title: Developmental stage specific chromosome architecture in human erythroid cells (ChIP-seq)

city: Guangzhou

first: Peng

last: Huang

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

summary: Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and find that globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detect distinct folding patterns at the developmentally controlled b-globin locus. Specifically, new fetal stage-specific contacts are uncovered between a region separating the fetal (g-) and adult (b-) globin genes (encompassing the HBBP1 and BGLT3 non-coding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus. In contrast, in adult cells the HBBP1-BGLT3 region contacts the embryonic e-globin gene, physically separating the fetal globin genes from the enhancer (LCR). Removal of the HBBP1 gene strongly reactivates g-globin expression, accompanied by increased LCR-g-globin and decreased BGLT3-e-globin interactions, mimicking the effects of deleting the fetal globin repressor BCL11A. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.

overall_design: We compared the genome wide CTCF binding profiles of fetal and adult human erythroblasts by ChIP-seq.

first: Gerd

last: Blobel


title: Developmental stage specific chromosome architecture in human erythroid cells

status: Public on Sep 18 2017

state: Guangdong

country: China

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The effect of early life antibiotic treatment in germ-free or SPF colonized C57BL/6 mice

city: New York

first: Thomas

middle: W

last: Battaglia

state: NY

address: 423 E 23rd Street

department: Medicine

country: USA

institute: NYU School of Medicine

summary: Broad-spectrum antibiotics are frequently prescribed to children. The period of early-childhood represents a time where the developing microbiota may be more sensitive to environmental perturbations, which thus might have long-lasting host consequences. We hypothesized that even a single early-life broad-spectrum antibiotic course at a therapeutic dose (PAT) leads to durable alterations in both the gut microbiota and host immunity. In C57BL/6 mice, a single early-life tylosin (macrolide) course markedly altered the intestinal microbiome, and affected specific intestinal T-cell populations and secretory IgA expression, but PAT-exposed adult dams had minimal immunologic alterations. No immunological effects were detected in PAT-exposed germ-free animals; indicating that microbiota are required for the observed activities. Transfer of PAT-perturbed microbiota led to delayed sIgA expression indicating that the altered microbiota is sufficient to transfer PAT-induced effects. PAT exposure had lasting and transferable effects on microbial community network structure. Together these results indicate the impact of a single therapeutic early-life antibiotic course altering the microbiota and modulating host immune phenotypes that persist long after exposure has ceased.

overall_design: Nanostring gene expression analysis was performed on RNA extracted from the terminal ileum of control and Tylosin-exposure germ-free and SPF mice.

first: Victoria

middle: E

last: Ruiz

first: Zachary

middle: D

last: Kurtz

first: Luc

last: Bijnens

first: Amy

last: Ou

first: Isak

last: Engstrand

first: Xuhui

last: Zheng

first: Tadasu

last: Iizumi

first: Briana

middle: J

last: Mullins

first: Christian

middle: L

last: Meuller

first: Ken

last: Cadwell

first: Richard

last: Bonneau

first: Guillermo

middle: I

last: Perez-Perez

first: Martin

last: Blaser


title: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (Perturbation-RNAseq)

city: Boston

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

summary: Concerted efforts over past decades have established a thorough understanding of the canonical somatic DNA methylation landscape as well as its systematic misregulation across most human cancers.  However, the underlying mechanism that directs this genome-scale transformation remains elusive, with no clear model for its acquisition or understanding of its potential developmental utility. Here we present base pair resolution analysis of global remethylation from the hypomethylated state of the preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions: while the proximal epiblast establishes a canonical CpG-density dependent pattern found in somatic cells, the extraembryonic epigenome becomes substantially more mosaic.  Moreover, this alternate pattern includes specific de novo methylation of hundreds of CpG island promoter containing genes that function in early embryonic development and are orthologously methylated across an extensive cohort of human cancers.  From these data, we propose a model where the evolutionary innovation of extraembryonic tissues in eutherian mammals required cooption of DNA methylation-based suppression as an alternate pathway to the embryonically utilized Polycomb group proteins, which otherwise coordinate germ layer formation in response to extraembryonic cues at the onset of gastrulation.  Moreover, we establish that this decision is made deterministically downstream of the promiscuously utilized, and frequently oncogenic, FGF signaling pathway and utilizes a novel combination of epigenetic cofactors.  Recruitment of this silencing mechanism to developmental genes during cancer therefore reflects the misappropriation of an innate regulatory pathway that may be spontaneously sampled as an alternate epigenetic landscape within somatic cells.

overall_design: Comparison of gene expression patterns in Extraembryonic Ectoderm and cancer

last: Smith

first: Julie

last: Dongahey

first: Davide

last: Cacciarelli

first: Franziska

last: Michor

first: Alexander

last: Meissner


title: Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation

status: Public on Sep 19 2017

city: Research Triangle Park

first: Pishun

last: Li

state: NC

address: 111 T.W. Alexander Drive

department: ESCBL

institute: National Institute of Environmental Health Sciences

type: Methylation profiling by high throughput sequencing


title: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (Perturbation-RRBS)

overall_design: Comparison of DNA methylation patterns in Extraembryonic Ectoderm and cancer

first: Zachary


title: A single early-in-life antibiotic course has long-lasting effect on microbial network topology and host immunity, in a murine model

first: Thomas

last: Battaglia


title: The effect of a single or multiple pulsed antibiotic exposure in C57BL/6 mice

overall_design: Nanostring gene expression analysis was performed on RNA extracted from the terminal ileum of control, PAT1 and PAT3 mice at week 7 of life.

first: Victoria

last: Ruiz

last: Kurtz

first: Luc

last: Bijnens

first: Amy

last: Ou

first: Isak

last: Engstrand


title: miCLIP, RNA-Seq, and Ribo-Seq in MOLM13 cells

first: Brian

middle: Frederick

last: Pickering

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: We studied the following conditions: m6A RNA methylation in MOLM13 AML cells; METTL3 deficiency on gene expression and translational efficiency

overall_design: miCLIP was performed on poly(A) mRNA from MOLM13 as previously described(see GSE63753), RNA-Seq and Ribo-Seq were performed on MOLM13 cells four days after lentiviral transduction with a control shRNA or two independent hairpins targeting METTL3 (shRNA#9 and shRNA#12).  All experiments were performed in biological triplicate.

middle: F

first: Michael

last: Kharas

first: Samie

middle: R

last: Jaffrey


title: Gene expression profile of A549 cells cultured under a new 3D culture conditions

status: Public on Sep 17 2017

city: Shiraoka-shi

first: Natsuki

last: Abe

state: Saitama

address: Shiraoka 1470

country: Japan

institute: NISSAN CHEMICAL INDUSTORIES, LTD

summary:
Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval.  Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that is suitable for imaging analysis and improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of LA717, a seaweed-derived polysaccharide.
Gene microarrays were used to observe the global gene expression in A549 cells cultured with adhesion condition (2D, control) or with low adhesion condition (LA717) and identified distinct classes of up or down-regulated genes.

overall_design: A549 cells were cultured for 7 days in three different conditions as follows. (1) Normal attachment plate with normal medium (as control), (2) low-attachment plate with normal medium, (3) low-attachment plate with LA717 containing medium. Each sample was collected three times.


title: Genome-wide maps of H3K9me3 with tethered heterochromatin machinery

status: Public on Sep 16 2017

city: Eugene

first: Jordan

middle: David

last: Gessaman

state: OR

address: 355 Streisinger Hall

department: Biology, Institute of Molecular Biology

institute: University of Oregon

summary: Purpose: The goal of this study is to characterize the domain(s) of H3K9me3 induced by artifical localization of heterochromatin factors in wild-type and mutant backgrounds.

overall_design: Methods: ChIP-seq was performed on each sample (H3K9me3 ChIP; six samples total). qRT-PCR validation was done with SYBR Green reagent.

first: Eric

middle: U

last: Selker


title: mRNA and lncRNA expression in cholangiocarcinoma

first: Bowei

last: Han

address: No. 651, Dongfeng Road East

institute: SUN YAT-SEN UNIVERSITY CANCER CENTER

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

summary: Long noncoding RNAs (lncRNAs) are known to play important roles in different cell contexts, including cancers. However, little is known about lncRNAs in cholangiocarcinoma (CCA), a cholangiocyte malignancy with poor prognosis, associated with chronic inflammation and damage to the biliary epithelium. This study determined whether lncRNAs were dysregulated and participated in disease diagnosis or pivotal inflammation pathways through a genome-wide lncRNA screening and functional analysis. We firstly identified a large number of lncRNAs abnormally expressed between 9 pairs of cancerous and adjacent tissues of CCA, and between intra-hepatic CCA and extra-hepatic CCA through a genome-wide profiling. Our findings show that lncRNAs may be potential biomarkers of CCA progression.

overall_design: LncRNA and mRNA expression profile of 9 pairs of cancerous and adjacent tissues of cholangiocarcinoma were identified using RNA microarray. 3 normal bile duct tissue were used as normal control.

first: Yue-Qin

last: Chen

first: Wentao

last: Wang


title: AltitudeOmics gene expression data

city: Aurora

first: Robert

middle: C

last: Roach

state: CO

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

institute: University of Colorado

summary: Acclimatization to high altitude over 21 days, and upon re-ascent 7 and 21 days post-descent. See Subudhi et al. (2014) PLoS One 9(3):e92191, PMCID PMC3962396, PMID 24658407 for experiment details.

overall_design: 112 total samples representing 21 subjects at 7 time points (not all subjects represented at all time points) were taken. Significance was determined by change vs. baseline (sea level). Genes represented by probesets showing significant change vs. baseline (Benjamini-Hochberg FDR q-value less than or equal to 0.01) at any time point were subject to WGCNA clustering.

first: Daniel

last: Dvorkin


title: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer

first: Jiantao

last: Shi


title: ncRNA transcription-induced changes in nuclear architecture directs with high precision enhancer-promoter interaction

city: La Jolla

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

department: Biology

institute: UCSD

summary: It is now well established that transcriptional enhancers dictate with high precision  lineage-specific programs of gene expression. However, it has remained an enigma as to  how distally located enhancers, while separated by vast genomic distances, selectively  target their cognate promoters. To explore the mechanism that underpins this  precision-directed targeting we have examined the nuclear architecture of a  super-enhancer that regulates the expression of Bcl11b. Bcl11b is a transcriptional  regulator that specifies T cell fate and suppresses T-cell malignancy. We show that in T  cell progenitors the Bcl11b super-enhancer is located at the nuclear lamina in a  transcriptionally silent environment. We found that during T cell commitment the  super-enhancer repositioned from the lamina to the transcriptionally permissive  compartment. In search for candidate factors that reposition the super-enhancer we  identified ThymoD (Thymocyte-Differentiation Factor). ThymoD expression pattern in T cell progenitors immediately precedes that of Bcl11b. We  show that ThymoD transcription is required to activate Bcl11b expression, to promote T  cell fate, and to suppress the development of T cell malignancy. We found that ThymoD  acts in cis to reposition the Bcl11b super-enhancer from the lamina to the nuclear interior.  We demonstrate that ThymoD brings the Bcl11b super-enhancer and promoter into close  spatial proximity by modulating CTCF and cohesin occupancy and chromatin folding  across the Bcl11b intergenic region. These data reveal how ncRNA transcription  modulates nuclear location and chromatin folding permitting distally located enhancers to  select with high precision their cognate promoter regions.

overall_design: Adult hematopoietic stem cells (aHSCs) were obtained from either WT or ThymoD+/p(A) or ThymoD p(A)/p(A) bone marrow. aHSCs were cultured on OP9-DL1 stromoal cells with Flt3-L and IL7. DN2 cells were sorted by AriaII. 6 ATAC samples from in-vitro cultured DN2 cells  (duplicates, WT, ThymoD +/p(A) and ThymoD p(A)/p(A)), 6 RNAseq samples from in-vitro cultured DN2 cells  (triplicates, WT, ThymoD p(A)/p(A)), 6 SMC3 ChIP-seq samples from in-vitro cultured DN2 cells  (duplicates, WT, ThymoD +/p(A) and ThymoD p(A)/p(A)), 4 CTCF ChIP-seq samples from in-vitro cultured DN2 cells  (WT, duplicates ThymoD+/- and ThymoD p(A)/p(A)), 3 H3K4me1 ChIP-seq samples from in-vitro cultured DN2 cells  (WT, ThymoD +/p(A) and ThymoD p(A)/p(A)), 3 H3K4me3 ChIP-seq samples from in-vitro cultured DN2 cells  (WT, ThymoD+/- and ThymoDp(A)/p(A)), 3 H3.3 ChIP-seq samples from in-vitro cultured DN2 cells  (WT, ThymoD+/- and ThymoDp(A)/p(A)), 2 Hi-C samples from in-vitro cultured DN2 cells (WT and ThymoDp(A)/p(A)). This study includes a re-analysis of Hi-C samples GSM987816 and GSM987818 from GSE40173. Tag counts for the re-analyzed HiC samples and the wildtype HiC sample (GSM2418375) were normalized to the sample with lowest sequencing depth. For multipotent progenitors (GSM987816), pro-B (GSM987818) and wild-type DN2 (GSM2418375) comparisons a map resolution of 50 kb was chosen to ensure that > 80% of loci were associated with at least 1000 genomic contacts. The processed data files for the re-analyzed samples are available on the series record.

first: Takeshi

last: Isoda

first: Amanda

last: Moore

first: Vivek

last: Chandra

first: Masatoshi

last: Aida

first: Matthew

last: Denholtz

first: Zhaoren

last: He

first: Jan

middle: P

last: van Hamburg

first: Kathleen

middle: M

last: Fisch

first: Aaron

middle: N

last: Chang

first: Cornelis


title: White adipose tissues: amphiregulin overexpression

status: Public on Sep 15 2017

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary: Transcriptional profiling of transgenic mice specifically expressing amphiregulin in white adipose tissues. The objective of this study is to explore gene expression profiles of adipose tissues in response to amphiregulin overexpression.

overall_design: Noriyuki, Yanaka


title: An NF-κB-dependent, lineage-specific transcriptional program regulates Treg identity and function

first: Hyunju

last: Oh

address: 701 West 168th Street

department: Microbiology and Immunology

institute: Columbia University Medical Center


title: Neuromedin U receptor-1 amplifies inflammatory lung innate lymphoid cells

city: Cambridge

first: Samantha

last: Riesenfeld

state: MA

address: 415 Main St

institute: Broad Institute

summary: Type 2 innate lymphoid cells (ILC2s) promote mucosal homeostasis, yet also contribute to pathologic type 2 inflammation in allergic asthma. Alarmin cytokines produced by damaged and stressed epithelial cells, such as IL-25, activate ILC2s, but it remains unclear if these cytokines are unique in switching homeostatic ILC2s into pro-inflammatory cells that drive tissue inflammation. To identify molecular cues that modulate ILC responses to alarmins, we collected single-cell RNA-seq profiles of lung-resident ILCs at steady state and after in vivo stimulation. Computational and functional analysis identified that ILC2s express the neuropeptide receptor Nmur1. Neuromedin U (NMU), the ligand of Nmur1, activates ILCs in vitro, and when co-administered with IL-25 in vivo, NMU dramatically amplifies allergic inflammation and induces ILC2 expansion.  Finally, loss of NMU/Nmur1-signaling reduces ILC2 frequency and effector function following allergen challenge in vivo. Our results demonstrate that Nmur1 signaling modifies alarmin-mediated ILC2 responses to promote pro-inflammatory ILCs, and highlights the importance of neuro-immune crosstalk in allergic inflammatory responses at mucosal surfaces.

overall_design: For one set of experiments C57BL/6 mice were given PBS, IL-25, IL-33, NMU or NMU+IL-25 intranasally daily for 3 consecutive days. For another set of experiments, wildtype or Nmur1-deficient C57BL/6 mice were given PBS or house dust mite extract intranasally daily on days 0, 7, 8 and 9. In all cases, one day after the last treatment, lungs from mice of the same treatment group were pooled and enriched for CD90.2+ cells. Innate lymphoid cells (live CD45+ Lineage- CD90.2+ CD127+) were then isolated by fluorescence-activated cell sorting and analyzed by droplet-based 3' scRNA-seq (10x) and full-length scRNA-seq (SMART-Seq2). Two biologic replicates exist for each sample.


title: The CCR4-Not complex is a tumor suppressor in Drosophila melanogaster eye cancer models

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: The CNOT3 protein is a subunit of the CCR4-Not complex, a cytoplasmic protein complex mediating mRNA deadenylation as the first step in mRNA degradation. We recently identified CNOT3 loss-of-function mutations in patients with T-cell acute lymphoblastic leukemia (T-ALL). However, it is not clear yet how loss of this gene is involved in cancer development. Here we use different Drosophila melanogaster eye cancer models to study the potential tumor suppressor function of Not3, the CNOT3 orthologue, as well as other members of the CCR4-NOT complex. We show that not only Not3 but also the structural components Not1 and Not2, as well as the deadenylases Twin and Pop2 all behave as tumor suppressor genes. Moreover, RNA-sequencing analyses revealed that Not3 loss leads to increased expression levels of genes involved in DNA replication and ribosome biogenesis pathways, and that CycB is a Not3 target gene in our cancer models. Furthermore, we were able to confirm those results on human T-ALL cell lines, pointing out the conserved function of Not3 in both model systems and in tumor development. Together, our data establish a critical role for Not3 and the entire CCR4-NOT complex as a tumor suppressor.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: RNA-sequencing in Drosophila Melanogaster and in 2 human cell lines, knock-down of Not3/CNOT3 gene

first: Carmen

last: Vicente

first: Rocco

last: Stirparo

last: Cools


title: Expression data for LDHA KD 4T1 cells

city: ANN ARBOR

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher PL

department: Surgery

institute: University of Michigan

summary:
LDHA is key enzyme for tumor glycolysis metabolism and knocking down LDHA would change a lot of gene expression
We used microarrays to detail the global gene expression in 4T1 cells with LDHA knocked down by shRNA

overall_design: LDHA was knocked down by shRNA and positive cells were selected by 10µg/ml puromycin and mixed together

first: Wei

last: Li

first: Christopher

last: Krebs


title: Expression data from mouse adrenal glands extracted from wild-type (WT) and Cyp11b2tm1.1(cre)Brlt;Prkar1afl/fl(KO) adrenals

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

country: France

institute: CNRS, INSERM, Université Clermont Auvergne

summary:
We demonstrate that PKA signalling drives zonal conversion within adult adrenocortical lineage in a sexually dimorphic manner. Our data establish that Prkar1a genetic ablation (leading to constitutive PKA activation) in the adult adrenocortical lineage leads to endocrine hyperactivity and accelerates adrenal cortex renewal. This results in increased zona fasciculata differentiation and final conversion into reticularis-like zone. This phenomenon relies partly on sex-dependent mechanisms of cortical renewal, on which the male androgenic milieu exerts a repressive action through induction of WNT signalling, which in turn antagonizes PKA signalling and cortical cell turnover.
We used microarrays to analyse gene expression in response to Prkar1a gene ablation in the adult adrenocortical cell lineage in both female and male mice and explored the effects of orchidectomy (GDX).

overall_design: Adrenal glands were dissected from female KO (4), female WT (4), male KO (4), male WT (4), male KO GDX (4) and male WT GDX (4)

first: Pierre

last: Val


title: Expression data from bone marrow-derived cells

city: Osaka

first: Kiyoshi

last: Higashi

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co. Ltd.

summary: We used microarrays to identify genes in the migrated bone marrow-derived cells by G-CSF

overall_design: Bone marrow-derived cells migrating to liver tissue were collected from mice exposed to carbon tetrachloride and G-CSF

first: Kayo

last: Sumida


title: Estimating DNA methylation heterogeneity in bisulfite sequencing data

city: Taipei

first: Moloya

last: Gohain

state: Taipei

address: 128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT

department: INSTITUTE OF PLANT AND MICROBIAL BIOLOGY

country: Taiwan

institute: ACADEMIA SINICA

summary: We extended the mathematical models of measuring biodiversity to estimate DNA methylation heterogeneity in a cell population. We propose a model-based approach (abundance-based, phylogeny-based and pairwise similarity-based heterogeneity) and consider similarity in DNA methylation patterns from individual cells to evaluate heterogeneity that overcomes biases due to missing data. We also applied commonly used non-model based method (methylation entropy) and other reported methods of estimating methylation heterogeneity such as single-cell based approach to evaluate methylation heterogeineity.

overall_design: The performance of model-based methods for estimation of methylation heterogeneity is exemplified by artificial data, and compared by real datasets from normal and tumor tissue profiled by reduced representation bisulfite sequencing (RRBS).

first: De-Hua

last: Chen

first: Jui-Hsien

last: Lu

first: Wen-Wei

last: Liao

first: Pao-Yang


title: Single-cell RNA-seq analysis of human CD14+ monocytes

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

summary: We performed single-cell RNA-seq on CD14+ monocytes isolated from the blood of healthy donors. Using the 10x chromium technology, we analyzed 425 and 431 cells from 2 individual donors.

overall_design: Peripheral Blood Mononuclear Cells (PBMC) were prepared by centrifugation on a Ficoll gradient. Blood CD14+ monocytes were isolated from healthy donors’ PBMC by positive selection using magnetic beads. Monocytes were 93-95% CD14+CD16- as assessed by flow cytometry. Cellular suspensions (1700 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol.

first: Tsing-Lee

last: Tang-Huau

first: Mylène

last: Bohec

first: Paul

last: Gueguen

first: Christel

last: Goudot


title: Gene expression profile of A549 cells cultured with LA717

first: Natsuki

last: Abe

summary:
Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval.  Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that is suitable for imaging analysis and improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of LA717, a seaweed-derived polysaccharide.
Gene microarrays were used to observe the global gene expression in A549 cells cultured with or without LA717 and identified distinct classes of up or down-regulated genes.

overall_design: A549 cells were cultured for 7 days in normal attachment plates with normal medium (as control) or normal attachment plate with LA717 containing medium. Each sample was collected three times.


title: Transcriptomic analysis of in vitro-generated human monocyte-derived cells

summary: We analyzed the transcriptomes of human dendritic cells and macrophages derived from monocytes using MCSF + IL-4 + TNFa, or IL-34 + IL-4 + TNFa, or dendritic cells derived from monocytes using GMCSF + IL-4.

overall_design: We used as precursor cells the monocytes purified from the blood of 6 different donors. The data set contains therefore 6 biological replicates for each population of monocyte-derived cells analyzed.


title: Expression data from regenerating liver tissue

summary: We used microarrays to identify genes in regenerating mouse liver after OGFRL1-expressing cell administration

overall_design: Regenerating mouse liver tissue were prepared from EGFP- or OGFRL1-expressing cell administration


title: Epigenetic analysis of TCR signaling [Dnase-Seq]

city: Freiburg

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: DNaseI-Sequencing of unstimulated and PMA/Ionomycin-stimulated human T-blast cells

overall_design: Sequencing of DNaseI assays blast-cultured (via initial PHA stimulation) human PBMC with or without PMA+Ionomycin restimulation

first: Ruth

last: Brignall

first: Sarah

last: Bevington

first: Bethany

last: Gorman

first: Angela

middle: O

last: Pisco

first: James

last: Bagnall

last: Boddington

first: William

last: Rowe

first: Hazel

last: England

first: Kevin

last: Rich

first: Lorraine

last: Schmidt

first: Nigel

last: Dyer

first: Mark

last: Travis

first: Sascha

last: Ott

first: Dean

middle: A

last: Jackson

first: Peter

last: Cockerill

first: Pawel

last: Paszek


title: Integrated Transcriptomic and Proteomic Dynamics of Everolimus Treatment in B Lymphoblastoid Cells

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: The investigation aims to profile the molecular dynamics of Everolimus treatment in cells.  Specifically, a B-lymphoblast cells line was treated with Everolimus and sampled every half-hour over a 12 hour period. Treated and untreated cells were processed to extract RNA and protein that were subsequently used in high-throughput analysis of the transcriptome (RNA-Sequencing) and proteome (mass spectrometry).

overall_design: Examination of dynamics in a treated cell line and a parallel untreated controlline, both sampled over 12hrs every half hour. Validation using a new repeated experiment, with treated and untreated tracks, sampled over 6 selected time points.

first: Lavida

middle: K

last: Brooks


title: Identification of kidney transplant patients at risk for cutaneous squamous cell carcinoma by differentially methylated regions in T cells

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

type: Methylation profiling by genome tiling array

summary:
We aim to discover differentially methylated regions (DMRs) in peripheral T cells involved in de novo cSCC development after kidney transplantation. This was a retrospective study on biobank patient material.
We matched kidney transplant patients with (future) cSCC to those without cSCC and studied genome-wide DNA methylation (450k arrays) of T cells before transplantation.

overall_design:
Pure T cell samples of 54 patients were analyzed. No replicates are included, all samples are unique. Kidney transplant patients with a (future) cSCC were matched to control kidney transplant patients without cSCC. All these samples were taken before transplantation.

In addition to the comparison between cSCC and non-cSCC samples, we also studied samples of 11 cSCC patients of which a sample was available both before and after transplantation to asses the stability of the DNA methylation results after transplantation


title: Effect of long-term sodium arsenite treatment on transcriptomic profiles in progenitor and differentiated HepaRG cells.

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Inorganic arsenic, a ubiquitous environmental contaminant of food and drinking water, is a human carcinogen associated with lung, liver, prostate, renal, and bladder cancers.  It has been postulated that inorganic arsenic targets stem cells or partially differentiated progenitor cells, causing their oncogenic transformation.  This is proposed to be one of the key mechanisms in arsenic-associated carcinogenesis; however, the underlying mechanisms for this process remain largely unknown.  To address this question, human liver HepaRG cells, at progenitor and differentiated states, were continuously treated with a non-cytotoxic concentration of 1 μM sodium arsenite (NaAsO2).  Briefly, in Experiment 1, three days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 25 days.  In Experiment 2, fourteen days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 14 days.  In Experiment 1 and Experiment 2, control and NaAsO2-treated cells were harvested on the 28th day after the initial seeding.  In Experiment 3, twenty-eight days after the initial seeding, the terminally-differentiated cells were treated continuously with 1 μM NaAsO2 for an additional 14 days and then harvested. Transcriptomic analysis of NaAsO2-treated progenitor-like HepaRG cells (Experiment 1 and Experiment 2) identified 743 and 639 differentially expressed genes, respectively, among which 343 genes were expressed in common. Pathway analysis of common differentially expressed genes demonstrated a substantial inhibition of cellular metabolic pathways, mainly lipid and xenobiotic metabolism, and cell death pathways.  In contrast, cell proliferation, cell survival, and inflammation, were substantially activated. Treatment of differentiated HepaRG cells with NaAsO2 (Experiment 3) resulted in prominent gene expression changes, with a total of 1058 transcripts being significantly different from the control HepaRG cells.  Pathway analysis of differentially expressed genes in NaAsO2-treated cells differentiated HepaRG cells showed activation of cellular death-associated pathways and inhibition of cell survival and cell proliferation.

overall_design: In Experiment 1, three days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 25 days.  On the 28th day after the initial seeding, cells were harvested by mild trypsinization, washed in phosphate-buffered saline (PBS), and frozen immediately at -80°C for subsequent analyses. In Experiment 2, fourteen days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 14 days.  On the 28th day from the beginning of the study, cells were harvested by mild trypsinization, washed in PBS, and frozen immediately at -80°C for subsequent analyses. In Experiment 3, twenty-eight days after the initial seeding, the terminally-differentiated cells were treated continuously with 1 μM NaAsO2 for an additional 14 days.  The cells were then harvested by mild trypsinization, washed in PBS, and frozen immediately at -80°C for subsequent analyses. Following the treatment, gene expression profiles of control and s NaAsO2-treated HepaRG cells was examined.

first: Kostiantyn

last: Dreval

first: Orish

middle: E

last: Orisakwe

first: Frederick

last: Beland

first: Daniel

last: Doerge

first: Igor

last: Pogribny


title: Expression profiling analyses of ECF sigma factor of Porphyromonas gingivalis W83

status: Public on Sep 14 2017

city: Loma Linda

first: Yuetan

last: Dou

state: CA

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

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

platform_organism:
Porphyromonas gingivalis
Porphyromonas gingivalis W83

overall_design: Refer to individual Series


title: Expression profiling analyses of ECF sigma factor PG1660 mutant of Porphyromonas gingivalis W83

summary:
To study the expression profile of ECF sigma factor PG1660 mutant under anaerobic conditions and hydrogen peroxide stress conditions compared to the wild-type W83 by using DNA-microarray.
The role of ECF sigma factor PG1660 involved in oxidative stress was published Yuetan Dou, Devon Osbourne, Rachelle McKenzie, Hansel M Fletcher. (2010) Involvement of extracytoplasmic function sigma factors in virulence regulation in Porphyromonas gingivalis W83. FEMS Microbiology Letter, 312(1):24-32.

overall_design: 6 array sets were used for W83 under anaerobic conditions; 3 were used for PG1660 mutant under anaerobic conditions; 3 were used for W83 under hydrogen peroxide stress conditions; 3 were used for PG1660 mutant under hydrigen peroxide stress conditions; 3 were used for ECF sigma factors PG0162PG1660 mutant under anaerobic conditions

first: Charles

last: Wang

first: Hansel

last: Fletcher


title: Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment

city: changsha

first: Gang

last: Gao

address: No. 348, West Xianjiahu Road,

institute: Institue of bast fiber crops,Chinese academy of agricultural science

summary: Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage  (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.

overall_design: Root samples of terrestrial ramie, and different development stage of hydrophonic ramie were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. These clean reads were then de novo assembled into unigenes and annotated with the 7 functional databases.  Gene expression level of each sample were  quantified using BGISEQ500 platform to help understand the distribution of aquatic root development related genes from macro level.

first: Aiguo

last: Zhu


title: Inhibition of the oncogenic fusion protein EWS-FLI1 causes G2/M cell cycle arrest and enhanced vincristine sensitivity in Ewing sarcoma

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: A chimeric fusion between the RNA binding protein EWS and the ETS family transcription factor FLI1 (EWS-FLI1), created from a chromosomal translocation, is implicated in driving the majority of Ewing sarcomas (ES) by modulation of transcription and alternative splicing. The small molecule YK-4-279 inhibits EWS-FLI1 function and induces apoptosis. We tested 69 anti-cancer drugs in combination with YK-4-279 and found that vinca alkaloids exhibited synergy with YK-4-279 in five ES cell lines. The combination of YK-4-279 and vincristine reduced tumor burden and increased survival in mice bearing ES xenografts. We determined that independent drug-induced events converged to cause this synergistic therapeutic effect. YK-4-279 rapidly induced G2/M arrest, increased the abundance of cyclin B1, and decreased EWS-FLI1–mediated expression of microtubule-associated proteins, which rendered cells more susceptible to microtubule depolymerization by vincristine. YK-4-279 reduced the expression of the EWS-FLI1 target gene encoding ubiquitin ligase UBE2C, and this in part contributed to the increase in cyclin B1. Biochemical assays revealed that YK-4-279 also increased the abundance of proapoptotic isoforms of MCL1 and BCL2, presumably through inhibition of alternative splicing by EWS-FLI1, thus promoting cell death in response to vincristine. Thus a combination of vincristine and YK-4-279 might be therapeutically effective in ES patients.

overall_design: Examination of mRNA profiles of TC32 on knockdown of EWS-FLI1 or treatment with YK-4-279: 3 samples Total: 1 TC32 WT Control, 1 TC32 shEF, 1 TC32 YK

first: Stefan

last: Zöllner

first: Saravana

last: Selvanathan

middle: T

first: Ryan

last: Commins

first: Sung-Hyeok

last: Hong

first: Eric

last: Moseley

first: Sydney

last: Parks

first: Jessica

last: Haladyna

first: Hayriye

middle: V

last: Erkizan

first: Uta

last: Dirksen

first: Michael

middle: D

last: Hogarty

first: Aykut

last: Üren

first: Jeffrey

last: Toretsky


title: Cilia-dependent GLI processing in neural crest cells is required for tongue development

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: We report the RNA profiles of both control and Kif3a f/f; Wnt1-Cre mandibular prominences of the murine face at  embryonic day E11.5. We sought to determine the gene expression changes which occurr in the mandibular prominence when primary cilia are lost on neural crest cells.

overall_design: The mandibular prominence from 10 control e11.5 embryos were collected and pooled, and 10 mutant e11.5 embryos were collected and pooled. RNA-seq was performed on these samples.

first: Grethel

last: Millington

first: Kelsey

middle: H

last: Elliott

first: Ya-Ting

last: Chang

first: Ching-Fang

first: Andrzej

last: Dlugosz


title: The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Polycomb group proteins are transcriptional repressors that control cell identity and development. In mammals, at least five different CBX proteins are believed to associate with the core Polycomb repressive complex 1 (PRC1). CBX6 and CBX7 are the most highly expressed CBX proteins in embryonic stem cells (ESCs), yet little is known about the function of CBX6 in these cells. Here we show that CBX6 is an essential regulator of ESC identity, since ablation of CBX6 function destabilizes the pluripotency network and triggers differentiation. At the molecular level, CBX6 is linked to the canonical PRC1 (cPRC1) complex; however, contrary to expectations, our results indicate that CBX6 also has a non-canonical PRC1 function. Taken together, our findings reveal that CBX6 is an essential component for ESC biology and contributes to the structural and functional complexity of the PRC1 complex.

overall_design: List of ChIPseq samples (Cbx6/Cbx7/Ring1b) and RNAseq samples (control and Cbx6 knock-down)

first: Alexandra

last: Santanach

first: Luciano

last: DiCroce


title: Lineage-specific genetic innovations streamline the genomes of Armillaria species to pathogenesis

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

summary: Armillaria species are devastating forest pathogens that are among the largest terrestrial organisms on Earth. They explore hosts and achieve immense colony sizes by rhizomorphs, root-like multicellular structures of clonal dispersal. To resolve the genetic bases of their unique biology, we sequenced and analyzed genomes of 4 Armillaria species and performed RNA-Seq on 7 invasive and reproductive developmental stages. Comparison with 22 basidiomycete fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose degrading enzymes and lineage-specific genes involved in rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome and share their morphogenetic machinery with fruiting bodies, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria has drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

overall_design: 30 samples corresponding to 10 developmental stages were analyzed. Each developmental stage contains 3  biological replicates.

first: Gyorgy

last: Sipos

first: Arun

last: Prasanna

first: Mathias

last: Walter

first: Eoin

last: O'Connor

first: Krisztina

last: Krizsan

first: Brigitta

last: Kiss

first: Jacky

last: Hess

first: Torda

last: Varga

first: Jason

last: Slot

first: Robert

last: Riley

first: Bettina

last: Boka

first: Daniel

last: Rigling

first: Kerrie

last: Barry

first: Juna

last: Lee

first: Sirma

last: Mihaltcheva

first: Kurt

last: LaButti

first: Anna

last: Lipzen

first: Rose

last: Waldron

first: Nicola

last: Moloney

first: Christoph

last: Sperisen

first: Laszlo

last: Kredics

first: Csaba

last: Vagvolgyi

first: Andrea

last: Patrignani

first: David

last: Fitzpatrick

first: Istvan

last: Nagy

first: Sean

last: Doyle

first: James

last: Anderson

first: Igor

last: Grigoriev

first: Ulrich

last: Guldener

first: Martin

last: Munsterkotter

middle: G


title: PMP22 antisense oligonucleotides reverse clinical, pathological, and molecular features of Charcot-Marie-Tooth disease type 1A

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: RNA sequencing data from sciatic nerves of C22 and wildtype littermates

overall_design: RNA sequencing of sciatic nerves from C22 and wildtype littermates at 5 weeks of age (5 wk), before treatment with antisense oligonucleotides against PMP22, and at 9 weeks after treatment or 15 wk-old mice

first: Hien

last: Zhao

first: Karli

last: Ikeda-Lee

first: Steven

last: Kuntz

first: Joel

last: Li

first: Apoorva

last: Mohan

first: Aneeza

last: Kim

first: Gene

last: Hung

first: Mark

last: Scheideler

first: Steve

last: Scherer

first: John

last: Svaren

first: Eric

last: Swayze

first: Holly

middle: B

last: Kordasiewicz


title: miRNA expression profiling of thymus samples from myasthenia gravis patients

city: Washington DC

first: Manjistha

last: Sengupta

state: District of Columbia

address: 2300 Eye Street NW, Ross Hall,  Room #723

department: Neurology

institute: George Washington University

summary:
Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease.
A large proportion of MG patient show the presence of ectopic germinal centers (GC) in thymus that are absent in normal individuals. However, the exact mechanism how this change in thymus morphology is triggered and if this is related to pathophysiology of the disease remains unknown.
In this study we have compared the mRNA profile of thymus samples obtained during a clinical trial (Thymectomy Trial in Non-Thymomatous Myasthenia Gravis Patients Receiving Prednisone Therapy. ClinicalTrials.gov Identifier: NCT00294658).
We have compared the miRNA profile of thymus samples that have distinct germinal centers with those that lack them using Affymetrix miRNA array 4.0 to identify the differentially expressed genes with in the two groups.

overall_design:
Sixteen frozen tissue samples collected during MGTX trial were cryo-sectioned and were stained with haematoxylin and eosin to examine morphological features and presence of germinal centers.
The H and E sections were evaluated by two blinded observers and graded depending on presence (Grades 1-4) or absence of germinal centers (Grade 0). Total RNA including small RNA was isolated from the remaining tissue using mirVana miRNA isolation kit.
The RNA samples were processed and applied to Affymetrix miRNA array 4.0. Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.

first: Bi-Dar

last: Wang

first: Norman

last: Lee

first: Linda

middle: L

last: Kusner

first: Henry

middle: J

last: Kaminski


title: Genome-wide mapping of SIN3A binding sites by ChIP-seq in HUVEC exposed to hypoxia

city: Madrid

first: Luis

last: del Peso

state: Madrid

address: Arzobispo Morcillo

department: Biochemistry

institute: Universidad Autonoma de Madrid

summary: Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia. SIN3A interference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.

overall_design: ChIP-Seq analysis of SIN3A binding in normoxia and hypoxia in HUVEC cells compared with their input as a control. The data is from a single biological replicate.

first: María

last: Tiana


title: DNA methylation in demyelinated multiple sclerosis hippocampus

city: Cleveland

first: Ranjan

last: Dutta

address: 9500 Euclid Avenue, NC-30

department: Neuroscience

institute: Lerner Research Institute

summary: Genome wide DNA methylation profiling of genomic DNA isolated from hippocampus of multiple sclerosis patients were hybridized to Illumina HumanMethylation450 Beadchip arrays.  DNA methylation profiles across approximately 45,000 CpGs were compared between 8 myelinated and 7 demyelinated tissues .

overall_design: Bisulphite converted DNA from the 15 samples were hybridised to the Illumina Human Methylation450 Beadchip arrays


title: IKKα is essential for the development and maintenance of Marginal  zone and Follicular B cells

city: Boston

first: Mumtaz

last: Yaseen

address: 800 Washington st

institute: Tufts University Medical Center

summary: IKKα kinase is essential for the B cell maturation and secondary lymphoid organ development. In the current study, we evaluated the role of IKKα in the marginal zone and follicular B lymphocyte development by genetically deleting IKKα from the B cell lineage using CD19-Cre mice. The loss of IKKα did not affect the normal development of early B cell progenitors. However, a significant decline was observed in the percentage of immature B lymphocytes, mature marginal zone and follicular B cells along with a severe disruption of splenic marginal and follicular B cell zones. A gene expression analysis performed on the RNA extracted from the newly formed B cells (B220+IgMhi) revealed that IKKα deficiency produces significant changes in the expression of genes involved in MZ and FO B lymphocyte survival, homing and migration. And several among those genes identified belong to G protein family. Specifically, we validated the upregulated expression of regulator of G protein signaling 13 (RGS13), which is a GTPase activating protein (GAP) that negatively regulates G protein signaling and impede B cell migration. Likewise, promigratory B lymphocyte receptor, the sphingosine-1-phosphate receptor 3 (SIPR3) that couple to Gαi showed significantly reduced expression. In addition, an in silico analysis of gene product interactions revealed NF-κB signaling pathways to be a major gene regulating networks perturbed with IKKα deletion. Taken together, this study reveals IKKαNF-κB and G protein signaling axis to be central for the MZ and FO B cells survival, maintenance, homing and migration.

overall_design: We have two groups, an experimental and control group. RNA was extracted from newly formed B cells (B220+IgMhi) and subjected to hybridization on affy chip

middle: Y

last: Balkhi

first: Jami

last: Willette-Brown

first: Yinling

last: Hu


title: Transcriptome analysis and microRNAs profile of mesodermal iPSCs derived progenitors

city: Leuven

first: Giorgia

last: Giacomazzi

address: Herestraat 49

institute: KUleuven

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesodermal iPSC derived progenitors (MiPs) obtained from human fetal fibroblasts and skeletal muscle mesoangioblasts show a different myogenic potential in vitro and when injected in vivo in mice model of Muscular Dystrophy. MAB-MiPs hold greater myogenic commitment compared to f-MiPs, showed by increased engraftment and regeneration of the hindlimb muscle.  Here we report that RNA sequencing of MiPs and of induced pluripotent stem cells (iPSCs) of origin allows identification of genes differentially regulated between fibroblast and MABs progenies that might be responsible for the different contribution to muscle regeneration. MicroRNA- sequencing of the same cell lines further allowed a selection of a set of miRNAs that can drive the myogenic propensity of MiPs in vivo and identification of promyogenic  and antimyogenic  miRNA cocktails.  Manipulation of the selected miRNAs improved the engraftment and regeneration of MiPs. Additional RNA-sequencing after the treatment with the defined promyogenic and antimyogenic cocktails unraveled additional information on the pathways modulated by the selected factors.

overall_design: mRNA and microRNA profile of n=3 f-MiPs, f-iPSCs, MAB-MiPs, MAB-iPSCs and additional mRNA profile of n=3 f-MiPs and MAB-MiPs before and after treatment with antimyogenic and promyogenic cocktails.

first: Bryan

last: Holvoet

first: Sander

last: Trenson

first: Ellen

last: Caluwé

first: Bojana

last: Kravic

first: Hanne

last: Grosemans

first: Alvaro

last: Cortes Calabuig

first: Christophe

last: Deroose

first: Danny

last: Huylebroeck

first: Said

last: Hashemolhosseini

first: Stefan

last: Janssens

first: Elizabeth

last: McNally

first: Mattia

last: Quattrocelli

first: Maurilio

last: Sampaolesi


title: Long non-coding RNA HOTAIR promotes cell migration by upregulating insulin growth factor-binding protein 2 in renal cell carcinoma

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

institute: Miyagi Cancer Center

summary: Renal cell carcinoma (RCC) is one of the most lethal urologic cancers. About one-third of RCC patients already have distal metastasis at the time of diagnosis. There is growing evidence that Hox antisense intergenic RNA (HOTAIR) plays essential roles in metastasis in several types of cancers. However, the precise mechanism by which HOTAIR enhances malignancy remains unclear, especially in RCC. Here, we demonstrated that HOTAIR enhances RCC-cell migration by regulating the insulin growth factor-binding protein 2 (IGFBP2) expression. HOTAIR expression in tumors was significantly correlated with nuclear grade, lymph-node metastasis, and lung metastasis. High HOTAIR expression was associated with a poor prognosis in both our dataset and The Cancer Genome Atlas dataset. Migratory capacity was enhanced in RCC cell lines in a HOTAIR-dependent manner. HOTAIR overexpression accelerated tumorigenicity and lung metastasis in immunodeficient mice. Microarray analysis revealed that IGFBP2 expression was upregulated in HOTAIR-overexpressing cells compared with control cells. The enhanced migration activity of HOTAIR-overexpressing cells was attenuated by IGFBP2 knockdown. IGFBP2 and HOTAIR were co-expressed in clinical RCC samples. Our findings suggest that the HOTAIR-IGFBP2 axis plays critical roles in RCC metastasis and may serve as a novel therapeutic target for advanced RCC.

overall_design: HOTAIR-overexpressing (HOTAIR1-3) and control (EV1-4) ACHN cells

first: Hiromichi

last: Katayama

first: Rie

last: Shibuya

first: Mao

last: Nakamura

first: Mai

last: Mochizuki

first: Kazunori

last: Yamaguchi

first: Sadafumi

last: Kawamura

first: Tatsuo

last: Tochigi

first: Ikuro

last: Sato

first: Takamasa

last: Okanishi

first: Kunie

last: Sakurai

first: Wataru

last: Fujibuchi

first: Yoichi

last: Arai

first: Kennichi

last: Satoh


title: IGF2 mRNA Binding Protein-2 is a tumor promoter that drives cancer proliferation through its client mRNAs IGF2 and HMGA1

first: Ning

last: Dai

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The gene encoding the IGF2 mRNA binding protein-2/IMP2 is amplified and overexpressed in many cancers, accompanied by a poorer prognosis. Mice deficient in IMP2 exhibit a longer lifespan and a reduced tumor burden at old age. Herein we show in a diverse array of cancer cells that IMP2 overexpression stimulates and IMP2 elimination diminishes proliferation by 50-80%. In addition to its known ability to promote IGF2 abundance, we find that IMP2 strongly promotes IGF action, by binding and stabilizing HMGA1 mRNA. The HMGA1 DNA binding protein, a known oncogene, suppresses the abundance of IGFBP2 and Grb14, inhibitors of IGF action. IMP2 stabilization of HMGA1 mRNA plus IMP2 stimulated IGF2 production synergistically drive cancer cell proliferation and account for IMP2’s tumor promoting action. IMP2’s ability to promote proliferation and IGF action requires mTOR-catalyzed IMP2 phosphorylation.

overall_design: Cell proliferation with/without IMP2 in mouse embryo fibroblasts  cells.

first: Fei

last: Ji

first: Jason

last: Wright

first: Liliana

last: Minichiello

first: Ruslan

last: Sadreyev

first: Joseph

last: Avruch


title: VTA and NAC labeled ribosome from mPFC

city: PALO ALTO

first: Li

last: Ye

state: California

address: 1050 Arastradero Rd Bulding B

institute: Stanford University

summary:
Projection-dependent ribosome profling from mouse mPFC.
Ribosome from NAC- and VTA- projecting mPFC cells were immunoprecipited using GFP-trap (Chromotech). Translating mRNA was isolated and analyzed

overall_design: Cre-dependent ribosome TRAP mice were injected with CAV2-Cre in NAC and VTA. Projection-dependent ribosome labeling was enabled by isolating mPFC. Ribosome was genetically tagged with GFP in the activated cells and could be immunologically purified.

first: Karl

last: Deisseroth


title: Genome-wide Regulation of Electro-acupuncture on the Neural Stat5-loss-induced Obese Mice

city: Nanjing

first: Bing-Mei

last: Zhu

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing university of Chinese Medicine

summary:
Purpose: Acupuncture is reported to be effective in treating obesity related illnesses, but its mechanism is still unclear. To investigate this mechanism we applied electro-acupuncture (EA) in a mouse model of obesity and used RNA-seq to identify molecular consequences.
Methods: Adult male mice (17w)  were divided into three groups: Stat5fl/fl, Stat5NKO, Stat5NKO+EA groups, hypothalamus and Epi-WAT mRNA profiles of  mice in each group were generated by deep sequencing,using Illumina Hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the mouse genome (UCSC mm9) and identified transcripts in the Stat5fl/fl, Stat5NKO and Stat5NKO+EA mice  with TopHat and Cufflinks workflow respectively.  Genes with lower than one FPKM (average fragments per kilobase of transcript per million fragments mapped) were filtered out. Up-regulation and down-regulation were defined as a relative transcription level above Log2 fold change (FC) ≥ |±1| and P value <0.05.
Conclusions: Our results provided, for the first time, insight into genomic networks of obesity and their modulation by electro-acupuncture, which in turn reveals potential mechanisms that explain acupuncture-induced weight-loss.

overall_design: Hypothalamus and Epi-WAT mRNA profiles of  Stat5fl/fl, Stat5NKO and Stat5NKO+EA  mice were generated by Hiseq 2000, all groups included three samples.

first: Shu-Ping

last: Fu

first: Hao

last: Hong

first: Chen-Jun

last: Hu

first: Hou-xi

last: Xu


title: Early gestational maternal low-protein diet diminishes hepatic response to fasting in young adult male mice

city: Tokyo

first: Noriko

last: Sato

address: 1-5-45, Yushima, Bunkyo-ku

department: Molecular Epidemiology & Epigenetic Epidemiology

institute: Medical Research Institute, Tokyo Medical and Dental University

summary: Maternal low-protein (MLP) diet can lead to hepatic steatosis, which only develops with ageing. It is still unclear whether the young offspring show any signs of past exposure to prenatal adverse conditions. We hypothesized that early nutritional insult would first affect the dynamic responsiveness to nutritional challenges rather than the static state. We analyzed the transcriptome and metabolome profiles of the hepatic response to fasting/refeeding in young male mice offspring to identify changes induced by early gestational MLP diet. Restricted MLP exposure strictly to early gestation was achieved by the embryo transfer method. As a result, significant transcriptional differences between control and MLP pups were found only in the fasted state. The fasting-induced upregulation of genes for long-chain fatty acid metabolism and of stress response genes related to protein folding were significantly diminished in MLP pups. Gene Set Enrichment Analysis showed that peroxisome proliferator activated receptor  (PPAR)-mediated induction was impaired in fasted MLP pups. Lipid profiling showed that the hepatic signature of triacylglycerols was shifted to longer acyl-chains and higher saturation by the MLP diet. Taken together, early gestational MLP diet affected the hepatic dynamic response to nutritional stress in seemingly healthy young offspring, accompanied with partial deterioration of PPAR action.

overall_design: This study tested whether early gestational maternal low protein diet affects hepatic metabolism even in seemingly healthy young offspring. We subjected offspring to fasting stress to uncover difference in the dynamic hepatic response, caused by early gestational MLP diet. Liver RNA expression profiles were compared between Ctrl and MLP pups, at the three nutritional conditions (ad libitum fed, fasted and refed)

first: Katsuko

last: Sudo


title: Differential gene expression array between primary and cultured human bone marrow MSCs

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: Investigation of differential gene expression array between primary and cultured human bone marrow MSCs as adherent cells (P0 and P3) or spheres (P0 and P3)

overall_design: Total RNA obtained from sorted lin-CD45-CD31-CD71-CD235a-CD271+ cells primary cells (n=3), from cultured adherent cells (P0; n=4, P3; n=4) and from sphere cultured cells (P0; n=4, P3; n=4)

first: Roshanak

last: Ghazanfari

first: Dimitra

last: Zacharaki

first: Stefan

last: Scheding


title: Spleen transcriptional profiling of Mus musculus BALB/c strain after DNA vaccination against influenza H5N1

city: Warsaw

first: Róża

last: Sawicka

address: Pawinskiego

department: Department of Protein Biosynthesis

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: Hemagglutinin of the influenza virus is the main external glycoprotein. This very immunogenic protein is the target of the most anti-influenza vaccines. DNA vaccines are new alternative to conventional inactivated ones. Four DNA vaccines were tested. Each tested variant was based on the pCI vector with nucleotide sequence encoding hemagglutinin from A/swan/Poland/305-135V08/2006 (H5N1, clade 2.2). In K3/pCI, GK/pCI and HAneo/pCI the different optimization algorithms of hemagglutinin encoding sequence without amino acids change were tested. In 3NF/pCI the NFkappaB binding sites flanking the expression cassette were included in order to improve the nuclear transfer. Comparative transcriptome analysis of mice vaccinated the following vaccine HAneo/pCI,K3/pCI, GK/pCI or 3NF/pCI versus empty vector demonstrated minor changes in genes expression pattern. Most genes were expressed on the similar level in the vaccinated individuals and in the control mice. Small number of genes in particular variants showed the expression different than in the control mice. In general, the identified genes with the changed expression included some genes involved in metabolic processes and none of them seem to induce any undesirable pathways nor disease.

overall_design: 6-8 weeks female mice BALB/c strain were used in the experiments. Three independent biological replicates of total RNA were isolated for each vaccine variants: HAneo/pCI, K3/pCI and 3NF/pCI and two independent biological replicates of total RNA were isolated from negative control group - empty vector and group GK/pCI. The spleen samples were collected 3 days after the booster DNA vaccination against influenza virus, each of dose was 20ug of plasmid DNA per mouse. Totally, 13 samples of RNA was prepared.

first: Agnieszka

last: Sirko

first: Anna

last: Fogtman

first: Marta

last: Koblowska


title: In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: The genes of the non-phosphorylative L-rhamnose catabolic pathway have been identified for several yeast species. In Pichia stipitis, all L-rhamnose pathway genes are organized in a cluster, which is conserved in Aspergillus niger, except for the lra-4 ortholog (lraD). The A. niger cluster also contains the gene encoding the L-rhamnose responsive transcription factor (RhaR) that has been shown to control the expression of genes involved in L-rhamnose release and catabolism. In this paper, we confirmed the function of the first three putative L-rhamnose utilisation genes from A. niger through gene deletion. We explored the identity of the inducer of the pathway regulator (RhaR) through expression analysis of the deletion mutants grown in transfer experiments to L-rhamnose and L-rhamnonate. Reduced expression of L-rhamnose-induced genes on L-rhamnose in lraA and lraB deletion strains, but not on L-rhamnonate (the product of LraB), demonstrate that the inducer of the pathway is of L-rhamnonate or a compound downstream of it. Reduced expression of these genes in the lraC deletion strain on L-rhamnonate show that it is in fact a downstream product of L-rhamnonate. This work showed that the inducer of RhaR is beyond L-rhamnonate dehydratase (LraC) and is likely to be the 2-keto-3-L-deoxyrhamnonate.

overall_design: This study aim to characterize in vivo the genes involved in the rhamnose metabolism and the regulator in Aspergillus niger by studing the gene expression values of the mutants and the reference strains. Mutant strains of the putative rhamnose metabolic and regulatory genes (lraA, lraB, lraC, rhaR) and reference strain were grown on L-rhamnose. Samples were taken after 2 hours of incubation.

first: Claire

last: Khosravi

first: Roland

last: Kun

first: Jaap

last: Visser

first: Maria Victoria

last: Aguilar-Pontes

middle: P

first: Evy

last: Battaglia


title: Regulated Ire1-dependent mRNA decay requires no-go mRNA degradation to maintain endoplasmic reticulum homeostasis in S. pombe

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: The unfolded protein response (UPR) continually monitors the protein folding capacity of the endoplasmic reticulum (ER). In S. pombe, Ire1, an ER membrane-resident kinase/endoribonuclease, utilizes a mechanism of selective degradation of ER-targeted mRNAs (RIDD) to maintain ER homeostasis. Here, we used a genetic screen to identify factors critical to the Ire1-mediated UPR response in S. pombe and found several proteins, Dom34, Hbs1 and SkiX, previously implicated in ribosome rescue and the no-go-decay (NGD) pathway. Ribosome profiling in ER-stressed cells lacking these factors revealed that Ire1-mediated cleavage on ER-associated mRNAs results in ribosome stalling on the cleaved transcript and, ultimately in full mRNA degradation.  The process engages mechanisms of precise, iterated cleavage of the mRNAs and ribosome rescue. This clear signature allowed us to discover hundreds of novel mRNA targets of Ire1. Our results reveal that the UPR in S. pombe executes RIDD in an intricate interplay between Ire1, translation, and the NGD surveillance pathway, and establish a critical role for NGD in maintaining ER homeostasis.

overall_design: 16 samples are included in the study (8 mRNA-Seq samples and 8 ribosome footprinting samples). Read sizes were examined for lengths of 15-18 nt and 25-34 nt for all profiling samples and reads were aligned by 5' ends for mRNA-Seq and 3' ends for profiling.

first: Philipp

last: Kimmig

first: Peter

last: Walter

first: Rachel

last: Green


title: Analysis of the miR-34 family functions in breast cancer reveals annotation error of miR-34b

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: The miR-34 family of microRNAs consisting of miR-34a, miR-34b and miR-34c are tumour suppressors. The annotated human miR-34b-5p has one additional base at the 5’ end of the common miR-34 family seed sequence, compared to miR-34a-5p and miR-34c-5p. This extra base results in a shift of the seed sequence, which would affect the target gene repertoire and have functional consequences. During our studies of miR-34 functions, we investigated the precise sequence of mature miR-34b-5p in human cells by deep sequencing. We found that a miR-34b-5p without the extra base was the predominant form in both non-malignant and malignant cells derived from several human tissues, indicating that the miR-34b annotation is misleading. We evaluated the functional implications of the seed shift, by comparing the effect of mimics representing the alternative miR-34b-5p sequences in MDA-MB-231 cells. In contrast to the annotated miR-34b, the endogenously expressed miR-34b displayed tumour suppressive characteristics in vitro similarly to miR-34c. These data demonstrate the importance of determining the precise sequence of a mature microRNA before exploring miRNA functions.

overall_design: Investigation of miR-34 family functions.

first: Marie

last: Engkvist

first: Eva

middle: W

last: Stratford

first: Susanne

last: Lorenz

first: Ola

last: Myklebost

first: Else

last: Munthe


title: Human Non-Small Cell Lung Cancer cells: Control vs gefitinib treated cells

status: Public on Sep 13 2017

city: Helsinki

first: Liang

last: Wang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

summary:
Total gene expression difference after treatment gefitinib for 24 h compared to control NSCLCs
To determine which proteins are responsible for the differences in glutamine metabolism in response to the gefitinib treatment between gefitinib-sensitive and gefitinib-resistant cells

overall_design: After separately treatment with 20 µM and 20 nM gefitinib in A549 and PC-9 cells for 24 h, both mRNA from control and gefitinib treated cells were transcripted for DNA microarray analysis.

first: Wen

last: Peng

first: Tianming

last: Wu

first: Pengchi

last: Deng

first: Ying

last: Zhao


title: Cell Cycle Proteins Control Production of Neutrophil Extracellular Traps (NETs)

city: Berlin

first: Brian

last: Caffrey

address: Ihnestrasse 63-73

institute: Max Planck Institute for molecular Genetics

summary: Microarray expression profiling of unstimulated human neutrophils from 8 healthy donors

overall_design: Gene expression was analyzed in human neutrophils purified from blood.

first: Arturo

last: Zychlinsky

first: Borko

last: Amulic


title: Nup153 defines neural identity through cooperative transcriptional control with Sox2

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

institute: German Center for Neurodegenerative Diseases

summary: Through RNA interference and genome-wide Nup153 binding studies, we found that Nup153 and Sox2 bind and co-regulate hundreds of genes. Furthermore, we found that Nup153 exhibits binding location dependent spatially distinct transcriptional control by differentially regulating expression when bound to the promoter region or to the transcription end site (TES). These results establish Nup153 not only as a novel transcriptional co-regulator of Sox2 but also as a key player in the regulation of cell fate by directly modulating gene expression.

overall_design: ChIP was performed on neural progenitor cells using antibodies against Nup153, FLAG-Nup153, H3K4Me3, or IgG. ChIPmentation was perfromed  using an antibody against Sox2 on NeuPCs treated with shNup153 or shControl.  RNA-seq was performed on NPCs treated with shNup153 or shControl. Atac-seq was performed on NPCs treated with shNup153 or shControl.

first: Sara

last: Linker

first: Jonathan

last: Hsu

first: Fred

last: Gage


title: Comparison of embryonic samples (E18) vs. adult (34 weeks old) lacrimal gland transcriptome

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

institute: Inserm

summary: As an element of the lacrimal apparatus, the lacrimal gland (LG) produces the aqueous part of the tear film, which protects the eye surface. Therefore, a defective LG can lead to serious eyesight impairment. Up to now, little is known about LG morphogenesis and subsequent maturation. In this study, we delineated elements of the cellular and molecular events involved in LG formation by using three epithelial markers, namely aSMA, Krt14 andKrt19. While aSMA marked a restricted epithelial population of the terminal end buds (TEBs) in the forming LG, Krt14 was found in the whole embryonic LG epithelial basal cell layer. Interestingly, Krt19 specifically labelled the presumptive ductal domain and subsequently, the luminal cell layer. By combining these markers, the Fucci reporter mouse strain and genetic fate mapping of the Krt14+ population, we demonstrated that LG epithelium expansion is fueled by a patterned cell proliferation, and to a lesser extent by epithelial reorganization and possible mesenchymal-to-epithelial transition. We pointed out that this epithelial reorganization, which is associated with apoptosis, regulated the lumen formation. Finally, we showed that the Notch signalling inhibition prevented the ductal identity from setting, and leads to a LG covered by ectopic TEBs. Taken together our results bring a deeper understanding on LG morphogenesis, epithelial domain identity, and organ expansion.

overall_design: 6 samples were analysed, 3 embryonic samples (biological triplicates, E18) and 3 adult samples (biological triplicates, 34wks old). Embryonic samples were composed of at least 10 LGs (5 individuals) pooled together. Samples were collected for RNA extraction and hybridization on Affymetrix microarrays (MTA1).

first: Alison

last: Kuony


title: Arraystar lncRNA and mRNA array data for H9c2 myocytes from Hypoxia/reoxygenation model

city: WenZhou

first: Bozhi

last: Ye

state: ZheJiang

address: 2 Fuxue Road

department: Department of Cardiology

institute: the First Affiliated Hospital of WenZhou Medical University

summary: Ischemia reperfusion (I/R) promotes the severity of cardiomyocyte injur. Our study provides a potential new therapeutic strategy to alleviate ischemia reperfusion injury.

overall_design: Hypoxia/reoxygenation (H/R) induced gene expression in H9c2 myocytes was measured at hypoxic condition (1% O2, 5% CO2, and 94% N2) for 1 h and then under normoxic condition for 3 h and normoxic group. Three independent experiments were performed at each group.

first: Zhouqing

last: Huang


title: Sources to variability in circulating human miRNA signatures

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: There is an increasing number of studies proposing microRNAs (miRNAs) circulating in patient sera as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurological pathologies and others. Numerous collections of biospecimens have been established throughout the world providing access to the precious samples required for biomarker development. To further explore the validation- and translational process of miRNA biomarkers it is indispensable to understand the variability of circulating miRNAs in undiseased individuals.   We determined longitudinal and genome-wide miRNomes of 90 serum samples from the Janus Serum Bank in Norway, that have been stored from 23 up to 40 years at -25 degrees Celsius. Three serum samples each collected approximately 5 years apart from 30 individuals were profiled with microarrays, allowing insights into inter-individual variability, age dependent miRNA variability and the impact of storage length and pre-processing. A significant proportion of the miRNAs was affected by the age of the blood donor and a not negligible, albeit small, part of the miRNome by the storage time. A substantial part of miRNAs was differentially abundant between individuals, independent of the time when samples were collected. Stepwise filtering of the 529 miRNAs that were detected in serum samples highlighted 168 miRNAs dependent on the time point, further 56 significant between individuals and another 169 varying dependent on the sampling procedure. While the afore mentioned miRNA groups contain generally interesting and biologically important miRNAs the remaining set of 135 miRNAs with overall lowest variability between healthy individuals and across a long life span, and independent of sampling processes and storage length seems to constitute very promising biomarker candidates.

overall_design: Serum samples of 30 individuals collected over a time of approx. 10 years, 3 time points per individual

first: Andreas

last: Keller


title: Transcriptome analysis by expression microarrays of breast cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

city: Koto

first: Nobuyuki

last: Fukui

state: Tokyo

institute: Japanese Foundation For Cancer Research

summary: We performed the expression microarray experiments for mRNA of breast cancer tissue.

overall_design: Messenger RNA were extracted from primary tumor of 29 breast cancer patients, hybridized and scanned with Affymetrix Human Genome GeneChip U133 Plus 2.0 array.

first: Yoshio

last: Miki


title: Genome-wide profiling of genes during differentiation of wild type (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs and Mageb16-depleted (KD) ESCs

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

summary: The Melanoma-associated Antigen gene family (MAGE) generally encodes for tumour antigens. We recently have identified one of the MAGE gene members, Mageb16 to be highly expressed in undifferentiated murine embryonic stem cells (mESCs). The role of Mageb16 for the differentiation of the pluripotent stem cells is completely unknown. Here we demonstrate that Mageb16 (41 kDa) is distributed in cytosol and/or in surface membrane in undifferentiated mESCs. A transcriptome study was performed with differentiated short hairpin RNA (shRNA)-mediated Mageb16 knockdown (KD ESCs) and scrambled control (SCR) ESCs until a period of 22 days. Mageb16 KD ESCs mainly differentiated towards mesodermal derivatives such as cardiovascular lineages. Mesoderm-oriented differentiation initiated biological processes such as adipogenesis, osteogenesis, limb morphogenesis and spermatogenesis were significantly enriched in the differentiated Mageb16 KD ESCs. Cardiomyogenesis in differentiated KD mESCs was stronger when compared to differentiated SCR and wild mESCs. The expression of non-coding RNA (ncRNA) Lin28a and other epigenetic regulatory genes, nucleocytoplasmic trafficking and genes participating in spermatogenesis have also declined faster in the differentiating Mageb16 KD ESCs. We conclude that Mageb16 plays a crucial role for differentiation of ESCs, specifically to the mesodermal lineages. Regulative epigenetic networks and nucleocytoplasmic modifications induced by Mageb16 may play a role for the critical role of Mageb16 for the ESCs differentiation.

overall_design: RNA from undifferentiated WT ESCs, SCR ESCS and KD ESCs (d0) as well as of 2-, 4-, 12-, 15- and 22-days EBs was isolated and gene expression was analysed by the Affymetrix (Mouse 430 2.0) chip.

first: John

middle: A

last: Gaspar


title: Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells

first: Yuka

last: Kanno

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we demonstrate that the signal-dependent transcription factor STAT5 is critical for accumulation of all known ILC subsets in mice, and reveal a hierarchy of STAT5 dependency for populating lymphoid and non-lymphoid tissues. We also apply transcriptome and genomic distribution analyses to define a STAT5 gene signature in NK cells, the prototypical ILC subset, and provide a systems-based molecular rationale for its key functions downstream of IL-15. Additionally, we uncover surprising features of STAT5 behavior, most notably, the wholesale re-distribution that occurs when NK cells shift from tonic signaling to acute cytokine-driven signaling, and its genome-wide coordination with T-bet, another key transcription factor in ILC biology. Collectively, our data position STAT5 as a central node in the transcription factor network that instructs ILC development, homeostasis and function, and provide mechanistic insights on how it works at cellular and molecular levels.

overall_design: This dataset includes 22 individual samples of RNAseq or STAT5 ChIPseq data from ex vivo or cytokine-treated NK cells. Each culture condition includes at least 2 biological replicates per genotype.

first: A

last: Villarino

first: H

last: Sun

first: G

last: Gutierrez-Cruz

first: S

last: Brooks

first: Y

first: J

last: O'Shea


title: ColoCare Project: Epigenome-wide analysis of DNA methylation in colorectal cancer and adjacent mucosa tissues

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Within the ColoCare Project we obtained genome-wide DNA methylation profiles from 149 mucosa and 112 colorectal cancer tissues using Illumina HumanMethylation450k BeadChips. DNA methylation profiles were analysed by patient characteristics, lifestyle and exposures.

overall_design: Colorectal cancer patients were recruited at the University Hospital of Heidelberg. Genomic DNA from 149 mucosa and 112 tumor samples were analyzed, including 105 tumor-mucosa pairs. For one patient 3 replicates coming from different chips were included.

first: Cornelia

middle: M

last: Ulrich

first: Karin

last: Michels

first: Melanie

last: Boerries


title: Transcriptome analysis of cellobiose-positive isolates of L. lactis MG1363

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

institute: RUG

summary:
Transcriptomes of L. lactis MG1363ΔcelBΔptcCΔ0963 containing either an IS905 or a gfp integrated into llmg_1239 (pseudo_39) were compared to that of MG1363 with a Pcel (llmg_0186)up-mutation
An integration of IS905 into a gene coding for a transcriptional repressor led to activation of the repressed gene cluster coding for a plant sugar utilization pathway. The strain is further characterized using DNA MicroArrays.

overall_design: Cellobiose-positive derivatives of L. lactis MG1363ΔcelBΔptcCΔ0963 grown in M17-cel to mid-exponential phase. Two strains with either IS905 or gfp integration in llmg_1239 were compared to the original strain.

first: Jan

last: Kok

first: Oscar

last: Kuipers


title: Transcriptional repression in hypoxia is mediated by the Sin3A histone deacetylase complex

city: Madrid

first: Luis

last: del Peso

address: Arzobispo Morcillo

institute: Universidad Autonoma de Madrid

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

overall_design: Refer to individual Series


title: gene profiling changes induced by regulation of Brachyury expression

status: Public on Sep 12 2017

city: Shanghai

first: Chen

last: Su

state: Please select...

address: Fengyang Road

institute: Changzheng Hospital

summary:
Chordoma is a rare malignant bone tumor on axial skeleton, locally invasive and has a high rate of recurrence. Despite extensive studies, the mechanisms of tumor recurrence after surgical intervention, as well as resistance to radiation and chemotherapy, remain elusive. In this study, cell lines PCH1 and PCH2 were established and characterized by chordoma specific markers. We found that the embryonic transcription factor brachyury inhibits taxol induced apoptosis in different cells, including PCH1 and U2OS cells. Brachyury regulated genes were identified in PCH1 and U2OS using microarray.
Brachyury is an embryonic transcription factor involved in embryo development. We emplored the downstream genes related to apoptosis of Brachyury by microarray in different cell lines: U2OS, PCH1 and H460.

overall_design: U2OS (Mock & Brachyury Overexpression), H460(NC & Brachyury silencing), PCH1 (Mock & Brachyury Overexpression & Brachyury silencing)

last: su

first: Jiao

last: jian


title: Transcriptome analysis of 7l-treated leukemic cells

city: Tianjin

first: Ding

last: Yahui

state: Tianjin

address: weijin Road 94

institute: nankai university

summary: To analyze the molecular mechanisms by which 7l may induce apoptosis, microarray gene expression profiling of 7l treated KG1a cells was performed.

overall_design: 7l induced gene expression in KG1a cell was measured at 24 hours after exposure to doses of 2µM. Each sample was performed in triplicate.

first: Yahui

last: Ding

first: Weizhi

last: Ge


title: cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

summary: Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell-types, but obtaining APA maps from individual cell-types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell-types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines.  Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell-types and cellular states within the brain.

overall_design:
Samples GSM2467568-GSM2467582: cTag-PAPERCLIP libraries were generated from brain or liver samples of different mouse strains.
Samples GSM2683273-GSM2683281: RNA-seq libraries were generated from isolated mouse brain microglia or dissected mouse embryonic brain cortex.

first: Robert

last: Darnell


title: An NF-kB-dependent, lineage specific transcriptional program regulates Treg identity and function [ChIP-seq]

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: NF-kB p65 ChIPseq revealed differential binding of p65 in Treg vs Tconv upon TCR stimulation

overall_design: Duplicate of ChIPseq. One input and four samples for each dataset. Samples include conventional T cells (Tconv) with our without CD3/CD28 stimulation and regulatory T cells with or without CD3/CD28 stimulation.

first: Hyunju

last: Oh

first: Yenkel

last: Grinberg-Bleyer

first: Sankar

last: Ghosh


title: ChIP Seq analysis of H3K4me3 and H3K79me3 in euploid and aneuploid Saccharomyces cerevisiae

city: Baltimore

first: Wahid

last: Mulla

address: 855 North Wolfe Street

institute: Johns Hopkins University

summary: Aneuploidy and epigenetic alterations have long been associated with carcinogenesis, but it was unknown whether aneuploidy could disrupt the epigenetic states required for cellular differentiation. In this study, we found that ~3% of random aneuploid karyotypes in yeast disrupt the stable inheritance of silenced chromatin during cell proliferation. Karyotype analysis revealed that this phenotype was significantly correlated with gains of chromosomes III and X. Chromosome X disomy alone was sufficient to disrupt chromatin silencing and yeast mating-type identity as indicated by a lack of growth response to pheromone. The silencing defect was not limited to the cryptic mating type loci but was associated with global changes in histone modifications and chromatin localization of Sir2 histone deacetylase. The chromatin-silencing defect of disome X can be partially recapitulated by increasing the copy number of several genes on chromosome X. These results suggest that aneuploidy can directly cause epigenetic instability and disrupt cellular differentiation.

overall_design: WT haploid and disome X yeast strains were grown in YPD to mid-log phase and harvested for genome-wide ChIP studies of histone modifications H3K4me3 and H3K79me3 in duplicate.

first: Chris

last: Seidel


title: FOXF1 transcription factor promotes lung regeneration after partial pneumonectomy

city: Cincinnati

first: Craig

middle: Steven

last: Bolte

state: Ohio

address: 3333 Burnett Ave

department: Center for Lung Regenerative Medicine

institute: Cincinnati Children's Research Foundation

summary: FOXF1, a member of the forkhead box family of transcription factors, has been previously shown to be critical for lung development, homeostasis, and injury responses. However, the role of FOXF1 in lung regeneration is unknown. Herein, we performed partial pneumonectomy, a model of lung regeneration, in mice lacking one Foxf1 allele in endothelial cells (PDGFb-iCre/Foxf1fl/+ mice). Endothelial cell proliferation was significantly reduced in regenerating lungs from mice deficient for endothelial Foxf1. Decreased endothelial proliferation was associated with delayed lung regeneration as shown by reduced respiratory volume in Foxf1-deficient lungs. FACS-sorted endothelial cells isolated from regenerating PDGFb-iCre/Foxf1fl/+ and control lungs were used for RNAseq analysis to identify FOXF1 target genes. Foxf1 deficiency altered expression of numerous genes including those regulating extracellular matrix remodeling (Timp3, Adamts9) and cell cycle progression (Cdkn1a, Cdkn2b, Cenpj, Tubb4a), which are critical for lung regeneration. Deletion of Foxf1 increased Timp3 mRNA and protein, decreasing MMP14 activity in regenerating lungs. ChIPseq analysis for FOXF1 and histone methylation marks identified DNA regulatory regions with the Cd44, Cdkn1a, and Cdkn2b genes, indicating they are direct FOXF1 targets. Thus FOXF1 stimulates lung regeneration following partial pneumonectomy via direct transcriptional regulation of genes critical for extracellular matrix remodeling and cell cycle progression.

overall_design: ChIPseq on quiescent MFLM-91U cells;  RNAseq on FACS-sorted endothelial cells (CD45-CD31+CD326-) from Foxf1fl/+ and PDGFb-iCre Foxf1fl/+ lungs 4 days after partial pneumonectomy surgery.

first: Jagannathan

last: Sajjeev

first: Logan

last: Fulford

first: Artem

last: Barski

first: Vladimir

last: Kalinichenko


title: The profile of exosomal and cellular miRNA in ovarian cancer cell lines

city: Tokyo

first: Akira

last: Yokoi

state: Tokyo-to

address: 5-1-1 Tsukiji, Chuo-ku

department: Group for Research of Molecular Functions and Targets

institute: National Cancer Center　Research Institute

summary: To check the profile of exosomal and cellular miRNA in ovarian cancer cell lines, total RNA were extracted from exosomes and cells. Thirteen ovarian cancer cell lines (A2780, ES-2, CAOV3, SKOV3, OV-90, OAW42, MCAS, COV362, RMG-1, RMUG-S, KURAMOCHI, NIH-OVCAR3 and A2780cis) were investigated, and HOSE1, HOSE2 and HOSE3 (human ovarian surface epithelim cell lines) were used as control.

overall_design: To check the profile of exosomal and cellular miRNA in ovarian cancer cell lines, total RNA were extracted from exosomes and cells. Microarray analysis was performed using 50 ng of exosomal miRNAs and 100 ng of cellular miRNAs.

first: Yusuke

last: Yoshioka

last: Yamamoto

first: Takahiro

last: Ochiya

first: Mitori

last: Hiratsuka


title: A mouse model for embryonal tumors with multilayered rosettes uncovers the therapeutic potential of Sonic-hedgehog inhibitors

status: Public on Sep 11 2017

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

institute: University Medical Center Hamburg-Eppendorf

summary:
Embryonal Tumors with Multilayered Rosettes (ETMRs) have recently been described as a new entity of rare pediatric brain tumors with fatal outcome. We show here that ETMRs are characterized by a parallel activation of Shh- and Wnt-signaling. Co-activation of these pathways in murine neural precursors is sufficient to induce ETMR-like tumors in vivo that resemble their human counterparts based on histology and global gene expression analyses, and point to apical radial glia cells as the possible tumor cell-of-origin. Overexpression of LIN28A, which is a hallmark of human ETMRs, augments Sonic Hedgehog (Shh)- and Wnt-signaling in these precursor cells through downregulation of let7-miRNA, and LIN28A/let7a interaction with the Shh-pathway was detected at the level of Gli mRNA. Finally, human ETMR cells that were transplanted into immunocompromised host mice were responsive to the Shh-inhibitor Arsenic trioxide (ATO). Our findings provide a novel mouse model to study this tumor type, demonstrate the driving role of Wnt- and Shh-activation in the growth of ETMRs and propose downstream inhibition of Shh-signaling as a therapeutic option for patients with ETMRs.
Gene expression data of hGFAP-cre::Ctnnb1(ex3)Fl/+SmoM2Fl/+ , hGFAP-cre::SmoM2Fl/+ , hGFAP-cre::Ctnnb1(ex3)Fl/+  and Control mice

overall_design: Forebrain tumors and forebrain tissue of P0 mice

middle: E

first: Annika

middle: K

last: Wefers

first: Sander

last: Lambo

first: Edoardo

last: Bianchi

first: Marie

last: Bockstaller

first: Mario

last: Dorostkar

first: Valerie

last: Meister

first: Pia

last: Schindler

first: Andrey

last: Korshunov

first: Katja

last: von Hoff

first: Johannes

last: Nowak

first: Monika

last: Warmuth-Metz

first: Marlon

last: Schneider

first: Ingrid

last: Renner-Müller

first: Daniel

last: Merk

first: Mehdi

last: Shakarami

first: Tanvi

last: Sharma

first: Lukas

last: Chavez

first: Rainer

last: Glass

first: Jennifer

last: Chan

first: M

last: Taketo

first: Philipp

first: Marcel

last: Kool

first: U

last: Schüller


title: Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of androgen receptor (AR) blockade by the glucocorticoid receptor (GR). In contrast to fixed genomic alterations, here we show that GR-mediated antiandrogen resistance is adaptive and reversible due to regulation of GR expression by a tissue-specific enhancer. GR expression is silenced in prostate cancer by a combination of AR binding and EZH2-mediated repression at the GR locus, but is restored in advanced prostate cancers upon reversion of both repressive signals. Remarkably, BET bromodomain inhibition resensitizes drug-resistant tumors to Enz by selectively impairing the GR signaling axis via this enhancer. In addition to revealing an underlying molecular mechanism of GR-driven drug resistance, these data suggest that inhibitors of broadly active chromatin-readers could have utility in nuanced clinical contexts of acquired drug resistance with a more favorable therapeutic index.

overall_design: A total of 45 samples were analyzed (905L = LNAR'; 924R = LREX'). For ChIP-seq, histone modification (H3K4me1, H3K4me3, H3K27ac, H3K27me3) ChIP and BRD4 ChIP was performed on cell lines with or without Enz treatment; input used to normalize. Chem-Seq using bio-JQ1 was performed on cell lines with or without Enz treatment. RNA-seq was performed on in vivo LNAR' or LREX' tumors treated with vehicle or JQ1 (n=4 tumors analyzed per treatment condition)

first: Neel

last: Shah

first: Charles

last: Sawyers

first: Ping

last: Wang


title: Methylation and expression datasets of human myeloid-derived suppressor cells and dendritic cells derived from monocytes

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)


title: Distinct cell cycle control in naïve and primed mouse pluripotency

city: Nijmegen

first: Menno

last: ter Huurne

address: Geert Grooteplein 26

department: Molecular Biology

institute: Radboud University Nijmegen

first: Henk

last: Stunnenberg