title: CD95/Fas increases stemness in cancer cells by inducing a STAT1 dependent Type I interferon response


title: Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification

status: Public on Oct 10 2016

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CD95/Fas increases stemness in cancer cells by inducing a STAT1 dependent Type I interferon response [array]

status: Public on Feb 16 2017

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: CD95 was found to be important for both the formation of CSCs and their maintenance.  Using a stable isotope labeling by amino acids in cell culture (SILAC) analysis  we have now identified STAT1 as a critical gene that mediates the CSC-driving activity of CD95.  We report that chronic stimulation of CD95 by either agonist antibodies, soluble CD95L or stably  expressed membrane CD95L causes both serine and tyrosine phosphorylation of STAT1 and activation  of STAT1 regulated genes. The genes most significantly induced were part of an interferon (IFN)-related  DNA damage resistance signature (IRDS) recently identified in a radiation resistant squamous cell  carcinoma cell line Nu61 when compared to parental SCC61 cells. The IRDS was found to strongly correlate with therapy resistance (chemotherapy and radiation) in multiple cancer cells as well as in 5 human  primary cancers. We now report that CD95 stimulation of breast cancer cell lines or the SCC61 cells induces  the upregulation of Type I IFNs that bind to both Type I receptors IFNAR1 and IFNR2 resulting in activation  of JAK kinases, activation of STAT1 and induction of a number of STAT1-regulated genes. This process can be  inhibited by active caspases. Consequently, we identified Type I IFNs as drivers of cancer stemness.  Knockdown of STAT1 using either siRNAs or shRNAs, or deleting two independent sites in the STAT1 gene in MCF-7  cells using the CRIPSR/Cas9 gene editing system resulted in a loss of the ability of CD95 to increase stemness.  This identifies STAT1 as a critical mediator of the CSCs-inducing activity of CD95.

overall_design: Two replicates per condition

middle: E

first: Abdul

middle: S

last: Qadir

first: Paolo

last: Ceppi


title: Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification [Mouse smallRNA-Seq]

summary: Primordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells (PGCLCs). Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster. The dynamics of specification and epigenetic reprogramming show species-specific differences, in particular markedly slower reprogramming kinetics in the human germline. Differences in developmental kinetics between species may be explained by differential regulation of epigenetic modifiers. Our work establishes a robust and faithful experimental system of the early events of epigenetic reprogramming and its regulation in the germline.

overall_design: smallRNA-seq of mouse in vitro PGC-like cells, PGCs and ESCs

first: Rebecca

middle: V

last: Berrens

first: Ferdinand

last: von Meyenn

first: Wolf

last: Reik


title: Injury-activated endocardium plays structural and signalling roles in zebrafish heart regeneration

status: Public on Mar 31 2017

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

summary: The zebrafish heart remarkably regenerates after a severe ventricular damage followed by inflammation, fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D-whole mount imaging in injured hearts revealed that GFP-labelled endocardial cells in ET33mi-60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury (dpci). Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury, endocardial cells strongly up-regulate the Notch pathway ligand delta like4 (dll4) and the Notch receptors notch1b, notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain- and loss-of-function experiments revealed that Notch is required for the organization of the endocardium, attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration.

overall_design: RNA was extracted from apical tip of heart ventricles 72h after cryoinjured adult zebrafish heart treated with DMSO (Controls) or RO gamma secretase inhibitor at 24 and 48h post injury.

first: Juliane

last: Münch

first: Dimitrios

last: Grivas

first: Alvaro

last: González-Rajal

first: José

last: Luis de la Pompa


title: Sequential Notch activation regulates ventricular chamber development

status: Public on Feb 12 2016

summary: Ventricular chambers are essential for the rhythmic contraction and relaxation that occurs in every hearbeat throughout life. Congenital abnormalities in ventricular chamber formation cause severe human heart defects. How the early trabecular meshwork of myocardial fibres forms and subsequently develops into mature chambers is still poorly understood. Here we show that Notch signalling first connects chamber endocardium and myocardium to sustain trabeculation and later coordinates ventricular patterning and compaction with coronary vessel development to give rise to the mature chamber via a temporal sequence of ligand signalling determined by the glycosyltransferase Manic Fringe (Mfng). The early endocardial expression of Mfng favours Dll4-Notch1 signalling, Which induces trabeculation in the developing ventricle.Ventricular maturation and compaction in turn require Mfng and Dll4 downregulation in the endocardium, Which allows myocardial Jag1- And Jag2- Signalling to Notch1 in this tissue.Timely and spatial perturbation of this signalling equilibrium severely disrupts heart chamber formation. Our results open a new research avenue into the pathogenesis of cardiomyopathies.

overall_design: Dll4 and Notch1 conditional KOs using Nfact1 and/or Tie2 driven Cre expression: RNA was isolated from pooled whole hearts of 8 (Nfact1) or 9 (Tie2) E9.5 embryos per replicate. Dll4flox;Nfatc1-Cre and WT siblings (4 KO and 4 WT replicates), Notch1flox;Nfatc1-Cre and WT siblings (3 KO and 2 WT replicates), Dll4flox;Tie2-Cre and WT siblings (3 KO and 3 WT replicates). Jag1, Jag2 and Jag1Jag2 conditional KOs using cTnT driven Cre expression: RNA was isolated from pooled heart ventricles of 4 E15.5 embryos per replicate. Jag1flox;cTnT-Cre and WT siblings (3 KO and 3 WT replicates), Jag2flox;cTnT-Cre and WT siblings (3 KO and 2 WT replicates). Jag1flox;jag2flox;cTnT-Cre and WT siblings (3 KO and 2 WT replicates). MFng Gain Of Function using Tie2 driven Cre expression: RNA was isolated from pooled heart ventricles of 4 E15.5 embryos per replicate. MFng;Tie2-Cre and WT siblings (4 GOF and 4 WT replicates). For Dll4, Noth1 and Jag1 KOs, libraries were prepared using the standard Illumina TrueSeq RNASeq library preparation kit and sequenced in a GAIIx Illumina sequencer using a 75bp single end elongation protocol. For Jag2 and Jag1Jag2 KOs and MFng GOF libraries were prepared prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina and sequenced in a HiSeq2500 Illumina sequencer using a 61bp single end elongation protocol

first: Gaetano

last: D'Amato

first: Guillermo

last: Luxán

first: Gonzalo

last: del Monte

first: Beatriz

last: Martínez-Poveda

first: Carlos

last: Torroja

first: Wencke

last: Walter

first: Matthew

last: Bochter

first: Rui

last: Benedito

first: Susan

last: Cole

first: Fernando

last: Martinez

first: Anna-Katerina

last: Hadjantonakis

first: Akiyoshi

last: Uemura

first: Luis

middle: J

last: Jiménez-Borreguero

middle: L


title: Classical dendritic cells are required for dietary antigen-mediated peripheral regulatory T cell and tolerance induction II

status: Public on Mar 28 2016

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Oral tolerance prevents pathological inflammatory responses towards innocuous foreign antigens via peripheral regulatory T cells (pTreg cells). However, whether a particular subset of antigen-presenting cells (APCs) is required during dietary antigen exposure to instruct naïve CD4+ T cells to differentiate into pTreg cells has not been defined. Using myeloid lineage-specific APC depletion in mice, we found that monocyte-derived APCs are dispensable, while classical dendritic cells (cDCs) are critical for pTreg cell induction and oral tolerance. CD11b¬– cDCs from the gut-draining lymph nodes efficiently induced pTreg cells, and conversely, loss of IRF8-dependent CD11b– cDCs impaired their polarization, although oral tolerance remained intact. These data reveal the hierarchy of cDC subsets in pTreg cell induction and their redundancy during oral tolerance development.

overall_design: Sorted naïve CD45.1 OT-II CD4 T cells  were co-cultured with four dendritic cell subpopulations sorted from mouse mesenteric lymphnodes. 24h later OT-II cells  were sorted again and compared in their gene expression profile.

first: Daria

last: Esterházy

first: Jakob

last: Loschko

first: Mariya

last: London

first: Veronica

last: Jove

first: Daniel

last: Mucida


title: RNA-seq of hESC samples upon loss of UPF1.

status: Public on Jun 17 2016

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

summary: Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-b and BMP signaling, which we found NMD acts through to influence definitive endoderm vs. mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages.

overall_design: Examination of differential gene expression in hESCs upon loss of UPF1.

first: Chih-Hong

last: Lou

first: Jennifer

last: Chousal


title: Wild - type and PU.1 Q202L mutant mice ST - HSC (lin- c-kit+ Sca-1+ CD150- CD48-) and GMP (lin- c-kit+ Sca-1- CD16/32hi CD34+)

status: Public on Mar 07 2016

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

summary: Identification of differentially regulated genes in the PU.1 Q202L point mutant that disrupts association with c-Jun. The goal was to identify PU.1 target genes that depend on the co-activation of PU.1 by c-Jun. Mice have normal ST-HSC but lack normal GMP, so a population of GMP-like cells was used in the mutant.

overall_design: Sorted cell populations from homozygous PU.1 Q202L

first: Xinhui

last: Zhao

first: Boris

last: Bartholdy

first: Yukiya

last: Yamamoto

first: Erica

middle: K

last: Evans

first: Meritxell

last: Alberich-Jorda

first: Philipp

last: Staber

first: Touati

last: Benoukraf

first: Pu

last: Zhang

first: Junyan

first: John

middle: D

last: Crispino

first: Trang

last: Hoang

middle: A

middle: G

last: Tenen


title: mRNA and miRNA expression data from human Ewing's sarcoma (ES)

status: Public on Jul 14 2015

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

country: Japan

institute: Oita University

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

platform_organism:
Homo sapiens
synthetic construct


title: microRNA Expression data from human Ewing's sarcoma (ES)

summary:
To explore possible oncogenic factors in ES, we used a microarray-based approach to profile changes in the expression of miRNAs in five ES cell lines and human mesenchymal stem cells (hMSCs).
We used a microarray-based approach to profilein the mRNA expression of ES

overall_design: Human ES cell lines were analyzed with genome-wide expression arrays.

first: Kazuhiro

last: Tanaka


title: mRNA Expression data from human Ewing's sarcoma (ES)

summary:
To explore possible oncogenic factors in ES, we used a microarray-based approach to profile changes in the expression of mRNAs in five ES cell lines and human mesenchymal stem cells (hMSCs).
We used a microarray-based approach to profilein the mRNA expression of ES


title: Mistimed sleep disrupts circadian regulation of the human blood transcriptome

status: Public on Jan 23 2014

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

summary: 22 healthy volunteers without sleep disorders were resident in an environmental scheduling facility and participated in a forced-desynchrony protocol, in which the sleep-wake cycle and the associated fasting-feeding cycle is scheduled to a 28-hour period, of which one third (i.e. 9h 20min) is scheduled for sleep. Under these conditions, during which light levels in the waking episode are kept low and sleep is scheduled in darkness,  the phase of the melatonin rhythm occurred at approximately the same clock time during the first (D1) and fourth (D4) 28-h cycle and there were no major changes in either the amplitude or the waveform of this rhythm. During D1 and D4 7 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 287 samples comprising 22 human subjects, for which 14 samples across multiple time-points/sleep condition were collected.

first: Carla

last: Moller-Levet

first: Simon

last: Archer

first: Giselda

last: Bucca

first: Ana

last: Slak

first: Renata

last: Kabiljo

first: Daan

last: van der Veen

first: Alpar

last: Lazar

last: Groeger

first: Nayantara

last: Santhi

first: Malcolm

last: von Schantz

first: Colin

middle: P

last: Smith

first: D

last: Dijk


title: The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

status: Public on Jun 21 2016

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

country: Canada

institute: McGill University

summary: Nitrogen (N) fertilization is an important abiotic factor for the growth of potato (S. tuberosum) because of its potential effects on yield. Because excess N in the soil runs off into water systems and negatively impacts the environment, studies on N use by the plant are key to decrease N-fertilizer use. Three commercial potato cultivars (Shepody, Russet-Burbank and Atlantic) were grown under two different rates of applied N-fertilizer (0 kg N ha-1 and 180 kg N ha-1) to obtain more information on the underlying gene regulation mechanisms associated with N. Plants with no added N had significantly lower concentrations of petiole nitrates, chlorophyll level indices, biomass and yield per hectare. Total mRNA samples were taken at two different time-points during the growth season and used for sequencing. The results for each cultivar and time-point were analysed separately to find differentially expressed genes. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed in plants from all potato cultivars when they were grown with added N-fertilizer. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed to find overrepresented motifs using three motif discovery algorithms (Seeder, Weeder and MEME). Nine different motifs were found, indicating potential gene regulatory mechanisms for potato under N-deficiency.

overall_design: Differential gene expression in leaf tissue of S. tuberosum from three different cultivars (Shepody, Russet-Burbank and Atlantic), at two different time points, with four repetitions per treatment, using an Illumina HiSeq 2000.

first: Helen

middle: H

last: Tai

first: Martin

last: Lague

first: Jose

last: Galvez

first: Bernie

last: Zebarth


title: Genetic identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue [Illumina SNP array]

status: Public on Jun 27 2011

first: Christopher

middle: David

last: Brown

department: Human Genetics

institute: University of Chicago

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

summary: Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. We have conducted two independent studies to identify genetic, including both SNPs and copy-number variants, and environmental determinants of human liver gene expression variation. We analyzed two sets of primary livers (primary dataset: n=220; replication dataset: n=60) using Agilent and Illumina expression arrays and Illumina SNP genotyping (550K). At least 30% of genetic and non-genetic factors that meet genome-wide significance (p <1 x10-9) in one study fail to replicate in the second study, suggesting that artifacts, like unknown SNPs that affect RNA-probe hybridization or hidden confounding variables, often result in statistically significant but biologically irrelevant correlations. These data confirm the value of independent replications to enrich for truly predictive eQTLs, and given our study design we are able to identify hundreds of reproducible correlations. We show that such information can be used to provide insights into disease-relevant phenotypes, with specific examples including eQTLs related to lipid levels (e.g. LDL cholesterol), immune system function (e.g. HLA), and drug response (e.g. warfarin). Furthermore, in the interest of both fine-mapping and mechanistic annotation, we hypothesized that promoters and 3’UTRs are enriched for causal eQTL variants. Therefore, we re-sequenced the promoter and 3’UTR regions of 25 genes with eQTLs, cloned each discovered haplotype, and quantified their impact on transcription using a luciferase-based assay. These data reveal multiple examples of robust, haplotype-specific in vitro functional differences that correlate directly with in vivo expression levels. This suggests that many eQTLs can be rapidly fine-mapped to one or a few single-nucleotide variants and mechanistically characterized using such assays. Integration of functional assays with eQTL discovery, and eQTLs with complex trait associations, is a powerful means to exploit GWAS data and improve their biological interpretability.

overall_design: RNA expression levels were quantified on Agilent gene expression microarrays for 224 normal human livers.  Genotypes were also derived from these samples using Illumina SNP chips.  Expression quantitative trait loci were identified by genome wide association mapping.

first: Federico

last: Innocenti


title: Resveratrol supplementation does not improve metabolic function in non-obese women with normal glucose tolerance

status: Public on Jan 02 2013

city: St. Louis

first: C. Charles

last: Gu

address: 660 S Euclid Ave

institute: Washington University

summary: Resveratrol has been reported to improve metabolic function in metabolically-abnormal rodents and humans, but has not been studied in non-obese people with normal glucose tolerance.  We conducted a randomized, double-blind, placebo-controlled trial to evaluate the metabolic effects of 12 weeks of resveratrol supplementation (75 mg/day) in non-obese, postmenopausal women with normal glucose tolerance.  Although resveratrol supplementation was well-tolerated and increased plasma resveratrol concentration without adverse effects, it did not change body composition, resting metabolic rate, plasma lipids, or inflammatory markers.  A two-stage hyperinsulinemic-euglycemic clamp procedure, in conjunction with stable isotopically-labeled tracer infusions, demonstrated that resveratrol did not increase liver, skeletal muscle, or adipose tissue insulin sensitivity.  Consistent with the absence of in vivo metabolic effects, resveratrol did not affect its putative molecular targets, including AMPK, Sirt1, Nampt, and Pgc-1α, in either skeletal muscle or adipose tissue.  These findings demonstrate that resveratrol supplementation does not have metabolic effects in non-obese women.

overall_design: We compared gene expression profile in subcutaneous abdominal adipose tissue and skeletal muscle (vastus lateralis) biopsy samples obtained from non-obese people before and after 1) placebo (PLC), 2) resveratrol (RES), and 3) calorie restriction (CR) intervention.

first: Jun

last: Yoshino

first: Caterina

last: Conte

first: Luigi

last: Fontana

first: Bettina

last: Mittendorfer

first: Shin-ichiro

last: Imai

first: Kenneth

middle: B

last: Schechtman

first: C

middle: C

first: Iris

last: Kunz

first: Flippo

middle: R

last: Fanelli

first: Bruce

middle: W

last: Patterson

first: Samuel

last: Klein


title: De novo assembly in defense against pests in Pinus massoniana

status: Public on Aug 24 2015

city: Nanning

first: Ying

last: Hu

address: Daxue

country: China

institute: Guangxi University

summary: We sequenced mRNA from the insect-resistant and poor insect resistance Pinus massoniana to discover metabolic pathways and genes that are involved in defense against pests.

overall_design: Examination of mRNA levels in strain insect-resistant and poor insect resistance Pinus massoniana

first: Hu

last: Chen

first: Zhangqi

last: Yang


title: Classical dendritic cells are required for dietary antigen-mediated peripheral regulatory T cell and tolerance induction

first: Thiago

last: Oliveira


title: Neoadjuvant anastrozole alone or with gefitinib in early breast cancer

status: Public on Jan 08 2014

city: Hørsholm

first: Thomas

last: Jensen

address: Venlighedsvej 1

department: lab

country: Denmark

institute: MPI

summary: Trial 223 was a placebo-controlled trial of neoadjuvant anastrozole  alone or with gefitinib in early breast cancer. We used patients from  arm B and C: anastrozole 1mg/d for the duration of the 16 week period  plus placebo 1 tablet/d orally for 2 weeks. Patients in arm B were  followed by gefitinib 250mg/d orally for 14 weeks whereas patients in  arm C continued with placebo for 14 weeks.

overall_design: 96 samples

first: Steen

last: Knudsen

first: Anker

last: Hansen

first: Wiktor

last: Mazin

first: Justin

last: Lindemann

first: Naomi

last: Laing

first: Elizabeth

last: Anderson