPR/Cas9-directed gene editing in NES cells. Transcriptomic and proteomic analyses suggest that p62 is essential for neuronal differentiation by controlling the metabolic shift from aerobic glycolysis to oxidative phosphorylation required for neuronal maturation. This shift is blocked by the failure to sufficiently downregulate lactate dehydrogenase expression due to the loss of p62, possibly through impaired Hif-1α downregulation and increased sensitivity to oxidative stress. The findings implicate an important role for p62 in neuronal energy metabolism and particularly in the regulation of the shift between glycolysis and oxidative phosphorylation, required for normal neurodifferentiation.

overall_design: Transcriptomes of neuroepithelial stem cells in an undifferentiated (0d) and differentiated state (4d) were generated in triplicates on an Illumina HiSeq 2500.

first: Javier

last: Calvo-Garrido

first: Camilla

last: Maffezzini

first: Paula

last: Clemente

first: Elias

last: Uhlin

first: Malin

last: Kele

first: Henrik

last: Stranneheim

first: Nicole

last: Lesko

first: Helene

last: Bruhn

first: Per

last: Svenningsson

first: Anna

last: Falk

last: Wedell

first: Christoph

last: Freyer

last: Wredenberg


title: small RNA seq profile of DG and CA region of mice subjected to 2 or 10 weeks of environmental enrichment and their respective home cage controls

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

country: Germany

institute: DZNE Goettingen

summary: Physical exercise in combination with cognitive training is known to improve memory function and lower the risk for various complex diseases including Alzheimer’s disease. Here we show that prolonged exposure of mice to such an environmental enrichment paradigm mediates long-lasting beneficial effects on memory function and synaptic plasticity even after the end of enrichment training and also provides a cognitive advantage to the offspring. We furthermore show that this effect is mediated via changes in sperm RNA involving the expression of miR-212/132.

overall_design: small RNA profile from adult animals (hippocampal DG or CA region) subjected to 2 weeks or 10 weeks of enrvironmental enrichment

last: Benito-Garagorri

first: Cemil

last: Kerimoglu

first: Andre

last: Fischer


title: The Wnt/ß-catenin axis modulates early BBB development by fine-tuning TGFß signalling through ADAMTSL2

city: Stockholm

first: Julianna

middle: MV

last: Kele-Olovsson

address: Nanna Svartz väg 2

department: Physiology and Pharmacology

institute: LICR ltd and Karolinska Institutet

summary: The Wnt/ß-catenin pathway is orchestrating the development of the blood-brain barrier (BBB), but its downstream mediators have remained elusive. To identify potential effectors, we generated an endothelial cell specific Axin1 over-expressing mouse model, AOEiEC. We found that in AOEiE mice Wnt/ß-catenin signalling was down regulated leading to premature regression and remodelling without directly compromising BBB integrity. Interestingly, by comparing transcriptomes of endothelial cells from control and AOEiEC mice, we identified Adamtsl2 as a novel Wnt/ß-catenin-induced, secreted factor, important for stabilizing the cerebral vasculature during development. Importantly, loss-of-function and gain-of-function experiments revealed that Adamtsl2 alone was sufficient to rescue CNS vascular defects seen upon Wnt-signalling inhibition. Furthermore, using various cell and animal models we demonstrate that Adamtsl2 exerts its function by fine-tuning the TGFβ signalling pathway in CNS vessels. In conclusion, this study implicates Adamtsl2 as a mediator of Wnt/ß-catenin signalling during BBB development by linking it to TGFβ signalling.

overall_design: We performed RNA-seq for wildtype E14.5 mouse embryos and ones overexpressing Axin1

first: Mike

last: Hupe

first: Jan

last: Stenman

first: Minerva

last: Xueting-Li

first: Belma

last: Hot


title: Epigenetic effects of acrylamide exposure in mice

status: Public on Jan 30 2019

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

summary: Acrylamide, a high-production-volume chemical and food contaminant in baked and fried carbohydrate-rich foods has been classiﬁed as a “Group 2A carcinogen” (probable human carcinogen) by the IARC. The carcinogenicity of acrylamide is attributed to its well-recognized genotoxicity; however, evidence suggests that acrylamide may also induce non-genotoxic alterations.  In the present study female B6C3F1 mice were exposed to 0.70mM acrylamide in drinking water for 28 days and genotoxic and transcriptomic effects were investigated in the lung, a target organ for acrylamide carcinogenicity in mice, and the liver, a non-target organ.  Acrylamide exposure resulted in a dose-dependent formation of N7-(2-carbamoyl-2-hydroxyethyl)guanine and N3-(2-carbamoyl-2-hydroxyethyl)adenine in lung and liver DNA at the similar levels.  In contrast, whole genome gene expression profiles in the lungs and livers revealed the tissue-specific gene expression alterations.  By using a SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent Technologies), we identified 123 and 363 genes that were found to be differentially expressed in the lungs and livers of acrylamide-treated mice; however, only 5 genes were in common between the organs.  A detailed analysis of differentially expressed genes revealed that the major difference in the effect of acrylamide on the transcriptome in the lungs and livers was related to a different trend of gene expression changes.  In the lungs, acrylamide exposure caused an inhibition of gene expression (54 up-regulated and 69 down-regulated genes), whereas the opposite effect, characterized by twice the number of up-regulated as compare to down-regulated genes (245 up-regulated and 118 down-regulated), was found in the livers of exposed mice.

overall_design: Transcriptomic profile in the liver of female mice treated with acrylamide (n=3). Age-matched control samples were also analyzed (n=3).

first: Volodymyr

last: Tryndyak

first: Frederick

last: Beland

first: Alexandra

last: Antunes

first: Igor

middle: P

last: Pogribny


title: RNA Sequencing of mouse Purkinje cells across postnatal development

city: Oxford

first: Esther

last: Becker

address: Sherrington Road

country: United Kingdom

institute: University of Oxford

summary: We analyzed Purkinje cell transcriptome dynamics in the developing mouse cerebellum during the first three postnatal weeks, a key developmental period equivalent to the third trimester in human cerebellar development. Our study represents the first detailed analysis of developmental Purkinje cell transcriptomes and provides a valuable dataset for gene network analyses and biological questions on genes implicated in cerebellar and Purkinje cell development.

overall_design: Laser capture microdissection was employed to obtain a highly enriched population of cerebellar Purkinje cells. Deep sequencing was performed on RNA isolated from 1000 Purkinje cells at five developmental timepoints (postnatal days P0, P4, P8, P14 and P21) in triplicate.

first: Harry

last: Clifford

last: Dulneva

first: Chris

last: Ponting

first: Wilfried

last: Haerty

middle: B


title: Stenotrophomonas maltophilia differential gene expression in synthetic cystic fibrosis sputum identifies shared and cystic fibrosis strain-specific expression responses to the sputum environment

city: Burlington

first: Korin

last: Eckstrom

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

summary: We characterized the transcriptional responses of three S. maltophilia strains during exposure to synthetic CF sputum media (SCFM2) to gain insight into how this organism interacts with the host in the CF lung. These efforts led to the identification of 881 transcripts differentially expressed by all three strains, many of which reflect different metabolic pathways used by S. maltophilia in sputum, and altered stress responses. The latter correlated with increased resistance to peroxide exposure after pre-growth in SCFM2. We also compared the SCFM2 transcriptomes of two S. maltophilia CF isolates with the SCFM2 transcriptome of the acute infection model strain, S. maltophilia K279A, allowing us to identify CF isolate-specific signatures in differential gene expression that may be suggestive of adaptation to the CF lung. Each strain also possessed genes not shared by the other two and here we show that expression of some of the accessory genes in each strain are changed in response to SCFM2. Collectively, this work details the response of S. maltophilia to the CF lung environment, identifying potential survival strategies and metabolic pathways used by S. maltophilia during infections.

overall_design: Examination of response to two media types (SCFM2 and lactate) in three bacterial strains (GW273, GW275, and K279a)

first: Graham

last: Willsey

first: Annette

last: LaBauve

first: Lauren

last: Hinkel

first: Kristin

last: Schutz

first: John

middle: J

last: LiPuma

first: Matthew

last: Wargo


title: Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States.

city: Seattle

first: David

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Epigenomic analysis of naïve human embryonic stem cells including histone modificatinos and 3D genomic architecture

overall_design: Five histone modifications on two cell types, ChIP-seq for enhancers in four additional cell types, Dnase-HiC in naïve human embryonic stem cells

first: R

middle: D


title: Expression of tissue-restricted human genes following signaling or chromatin perturbations [kinase screen]

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

department: UMR7216 "Epigenetics and Cell Fate"

country: France

institute: CNRS-Université Paris Diderot - Sorbonne Paris Cité

summary: The goal of the study was to determine whether perturbations in signaling pathways or chromatin regulators were sufficient to induce the illegitimate expression of tissue-restricted genes in primary human cells

overall_design: Two screens were conducted. IMR90 cells were infected with a collection of 192 genetically activated kinases (Addgene# 1000000012), or transfected with 164 distinct siRNA pools. Total RNA was extracted and analyzed by Nanostring

first: Pierre-antoine

first: Olivier

last: Kirsh


title: Expression of tissue-restricted human genes following signaling or chromatin perturbations

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

overall_design: Refer to individual Series


title: Systems analysis of hepatic insulin resistance identifies RGS4 as a key mediator of metabolic adaptation

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

summary: We profiled the transcriptomes of chow diet-fed and high-fat diet-fed mice across insulin stimulation time points. We also profiled the effects of metformin treatment on mouse liver transcritomes. Our temporal analyses of chow-diet and 16 week high-fat diet transcriptomics following insulin stimulation uncovered several regulator of G-protein signaling genes, particularly Rgs4, that are specifically regulated transcriptionally in HFD livers following insulin stimulation. We validated these findings with additional assays of RGS4 mRNA and protein levels and characterized this molecule's role in regulating hepatic insulin responses in mice.

overall_design: Liver mRNA was profiled by sequencing from chow diet and 6 week and 16 week high-fat diet mouse livers. We sampled time points following insulin stimulation as well as following treatment with metformin. At least three mice per group/time point were used for statistical analyses.

first: Norman

last: Kennedy


title: Expression of tissue-restricted human genes following signaling or chromatin perturbations [sirna screen]


title: Gene expression profile in response to HIF-1α inhibition together with PPARα activation and the postnatal factors (T3, IGF-1 and dexamethasone) in hiPSC-CMs

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

summary:
Methods: RNA-seq libraries were prepared using the Illumina TruSeq technology. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq2500 system. Reads were mapped on the Human Genome Reference (GRCh38) and normalized expression table was generated.
Results: Among differentially expressed genes, compared with DMSO-treated hiPSC-CMs, 505 genes were upregulated in FM+WY+TID-treated hiPSC-CMs, with 72 genes commonly upregulated in both FM+WY+TID-treated hiPSC-CMs and LV groups and 949 genes were downregulated in FM+WY+TID-treated hiPSC-CMs and 2137 genes were downregulated in LV, with 437 genes downregulated in both FM+WY+TID-treated hiPSC-CMs and LV compared with DMSO-treated hiPSC-CMs .
Conclusions: Data demonstrate increased expression of genes associated with many metabolic processes which are also highly enriched in human pediatric heart samples including many interconnected metabolic processes that are upstream of lipid metabolism and FAO, agreeing with the shift to FAO for energy utilization in more mature CMs, and decreased expression of genes involved in developmental processes, adhesion and signaling in both FM+WY+TID-treated hiPSC-CMs and LV. The overlap in both upregulated and downregulated genes in both groups confirmed an advanced degree of cardiomyocyte maturation in response to FM+WY+TID.

overall_design: RNA-sequencing analysis was performed to compare global gene expression profiles of hiPSC-CMs at differentiation day 28 with maturation factors (FM+WY+TID) treatment (Treat)  vs. DMSO treatment (DMSO) vs. left ventricle tissue sample (LV).

first: Cinsley

last: Gentillon

first: Meixue

last: Duan

first: Gregory

last: Gibson

first: Chunhui

last: Xu


title: Decoding the 5’ nucleotide bias of PIWI-interacting RNAs (piRNAs)

first: Astrid

middle: Desiree

last: Haase

state: Maryland (MD)

address: 8 Center Drive, Bldg 8 1A04

department: NIDDK

institute: NIH

summary: Analysis of Piwi-piRNAs that assocaite with wild type Piwi and specificity loop (SL) mutants in ovarian somatic sheath cells (OSC) and Droosphila ovaries.

overall_design: Small RNAs (~20-30nt) associated with Flag-HA-tagged Piwi proteins (wt and mutants) were purified and prepared for illumina sequencing.

first: Chad

last: Stein

first: Pavol

last: Genzor

first: Sanga

last: Mitra

first: Alexandra

last: Elchert

first: Leif

last: Benner

first: Sushil

last: Sobti

first: Jonathan

last: Ipsaro

first: Molly

last: Hammell

first: Leemor

last: Joshua-Tor


title: Hybrid vigour can be enhanced by delayed leaf senescence

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

summary: In agriculture hybrids are used extensively due to their superior performance in a number of traits such as seed yield, yet the molecular mechanisms underpinning their performance are not understood.  Recent evidence has suggested that a decrease in basal defence response genes regulated by reduced levels of the phytohormone salicylic acid (SA) may be important for hybrid vigour.  Decreasing levels of SA in the Arabidopsis accession C24 through the introduction of the SA catabolic enzyme NahG results in increased plant size phenocopying the increased size of C24/Ler F1 hybrids.  The increased growth of C24 NahG occurs during late development. Our transcriptome analysis of F1 hybrids and C24 NahG identified shared pathways associated with their size increase including decreased expression of defence response genes, SA biosynthetic genes, and SA response genes. In both C24 NahG and F1 hybrids we found decreased expression of key senescence transcription factors WRKY53, NAP and ORE1 and delayed senescence compared to C24. The delay in senescence resulted in an extension of active photosynthesis in the leaves of F1 hybrids compared to the parental lines allowing each leaf to produce more resources for the growth process.

overall_design: Samples analyzed included C24, C24B, Ler, C24 x Ler, C24 NahG 2, C24 NahG 3 and Ler NahG.  C24, Ler, Ler NahG and C24xLer all had three biological replicates.  C24B, C24 NahG 2 and C24 NahG 3 had two biological replicates.  C24 NahG 2 and C24 NahG 3 are two indepedent transgenic lines which ere sequenced at a later stage than the other samples.  These and were analyzed separately (eg. C24 B versus C24 NahG 2).  All biological replicates were made from 6-10 plants.


title: Hypoxic microenvironment activates GLI2 through synergistic action of TGF-β2 and HIF-1α to confer chemoresistance and poor clinical outcome in colorectal cancer

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore


title: Hypoxic microenvironment activates GLI2 through synergistic action of TGF-β2 and HIF-1α to confer chemoresistance and poor clinical outcome in colorectal cancer [IlluminaExpr_2_CAF_SF_SD208]

summary: Microenvironment has been suggested as an important factor contributing to how the colorectal cancer cells escape therapy, but the exact mechanism leading to chemoresistance remains elusive. Here, through modeling in vitro by cocultivation of patient-derived cancer associated fibroblasts (CAFs) with cancer stem cells (CSCs), we show that CAFs-secreted TGF-β2 is a key stromal factor that coordinates with hypoxia to promote CSC stemness and resistance to chemotherapy. GLI2, a key transcription factor of Hedgehog pathway, was identified as both necessary and sufficient in this process in which TGF-β and hypoxia-inducible factor (HIF-1α) synergize to directly induce GLI2 expression.  Conversely, CSC-secreted TGF-β is also important to support the growth of CAFs but instead induce death of normal fibroblasts, suggesting a reciprocal mechanism to selectively support the CAF-CSC interaction. Small molecule inhibition of both TGF-β and GLI2 effectively reversed the chemoresistance. Finally, expression of TGFB2/HIF1A/GLI2 gene signature as a functional readout of this resistance pathway defines worse clinical outcomes and predicts patients relapse. Our observations uncover a key role of TGF-β/HIF-1α/GLI2 in microenvironment-mediated chemoresistance and reveal novel biomarker and targeting strategies to identify and treat the high risk CRC patients.

overall_design: Total RNA obtained from colorectal patients-derived tumorspheres (TS) in coculture with cancer-associated fibroblast (CAF) treated with or without TGFBR inhibitor (SD208) are subject to expression microarray analysis using Illumina Gene Expression Sentrix BeadChip HumanHT-12_V4.

first: Yen-An

last: Tang

first: YuFeng

last: Chen

first: Siti

last: Yatim

first: Yi

last: Bao

last: Oguz

first: Puay

last: Lee

first: Sylvia

last: Mahara

first: Xiaojian

last: Wu

first: Qiang

last: Yu


title: Transcriptome profiling of HCC1937 vector and wtBRCA1 cell lines which were treated with OTX-015

city: Shanghai

first: Baoyuan

last: Zhang

state: Shanghai

address: Ruijin er road

department: Ruijin hospital

institute: Shanghai jiaotong university

summary:
Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with OTX-015.
Methods: HCC1937 vector and wtBRCA1 cells were treated with 5 micromolar OTX-015 for 24 hours. Total RNA was extracted and processed with NEBNext Ultra Directional RNA Library Prep Kit for cDNA library preparation. The data are in duplicate and raw data were generated by Illumina 2500 sequencer. The Fastq format data were then processed with Tophat for genome mapping. After getting the bam files, they were further analyzed with cuffdiff for gene expression of different groups.
Results: From the transcriotome profiling and analysis, we got gene expression data of DMSO control group and OTX-015 treatment group for the HCC1937 BRCA1 isogenic cell lines.
Conclusion: The gene expression data revealed the transcriptome variation by OTX-015 treatment.

overall_design: OTX-015 treated HCC1937 BRCA1 isogenic cells were used for RNA extraction and RNAseq analysis for transcriptome profiling

first: Joong

middle: S

last: Shim


title: Identification of p53-regulated genes in wild-type p53 or p53-null HCT116 cells

status: Public on Jan 29 2019

city: Tokyo

first: Koichi

last: Matsuda

address: 4-6-1, Shirokanedai, Minato-ku

institute: The University of Tokyo

summary: Microarray-based gene expression analysis of HCT116 p53+/+ and HCT116 p53−/− treated with doxorubicin to activate p53 in time-dependent manner.

overall_design: HCT116 p53+/+ and HCT116 p53−/− cells were treated with 2 μg/mL of doxorubicin for 2 hours. Total RNA was isolated at 12, 24, and 48 hours after the treatment; including non-treated cells (0 hour) as controls.

first: Yu-Yu

last: Liu

first: Chizu

last: Tanikawa

first: Takafumi

last: Miyamoto

first: H

last: Lo

first: Makoto

last: Hirata


title: Hypoxic microenvironment activates GLI2 through synergistic action of TGF-β2 and HIF-1α to confer chemoresistance and poor clinical outcome in colorectal cancer [IlluminaExpr_1_CAF_NF]

first: Gokce

last: OGUZ

summary: Analysis of gene expression profiles of three cancer-associated fibroblasts (CAFs) and four normal fibroblasts (NFs), which are derived from tumor tissues and adjacent normal mucosa of colorectal cancer patients, respectively.

overall_design: Total RNA obtained from three CAFs and four NFs are subject to expression microarray analysis using Illumina Gene Expression Sentrix BeadChip HumanHT-12_V4.

last: Tang


title: Interspecies chemical signalling in a methane-oxidizing bacterial community

first: Mitchell

middle: William

last: Pesesky

address: 616 NE Northlake Place

summary: Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide a carbon and energy source for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structure and function these communities. Here we show that many members of the Methylomonas genus possess a LuxR-type acyl-homoserine lactone (acyl-HSL) receptor/transcription factor highly homologous to MbaR from the quorum sensing (QS) system of Methylobacter tundripaludum, another methane-oxidizer that has been isolated from the same environment. We reconstitute this detection system in Escherichia coli and also use mutant and transcriptomic analysis to show that the receptor from Methylomonas species strain LW13 (LW13) is active and alters LW13 gene expression in response to the acyl-HSL produced by M. tundripaludum. These findings provide a molecular mechanism for how two species of bacteria that may compete for resources in the environment can interact in a specific manner through a chemical signal.

overall_design: In order to determine which genes MmsR regulates in response to acyl-HSL signal, we compared the transcriptome of exponentially growing LW13 in the presence or absence of 3-OH-C10-HSL. As a control for gene changes that are not the result of signal binding to MmsR, we constructed an unmarked, in-frame deletion of mmsR (∆mmsR) and also compared the transcriptome of this strain in the presence and absence of signal. For each condition, we sequenced the transcriptomes of two biological replicates.

first: Aaron

middle: W

last: Puri

first: Darren

first: Amy

last: Schaefer

first: Zheng

first: E

last: Greenberg

first: Mary

middle: E

last: Lidstrom


title: Genome-wide analysis of different response of the hepatocytes and oval cells induced by aflatoxin B1 exposure

city: Wuhan

first: Lei

address: 1095 Jiefang Avenue

institute: Tongji Hospital

summary: Analysis of genetic changes of hepatocytes and oval cells induced by HBV. The hypothesis tested in the present study was that hepatic progenitor cells (oval cells) are the founder cells of hepatocellular carcinoma(HCC). Results provide important information of the different responses of hepatocytes and oval cells to HBV expression during HBV-related hepatocarcinogenesis, such as up- or down-regulated oncogenes,tumor suppressor genes and signaling pathways.Results also provide new insights into the biology of human HCC.

overall_design: Total RNA obtained from primary cultured hepatocytes and oval cells isolated from the healthy and HBV transgenic mice.

first: Yan

last: Chen


title: Deficiency in the Phosphorylated Pathway of Serine Biosynthesis perturbs sulfur assimilation in Arabidopsis

status: Public on Jan 26 2019

city: Burjassot

first: Roc

last: Ros

state: valencia

address: Vicent Andres Estelles

department: Biologia Vegetal

country: Spain

institute: Universitat de Valencia

summary: Although the plant Phosphorylated Pathway of L-serine Biosynthesis (PPSB) is essential for embryo and pollen development, and for root growth, its metabolic implications have not yet been investigated in depth. A transcriptomics analysis of PPSB-deficient mutants at nighttime, where PPSB activity is thought to be more important, pointed the sulfate assimilation process. As sulfate assimilation takes place mainly during the light period, we also investigated this process in PPSB-deficient lines in the daytime. Key genes in the sulfate starvation response, such as the Adenosine 5’phosphosulfate reductase (APR) genes along with sulfate transporters (SULTR), especially those involved in sulfate translocation in the plant, were induced in the PPSB-deficient lines. However, sulfate content did not lower in these lines, and the steady-state level of glutathione (GSH) increased in roots. This scenario suggests that PPSB deficiency perturbs the sulfate assimilation process between tissue/organs. Alteration of thiol distribution in leaves from different developmental stages, and between aerial parts and roots in plants with reduced PPSB activity provided confirmatory support for this idea. Flux analysis indicated that diminished PPSB activity caused an enhanced flux of 35S into thiol biosynthesis especially in roots. GSH turnover also accelerated in the PPSB-deficient lines, which supports the notion that not only biosynthesis, but also transport and allocation of thiols were perturbed in the PPSB mutants. Our results suggest that PPSB is required for sulfide assimilation in specific heterotrophic tissues and that lack of PPSB activity perturbs sulfur homeostasis between photosynthetic and non-photosynthetic tissues.

overall_design: Aerial parts and roots of Arabidopsis wild type plants and mutants of the phosphoserine phosphatase were compared, in triplicate. The sequencing step was performed using a SOLID 5500XL equipment of 75 nucleotides using the Exact Call Chemistry.

first: Armand

last: Anoman

first: María

last: Flores-Tornero

first: Ruben

middle: M

last: Benstein

first: Samira

last: Blau

first: Sara

last: Rosa-Téllez

first: Andrea

last: Bräutigam

first: Alisdair

last: Fernie

first: Jesús

last: Muñoz-Bertomeu

first: Sören

last: Schilasky

first: Andreas

last: Meyer

first: Stanislav

last: Kopriva

first: Juan

last: Segura

first: Stephan

last: Krueger


title: Genome-wide gene expression analysis in treatment for 24 h with 40 μM APR-246 in ARID1A-WT and ARID1A-KO HCT116 cells.

status: Public on Jan 28 2019

city: Chuo-ku

first: Takashi

last: Kohno

state: Tokyo

address: 1-1, Tsukiji 5-chome

institute: National Cancer Center Research Institute

summary: To explore the sensitivity of ARID1A-KO cells to APR-246

overall_design: 7 samples are analyzed.

first: Hideaki

last: Ogiwara


title: miR-140 mutation and skeletal dysplasia [RNA-seq]

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA–target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs.

overall_design: RNA sequencing (RNA-seq) in chondrocytes with miR-140 G mutation or deletion

middle: I

first: Giedre

last: Grigelioniene

first: Tatsuya

last: Kobayashi


title: A novel non-canonical signaling pathway mediates TGF-β1-induced glucocorticoid insensitivity in epithelial cells

status: Public on Jan 27 2019

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

summary: Limited therapeutic responses to glucocorticoids in chronic inflammatory disease are partly attributable to interleukins and transforming growth factor-β1 (TGF-β1). Global inhibition of TGF-β1 carries known risks, including autoimmune disease.  Here we elucidate the signaling pathway subserving modulation of glucocorticoid activity by TGF-β1. The proteomic response of airway epithelial cells to TGF-β1 revealed 24 candidate proteins of which 3 were prioritized by exclusion of changes induced by: TGF-β2, which lacks the modulatory activity of TGF-β1 and TGF-β3; and those of TGF-β1 that were prevented by small molecule inhibitors of non-canonical TGF-β1 signaling, that did not prevent glucocorticoid modulation. Pharmacological and genetic approaches establish that TGF-β1-induced glucocorticoid insensitivity is mediated by a novel signaling cascade involving LIM domain kinase 2 mediated phosphorylation of phospho-cofilin1 that activates phospholipase D to generate the effector(s) (lyso)phophatidic acid. This study identifies several promising drug targets that potentially enable safe modulation of TGF-β1 in chronic inflammatory diseases.

overall_design: Biological triplicates of BEAS-2B cell lines treated with Dexamethasone, TGFbeta1 and a combination of Dexamethasone +TGFbeta1 were compared among themselves and with an untreated control

first: Meina

last: Li

first: Christine

middle: R

last: Keenan

middle: H

last: Lopez Campos

first: Jonathan

last: Magnum

first: Danica

last: Radojicic

first: Yuxiu

middle: C

last: Xia

first: Shenna

middle: Y

last: Langenbach

first: Trudi

last: Harris

first: Alastair

middle: G

last: Stewart


title: The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: ChIP-seq of CP190, Su(Hw), Mod(mdg4) for genome-wide overlap with CLAMP

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Chromatin insulators are DNA-protein complexes that establish higher order independent DNA domains to influence transcriptional regulation. Insulators are defined by two different functions: they can block communication between an enhancer and a promoter and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy-insulator complex contains three core components: Su(Hw), CP190 and Mod(mdg4)67.2. Here we identify a novel role for Chromatin-linked adaptor for MSL proteins (CLAMP) in promoting gypsy chromatin insulator function. When Clamp is depleted by RNAi, gypsy-dependent enhancer blocking activity decreases and barrier activity is reduced in all tissues. Furthermore, Clamp RNAi knockdowns and mutation result in disorganized insulator complex localization in the nucleus. Co-immunoprecipitation experiments showed that CLAMP physically associates with core gypsy-insulator proteins. Co-localization of CLAMP with gypsy components on polytene chromosomes and ChIP-seq analysis demonstrates co-localization of CLAMP with a subset of insulator sites across the genome. Thus, our findings suggest a ubiquitous, genome-wide role for CLAMP in promoting gypsy-dependent chromatin insulator activity.

overall_design: Examination of overlapping of CLAMP with insulator proteins Su(Hw), CP190 and Mod(mdg4) genome wide in Kc167 embryonic cell lines.

first: Indira

last: Bag

first: Ryan

last: Dale

first: Elissa

last: Lei


title: DNA Hypermethylation at Loci Associated with Diabetes, Obesity and Cardiac Abnormalities in CD3+ Lymphocytes of Intrauterine Growth Restricted Newbors

status: Public on Jan 25 2019

city: Bronx

first: Maureen

middle: J

last: Charron

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

summary: Intrauterine growth restriction (IUGR) is associated with increased susceptibility to obesity, metabolic syndrome and type 2 diabetes. Although the mechanisms underlying the fetal origin of metabolic disease are poorly understood, evidence suggests epigenomic alterations play a critical role. We sought to identify changes in DNA methylation patterns that define IUGR in CD3+ T-cells purified from umbilical cord blood obtained from appropriate for gestational age (Control) and IUGR male newborns using a genome-wide assay. We identified a global shift towards hypermethylation in IUGR compared to Control newborns targeted to regulatory regions of the genome.

overall_design: DNA methylation was assessed globally at specific CpG sites in CD3+ T cell from human cord blood obtained from 7 IUGR and 8 Control male newborns.

first: Yoshinori

last: Seki

first: Lyda

last: Williams


title: Altered oligodendrocyte heterogeneity in Multiple sclerosis.

status: Public on Jan 23 2019

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

summary: Oligodendrocyte (OL) pathology is increasingly implicated in neurodegenerative diseases, as they are involved in metabolic support of axons and functional cross-talk with other brain cells. Rodent OLs are heterogeneous, with developmental and biological differences, but the extent of heterogeneity in the normal human brain and its contribution to any changes of disease remains unknown. Here we performed single nuclei RNA-sequencing (snRNA-seq) from white matter (WM) areas of post mortem human brain both in control (Ctr) and multiple sclerosis (MS) patients. We identified several sub-clusters of oligodendroglia in the Ctr human WM, some similar to those in mouse, and defined new markers for these. Strikingly, some of these sub-clusters were under-represented in MS tissue, while others were more prevalent than in controls. There was a lack of OL precursor cells (OPCs) and OLs in an intermediate stage of differentiation in MS lesions and in normal appearing white matter (NAWM), suggesting either depletion by the disease or by a regenerative response. The differences in mature OL sub-clusters indicate different functional states of OLs in MS tissue and, as this is similar in NAWM to lesions, that MS is a more diffuse brain disease than the focal demyelinating lesions suggest. We were also able to identify new markers of different MS lesion subtypes. Our findings of an altered heterogeneity of oligodendroglia in MS may have an important contribution to our understanding of disease progression and may alter therapeutic approaches to MS.

overall_design:
We isolated single nuclei from white matter post-mortem tissue from 5 non-neurological control samples (Ctrl) and post-mortem tissue from 4 progressive Multiple sclerosis (MS) patients. We got a total of 20 samples, which in the MS samples included different non-lesioned (normal appearing white matter) and lesioned (active lesions, chronic active lesions, chronic inactive lesions and remyelinating lesions) based on pathology, to address the cellular and functional differences between the two groups.
Note from submitter: Since the data is from human patients, we will submit the raw data to dbGap, that allows human sequence data

first: Sarah

last: Jäkel

first: Ana

last: Falcao

first: David

last: van Bruggen

first: Ka

last: Lee

first: Irene

last: Knuesel

first: Dheeraj

last: Malhotra

first: Charles

last: ffrench-Constant

first: Anna

first: Gonçalo

last: Castelo-Branco


title: Gene Expression Analysis in NIH3T3 cells with control or RPRD1B knockdown

city: San Francisco

first: Melanie

last: Ott

state: CA

address: 1650 Owens Street, 5th Floor

department: Virology and Immunology

institute: Gladstone Institutes

summary: To investigate the role of RPRD1B in regulating gene expression in NIH3T3 cells.

overall_design: Examination of mRNA expression levels in cells with control or RPRD1B knockdown NIH3T3 cells

first: Ibraheem

last: Ali


title: Bilin-dependent photoacclimation in Chlamydomonas reinhardtii

status: Public on Jan 24 2019

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: Linear tetrapyrrole (bilin)-based phytochrome sensors optimize photosynthetic light capture by mediating massive gene reprogramming in land plants, yet surprisingly, many sequenced chlorophyte (green) algae lack phytochrome genes. Previous studies on the heme oxygenase (hmox1) mutant of Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is needed for regulation of a limited nuclear gene network implicated in oxygen detoxification during dark to light transitions. The hmox1 mutant is unable to grow photoautotrophically and poorly acclimates to increased illumination even in the presence of acetate. Here we show that these phenotypes reflect the reduced accumulation of PSI reaction centers as well as a loss of PSI and PSII antennae complexes during photoacclimation. Phenotypically, the hmox1 mutant is similar to the chlorophyll biosynthesis mutants, gun4, crd1 and cth1. However, many of the hmox1 phenotypes can be rescued by the application of exogenous biliverdin IXα, the bilin product of HMOX1; this rescue is independent of photosynthesis but strongly dependent upon blue light. RNA-Seq comparisons of hmox1, 4A+ wild type and two genetically complemented lines also reveal that bilins restore regulation of a small network of photosynthesis-associated nuclear genes. These include genes responsible for chlorophyll biosynthesis (CHLI1/2), PSI light-harvesting (LHCA4) and naphthoquinone metabolism (MEN2), all of which show reduced photoinduction in the hmox1 mutant. We propose that a bilin-based, blue light sensory system is responsible for the maintenance of a functional photosynthetic apparatus in light-grown C. reinhardtii. This critical and possibly ancestral role for bilins may be responsible for retention of bilin biosynthesis in all eukaryotic photosynthetic species.

overall_design: We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXα before and after transfer to low light.

first: Tyler

last: Wittkopp

first: Deqiang

last: Duanmu

first: Stefan

last: Schmollinger

first: Wei

last: Hu

first: Qiuling

last: Fan

first: Ian

last: Blaby

last: Casero

first: Matteo

last: Pellegrini

first: Arthur

last: Grossman

first: J

last: Lagarias

first: Michael

middle: T

last: Leonard

first: Sean

middle: D

last: Gallaher


title: Distinct vascular genomic effects of proton and gamma radiation

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: We performed comparative RNA sequencing of the early (4 hrs) dose response (0.5 – 200 cGy whole body dose, 10 dose levels) of the mouse aorta to proton and gamma radiation. Total-body proton radiation of conscious animals was performed using a proton beam produced by a cyclotron system, while total-body gamma radiation of animals was performed using a Caesium-137 gamma source. A trend analysis identified genes that showed a dose response, using data permutation to estimate a false discovery rate (q-value) for each gene. We identified 29 and 194 genes (q-value ≤ 0.1) that were upregulated with increasing doses of proton and gamma radiation, respectively. No genes were down-regulated. While fewer genes were dose-responsive to proton radiation, the magnitude of the effect was greater than with gamma radiation. These highly responsive genes were enriched for pathways involved in the response to DNA damage, apoptosis, cellular stress and inflammation (p < 0.01). Gamma radiation responsive genes included the same pathways, but extended to genes in vasculature specific pathways. Genes responsive to both radiation types (19 genes at q-value ≤ 0.1) showed almost perfectly superimposable dose-response relationships. We observed the same superimposable dose response relationship of gamma and proton radiations in a subset of genes validated by quantitative PCR not only in the aorta but also in liver, lung, heart and kidney.     Despite a relative similar relative biological effectiveness of protons and gamma photons and the activation of canonical radiation response pathways by both radiation types, we detected marked differences in the genomic response. It seems plausible that these genomic differences translate into differences in the biological processes leading to cardiovascular pathologies.

overall_design: RNA-Seq 20 samples, mouse aorta. 10 mice were treated with ten different centigrays of gamma radiation and 10 mice were treated with ten different centigrays of high energy protons (0 cGy, 5 cGy, 10 cGy, 25 cGy, 50 cGy, 75 cGy, 100 cGy, 125 cGy, 150 cGy, 200 cGy). One sample per dose.

first: Emanuela

last: Ricciotti

first: Dimitra

last: Sarantopoulou

first: Jenine

last: Sanzari

first: Gabriel

last: Krigsfeld

first: Amber

last: Ahmad

first: Ann

last: Kennedy

first: Tilo

last: Grosser


title: Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer [Repli-seq]

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research

summary: DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.

overall_design: Repli-Seq was conducted in 2 human prostate cell lines: normal prostate epithelial cells (PrEC) and prostate cancer cells (LNCaP)

first: Susan

last: Clark


title: LINE-2 transposable elements are a source of functional human microRNAs and target sites

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

institute: Lund University

summary: Transposable elements (TEs) are dynamically expressed at high levels in multiple human tissues, but the function of TE-derived transcripts remains largely unknown. In this study, we identify numerous TE-derived microRNAs (miRNAs) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (AGO2 RIP-seq) on human brain tissue. Many of these miRNAs originated from LINE-2 (L2) elements, which entered the human genome around 100-300 million years ago. We found that L2-miRNAs derive from the 3’ end of the L2 consensus sequence and thus share very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3’UTR. In line with this, we found that many protein-coding genes carry fragments of L2-derived sequences in their 3’UTR: these sequences serve as target sites for L2-miRNAs. L2-miRNAs and their targets were generally ubiquitously expressed at low levels in multiple human tissues, suggesting a role for this network in buffering transcriptional levels of housekeeping genes. Interestingly, we also found evidence that this network is perturbed in glioblastoma. In summary, our findings uncover a TE-based post-transcriptional network that shapes transcriptional regulation in human cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Small and total RNA sequencing data from AGO-RIPseq experiments on human glioblastoma and cortex tissue, mouse brain tissue and ESCs-derived neurons.

first: Rebecca

last: Petri

middle: L

last: Brattås

first: Yogita

last: Sharma

first: Marie

last: Jönsson

first: Karolina

last: Pircs

first: Johan

last: Bengzon

last: Jakobsson


title: Extra deep sequencing of GL261 and LLC1 murine cell lines for the purpose of fusion detection

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

summary: RNA from GL261 (glioma) and LLC1 (Lewis Lung carcinoma) samples were sequenced at a depth of 142M and 188M paired reads, respectively.

overall_design: RNA-sequencing data were used to detect fusions capable of producing proteins containing neoantigens.

first: S

middle: K

last: Rathe

first: J

last: Johnson

first: F

last: Popescu

first: A

last: Watson

first: D

middle: A


title: Hepatic gene expression analysis from rats with chronic sleep restriction

first: Aalim

last: Weljie

address: 3400 Civic Center Blvd

summary: We report the change in gene expression in rat liver post chronic sleep restriction. Rats were sleep restricted by for 5 days by forced activity protocol. We found changes in genes related to NAD metabolism (Nampt), TCA cycle (Acly) and methionine metabolism (Msrb2 and Mtr)

overall_design: Examination of differential expression from liver of rats undergoing forced activity plus sleep restriction and force activity only

first: Arjun

last: Sengupta

first: Seth

last: Rhoades

first: Eun-Ji

last: Kim

first: Greg

last: Grant

first: Peter

last: Meerlo


title: miR-140 mutation and skeletal dysplasia [SmallRNA-seq]

first: Hiroshi

last: Suzuki

overall_design: Small RNA sequencing (SmallRNA-seq) in chondrocytes with miR-140 G mutation or deletion


title: A developmental model of human early cardiac valvulogenesis

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

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

overall_design: Refer to individual Series


title: Core Binding Factor β Is Required For Group-2 Innate Lymphoid Cell Activation

city: ALBANY

first: Xiaofei

last: Shen

state: New York

address: 47 NEW SCOTLAND AVENUE

department: Immunology & Microbial Diseases

institute: Albany Medical College

summary: Group-2 innate lymphoid cells (ILC2) are tissue-resident, long-lived innate effector cells implicated in allergy and asthma. Upon activation, mature ILC2 rapidly secret large amounts of type-2 cytokines and other effector molecules. The molecular pathways that drive ILC2 activation are not well understood. Here we report that the transcriptional controller Core-binding factor β (CBFβ) is required for ILC2 activation. Deletion or inhibition of CBFβ did not impair the maintenance of ILC2 at homeostasis, but abolished ILC2 activation during allergic airway inflammation. Treatment with CBFβ inhibitors prevented ILC2-mediated airway hyperresponsiveness in a mouse model of acute Alternaria allergen inhalation. CBFβ promoted expression of key ILC2 genes at both transcriptional and translational levels. CBF transcriptional complex directly bound to Il13 and Vegfa promoters and enhancers, and controlled gene transcription. CBFβ further promoted ribosome biogenesis and enhanced gene translation in activated ILC2. Together, these data establish an essential role for CBFβ in ILC2 activation.

overall_design: Gene expression comparison between CRISPR-mediated non-target control and CBFβ knockout ILC2 line

first: Mingwei

last: Liang

first: Qi

last: Yang


title: Mean expression levels of RNA in cells receiving WT-Cas9 and Mutant Cas9 along with gRNA targeting MIAT locus.

city: Pittsburgh

first: Samira

last: Kiani

state: Pennsylvania

address: A809-B Scaife Hall 3550 Terrace Street Pittsburgh

department: Division of Experimental Pathology

institute: University of Pittsburgh

summary: In this study, we report pre-existing human CD8+ T cell immunity to Streptococcus pyogenes Cas9 in the majority of healthy individuals screened.  In a proof-of-principle study, we demonstrate that Cas9 protein can be modified to eliminate immunodominant epitopes through targeted mutation while preserving its function and specificity. The data presented here show the functionality of this Mutant Cas9 compared to WT-Cas9 when targeting an endogenous locus.

overall_design: Mammalian cells (Hek293FT) received either WT-Cas9 or a mutant Cas9 along with activator domains and gRNA targeting endogenous MIAT locus. The goal of the experiment was comparing activation capacity of the mutant Cas9 with the WT-Cas9. Activation levels were assessed 3 days post transfection using RNA-seq and qRT-PCR.

first: Jin

last: Park

first: Karen

last: Anderson


title: RNA Sequencing of Btz knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

status: Public on Jan 22 2019

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.

overall_design: polyA mRNA -seq in conditions with the indicated knockdown treatments

first: Akhtar

last: Junaid

first: Kreim

last: Nastasja


title: An evolutionarily conserved function of the pre-mRNA splicing regulator TNPO3 for T cell development

city: Freiburg

first: Andreas

middle: S.

last: Richter

address: Stuebeweg 51

department: Bioinformatics Unit

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: All vertebrates possess lymphocytes, enabling the functional interrogation of this evolutionarily conserved organizing principle of adaptive immunity in non-mammalian species. A forward genetic screen in zebrafish indicated that a mutation of tnpo3, encoding a regulator of alternative splicing of pre-mRNAs, specifically impaired intrathymic T cell development. In mouse T cells, Tnpo3 deficiency predominantly disrupted the splicing of genes encoding RNA-binding motifs, and it specifically blocked the splicing of Va11, associated with reduced numbers of peripheral T cells and the complete loss of iNKT cells. Our results reveal an evolutionarily conserved function of a pre-mRNA processing factor for T cell development, uncovering a previously unappreciated checkpoint during the formation of mature mRNAs of the Tcra gene.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: We identified a loss-of-function mutation in the zebrafish tnpo3 gene. We also generated conditional knock-out mice using a floxed allele of Tnpo3 and Lck:Cre (Orban et al., 1992) to eliminate Tnpo3 in the αβ lineage of T cells. Under these conditions, complete inactivation of the Tnpo3 gene was achieved. RNA was prepared from three replicates of wild-type and mutant zebrafish. RNA was also prepared from three replicates of CD4-positive and CD4/CD8-double-positive thymocytes of heterozygous (Tnpo3fl/+; Lck:Cre) and homozygous (Tnpo3fl/fl; Lck:Cre) mutant mice. RNAs were subjected to RNA-seq analysis and examined for differentially expressed genes and alternative splicing events.

first: Norimasa

last: Iwanami

middle: S

first: Katarzyna

last: Sikora

first: Thomas

last: Boehm


title: ChIP of PolII in S2R+ cells depleted for EJC components or RnpS1 [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Pol II ChIP in control, Mago, Y14, Btz, and eIF4AIII knockdown S2R+ cells


title: DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: DRB-4SU seq of Ctrl and Mago condition in 2 replicates. The 4SU labelling was perofromed for 6 minutes. During the enrichment of the biotinylated RNA on streptavidin beads, the RNA was digested with RNAse T1 to > 100bp to improve the resolution.


title: ChIP of PolII from cells with Mago knockdown, control knockdown, and RnpS1 knockdwon [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Pol II ChIP in  control and Mago depleted S2R+ cells, in duplicates

first: Junaid

last: Akhtar

first: Nastasja

last: Kreim


title: Mnase Sequencing [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Micrococcal nucelase digestion of S2R+ cells in control and Mago knockdown conditions


title: Transcriptomic profile of circulating CD8 T cells in donors with ZIKV infection

city: La JOLLA

first: Alba

last: Grifoni

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Insitute for allergy and immunology

summary: The pandemic rise of Zika virus (ZIKV) has recently commanded the attention of the general public and medical research community alike . The characterization of exact molecular components of immune response associated may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of  ZK-specific CD8 T cells after stimulation with ZK specific peptides comparing it with a generic stimulation with anti-CD3/CD28. Transcriptomic profiling using RNA sequencing was performed on CD8 T cells producing IFNg in comparison with non IFNg producing cells isolated from individuals with Zika infections from  endemic areas of Puerto Rico and US travellers.

overall_design: RNA-sequencing of sorted CD8  T cells from cryopreserved PBMC of 16 subjects with ZIKV infection.

first: Daniela

last: Weiskopf

first: John

last: Pham

first: Gregory

last: Seumois

first: Jason

last: Greenbaum

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette


title: DNA microarray analyses on Schizosaccharomyces pombe Wild type, Δpka1, Δcgs1, and Δppt1 strains.

city: Matsue

first: Ikuhisa

last: Nishida

state: Shimane

address: 1060 Nishikawatsu

department: Life Sciences

institute: Shimane University

summary:
We explored the possibility that the cAMP/PKA pathway affects the expression of the genes involved in Coenzyme Q10 synthesis and other related metabolic pathways. To that end, we performed microarray analyses on Δpka1, Δcgs1, and Δppt1 strains.
An article under submission

overall_design: Examination of gene expression profiles in 4 cell types. The experiment was duplicated.

first: Kazumasa

last: Yokomi

first: Tomohiro

last: Kaino

first: Makoto

last: Kawamukai


title: ChIP of eif4AIII_HA and Y14_HA with Ctrl_HA [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

first: Jean-Yves

last: Roignant

overall_design: ChIP-Seq of HA tagged Y14 and eIF4AIII  along with HA alone controls. Inculded are also the corresponding input controls.

first: Akhtar

last: Junaid

first: Kreim

last: Nastasja


title: ChIP of K4Me3 in Ctr condition and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: K4Me3 ChIP in  control and Mago depleted S2R+ cells, in duplicates


title: ChIP of RnpS1_HA [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: ChIP-Seq of HA tagged RnpS1 with and without RNAseT1 treatment, along with the input control

first: Junaid

last: Akhtar


title: polyA RNA -Seq [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

first: Nastasja

last: Kreim


title: ChIP of Mago [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: ChIP-Seq of HA tagged Mago and HA-Tag alone with and without RNAseT1 treatment. Included are also the corresponding input controls.


title: ChIP of PolII in HeLa cells [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

overall_design: Total PolII ChIP in  control and Magoh depleted HeLa cells.


title: DRB-4sU seq in control and Mago depleted S2R+ cells [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]


title: FGM4 is the cluster-specific transcriptional regulator of FG3_54

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

summary:
Purpose: To assess global changes in gene expression in response to FGM4
Methods: mycelium mRNA profiles of 3-day-old wild-type PH-1,∆fgm4,WT-OE::FGM4 and ∆fg3_54-OE::FGM4 were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.
Results: We mapped more than 31 million clean sequence reads per sample to the Fusarium graminearum PH-1 genome. RNA-seq data confirmed that expression of all FG3_54 cluster member genes was elevated in WT-OE::FGM4 compared to the remaining strains, while expression of neighboring genes outside the cluster remained unchanged.
Conclusions: Our study represents that FGM4 functions as a cluster-specific transcriptional regulator.

overall_design: mRNA profiles of 3-day-old Fusarium graminearum mycelia growing in YEPD medium were generated by deep sequencing using Illumina HiSeq 2500 Sequencing System.

first: Lei-Jie

last: Jia

first: Dong

last: Zhang

first: Wei-Hua


title: A developmental model of human early cardiac valvulogenesis (I)

first: michel

last: PUCEAT

summary: One third of cardiac congenital diseases affect cardiac valves. Genetically modified mice have advanced our understanding of valve development and related pathologies. However, little is known with regard to human valve development.We aimed to derive a novel human pluripotent stem cell model in order to decode the early steps of human valvulogenesis. Human MesP1+mesodermal cells were differentiated toward the fate of second heart field progenitors and then to a selected population of pre-valvular endocardial cells. Gene arrays revealed that these human prevalvular cells (HPVC) express patterns of genes similar to those expressed in the atrioventricular canal (AVC) endocardium of E9.0 mouse embryos. In mice this developmental time precedes endocardial mesenchymal transition (EndoMT),which is required for mature valve formation. HPVC treated with BMP2, cultured onto chick or mouse AVC cushions, or transplanted into the outflow tract or AVC of embryonic chick and mouse hearts, underwent EndoMTin both a Notch-dependent and independent-manner and expressed markers of valve mesenchymal cells and fibroblasts. Similar to the previously described valve interstitial cells (VICs), HPVC also differentiate into tendinous/chondrogenic cells.   Our study indicates tha thuman pluripotent stem cells canrecapitulate early valvulogenesis and thus provide a powerful model to further decipher the origin and lineage contribution of different valvular cell types in humans.

overall_design: experiments were performed in triplicates; references are the HUES24 pluripotent stem cells.

first: Tui

last: Neri

first: Michel

last: Puceat


title: Next Generation Sequencing  of Wild Type and LXRα-Ser196 phosphorylation deficient Murine Hepatic Transcriptomes on a High Fat/High Cholesterol Diet

status: Public on Jan 21 2019

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

institute: University College London

summary: Liver X Receptors (LXRα and β) are ligand-activated transcription factors that play a key role in the control of lipid homeostasis, as well as modulation of immunity and inflammation. LXR activity can be regulated by posttranslational modifications, such as phosphorylation. This study aims to assess changes in the hepatic transcriptional profiles of mice that carry a whole-body phosphorylation deficient knock in mutant of LXRα  (S196A) compared to wild-type (WT) upon being fed a HFHC diet.

overall_design: Liver mRNA profiles of either wild-type (WT) or LXRα-S196A female mice after being fed a High Fat-High Cholesterol diet for 6 weeks. Three biological replicate samples for each group are included. WT samples are used as controls.

first: Natalia

last: Becares


title: Next Generation Sequencing  of Wild Type and LXRα-Ser196 phosphorylation deficient Murine Hepatic Transcriptomes on a Chow diet

summary: Liver X Receptors (LXRα and β) are ligand-activated transcription factors that play a key role in the control of lipid homeostasis, as well as modulation of immunity and inflammation. LXR activity can be regulated by posttranslational modifications, such as phosphorylation. This study aims to assess changes in the hepatic transcriptional profiles of mice that carry a whole-body phosphorylation deficient knock in mutant of LXRα  (S196A) compared to wild-type (WT) fed a chow diet.

overall_design: Liver mRNA profiles of either wild-type (WT) or LXRα-S196A 16-week old female mice on a chow diet. Three biological replicate samples for each group are included. WT samples are used as controls.


title: Circulating extracellular RNA markers of liver regeneration

status: Public on Jan 20 2019

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo S

institute: Mayo Clinic

summary:
Background and Aims: Although the liver can regenerate after sustaining injury, the tools to detect ongoing regeneration are lacking.  The restoration of the liver after hepatectomy involves rapid, sequential, and coordinated changes in gene expression that result in systemic and local changes, such as the activation of progenitor cell populations and proliferation of quiescent hepatocytes.  We postulated that changes in gene expression and regenerative programs could be activated within target cells through the transfer of extracellular RNA across cells or within the circulation, coordinating tissue response, and these extracellular RNA could represent biomarkers of the hepatic regenerative response.
Methods: We identified temporal changes in circulating extracellular RNA at selected time periods up to 24 hours after partial hepatectomy in mice.  (CD-1 males)
Results: A peak increase in extracellular RNA content occurred 6 hours after hepatectomy.  RNA sequencing was performed to identify the circulating extracellular non-coding RNA released after partial hepatectomy.  To identify candidate markers, we used bioinformatics analyses to find the enriched RNA  in the circulation after hepatectomy.  We then performed tissue expression analysis for selected non-coding RNA and correlated it to these findings.  Finally, a digital PCR assay was used to detect and quantify the expression of selected extracellular RNA in serum samples.
Conclusions: Extracellular RNA that were selectively enriched during acute regeneration were detected within the circulation and represent biomarkers of ongoing liver regeneration in mice.  The ability to detect ongoing active regeneration would benefit the evaluation of hepatic recovery after liver injury.

overall_design: Compare small RNA expression in time points after partial hepatectomy in CD-1 mice.

first: Irene

last: Yan


title: Myc activation in breast cancer is due to p53-loss and sustains self-renewal of cancer stem cells (ChIP-Seq)

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

summary:
Purpose: discover the downstream pathways and the mechanism of target activation by the p53:Myc axis in normal mammary and cancer stem cells
Methods: we performed ChIPseq experiments from NMuMG cells grown in adhesion under standard conditions
Results: the p53:Myc axis orchestrates its transcriptional response in mammary-epithelial cells via a dual and overlapping mechanism: i) a tightly controlled epistasis driven by p53 and executed by Myc, and ii) a co-operative double occupancy of their downstream effectors at different regulatory regions

overall_design: Examination p53 and Myc binding sites in murine mammary epithelial cells

first: Angela

last: Santoro

first: Thalia

last: Vlachou

first: Lucilla

last: Luzi

first: Cristina

last: Pasi

first: Linsey

last: Reavie

first: Giorgio

last: Melloni

first: Paola

last: Bonetti

first: Pier


title: Myc activation in breast cancer is due to p53-loss and sustains self-renewal of cancer stem cells (RNA-Seq)

summary:
Purpose: discover the downstream pathways and the mechanism of target activation by the p53:Myc axis in normal mammary and cancer stem cells
Methods: we established mammosphere culture from normal and tumoral murine mammary glands and extracted RNA for expression analysis at passage 3 of the serial replating assay
Results: These data demonstrate the existence of a set of 189 p53 and Myc common targets, which are implicated in the regulation of mitosis and are up-regulated in the ErbB2-tumor mammospheres, and suggest that these genes are crucial for the regulation of CSC numbers.

overall_design: Examination of expression profile in mammospheres derived from WT, L-MyCER, ErbB2-tumor and p53-/- murine mammary cells


title: ChIP-seq analysis of normal and HBx transgenic mouse liver

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

summary: A genome-wide integrated ChIP-seq analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in histone modification and RNA pol II enrichment pattern between cancer and normal liver cells.

overall_design:
High-throughput sequencing analysis of ChIP (H3, H3K4me3, H3K27me3, H3K36me3, RNA polymerase II) at 3 month old age mouse liver

Not all samples in this series have associated SRA records. For samples with unavailable fastq files (GSM2042663, GSM2042665, GSM2042666, GSM2042667), non-fastq formatted sequence files were submitted. These are available as sample supplementary files.

first: Sun-Min

last: Lee


title: Myc activation in breast cancer is due to p53-loss and sustains self-renewal of cancer stem cells

overall_design: Refer to individual Series


title: Tristetraprolin (TTP) regulated splenic transcriptome in "TTPΔARE" mice

status: Public on Jan 19 2019

city: Durham

first: Perry

last: Blackshear

address: 101 Alexander Dr.

institute: NIEHS

summary: Tristetraprolin (TTP)  binds to specific AU-rich elements in the 3'UTR of certain transcripts and regulates post-transcriptional gene expression by increasing the rate of mRNA turnover.  Here, we generated a novel TTP mouse line (TTPΔARE) with a 136 base deletion in the 3'UTR AU-rich region of TTP mRNA, which resulted in a moderate increase in TTP protein expression in many tissues.  In this study, we evaluated the effects of the moderate TTP overexpression on the overall pattern of gene expression in spleen, to investigate the effect of this mutation on mRNA targets of TTP under normal conditions.  We utilized "TTPΔARE" (136 b deletion in the 3'UTR AU-rich region of Zfp36 mRNA) mice that overexpress TTP and compared the transcriptomic changes to the littermate "WT" mice.  Spleen mRNA from four WT and four "TTPΔARE" mice were subjected to mRNA-Seq.  All the animals used in this study were males between the ages of 8-12 weeks and were on a C57BL/6 background.

overall_design: Examination of gene expression differences in mouse spleen from 4 wild-type and 4 TTPΔARE male mice aged 8-12 weeks

first: Sonika

last: Patial

first: Weichun

last: Huang

first: Debbie

last: Stumpo

first: Gordon

last: Flake


title: Genome-wide analysis of astrocyte XBP1 activation and regulation of transcriptional programs in CNS cells during EAE.

status: Public on Jan 18 2019

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

summary: We report XBP1 activation and regulation of pro-inflammatory signaling in astrocytes, microglia, and CNS-recruited pro-inflammatory monocytes during EAE.

overall_design: Analysis of RNA expression in astrocytes, microglia, and monocytes sorted by flow cytometry. Mice transduced with astrocyte-targeting lentiviruses encoding non-targeting or Xbp1-targeting shRNAs.

first: Emily

last: Tjon

first: Francisco

last: Quintana


title: Genome-wide analysis of XBP1 binding in astrocytes during EAE

summary: We report XBP1 activation and analysis of XBP1 binding to pro-inflammatory genes in astrocytes during EAE compared to naïve mice

overall_design: IP of XBP1 in astrocytes from EAE mice (n=3) versus naïve mice (n=2); IP samples were normalized to 10% input


title: Environmental control of astrocyte pathogenic activities in CNS inflammation

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


title: Time-dependent transcriptional changes in neutrophil phenotype

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC


title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing

first: Jean-Yves

last: Roignant

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Genome-wide analysis of chromatin profile in astrocytes isolated from EAE mice transduced with astrocyte-specific Xbp1-targeting or non-targeting lentiviruses.

summary: We report XBP1 activation and regulation of pro-inflammatory gene expression in astrocytes during EAE.

overall_design: Mice transduced with non-targeting (n=4) or Xbp1-targeting (n=3) lentiviruses. EAE induced in mice.


title: Transcriptome of neutrophils deficient in cxcr4 and arntl

summary: Our study aims to analyze time-dependent changes in neutrophil phenotype

overall_design: Blood neutrophils were isolated based on Ly6G staining, then standard RNA extraction procedures were performed. This samples were extracted at ZT13.

first: A

last: Hidalgo

first: J

middle: M

last: Adrover


title: Determining the impact of the Bromodomain and extra-terminal inhibitor JQ1 on the GATA2 cistrome in castrate-resistant prostate cancer

status: Public on Jan 17 2019

city: Cambridge

first: Lewis

last: Chaytor

address: Hutchison/MRC Research Centre, Cambridge biomedical campus

department: Department of Oncology

institute: Cambridge University

summary: To determine the impact of the Bromodomain and extra-terminal (BET) inhibitor JQ1 on the GATA2 cistrome in castrate-resistant prostate cancer we performed GATA2 ChIP-seq in the presence and absence of JQ1 and assessed differential binding upon JQ1 treatment for 24 hours. We first determined the GATA2 cistrome using our GATA2 ChIP-seq data. Overlapping this with previously published ChIP-seq data for the BET family of proteins (Asangani et al., 2014), we identified a substantial proportion of GATA2 genomic binding sites which are co-occupied by a BET protein. We then quantified differential binding of GATA2 upon JQ1 treatment genome-wide.

overall_design: Examination of GATA2 chromatin occupancy in the presence and absence of JQ1 in the VCaP cell line. Experiment was performed in duplicate. 30 million reads were sequenced for ChIP and Input samples.

first: Matthew

last: Simcock

first: Sirintra

last: Nakjang

first: Richard

last: Heath

first: Laura

last: Walker

first: Craig

last: Robson

first: Dominic

last: Jones

first: Luke

last: Gaughan