title: Widespread and precise epigenomic reprogramming in response to heat shock

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

summary: Gene expression is controlled by a variety of proteins (the epigenome) whose precise organization and mechanism of action at every promoter remains to be worked out. Here we examine a functionally diverse subset of these proteins: RSC (Rsc9), SAGA (Spt3), Hsf1, general transcription factors (GTFs), FACT (Spt16), and RNA polymerase (Pol) II, under normal and acute heat shock conditions, using the ultra-high resolution genome-wide ChIP-exo assay. Our findings indicate that canonically organized proteins reside at most genes and are rapidly reorganized upon heat shock. This includes association of SAGA with Hsf1 at upstream promoters regions, RSC movement from gene bodies to promoters, and Pol II accumulation at pre-existing melted promoter DNA. Surprisingly, most of these events are not coupled to changes in gene expression. In contrast, GTF occupancy tracks with gene expression level. Together, these findings reveal that the epigenome is reprogrammed by signaling events far beyond what is indicated by gene expression changes.

overall_design: Genome-wide analysis of yeast general regulatory factors by heatshock stress condition

first: Vinesh

last: Vinayachandran

first: Rohit

last: Reja

first: Matthew

middle: J

last: Rossi

first: Lila

last: Rieber

first: Chitvan

last: Mittal

first: Shaun

last: Mahony

first: B

middle: F

last: Pugh


title: Positively selected enhancer elements endow tumor cells with metastatic competence

status: Public on Jan 15 2018

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in signature enhancer-histone marks between near-isogenic pairs of high and low lung-metastatic osteosarcoma cells. We term these regions Metastatic Variant Enhancer Loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster non-randomly, indicating that activity of these enhancers and their associated gene targets is positively selected. Osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL associated gene expression.

overall_design: Examination of H3K4me1, H3K27ac, and Dnase I Hypersensitivity data in highly and non-metastatic osteosarcoma cell line pairs (n=5 pairs) as well as primary and metastatic tumors in human patients (n=5 pairs).  Global gene expression during metastatic progression in ex vivo model of lung metastasis was also examined for 3 cell line pairs.

first: James

last: Morrow

first: Alina

middle: R

last: Saiakhova

middle: C


title: OMICS assisted N-terminal proteoform and protein expression profiling upon methionine aminopeptidase 1 (MetAP1) deletion

status: Public on Jan 12 2018

city: Gent

first: Petra

last: Van Damme

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB

summary: Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition. The levels of iMet retention are inversely correlated with cellular proliferation rates. Further, despite the increased MetAP2 expression observed upon MetAP1 deletion and as inferred from the iMet retention profiles observed, MetAP2 was unable to restore processing of MS-, MP- and MA- N-termini, indicating the higher activity of MetAP1 over these N-termini. Proteome and transcriptome expression profiling point to differential expression of proteins implicated in lipid metabolism, cytoskeleton organization, cell proliferation and protein synthesis upon perturbation of MetAP activity.

overall_design: RNA sequencing of wild type (parental) and METAP1 knockout HAP1 cells.

first: Veronique

last: Jonckheere

first: Daria

last: Fijałkowska


title: Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

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

overall_design: Refer to individual Series


title: Comparison of GATA3 mutant and GATA3 wild type isogenic MCF-7 and CAMA1 breast cancer cell lines

city: Baltimore

first: Josh

last: Lauring

state: MD

address: 1650 Orleans Street, CRB1 Room 146

department: Oncology

institute: Dr.

summary: The GATA3 transcription factor is one of the most frequently mutated genes in breast cancer. Heterozygous mutations, largely frameshifting, are seen in 15% of estrogen receptor positive breast cancers, the subtype in which these mutations are almost exclusively found. Mouse studies have shown that Gata3 is critical for breast development and that GATA3 gene dosage affects breast tumor progression. Human patient data have shown that high Gata3 expression, a feature of luminal subtype breast cancers, is associated with a better prognosis. Although the frequency of GATA3 mutation suggests an important role in breast cancer development or progression, there is little understanding of how mutations in GATA3 affect its function in luminal breast epithelial cells and what gene expression changes result as a consequence of the mutations. Here, using gene editing, we have created two sets of isogenic human luminal breast cancer cell lines with and without a truncating GATA3 mutation. GATA3 mutation enhanced tumor growth in vivo but did not affect sensitivity to clinically used hormonal therapies or chemotherapeutic agents. We identified genes upregulated and downregulated in GATA3 mutant cells, a subset of which was concordantly differentially expressed in GATA3 mutant primary luminal breast cancers. Addback of mutant GATA3 recapitulated mutation-specific gene expression changes and enhanced soft agar colony formation, suggesting a gain of function for the mutant protein.

overall_design: Parental MCF-7 cells with endogenous heterozygous GATA3 D336fs*17 mutation are compared to two independently derived gene-edited GATA3 wild type clones. Biological replicates (independent cultures and RNA preparations) were run and array analysis was performed on two separate occasions using independent samples from these three cell lines. A separate comparison was performed between CAMA1 breast cancer cells and a single gene-edited clone with knock-in of the GATA3 D336fs*17 mutation on a single allele. Single replicates were compared for these CAMA1 and GATA3 mutant samples.


title: A glance over drug detoxification systems through the transcriptomic profiling of Mycobacterium tuberculosis during lipid metabolism

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

summary: Tuberculosis (TB) is currently the number one killer among infectious diseases worldwide. Lipids are abundant molecules during the infectious cycle of Mycobacterium tuberculosis (Mtb) and studies better mimicking its actual metabolic state during pathogenesis are needed. Though most studies have focused on the mycobacterial lipid metabolism under standard conditions (carbon source, drugs, stress), little is known about the transcriptome of Mtb in a lipid environment. Here we determine the transcriptome of Mtb H37Rv in a lipid-rich environment (mixture of cholesterol, palmitic, stearic and oleic acids), under aerobic and hypoxic conditions, using RNAseq technology. Lipids significantly induced the expression of 368 genes. A main core lipid response was observed involving efflux systems, iron caption and sulfur reduction. In co-expression with ncRNAs and other genes discussed below, may act coordinately to prepare the machinery conferring drug tolerance and increasing a persistent population. Our findings could be useful to tag relevant pathways for the development of new drugs, vaccines and new strategies to control TB.

overall_design: Three in vitro experimental conditions of Mycobacterium tuberculosis H37Rv were evaluated: exponential phase, stationary phase and hypoxic stage NRP1, each assay was tested in lipid conditions as treatment and in presence of dextrose as control. All samples had a biological replicate, yielding a total of 12 experimental samples.

first: Diana

middle: A

last: Aguilar-Ayala

first: Filip

middle: V

last: Nieuwerburgh

first: Sander

last: Willems

first: Dieter

last: Deforce

first: Juan

last: Palomino

last: Vandamme

first: Jorge

last: Gonzalez-Y-Merchand

first: Anandi

last: Martin


title: Genome-wide maps of Super-enhancers in TH9 cells by H3K27Ac and BRD4 CHIP-Seq.

status: Public on Jan 11 2018

city: Houston

first: xiang

last: xiao

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

summary: Th cell differentiation is transcriptionally regulated, relying on the induction of “lineage-defining” transcription factors. We report that formation of super-enhancers is critical in robust induction of Th9 cells and that assembly of the Il9 super-enhancers requires OX40-triggered chromatin H3K27 acetylation. Mechanistically, we found that OX40 costimulation induces RelB expression, which recruits the histone acetyltransferase p300 to the Il9 locus to catalyze H3K27 acetylation. This allows binding of the super-enhancer factor Brd4 to initiate assembly of the super-enhancer complex, which in turn drives robust Th9 induction. Thus, Th9 cells are induced in massive numbers upon OX40 costimulation and disruption of super-enhancers abolished Th9 induction in vitro and inhibited Th9-mediated allergic airway inflammation in vivo. Our data identify super-enhancers as a key mechanism of Th9 induction and uncover a new mechanism of Th cell differentiation.

overall_design: Analysis of H3K27Ac histone modifications and BRD4 binding in CD4+ T cells cultured in vitro under Th9 differentiation conditions for 48 hours in the presence or absence of OX40 ligation.

first: Xian

last: Li

first: Xiang

last: Xiao


title: Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [ChIP-Seq]

summary: We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and MCF7 ESR1-positive cell-lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR).

overall_design: Examination of ER binding in breast cancer cell lines with and without ESR1 mutations

first: Lesley-Ann


title: Microarray analysis of mRNA expression in E14.5 and E16.5 mouse ovaries with and without Coup-tfII (Nr2f2)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
COUP-TFII (NR2F2) is expressed in somatic cells in fetal ovary. To investigate the function of COUP-TFII , we used Cre-flox model to ablate Coup-tfII in the fetal ovaries
We performed microarray to compare gene expression profile between control and knockout ovaries.

overall_design: We established a tamoxifen inducible WT1-CreERT2; COUP-TFII flox/flox model to ablate Coup-tfII by injecting tamoxifen (2 mg/10g body weight) at E11.5 and E12.5. Control and knockout ovaries were collected at E14.5 and E16.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Fei

last: Zhao

first: Humphrey

last: Yao


title: A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary:
Polycomb group proteins regulate self-renewal and
differentiation in many stem cell systems. When
assembled into two canonical complexes, PRC1
and PRC2, they sequentially deposit H3K27me3
and H2AK119ub histone marks and establish repressive
chromatin, referred to as Polycomb domains.
Non-canonical PRC1 complexes retain RING1/
RNF2 E3-ubiquitin ligases but have unique sets of
accessory subunits. How these non-canonical complexes
recognize and regulate their gene targets
remains poorly understood. Here, we show that
the BCL6 co-repressor (BCOR), a member of the
PRC1.1 complex, is critical for maintaining primed
pluripotency in human embryonic stem cells
(ESCs). BCOR depletion leads to the erosion of
Polycomb domains at key developmental loci and
the initiation of differentiation along endoderm
and mesoderm lineages. The C terminus of BCOR
regulates the assembly and targeting of the
PRC1.1 complex, while the N terminus contributes
to BCOR-PRC1.1 repressor function. Our findings
advance understanding of Polycomb targeting and
repression in ESCs and could apply broadly across
developmental systems.

overall_design: Transcriptional Repression by the non-canonical PRC1.1 complex investigated by ChIP-Seq and RNA-Seq

first: Zheng

last: Wang

middle: D

first: Vivian

last: Bardwell

first: Natalia

last: Ivanova


title: RNA-seq data of soybean SKRP1 and AVR3C

city: Nanjing

first: Jie

last: Huang

state: Jiangsu

address: NO.1 Weigang

department: Plant Pathology

country: China

institute: Nanjing Agricultural University

summary: The process of RNA splicing influences many physiological processes including plant immunity. However, how plant parasites manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, physically binds to and stabilizes soybean (Glycine max) serine/lysine/arginine rich proteins GmSKRPs in vivo. The SKRPs are novel proteins that associate with spliceosome components, and are negative regulators of plant immunity. Analysis by RNA-seq data indicates that alternative splicing of pre-mRNAs from 401 soybean genes, including defense related genes, is altered in GmSKRP1 and PsAvr3c over-expressing lines compared to control plants. Representative splicing events mediated by GmSKRP1 and PsAvr3c are tested by infection assays or by transient expression in soybean plants. Our results show that a plant pathogen effector can reprogram host pre-mRNA splicing to promote disease, and we propose that pathogens evolved such strategies to defeat host immune systems.

overall_design: three independent soybean SKRP1 over-expression lines, three AVR3C over-expression samples and three GFP control samples

first: Suomeng

last: Dong


title: The role of LSD1 in Epithelial to Mesenchymal Transition: gene expression profiling and ChIP-seq

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra


title: The role of LSD1 in Epithelial to Mesenchymal Transition

summary: Complex regulatory networks control epithelial-to-mesenchymal transition (EMT) but the underlying epigenetic control is poorly understood. Lysine-specific demethylase 1 (LSD1) is a key histone demethylase that alters the epigenetic landscape. Here we explored the role of LSD1 in global epigenetic regulation of EMT, cancer stem cells (CSCs), the tumour microenvironment, and therapeutic resistance in breast cancer. LSD1 induced pan-genomic gene expression in networks implicated in EMT and selectively elicits gene expression programs in CSCs whilst repressing non-CSC programs. LSD1 phosphorylation at serine-111 (LSD1-s111p) by chromatin anchored protein kinase C-theta (PKC-θ), is critical for its demethylase and EMT promoting activity and LSD1-s111p is enriched in chemoresistant cells in vivo. LSD1 couples to PKC-θ on the mesenchymal gene epigenetic template promotes LSD1-mediated gene induction. In vivo, chemotherapy reduced tumour volume, and when combined with an LSD1 inhibitor, abrogated the mesenchymal signature and promoted an innate, M1 macrophage-like tumouricidal immune response. Circulating tumour cells (CTCs) from metastatic breast cancer (MBC) patients were enriched with LSD1 and pharmacological blockade of LSD1 suppressed the mesenchymal and stem-like signature in these patient-derived CTCs. Overall, LSD1 inhibition may serve as a promising epigenetic adjuvant therapy to subvert its pleiotropic roles in breast cancer progression and treatment resistance.

overall_design: 4 treatments (mock siRNA and LSD1 siRNA with or without PMA and TGF). 1 replicate each

first: Anjum

last: Zafar

first: Sudha

last: Rao


title: Transcription factor-dependent ‘anti-repressive’  mammalian enhancers exclude H3K27me3  from extended genomic domains

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
To define and assess the role of transcription factor binding at villus enhancers, we performed ATAC-seq and ChIP-seq.
We used RNA-sequencing to profile gene expression changes upon transcription factor loss. Loss of gene expression correlated with transcription factor-dependent enhancers and reveal the role of certain enhancers in H3K27me3 exclusion.

overall_design: ATAC-seq and ChIP-seq (H3K4me1, H3K4me2, H3K27ac, H3K27me3, H3K9me3, H3K4me3, CDX2, HNF1A, PBRM1, RNA PolII, SMARCC1, CTCF, MED1 and KDM6A) analysis of isolated mouse intestinal differntiated villus epithelial cells. RNA-seq analysis of mouse intestinal differentiated villus epithelial cells.

first: Madhurima

last: Saxena

first: Adrianna

middle: K

last: San Roman

first: Nicholas

last: O’Neill

first: Rita

last: Sulahian

first: Unmesh

last: Jadhav


title: Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression [ChIP-seq]

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary: Tissue regeneration relies on resident stem cells (SCs), whose activity and lineage choices are influenced by microenvironment. Exploiting the synchronized, cyclical bouts of tissue regeneration in hair follicles (HFs), we investigate how microenvironment dynamics shape the emergence of SC lineages. Employing epigenetic and ChIP-seq profiling, we uncover how signal-dependent transcription factors couple spatio-temporal cues to chromatin dynamics, thereby choreographing SC lineages. Using enhancer-driven reporters, mutagenesis and genetics, we show that simultaneous BMP-inhibitory and WNT signals set the stage for lineage choices by establishing chromatin platforms permissive for diversification. Mechanistically, when binding of BMP-effector pSMAD1 is relieved, super-enhancers driving HF-SC master regulators become silenced. Concomitantly, multipotent, lineage-fated super-enhancers silent in HF-SCs become activated by exchanging WNT-effectors TCF3/4 for LEF1. Throughout regeneration, lineage super-enhancers continue reliance upon LEF1, but then achieve specificity by accommodating additional incoming signaling effectors. Barriers to progenitor plasticity mount as diverse, signal-sensitive transcription factors shape LEF1-regulated super-enhancer dynamics.

overall_design: Mouse suprabasal TACs in mature hair follicle (Anagen VI) were FACS-purified for ChIP-sequencing.

first: Rene

last: Adam

first: Elaine

last: Fuchs


title: LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer

overall_design: 3 biological samples were analysed with one ChIP antibody.

first: Tara

last: Boulding


title: ISL1-binding sites in human ES cell-derived cardiomyocyte progenitor cells identified by ChIP-seq upon cardiac differentiation

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

summary: ChIP-Seq analysis of ISL1 binding sites in cardiomyocyte progenitor cells captured at day 5 of directed cardiac differentiation.

overall_design: hES cells (HuES6 background) are deficient in endogenous ISL1 but may express ISL1 under control of a doxycycline-inducible promoter. DOX was added at days 3 and 4 of high-efficiency cardiac differentiation and cells are harvested at day 5, the peak of endogenous ISL1 expression in wild-type cells. Analysed samples comprise a treatment sample expressing ISL1 (DOX added), a minus DOX control without ISL1 expression and an input control. Analysis of ISL1 binding sites in one treatment sample and two different negative controls. Each sample comprises pooled material from several independent experiments.

first: Boris

last: Greber

first: Roberto

last: Quaranta

first: Monika

last: Stoll


title: Learning and age-related changes in genome-wide H2A.Z binding in the hippocampus

status: Public on Jan 10 2018

city: Mississauga

first: Iva

middle: Toronto

last: Zovkic

state: Ontario

address: 3359 Mississauga Road North, CCT Building Room 4071

country: Canada

institute: University of Toronto Mississauga

summary: We characterize histone H2A.Z binding and RNA expression in the hippocampus of young (2.5 months) and aged (15.5 months) mice in response to contextual fear conditioning.

overall_design: We use ChIP to characterize H2A.Z binding under basal and learning-induced conditions in the hippocampus of young and aged mice. H2A.Z binding is compared to gene-expression levels in response to learning.

middle: B


title: Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression


title: Estrogen and high-fat diet induced alterations of endometrial transcriptome profile in ovariectomized C57BL/6 mice

city: Shanghai

first: Xiaojun

last: Chen

address: No. 419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

summary:
Unopposed estrogen stimulation and insulin resistance are known to play important roles in endometrial cancer (EC), but the relationship between these two factors and how they contribute to endometrial lesions is not completely understood. To investigate the endometrial transcriptome profiles and the associated molecular pathway alterations, we established an ovariectomized C57BL/6 mouse model treated with subcutaneous implantation of the 17-β estradiol (E2) pellet and/or high-fat diet (HFD) to mimic sustained estrogen stimulation and insulin resistance.
We used microarrays to detail the global program of gene expression underlying the  mice endometrium and indentified distinct classes of E2 and/or high-fat diet related ncRNA during this process.

overall_design: All mice received bilateral oophorectomy at 6-8 weeks after birth.The mice were then randomly divided into four groups and treated with normal chow diet, E2-releasing pellet implanted   subcutaneously, high-fat diet and E2-releasing pellet implanted subcutaneously plus high-fat diet for 12 weeks. Mice endometrium were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to investigate differential transcriptome and ncRNA profiles affected by estrogen and/or high-fat diet.

first: Yali

last: Cheng


title: Simple and Complex Centromeric Satellites in Drosophila Sibling Species

status: Public on Jan 08 2018

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appears to be present at all centromeres, and none of which is found only at centromeres. Although centromere sequences from a minichromosome have been identified and candidate centromere sequences have been proposed, the DNA sequences at native Drosophila centromeres remain unknown. Here we use native chromatin immunoprecipitation to identify the centromeric sequences bound by the foundational kinetochore protein cenH3, known in vertebrates as CENP-A. In D. melanogaster, these sequences include a few families of 5-bp and 10-bp repeats, but in closely related D. simulans, a partially overlapping set of short repeats and more complex repeats comprise the centromeres. The results suggest that a recent expansion of short repeats is replacing more complex centromeric repeats in the melanogaster subgroup of Drosophila.

sample_organism:
Drosophila melanogaster
Drosophila simulans

overall_design: We used native chromatin immunoprecipitation with anti-CENP-A antibodies to enrich for and sequence centromeric satellites bound by CENP-A in two sibling Drosophila species. We counted 71 candidate repeated sequences and their reverse complements to determine which were enriched in the immunoprecipitates.

first: Paul

last: Talbert

first: Sivakanthan

last: Kasinathan

first: Steven


title: S1P-dependent inter-organ trafficking of group 2 innate lymphoid cells supports host defense

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: Innate lymphoid cells (ILCs) are considered to be the innate counterparts of adaptive T lymphocytes and play important roles in host defense, tissue repair, metabolic homeostasis, and inflammatory diseases. ILCs are generally thought of as tissue-resident cells, but whether ILCs strictly behave in a tissue-resident manner or can move between sites during infection is unclear. We show here that IL-25- or helminthic infection-induced inflammatory ILC2s are not tissue-resident but circulating cells, which arise from resting ILC2s residing in intestinal lamina propria and then migrate to mesenteric lymph nodes, spleen, lung, and liver. IL-25 induces rapid proliferation of the intestinal ILC2s and a change in their sensitivity to S1P-mediated chemotaxis, leading to lymphatic entry, blood circulation, and accumulation in periphery sites, including the lung where they contribute to anti-helminth defense and tissue repair. Our finding of cytokine-driven expansion and migration of innate lymphocytes, a behavioral parallel to the antigen-driven priming, expansion, and migration of adaptive lymphocytes to effector sites in distant tissues, provides a significant advance in our overall understanding of ILCs and indicates that ILCs complement adaptive immunity by providing both local and distant site effector protection during infection.

overall_design: We examined the transcriptomes of BM ILC2 progenitors, lung nILC2s, IL-33-activated lung nILC2s, intestinal ILC2s, IL-25-induced lung iILC2s, and MLN iILC2s by RNA-Seq.

first: Yuefeng

last: Huang

first: Kairui

last: Mao

first: Xi

first: Ming-an

first: Takeshi

last: Kawabe

first: Weizhe

last: Li

first: Nicholas

last: Usher

first: Jinfang

last: Zhu

first: Joseph

last: Urban Jr

first: William

middle: E

last: Paul

first: Ronald

middle: N

last: Germain


title: DNA Methylation signatures in Panic Disorder

first: Elisabeth

middle: B.

last: Binder

state: DEUTSCHLAND

address: Kraepelinstraße 2-10

department: Dept. Translational Research in Psychiatry

institute: Max Planck Institute of Psychiatry

summary: An Epigenome-Wide Association Study (EWAS) was conducted to compare medication-free panic disorder (PD) patients (n=89) with healthy controls (n=76) in peripheral blood samples.

overall_design: Genomic DNA was extracted from peripheral blood. Bisulphite converted DNA was then hybridised to the Illumina Infinium HumanMethylation450 BeadChip to examine DNA methylation for each sample.

first: Angelika

last: Erhardt

first: Stella

last: Iurato


title: Dysregulated Signalling leads to altered cell migration: an oncogenic basis for the development of CCSK

city: Dublin

first: Maureen

last: O'Sullivan

state: Dublin 2

address: College Green

department: School of Medicine

country: Ireland

institute: Trinity College Dubiln

summary: The oncogenic mechanisms and tumour biology underpinning Clear Cell Sarcoma of Kidney (CCSK), the second commonest paediatric renal malignancy, are poorly understood and currently therapy depends heavily on Doxorubicin with cardiotoxic side-effects. Previously, we characterised the balanced t(10;17)(q22;p13) chromosomal translocation, identified at that time as the only recurrent genetic aberration in CCSK. This translocation results in an in-frame fusion of the YWHAE (encoding 14-3-3e) and NUTM2 genes, with a somatic incidence of 12%. Clinico-pathological features of that cohort suggested that this aberration might be associated with higher stage and grade disease. Since no primary CCSK cell line exists, we generated various stably transfected cell lines containing doxycycline-inducible HA-tagged-YWHAE-NUTM2, in order to study the effect of expressing this transcript. 14-3-3e-NUTM2-expressing cells exhibited significantly greater cell migration compared to mock-treated controls. Gene and protein expression studies conducted in parallel on this model system suggested dysregulation of signalling pathways as a basis to the migration changes. Importantly, by blocking these signalling pathways using anti-EGFR, anti-IGF1R and anti-PDGFa neutralising antibodies, the migratory advantage conferred by transcript expression was abrogated. These results support 14-3-3e-NUTM2 expression as a contributor to CCSK tumorigenesis and provide avenues for the exploration of novel therapeutic approaches in CCSK.

overall_design: Gene expression changes resulting from induction of the fusion gene were compared in mock- and doxycycline treated HEK293 and BJ-hTERT HA-YWHAE-NUTM2 cell lines at 24 and 72 hours. Total RNA was extracted from cell lines, assayed by NanoDrop (Thermo Scientific) and 200 ng was used for gene expression analysis using the Affymetrix® Human Gene 2.1 ST Array (Affymetrix, Santa Clara, CA, USA). The arrays were performed in triplicate and analysed using Bioconductor packages ‘oligo’ and ‘limma”.

first: Colin

middle: P

last: Kenny

last: O'Sulllivan


title: A method for the acute and rapid degradation of endogenous protein

city: Göttingen

first: Melina

last: Schuh

address: Am Fassberg 11

institute: Max Planck Institute for Biophysical Chemistry

summary: We developed Trim-Away as a a technique to degrade endogenous proteins acutely in mammalian cells without prior modification of the genome or mRNA. Trim-Away is able to remove unmodified native proteins within minutes of application by making use of the TRIM21 ubiquitin ligase that regognises antibody-protein complexes and harnesses the cellular degradation machinery. We performed transcriptome profiling (RNAseq) on NIH3T3 and NIH3T3-mCherry-mTRIM21 cells  following electroporation with non-targeting antibody (IgG), bovine serum albumin (BSA), or buffer (PBS). We found that a total of only 8 protein-encoding transcripts were consistently downregulated more than 2-fold in the NIH3T3-mCherry-mTRIM21 cells (Kdm5d, Ddx3y, Eif2s3y, Uty, Asb4, Fat4, Papss2 and Lama2), although we cannot rule out the possibility that this is an indirect consequence of lentivirus construct integration rather than a direct consequence of TRIM21 overexpression. Notably, transcripts encoding previously described ligands of TRIM21, IRF-3, IRF-5, Skp2, DAXX, DDX41, and SQSTM1 were not significantly increased or decreased upon overexpression of TRIM21. Our experiments suggest that the cells overexpressing TRIM21 behave similar to wild-types.

overall_design: mRNA profiles of NIH3T3 and NIH3T3-mCherry-mTRIM21 cells following electroporation with antibody (IgG), BSA or PBS were generated by deep sequencing, in triplicate, using a Illumina NextSeq 500 platform.

first: Dean

last: Clift

last: McEwan

first: Larisa

middle: I

last: Labzin

first: Vera

last: Konieczny

first: Binyam

last: Mogessie

first: Leo

last: James


title: Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression [RNA-seq]

first: Hanseul

last: Yang

overall_design: Mouse activated hair gem stem cells (by hair depilation, day3) were purified from wild-type, LEF1 single knock out, and LEF1/TCF7 double knock out mice. The sorted cells were analyzed by RNAseeq.

first: Rene

last: Adam

first: Elaine

last: Fuchs


title: Gene expression analysis of laser-captured epithelium and stroma from FVB mice and HPV16 E6/E7 transgenic mice under estrogen or control treatment regimens.

status: Public on Jan 09 2018

city: Madison

first: Johan

last: den Boon

state: WI

address: 330 North Orchard Street

department: Virology

institute: Morgridge Institute for Research

summary:
Affymetrix Mouse Genome 430 2.0 arrays were used to measure genome-wide gene expression levels. The results show that high-risk human papillomavirus oncogenes E6 and E7 reprogram the cervical cancer microenvironment independently of and synergistically with estrogen, a critical co-factor in cervical cancer development and maintenance.
Several potential estrogen-induced paracrine-acting factors were identified in the expression profile of the cervical tumor microenvironment. The microenvironment of estrogen-treated HPV-transgenic mice was significantly enriched for chemokine/cytokine activity and inflammatory and immune functions associated with carcinogenesis.

overall_design: Female reproductive tracts from wild type FVB and HPV16 E6/E7 transgenic mice were cryosectioned and used for laser-capture of cervical tissue. The mRNA levels were measured for a total set of 32 captures (5 untreated normal epithelium and stroma; 7 untreated transgenic epithelium and stroma; 3 estrogen-treated normal stroma; 5 estrogen-treated transgenic stroma).

first: Paul

last: Lambert

last: Ahlquist

first: Megan

last: Spurgeon


title: Cell-Type-Specific Survey of Epigenetic Modification by Tandem Chromatin Immunoprecipitation Sequencing

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary:
[Background]: Nervous system of higher eukaryotes is composed of numerous types of neurons and glia, which together orchestrate complex neuronal responses. However, the complex pool of cells usually poses analytic challenges to investigate gene expression profile and its epigenetic basis in specific cell type. Here we developed a novel method that enables cell-type-specific analyses of epigenetic modification using tandem chromatin immunoprecipitation sequencing (tChIP-Seq).

[Results]: FLAG-tagged histone H2B, a constitutive chromatin component, was firstly expressed in Camk2a-positive pyramidal cortical neurons and was used to purify the chromatin in a cell-type-specific manner. The subsequent chromatin immunoprecipitation using antibodies against H3K4me3—an active promoter mark—allowed us to survey neuron specific coding and noncoding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions as well as genes with unknown function expressed in cortical neurons.

[Conclusions]: tChIP-Seq thus provides a versatile approach to investigate epigenetic modifications of particular cell types in vivo.

overall_design: ChIP-Seq

first: Mari

last: Mito

first: Mitsutaka

last: Kadota

first: Kaori

last: Tanaka

first: Yasuhide

last: Furuta

first: Kuniya

last: Abe

first: Shinichi

last: Nakagawa


title: Substrate stiffness-dependent gene expression profile for cortical neurons

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

summary: We undertook mRNA microarray and gene ontology analyses to screen out substrate stiffness-dependent genes. Total mRNA were extracted from E17 cortical neurons grown on soft or stiff substrates at 5 or 16 hr time points. We identified 114 differentially-expressed mRNA transcripts in cells grown on 0.1 kPa and 20 kPa gels at the 5 hr time-point. Among them, 66 were upregulated in 0.1 kPa gel cultures and the remainder were downregulated (compared to cells grown on stiffer substrates).  The expressions of three endocytic genes (Cltc, Dab2, and Myo6) and four adhesion genes(Vcl, Robo2, Nrcam, and Cad11)  were confirmed by QGP and smRNA FISH.

overall_design: We collected total RNA extracted from E17 cortical neurons on different substrates with various stiffness ( 0.1,1,20 kPa gels and glass). Three independent experiments were performed at two time points (5 hr and 16 hr).

first: Ting-Ya

last: Chang

first: Chen

last: Chen

first: Ya-Chu

first: Chi-Huan

last: Lu

first: Min

last: Lee

first: Shao-Tzu

first: De-Yao

last: Wang

first: Aijun

first: Chin-Lin

last: Guo


title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells

city: Beijing

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

institute: Peking university

summary: Loss of organelle homeostasis is a hallmark of aging. However, it remains elusive how this occurs at transcriptional levels. Here, we report that human mesenchymal stem cell (hMSC) aging is associated with dysfunction of double-membrane organelles and downregulation of transcription factor ATF6. CRISPR/Cas9-mediated inactivation of ATF6 in hMSCs, not in human embryonic stem cells (hESCs), resulted in premature cellular aging, characteristic of loss of endomembrane homeostasis. Comparative transcriptomic analyses in hMSCs identify 145 constitutive and 112 tunicamycin-induced ATF6-regulated genes implicated in different layers of cellular homeostasis regulation. Notably, FOS was identified as one of the constitutive ATF6 responsive genes, downregulation of which contributes to accelerated hMSC senescence. Our study identifies a novel transcriptional program related to homeostatic regulation of membrane organelles, and provides mechanistic insights into aging-associated attrition of human stem cells.

overall_design: RNA Seq and ChIP-Seq

first: Wang

last: Si

first: Hu

last: Boqiang


title: A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia

city: Cold Spring Harbor

first: Yali

last: XU

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transient activation of tumor-associated macrophages boosts anti-tumor immunity

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary: Depletion of immunosuppressive tumor-associated macrophages (TAM) or reprogramming towards a pro-inflammatory activation state represent different strategies to therapeutically target this frequent myeloid population. Here we report that inhibition of colony-stimulating factor-1 receptor (CSF-1R) signaling sensitizes TAM to profound reprogramming in the presence of a CD40 agonist prior to their depletion. Despite the short-lived nature of macrophage hyperactivation, combined CSF-1R/CD40 stimulation of macrophages is sufficient to trigger a productive and durable T cell response in various mouse cancer models. The central role of macrophages in regulating T cell-dependent tumor rejections was substantiated by depletion experiments and transcriptomic analysis of ex vivo sorted TAM. Since CD40 expression on human TAM varies between different tumor types, co-expression of human CSF-1R and CD40 in colorectal adenocarcinoma and mesothelioma can serve as criteria to select these tumor types for clinical development

overall_design: Female C57BL/6N mice (6-8 weeks in age, obtained from Charles River) were inoculated with 106 MC38 colorectal adenocarcinoma tumor cells subcutaneously. Tumor growth curves were monitored by caliper measurement and once tumor size reached 250 mm3 in average, groups were allocated for antibody treatment. Ten mice/group were treated with 30 mg/kg IgG1 isotype control antibody clone MOPC-21 (BioXCell), 4 mg/kg anti-CD40 rat IgG2a antibody clone FGK45 (BioXCell), 30mg/kg anti-CSF-1R antibody clone 2G2, 4 mg/kg rat IgG2a control clone 2A3 (BioXCell). For depletion experiments 4mg/kg mouse anti-CD4 antibody clone GK1.5 (Biolegend), 4mg/kg anti-NK1.1 antibody clone PK136 (BioXCell) and 4mg/kg anti-CD8α antibody clone 53-6.7 (BioXCell) were administered when tumor size reached 190mm3 in average. Antibodies were given every second day for four times. In between doses two and three of the depleting antibodies, animals were further treated with vehicle control (0,9% sodium saline), MOPC21, FGK45, 2G2 or combination of FGK45 and 2G2. The anti-CSF-1R antibody or respective IgG1 control antibody were administered weekly until tumors regressed completely or animals reached termination criteria, while the anti-CD40 antibody was only administered once at day 11 simultaneously with the anti-CSF-1R antibody. All antibodies were given intraperitoneally. All procedures were performed in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and European Union directives and guidelines.

first: Sabine

last: Hoves


title: Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

status: Public on Jan 05 2018

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: The HMG-box protein Capicua (Cic) is a conserved transcriptional repressor that functions downstream of receptor tyrosine kinase (RTK) signaling pathways in a relatively simple switch: in the absence of signaling, Cic represses RTK-responsive genes by binding to nearly invariant sites in DNA, whereas activation of RTK signaling downregulates Cic activity, leading to derepression of its targets. This mechanism controls gene expression in both Drosophila and mammals, but whether Cic can also function via other regulatory mechanisms remains unknown. Here we characterize an RTK-independent role of Cic in regulating spatially restricted expression of Toll/IL-1 signaling targets in Drosophila embryogenesis. We show that Cic represses those targets by binding to suboptimal DNA sites of lower affinity than its known consensus sites. This binding depends on Dorsal/NF-kB, which translocates into the nucleus upon Toll activation and binds next to the Cic sites. As a result, Cic binds to and represses Toll targets only in regions with nuclear Dorsal. These results reveal a new mode of Cic regulation unrelated to the well-established RTK-Cic depression axis and implicate cooperative binding in conjunction with low-affinity binding sites as an important mechanism of enhancer regulation. Given that Cic plays a role in many developmental and pathological processes in mammals, our results raise the possibility that some of these Cic functions are independent of RTK regulation and may depend on cofactor-assisted DNA binding.

overall_design: ChIP-seq and ChIP-nexus was performed against cic, dl in Drosphila gd7 and toll10b mutants

first: Aikaterini

last: Papagianni

first: Marta

last: Forés

first: Wanqing

last: Shao

first: Nina

last: Koenecke

first: María

last: Andreu

first: Núria

last: Samper

first: Ze’ev

last: Paroush

first: Sergio

last: González-Crespo

first: Gerardo

last: Jiménez


title: Radiomic subtyping improves disease stratification beyond key molecular, clinical and standard imaging characteristics in patients with glioblastoma.

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary:
Background: To analyze the potential of radiomics for disease stratification beyond key molecular, clinical and standard imaging features in patients with glioblastoma.

Methods: Quantitative imaging features (n=1043) were extracted from the multiparametric MRI of 181 patients with newly-diagnosed glioblastoma prior to standard-of-care treatment (allocated to a discovery and validation set, 2:1 ratio). A subset of 386/1043 features were identified as reproducible (in an independent MRI-test-retest cohort) and selected for analysis. A penalized Cox-model with 10-fold cross-validation (Coxnet) was fitted on the discovery set to construct a radiomic signature for predicting progression-free and overall survival (PFS, OS). The incremental value of a radiomic signature beyond molecular (MGMT-promoter methylation, DNA-methylation subgroups), clinical (patients age, KPS, extent-of-resection, adjuvant treatment) and standard imaging parameters (tumor volumes) for stratifying PFS and OS was assessed with multivariate Cox-models (performance quantified with prediction error curves).

Results: The radiomic signature (constructed from 8/386 features identified through Coxnet) increased the prediction accuracy for PFS and OS (in both discovery and validation set) beyond the assessed molecular, clinical and standard imaging parameters (p≤0.01). Prediction errors decreased by 36% for PFS and 37% for OS when adding the radiomic signature (as compared to 29% and 27% with molecular + clinical features alone). The radiomic signature was - along with MGMT-status - the only parameter with independent significance on multivariate analysis (p≤0.01).

Conclusions: Our study stresses the role of integrating radiomics into a multi-layer decision framework with key molecular and clinical features to improve disease stratification and to potentially advance personalized treatment of patients with glioblastoma.

overall_design: The Illumina Infinium HumanMethylation450 array (Illumina, San Diego, USA) data from n=181 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Sturm et al. Cancer Cell. 2012 Oct 16;22(4):425-37)

first: Philipp

last: Kickingereder

first: Ulf

last: Neuberger

first: David

last: Bonekamp

first: Paula

middle: L

last: Piechotta

first: Michael

last: Götz

first: Antje

last: Wick

first: Annekathrin

last: Kratz

first: Russell

middle: T

last: Shinohara

last: Jones

first: Alexander

last: Radbruch

first: John

last: Muschelli

first: Andreas

last: Unterberg

first: Jürgen

last: Debus

first: Heinz-Peter

last: Schlemmer

first: Christel

last: Herold-Mende

first: Stefan

last: Pfister

last: von Deimling

first: Wolfgang

last: Capper

first: Klaus

middle: H

last: Maier-Hein

last: Bendszus


title: Arabidopsis thaliana AGO1 immunoprecipitated small RNA from Col0 plants transformed with a transgene expressing wild-type or a nuclear localized form of AGO1 fused to GFP.

status: Public on Jan 04 2018

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

type: Non-coding RNA profiling by high throughput sequencing

summary: Plant microRNAs undergo stepwise-nuclear maturation before engaging cytosolic sequence-complementary transcripts in association with the silencing-effector protein ARGONAUTE1(AGO1). How plant miRNAs translocate to the cytosol remains mysterious as does their cellular loading site(s) into AGO1. Here, we show that the N-termini of plant AGO1s contain a nuclear-localization (NLS) and nuclear-export signal (NES), which, in Arabidopsis thaliana (At) enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(Expo1)/NES-dependent nuclear export. Nuclear-only AtAGO1 contains the same 2’O-methylated miRNA cohort as its nucleo-cytosolic counterpart, but specifically interacts with the miRNA loading-chaperone HSP90. AtAGO1 nucleo-cytosolic shuttling is required for mature miRNA translocation and for miRNA-mediated silencing. We propose that plant miRNAs are matured, methylated, loaded into AGO1 in the nucleus, and exported cytoplasmically as AGO1:miRNA complexes in a CRM1(Expo1)/NES-dependent manner.

overall_design: 2 samples examined: Arabidopsis thaliana AGO1 immunoprecipitated small RNA Col0 from plants expressing pAGO1:GFP-AGO1 or pAGO1:GFP-AGO1ΔNES (2 replicates for each)

first: Nicolas

middle: G

last: Bologna

first: Raphael

last: Iselin

first: Luciano

last: Abriata

first: Nathan

last: Pumplin

first: Florence

last: Jay

first: Thomas

last: Grentzinger

first: Matteo

last: Dal Peraro

first: Olivier

last: Voinnet


title: TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary: Transition from primed to naive pluripotency is associated with dynamic changes in transposable element (TE) expression and demethylation of imprinting control regions (ICRs). In mouse, ICR methylation and TE expression are each regulated by TRIM28; however, the role of TRIM28 in humans is less clear. Here, we show that a null mutation in TRIM28 causes significant alterations in TE expression in both the naive and primed states of human pluripotency, and phenotypically this has limited effects on self-renewal, instead causing a loss of germline competency. Furthermore, we discovered that TRIM28 regulates paternal ICR methylation and chromatin accessibility in the primed state, with no effects on maternal ICRs. Taken together, our study shows that abnormal TE expression is tolerated by self-renewing human pluripotent cells, whereas germline competency is not.

overall_design: Examination of transcription, DNA methylation and chromatin accessibility of human ES cells for wild type and Trim28 knockout.

first: Yu

last: Tao

first: Ming-Ren

last: Yen

first: Amander

last: Clark


title: LNCaP treated with iBET

city: Sutton, London

first: Wei

last: Yuan

address: 15 Cotswold Road

institute: Institute of Cancer Research

summary: BRD4 belongs to the bromodomain and extraterminal (BET) family of epigenetic reader proteins that bind acetylated histones and regulate gene expression. Pharmacological inhibition of BRD4 by BET inhibitors (BETi) has indicated antitumor activity against multiple cancer types. We define a new function for BRD4 that is distinct from its established role in transcriptional gene regulation. We show that BRD4 is essential for the repair of DNA double-strand breaks (DSBs), and mediates the formation of oncogenic gene rearrangements by engaging the non-homologous end joining (NHEJ) pathway. Mechanistically, genome-wide DNA breaks are associated with enhanced acetylation of histone H4, leading to BRD4 recruitment, and stable establishment of the DNA repair complex. Loss of BRD4 function blocks the recruitment of multiple DNA repair proteins to the chromatin upon DNA damage, and thereby results in defective DNA repair. In support of this, we also show that in clinical tumor samples, BRD4 protein levels are negatively associated with outcome after prostate cancer (PCa) radiation therapy. Thus, in addition to regulating gene-expression, BRD4 is also a central player in the repair of DNA breaks, with significant implications for cancer therapy.

overall_design:
LNCaP cellline treated iBET at two different doses with duplicates
6 samples including 2 (replicates) LNCaP cell line treated with DMSO, 2  (replicates) LNCaP treated with iBET at 0.5uM,  and 2  (replicates) LNCaP treated with iBET at 2uM for 8 hours

first: Jon

last: Welti

first: Adam

last: Sharp

first: Johann

last: deBono


title: Influence of increased CacyBP/SIP level on gene expression pattern in HCT116 cells

city: Warsaw

first: Beata

middle: Alicja

last: Kądziołka

address: Pasteur 3 Street

department: Departament of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Gene expression analysis to search for genes which are up- and down-regulated after CacyBP/SIP overexpression in HCT116 cells

overall_design: Total RNA obtained from control HCT116 cells was compared to total RNA obtainded from HCT116 cells overexpressing CacyBP/SIP; 4 replicates

first: Konrad

middle: J

last: Dębski

first: Pawel

last: Bieganowski

first: Wieslawa

last: Leśniak

first: Anna

last: Filipek


title: Human bronchial epithelial cell lines: 16HBE14o- vs. beta/gammaENaC-16HBE14o-, Primary cells NHBE vs. DHBE-CF

status: Public on Jan 03 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Transcriptional profiling of human bronchial epithelial cell lines and primary cells.
Parental normal 16HBE14o- cells were stably transfected with beta/gammaENaC to generate beta/gammaENaC-16HBE14o- cells. NHBE and DHBE-CF were obtained from TaKaRa.

overall_design: Two-condition experiment, 16HBE14o- vs. beta/gammaENaC-16HBE14o- cells and NHBE vs. DHBE-CF cells. Biological replicates: One replicate per array.

first: Tsuyoshi

last: Shuto

first: Shunsuke

last: Kamei


title: A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (ChIP-seq)

first: Yali

last: XU

summary: Targeting of general coactivators, such as BRD4, is an emerging strategy to interfere with oncogenic transcription factors (TFs) in cancer. However, coactivator perturbations have the potential to influence the function of numerous TFs, thereby resulting in biological pleiotropy. Here we identify TAF12, an 18 kilodalton subunit of TFIID/SAGA coactivator complexes, as a selective requirement for acute myeloid leukemia (AML) progression. We trace this AML-specific dependency to a direct interaction between the TAF12/TAF4 histone-fold heterodimer and the transactivation domain of MYB, a TF with established roles in leukemogenesis. Ectopic expression of a histone-fold domain fragment of TAF4 can efficiently squelch TAF12 in cells, suppress MYB, and regress AML in mice. Our study reveals a strategy for potent MYB inhibition in AML and highlights how an oncogenic TF can be selectively neutralized by targeting a general coactivator complex.

overall_design: TAF2 and TAF10 ChIP-seq were performed using antibodies recognizing endogenous protein with input genomic DNA as control. FLAG-TAF12 ChIP-seq was performed in FLAG-TAF12 expressing cells.

last: Xu

first: Christopher

middle: R

last: Vakoc


title: Transcriptome analysis of FKBP25 siRNA-knockdown in cultured HEK 293 cells

city: Toronto

first: Mark

middle: D

last: Minden

address: 610 University Avenue

department: Medical Oncology & Hematology

institute: Princess Margaret Cancer Centre

summary: Peptidyl-prolyl isomerases (PPIs) are a superfamily of ubiquitous enzymes that catalyze the cis-trans interconversion of  Xaa-Pro peptide bonds. The functions of most PPIs remain uncharacterized. FKBP25, a mammalian PPI, localizes to the nucleus, binds nucleic acids, and associates with chromatin modifying enzymes. However, the role of this protein in transcriptional regulation remains unclear. To help address this question we present RNA-seq gene expression profiling in HEK293 cells transfected with siRNA targeting FKBP25 relative to a GFP-targeting negative control.

overall_design: Human embryonic kidney cells (HEK 293) were transfected with siRNA targeting FKBP25 or a GFP-targeting negative control and incubated for 72 h. Cells were harvested with trypsin, pelleted, and flash frozen before mRNA purification using the µMACs mRNA isolation kit (Miltenyl Biotec, Bergisch Gladbach, Germany). Purified mRNA was then analysed on an Agilent 2100 Bioanalyzer using Agilent 6000 RNA Nano Kit (Agilent Technologies, Santa Clara, California). cDNA was generated using the Superscript Double-Stranded cDNA Synthesis kit (ThermoFisher), 75bp paired-end libraries prepared using the Paired-End Sample Prep Kit (Illumina, San Diego, California) and then sequenced on a HiSeq 2000 sequencing system (Illumina).

first: David

last: Dilworth

last: Nelson


title: The Identification and Characterization of Sindbis Virus RNA:Host Protein Interactions

status: Public on Jan 02 2018

city: Louisville

first: Kevin

last: Sokoloski

state: KY

address: 505 S. Hancock St.

department: Microbiology and Immunology

institute: University of Louisville

summary: Arthropod-borne viruses, such as the members of genus Alphavirus, are a significant concern to global public health. As obligate intracellular pathogens, RNA viruses must interact with the host cell machinery to establish, and complete, their viral lifecycles. Despite considerable efforts to define the host/pathogen interactions essential for alphaviral replication, an unbiased and inclusive assessment of alphaviral RNA:protein interactions has not been undertaken. Moreover, the biological and molecular importance of these interactions, in the full context of their molecular function as RNA-binding proteins, has not been fully realized. The data presented here introduces a robust viral RNA:protein discovery method to elucidate the Sindbis virus (SINV) RNA:Protein host interface. Cross-Link Assisted mRNP Purification (CLAMP) assessment reveals an extensive array of host/pathogen interactions centered on the viral RNAs (vRNAs). After prioritization of the host proteins associated with the vRNAs, we identified the site of Protein:vRNA interaction via a CLIP-seq approach and assessed the consequences of the RNA:protein binding event of hnRNP K, hnRNP I, and hnRNP M in regards to viral infection. Herein we demonstrate that mutation of the prioritized hnRNP:vRNA interaction sites effectively disrupted the hnRNP:vRNA interaction. Correlating with disrupted hnRNP:vRNA binding, SINV growth kinetics were reduced relative to wild type parental viral infections in a vertebrate and invertebrate tissue culture models of infection. The molecular mechanism leading to reduced viral growth kinetics was found to be reduced vRNA accumulation and dysregulated structural gene expression. Collectively, this study further defines the scope and importance of the alphavirus host/pathogen vRNA:protein interactions.

overall_design: 5 CLIP-Seq samples in TOTAL- 2 Control Samples (Input and Empty), 3 immunoprecitations of hnRNP proteins (hnRNP K, I and M).

first: Autumn

last: Lapointe

first: Natasha

last: Gebhart

first: Megan

last: Meller

first: Richard

middle: W

last: Hardy


title: Gene expression profiling of colorectal cancer tissue samples.

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have analyzed the gene expression-based consensus molecular subtypes of colorectal cancer. These samples represent a subset of the total series analyzed.

overall_design: This subset consists of 174 colorectal cancer tissue samples analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Ina

middle: A

last: Eilertsen

first: Ragnhild

last: Lothe


title: Chromatin-Bound ARGONAUTE 1 Promotes Gene Transcription in Response to Various Stimuli in Arabidopsis

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: Conventional RNA interference (RNAi) pathways suppress eukaryotic gene expression at the post-transcriptional or transcriptional level. At the core of RNAi are small RNAs (sRNAs) and effector Argonaute proteins. Arabidopsis AGO1 is known to bind microRNAs (miRNAs) and post-transcriptionally repress target genes via mRNA cleavage and/or translational inhibition in the cytoplasm. Here, we report that AGO1 binds to the chromatin of transcriptionally active genes and promotes their transcription. We show that sRNAs and SWI/SNF are required for AGO1 binding to chromatin and its function in promoting gene transcription. Moreover, we show that various stimuli including plant hormones and stresses specifically trigger AGO1 binding to the stimulus-responsive genes. Finally, we show that AGO1 facilitates the induction of genes in the jasmonate (JA) signaling pathways and the activation of JA responses. Our findings reveal an unsuspected role for AGO1 in facilitating gene transcription in response to plant hormones and stresses.

overall_design:
We conducted AGO1 ChIP-seq with Arabidopsis wild-type (WT, Col-0) and ago1-36 seedlings under normal growth condition or treatment with MeJA, BTH, IAA, Flg22 or cold; RNA-seq with WT and ago1-36 seedlings under normal or MeJA treatment condition; Pol II, Pol II Ser2 and Pol II Ser5 ChIP-seq with WT and ago1-36; GRO-seq with WT and ago1-36; and small RNA-seq of nuclear AGO1-associated small RNAs purified from WT and coi1 under normal or MeJA treatment condition.
5 treatment conditions: Methyl jasmonate (MeJA), indole-3-acetic acid (IAA), Benzothiadiazole (BTH), flagellin22 (Flg22), 4 Centigrade (Cold).

first: Chang

last: Liu

first: Ying

last: Xin

first: Le


title: Genome-wide profiling of miRNA associated with BCR-FGFR1 fusion kinase driven stem cell leukemia and lymphoma I

status: Public on Jan 01 2018

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

summary: The BBC1 and BBC2 cell lines were isolated from pre-B-cell lymphoma models of a murine BCR-FGFR1 driven SCLL. miRNA profiles for BBC2 cells, were established using miRNA arrays. First, BBC2 cells were compared with FACS sorted, normal, murine splenic CD19+ B cells isolated from BALB/c mice, where upregulated and downregulated miRNAs in BBC2 cells were identified. We next investigated which of these miRNAs were affected by loss of FGFR1 function. Previously we showed that the FGFR inhibitor BGJ398 suppresses suppressed phosphoactivation of chimeric FGFR1 kinases. When BBC2 cells were treated with 50nM BGJ398 for 24 hours, up- and down-regulated miRNAs by FGFR1 signaling were identified. By comparasion of the two subsets of differentially expressed miRNAs, we were able to define core candidate miRNAs which appear to be regulated by BCR-FGFR1 in SCLL.

overall_design: The miRNA profiles of BBC2 cell sample and FACS sorted normal mouse CD19+ B cell sample were detected with miRNA microarray.

middle: K

first: Tianxiang

last: Hu


title: Expression profiling of Morc2b wt and Morc2b ko testes

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

summary: We report the effect of Morc2b inactivation on the transcriptome of testes at postnatal day 12 (PND12). We find 88 differentially expressed genes between wild type and Morc2b-/- testes

overall_design: RNA-seq of Morc2b+/- and Morc2b-/- testes at postnatal day 12 in biological quadruplicates (NextSeq500)

first: Xue

last: Jiangyang

first: Shi

last: Baolu

first: Zhou

last: Jian

first: Kasowitz

last: Seth D.

first: Zhang

last: Yuanwei

first: Liang

last: Guanxiang

last: Qinghua

first: Liu

last: Mingxi

first: Sha

last: Jiahao

first: Huang

last: Xiaoyan

first: Jeremy

last: Wang


title: RNA-seq study of mycolic acid deficiency in Corynebacterium glutamicum ATCC13869

city: Wuxi

first: Yunfei

last: Gao

address: Binhu district, Lihu Avenue 1800

institute: Jiangnan University

summary: We constructed mycolic acid synthesis key gene pks13 mutant strain and analyzed its impacts on whole cell at gene expression level compared to the wild-type ATCC13869.

overall_design: The Corynebacterium glutamicum ATCC13869 in-frame deletion pks13 mutant (renamed WG001) and wild-type ATCC13869 were analyzed by RNA-seq. All samples were cultivated in BHI medium until reaching exponential phase. Cultures were pooled for RNA extraction, library preparation and sequencing. qRT–PCR validation was performed using SYBR Green assays.

first: Xiaoyuan


title: Ythdf2-mediated m6A mRNA clearance modulates neural development in mice

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: We found that the proliferation and differentiation capabilities of NSPCs decrease significantly in Ythdf2 null mutants.To explore the underlying molecular mechanism, we performed transcriptomics and well-established m6A-methylome analyses of NSPCs dervied from wild type and Ythdf2-/- embryo brains. RNA-seq data revealed that expressions of genes enriched in neural development pathways were significantly disturbed. The inhibitory genes, like Flrt2, Ptprd, et al. in regulation of JAK-STAT cascade, which contributes to the neuroprotection and neurite outgrowth, showed increased gene expressions and m6A enrichment by m6A-seq. We identified that without the recognizing and binding of Ythdf2, the degradation of neuron differentiation related m6A-modified mRNAs were delayed in Ythdf2-/-, thereby disturbing the proliferation and differentiation of NSPCs. In summary, our findings uncovered that Ythdf2 modulates neural developmental via regulating the clearance of mRNA targets.

overall_design: Examination of gene expression levels and m6A levels in mRNAs in wild type and Ythdf2 deficient mouse E14.5 derived NSPCs

first: Xu

last: Zhao

first: Hailing

last: Shi

first: Zhike

last: Lu


title: Expression data of resident macrophages from the livers of wildtype mice and Melanocortin 4 receptor-deficient (MC4R-KO) mice with non alcoholic steatohepatitis (NASH)

city: Tokyo

first: Michiko

last: Itoh

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

institute: Tokyo Medical and Dental University

summary: There is a unique histological structure termed hepatic crown-like structure (hCLS), in which CD11c-positive macrophages surround dead or dying hepatocytes with large lipid droplets in NASH livers. To characterize gene expression patterns, we performed microarray analysis  using hepatic resident macrophages. CD11c-positive macrophages exhibited distinct polarization profiles from typical M1 and M2 macrophages, and there were clear differences in the gene expression profiles from CD11c-negative macrophages.

overall_design: F4/80 highly expressed resident macrophages were sorted based on the expression levels of CD11c from the livers of wildtype mice fed standard diet (SD) (CD11c-negative) and MC4R-KO mice fed Western diet (WD) for 20 weeks (CD11c-negative and positive).

first: Hideaki

last: Kato

first: Takayoshi

last: Suganami

first: Yoshihiro

last: Ogawa


title: Liver from CSF1-Fc- or PBS-treated neonatal rats and rat bone marrow derived macrophages

city: Brisbane

first: Katharine

last: Irvine

address: Translational Research Institute

institute: Mater Research Institute UQ

summary:
Signalling via the colony stimulating factor 1 receptor (CSF1R) controls the survival, differentiation and proliferation of macrophages which are a source of the somatic growth factor insulin growth factor 1 (IGF1). Treatment of newborn mice with CSF1 has previously been shown to produce an increase in somatic growth rate and we hypothesised that treatment of neonatal low birth weight (LBW) rats with CSF1 would do the same. Growth rates were not affected, yet CSF1 treatment caused an unexpectedly large, but reversible increase in liver size and hepatic fat deposition in both normal and LBW rats. By transcriptional profiling, we have highlighted numerous CSF1-regulated genes known to be involved in lipid droplet formation in the liver and novel candidate genes for further investigation. In contrast to mice and weaner pigs, CSF1 treatment did not increase hepatocyte proliferation in neonatal rats, rather the data were consistent with increased macrophage proliferation instead. This suggests that Kupffer cells promote lipid accumulation in neonates and treatment to ablate CSF1R signalling may reverse lipid accumulation in the liver.
Conclusion: Treatment of neonatal rats with CSF1 caused an increase in liver size and hepatic lipid accumulation, due to Kupffer cell expansion and/or activation rather than hepatocyte proliferation
Livers were harvested from neonatal rats on Day 6, following 5 days treatment with 1 ug/g porcine CSF1-Fc or PBS by subcutaneous injection. Bone marrow derived macrophages were generated in vitro by culture in CSF1.

overall_design: Whole liver from CSF1-FC-treated rats (n=4) and PBS-treated rats (n=2), and BMDM (n=3).

first: Clare

last: Pridans


title: Genome-wide microRNA profiling of HPV-positive self-samples: Promising triage markers for early detection of cervical cancer

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Offering self-sampling for HPV testing improves the effectiveness of current cervical screening programs. Molecular triage markers directly applicable on self-samples are needed to further stratify HPV-positive women at risk of cervical cancer (so-called triage) and to avoid over-referral and overtreatment. MicroRNAs (miRNAs) deregulation has been implicated in the development of cervical cancer, and represents a potential class of triage markers. However, it is unknown whether deregulated miRNA expression is reflected in self-samples. This study is the first to establish genome-wide miRNA profiles in HPV-positive self-samples to identify miRNAs that can predict the presence of CIN3 and cervical cancer in self-samples. Small RNA sequencing (sRNA-Seq) was conducted to determine genome-wide miRNA expression profiles in 73 HPV-positive self-samples of women with and without cervical precancer (CIN3). The optimal miRNA marker panel for CIN3 detection was determined by GRidge, a penalized method on logistic regression. Classification of sRNA-Seq data yielded a panel of 9 miRNAs with a combined Area Under the Curve (AUC) of 0.89 for CIN3 detection. Six out of nine miRNAs were validated by qPCR in 165 independent HPV-positive self-samples and resulted in a combined AUC of 0.72 for CIN3+ detection. This study shows that deregulated miRNA expression associated with CIN3 and cervical cancer  development can be detected in HPV-positive self-samples using genome-wide miRNA profiling. Further validation by qPCR indicates that miRNA expression analysis offers a promising novel molecular triage strategy for CIN3 and cervical cancer detection applicable to self-samples.

overall_design: Self-collected cervicovaginal lavage specimens from 24 women who were histologically diagnosed with a cervical intraepithelial neoplasia grade 3 (CIN3) lesion, and 32 control women with either histologically confirmed ≤CIN1 or that displayed HPV clearance combined with normal cytology in follow-up were analyzed  on an Illumina HiSeq 2500.

first: Barbara

middle: C

last: Snoek

first: Wina

last: Verlaat

first: Putri

last: Novianti

first: Mark

last: van de Wiel

first: Saskia

middle: M

last: Wilting

first: Nienke

middle: E

last: van Trommel

first: Leon

middle: F

last: Massuger

first: Willem

last: Melchers

first: Daniëlle

last: Heideman

first: Peter

last: Snijders

first: Chris

last: Meijer

first: Renske

last: Steenbergen


title: Hexavalent chromium disrupts chromatin organization and accessibility to CTCF sites in promoters of differentially expressed genes [ChIP-seq]

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Hexavalent chromium compounds are well-established respiratory carcinogens utilized in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal carcinogen, affecting millions of people throughout the world. Cr(VI) is genotoxic, by forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. We have used FAIRE to show that Cr(VI) elicits broad changes in chromatin accessibility resulting from disruption of the binding of transcription factors CTCF and AP-1 to their cognate sites in chromatin.  Here, we have used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase.seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and fuzziness, or changes in signal amplitude. Using ATAC to analyze changes in chromatin accessibility, we found that Cr(VI) opened differentially accessible chromatin domains in a dose-dependent manner. These domains were enriched for the previously identified binding motifs for CTCF and AP-1, many located in promoters of differentially expressed genes. Cr(VI)-enriched CTCF sites were confirmed by ChIP.seq and, when compared with ENCODE-validated CTCF site datasets from mouse liver, correlated with evolutionarily conserved similar sites occupied in vivo. Our results show that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent dysregulation of transcription may result from the disruption of CTCF binding and nucleosome spacing, suggesting that transcription regulatory mechanisms are primary Cr(VI) targets.

overall_design: Examination of 2 different chromium dosage in mouse models by different sequencing technology (ATAC-seq, ChiP-seq, MNase-Seq)

first: Andrew

last: VonHandorf

first: Francisco

last: Sánchez-Martín

first: Jacek

last: Biesiada

first: Xiang

last: Zhang

first: Alvaro

last: Puga


title: Hexavalent chromium disrupts chromatin organization and accessibility to CTCF sites in promoters of differentially expressed genes [MNase-Seq]


title: Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate in fission yeast

city: Ithaca

first: Gregory

middle: Thomas

last: Booth

state: New York

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: Post-translational modifications of the transcription elongation complex provide mechanisms to fine-tune gene expression, yet their specific impacts on RNA polymerase II regulation remain difficult to ascertain. Here, in Schizosaccharomyces pombe, we examine the role of Cdk9, and related Mcs6/Cdk7 and Lsk1/Cdk12 kinases, on transcription at base-pair resolution with Precision Run-On sequencing (PRO-seq).  Within a minute of Cdk9 inhibition, phosphorylation of Pol II-associated factor, Spt5 is undetectable.  The effects of Cdk9 inhibition are more severe than inhibition of Cdk7 and Cdk12, resulting in a shift of Pol II towards the transcription start site (TSS).  A time course of Cdk9 inhibition reveals that early transcribing Pol II can escape promoter-proximal regions, but with a severely reduced rate of only ~400 bp/min.  Our results in fission yeast suggest the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.

overall_design: Data represent 20 different treatments of various S. pombe strains performed in biological replicates. There are processed files for both replicates and combined replicate data for each experiment.

first: John

last: Lis

first: Robert

middle: P

last: Fisher

first: Pabitra

last: Parua

first: Miriam

last: Sanso


title: Profiling DNA methylation in nematodes

city: London

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

summary: DNA methylation in basal nematodes analysed by bisulfite sequencing

sample_organism:
Trichinella spiralis
Romanomermis culicivorax
Trichuris muris
Plectus sambesii

overall_design: Bisulfite sequencing of DNA extracted from adult nematodes


title: Hexavalent chromium disrupts chromatin organization and accessibility to CTCF sites in promoters of differentially expressed genes

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

overall_design: Refer to individual Series


title: H3K4me1 & H3K27ac ChIP on chip for Mouse E11.5 distal limb bud tissue

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

type: Genome binding/occupancy profiling by array

summary: Profiling H3K4me1 & H3K27ac histone modifications across the ZRS and a selection of limb development genes within Mouse E11.5 distal limb bud tissue.

overall_design: Chromatin Immunoprecipitation assay on custom mouse Agilent microarray. Two biological replicates per antibody for H3K4me1 and  H3K27ac.

first: S

last: Peluso


title: Mouse lung tissue: normal (WT) vs. CF (ENaC-Tg)

first: Satoshi

last: Kondo

summary:
Transcriptional profiling of mouse lung tissues.
C57BL/6J mice were airway-specifically transfected with betaENaC to generate betaENaC-Tg mice.

overall_design: Two-condition experiment, WT vs. ENaC-Tg cells of lung tissues. Biological replicates: One replicate per array.

first: Tsuyoshi

last: Shuto

first: Shunsuke

last: Kamei


title: ChIP-chip of  H3K4me1 and H3K27ac and transcription factors on E11.5 distal limb bud tissue or 14Fp cell line

type: Genome binding/occupancy profiling by genome tiling array


title: The E3 ubiquitin ligase HectD1 suppresses EMT and metastasis by targeting the +TIP protein ACF7 for degradation

city: montreal

first: Stephanie

last: Duhamel

state: Quebec

address: 110 avenue des pins ouest

institute: IRCM

summary: Cancer cells exploit the epithelial-to-mesenchymal transition (EMT) program toward metastasis. Cytoskeletal regulators are dually required in mesenchymal cells by promoting EMT-induced migration and sustaining the EMT program itself. In search for novel regulators of metastasis, we conducted an shRNA screen targeting a class of microtubule regulators, the plus-end tracking proteins (+TIPs). We show that the +TIP ACF7 is required for both the maintenance of EMT and to promote migration. We identified HectD1 as a potent E3 ubiquitin ligase mediating ACF7 degradation. Depletion of HectD1 robustly increases ACF7 protein levels and this is sufficient to enhance migration and EMT in cells, as well as facilitate metastasis in vivo. Ours results report the HectD1/ACF7 axis as a novel regulator of metastasis of breast cancer cells.

overall_design: Differential gene expression profile following ACF7 overexpression or Hetd1 depletion by RNA sequencing (Illumina HiSEq 2500)

first: J

last: Côté


title: Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

institute: QIMR Berghofer

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


title: Gene expression data from THP-1 cells expressing RKIP shRNA vs control

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: Myeloid sarcoma (MS) is a subform of acute myeloid leukemia (AML), where myeloid blasts infilitrate extramedullary tissues, a process that resembles the formation of metastases in solid tumors. RKIP has been shown to be a metastasis-suppressor gene. Identification of genes modulated by RKIP in human AML cells helps us to identify mechanisms how RKIP could be involved in the formation of MS.

overall_design: Total RNAs were extracted from THP-1 cells expressing RKIP shRNA and vector control. Affymetrix Human Gene 2.0 ST mRNA Arrays were performed to assess the gene expression and to identify the genes regulated by RKIP knockdown in human acute myeloid leukemia cells.

first: V

last: Caraffini

first: A

last: Zebisch

first: K


title: Arraystar lncRNA and mRNA microarray data for profiling of testis-specific long noncoding RNA in mice

city: Gwangju

first: Seonghyeon

last: Hong

address: 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Korea

department: School of Life Science

country: South Korea

institute: GIST

summary: LncRNA and mRNA expression profiles in five mouse tissues like brain, heart, kidney, liver and testis and three germ cell-related cell lines such as F9, GC-1 and GC-2

overall_design: LncRNAs and mRNAs expression profiles were analyzed in five mouse tissues and three germ cell-related cell lines with lncRNA microarray. Each of groups have three biological replicates.

first: C

last: Cho


title: Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient [Genotype]

summary: As organ-specific models of breast cancer bone metastasis do not exist, we established a novel breast cancer line was established from the ER-/PR-/HER2- bone metastasis from a breast cancer patient.  This cell line was characterized and compared to the primary tumour and/or normal mammary epithelial cells with regards to phenotypes (i.e. marker expression), gene expression and copy number variation.

overall_design:
Genomic DNA was isolated from the P7731 cell line the primary tumour and hybridised using the SNP arrays Illumina HumanCNV370-Duov1 DNA Analysis BeadChip (HumanCNV370v1)
Please note that the complete processed data is provided as sample supplementary text file.

first: Julie

last: Johnson

first: Darrell

last: Bessette

first: Jodi

last: Saunus

first: Chanel

last: Smart

first: Sarah

last: Song

first: Rebecca

last: Johnston

first: Sibylle

last: Cocciardi

first: Esdy

last: Rozali

first: Cameron

middle: N

last: Johnstone

first: Ana

last: Vargas

first: Katia

last: Nones

first: Peter

last: MacCallum

first: Kum

last: Khanna

first: Sunil

last: Lakhani

first: Georgia

last: Chenevix-Trench

middle: T

last: Simpson

first: Nic

last: Waddell


title: Transcriptome-wide profiling of translation efficiency using mRNA-seq and Ribo-seq in ER stress-induced NIH3T3 cells

first: Yumi

last: Woo

state: NY

summary: We report systematical profiling of translation efficiency in stress conditions of NIH3T3 cells.

overall_design: In this study, we pharmacologically induced ER stress by treatment of thapsigargin (THAP). Ribo-seq and RNA-seq were parallelly conducted in whole cells with DMSO- or THAP-treated NIH3T3 cells in duplicate.

first: Yu

first: Hojoong

last: Kwak


title: Novel targets in injured cord in an obese SCI rat model

city: Jackson

first: Michael

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

summary: In the present study, we sought to understand the impact of obesity/metabolic disease (high-fat induced) on spinal cord injury (SCI) by examining transcriptome. Adult, male Long Evans rats received either thoracic level contusion of the spinal cord or sham laminectomy and then were allowed to recover on normal rat chow for 4 weeks and further on HFD for an additional 8 weeks. Spinal cord tissues harvested from the rats were processed for Affymetrix microarray and further transcriptomic analysis.

overall_design: Male, Long Evans rats (400g) (Harlan, Indianapolis, IN) (N=10) werewere maintained on standard chow (#8640, Envigo, 3.0 kCal/g; 17% fat, 54% carbohydrate, 29% protein). Rats were assigned to either sham-laminectomy (Sham) or thoracic spinal cord injury (tSCI) group in a counterbalanced fashion based on body weight on the day prior to the start of surgery. Surgery was performed and animals were allowed to recover for 4 weeks following surgery. Rats were switched to a palatable, high-fat diet (HFD) (#D03082706, Research Diets, New Brunswick, NJ, 4.54 kCal/g; 40% fat, 46% carbohydrate, 15% protein) for the remainder of the study totaling 8 weeks.

first: Bernadette

last: Grayson


title: Genome-wide H3K4me3 and gene expression before and after methionine restriction in human cancer cells and mouse liver

city: Durham

first: Jason

last: Locasale

state: NC

address: Levine Science Research Center C270

department: Pharmacology and Cancer Biology

institute: Duke University

summary: In this study, we compared genomic H3K4me3 and gene expression profiles before and after methionine restriction in human cancer cells and mouse liver. The goals are to understand the influences of nutrient availability on genomic architecture of histone modification and gene expression.

overall_design: We compared H3K4me3 ChIP-seq and RNA-seq data in HCT116 cells cultured in medium containing high (100μM) and low (3μM) methionine, and in liver of C57BL/6J mice fed with diet containing high (0.86% Kcal) and low (0.12% Kcal) methionine.

first: Ziwei

last: Dai


title: Transcriptome-wide profiling of poly(A)-tail length, translation efficiency and mRNA stability using TED-seq, mRNA-seq, Ribo-seq and PRO-seq in ER stress conditions

summary: We report systematical profiling of translation efficiency and mRNA stability dependent on the dynamics of poly(A)-tail length in stress conditions of human cells. In this study, we developed a new feasible method measuring poly(A)-tail length called TED-seq and applied it to investigate the change of mRNA's poly(A)-tail lengths in ER stress pharmacologically induced by thapsigargin (THAP). Combined with other global RNA analyses such as RNA-seq, Ribo-seq and PRO-seq, we observed that ER stress induced lenthening poly(A)-tail length, in particular of ER-stress-regulators, upon ER stress. More specifically, these mRNAs are translationally de-repressed and more stabilized based on increase in poly(A)-tail length. We also identified that insoluble fractions which include stress-induced RNA-granules have overall shorter length of poly(A) tail. Taken together, our data suggest that poly(A)-tail lengths are dynamically regulated and influence both translation efficiency and mRNA stability in ER stress.

overall_design:
1) TED-seq (5 replicates) in cytoplasm and RNA granule fractions (3 replicates) of DMSO- or THAP-treated HEK293 cells
2) RNA-seq (4 replicates), Ribo-seq (4 replicates) and PRO-seq (2 replicates) in whole cells with DMSO- or THAP-treated HEK293 cells


title: Expression data from primary keratinocytes obtained from WT and keratinocyte specific Glut1-deficient mice

city: Dallas

first: Richard

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern


title: ChIP of transcription factor Etv4 (Pea3) Gabpa, Histone deacetylase HDAC2, Ep300 and Histone tails H3K4me1 and H3K27ac in E11.5 limb derived cell line (14Fp cell line)

first: Graeme

last: Grimes

summary: ChIP profiling of transcription factor Etv4 (Pea3) Gabpa, Histone deacetylase HDAC2, Ep300 and Histone tails H3K4me1 and H3K27ac in E11.5 limb derived cell line (14Fp ) across the ZRS and a selection of limb development genes

overall_design: Chromatin Immunoprecipitation assay on custom mouse Nimblegene microarray. Two biological replicates per antibody for HDAC2, ETV4, Ep300, GABPA, H3K4me1 and H3K27Ac.

first: S

last: Peluso


title: Global gene expression profiling of cardiac dendritic cells subsets

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Medicine

institute: University of Toronto

summary: Innate and adaptive immune cells modulate heart failure pathogenesis during viral myocarditis, yet their identity and functions remain poorly defined. In this study we characterized the phenotype, life-cycle and function of different conventional dendritic cells (cDC) populations in the heart, with focus on the 2 major subsets (CD103+ and CD11b+), which differentially rely on local proliferation and precursor recruitment to maintain tissue residency. Following viral infection of the myocardium, cDCs accumulate in the heart coincident with monocyte infiltration and loss of resident reparative embryonic-derived cardiac macrophages. cDC depletion abrogates antigen-specific CD8+ T cell proliferative expansion, transforming subclinical cardiac injury to overt heart failure. Importantly, these effects are mediated by BATF3-dependent CD103+ cDCs. Collectively, our findings definitively identify resident cardiac cDC subsets, define their origins, and implicate an essential role for CD103+ cDCs in antigen-specific T cell responses during viral myocarditis.

overall_design: Cardiac CD103+ and CD11b+ classical dendritic cells and MHC-II hi macrophages were sorted (n = 3 for each population). Global gene expression analysis was performed using the Affymetrix GeneChip® Mouse Gene 2.0 ST Array.


title: Expression data from primary keratinocytes obtained from WT and K14-Cre Glut1 KO mice [MoGene-2_0]

summary:
Glut1 is highly expressed in basal cells of keratinocytes, but the functions and regulation of Glut1 has not been explored, here we specifically ablate Glut1 in epidermal keratinocytes to elucidate the role of glucose transport in the skin.
We performed microarray analysis in WT and Glut1 deficient primary keratinocytes to determine the pathways might contribute to the impaired proliferation in Glut1 deficient keratinocytes,

overall_design: We harvested primary keratinocytes from 1 week old Glut1_fl/fl (Glut1 WT) (n=4) and Glut1_fl/fl K14 Cre (Glut-/-) (n=4) mice. Keratinocytes from each mice were seeded on one 10 cm dishes in complete KSFM medium. After 3 days, the cells were trypsinzed and reseed in new dishes with same cell number. The cells were harvested one day after harvesting. Two plates of cells of the same genotype were randomly harvested together, thus each genotype represents a combination of 2 biological replicates for microarray analysis.

first: Zhuzhen

last: Zhang


title: cAMP Signaling Regulates DNA Demethylation by Augmenting the Intracellular Labile Ferrous Iron Pool

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show that cAMP helps regulate cytosine demethylation through augmenting the intracellular labile ferrous iron pool.

overall_design: Examination of transcriptome and hydroxymethylome in cAMP treated schwann cells

first: Gaofeng

first: Vladimir

last: Camarena


title: PUVA pretreatment leads to significant reduction in imiquimod induced psoriatic phenotype with gene expression signature associated with senescence

first: Karin

last: Wagner

summary:
PUVA pretreatment leads to develop early senescence confirmed by p16, p21 and SA-β-GAL positivity which was completely normalised by longer gap.
Indicating that PUVA pretreatment causes conditioning set of genes that led to a marked delay in psoriasis development.

overall_design: To study the induction and phenotypes development of Aldara-mediated dermatitis in mice pretreated with PUVA in comparison to UVB

first: Nitesh

last: Shirsath

first: Michaela

last: Schlederer

first: Lukas

last: Kenner

first: Peter

last: Wolf


title: Expression data from Human Embrionic Stem Cells (hESC) from three different lines cultured on feeders or Matrigel with and without ROCK Inhibitor Y-27632

city: Barcelona

first: Gerardo

last: García-Díaz Barriga

state: Barcelona

address: Casanova 143

department: Biomedicine

country: Spain

institute: University of Barcelona

summary:
Microarray expression data from three different cell lines of human embrionic stem cells (Hs181, Hs293, Hs420), grown under feeder and feeder-free conditions (matrigel) with the addition of Y-27632 (ROCK Inhibitor)
We assessed the difference between cell lines and the impact of feeder-free vs matrigel conditions upon the addition of the ROCK Inhibitor Y-27632

overall_design: Cells from three different cell lines (Hs181, Hs293, Hs420) were grown for 1 day on the different experimental conditions described: Feeder, Matrigel, and Matrigel + Y-27632, then RNA was extracted

first: Andreas

last: Mezger

first: Josep

last: Canals


title: Gene expression profiles of embryonic kidneys and reconstructed organoids

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

institute: Kumamoto Univ.

summary: Understanding the developmental maturation processes of the embyonic kidney is important for functional validation of the pluripotent stem cell-derived kidney organoid. The microarray analysis offers a powerful, efficient and effective method for the creation of global gene expression profiles of the developing kidneys. Those gene expression data helps identifying the sets of genes that are serially upregulating or downregulating as the developmental progression, which should serve as the markers to monitor the regenerated kidney tissue maturity.

overall_design: ICR mice were used to isolate embryonic kidneys from embryos at E11.5, E13.5, E15.5, E17.5 and P0. To identify the stage dependently upregulating genes, each neighboring stage specimens were compared. The mouse ESC-derived nephron progenitors (iNP), ureteric bud (iUB) and E11.5 embryonic kidney stromal progenitors were reconstructed to induce kidney organoid. The gene expression  profiles of each embryonic kidneys, 7-day cultured E11.5 kidneys, reconstructed kidney organoids, and 7-day cultured reconstructed kidney organoids were compared to examine the developmental maturity.

first: Ryuichi

last: Nishinakamura


title: Gene expression from total and polysomal RNA fractions after ATO treatment in LN229 cells.

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

summary:
Arsenic trioxide (ATO) treatment leads to activation of mRNA translation through the MAPK-interacting kinase (MNK) signaling pathway.  Polysomal fractionation and microarray analysis allows for identification of transcripts undergoing active translation.   We identified the genes differentially enriched in untreated and ATO treated fractions.
In this dataset, we include expression data in untreated and ATO treated LN229 cells using either the total or polysomal RNA.

overall_design: LN229 cells were untreated or treated with ATO.  Cells were lysed and total RNA was collected.  Total RNA was then subjected to polysomal fractionation.   Each sample was performed in technical triplicates.  Data was then pooled and analyzed using the Transcriptome Analysis Console (TAC) from Affymetrix.  Coding genes with >1.5 increase in polysomal vs total RNA were then compared for untreated and ATO treated groups to generate lists of genes enriched in polysomal fractions.

first: Jonathan

middle: B

last: Bell

first: Leonidas

last: Platanias


title: Comparison of transcriptional responses to intracellular RNA and DNA between wild-type and RNase L KO cells

city: Seattle

first: Daniel

last: Stetson

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

summary:
Analysis of the response to intracellular nucleic acid ligands in wild-type versus RNase L KO cells showed that RNase L KO cells demonstrated an enhanced type I interferon
to RNA, but not DNA ligands. Previous studies suggest that mRNAs may be a target of RNase L regulation. To investigate the extent that RNase L activation regulates the
antiviral response by targeting of mRNAs, we performed microarray analysis comparing wild-type and RNase L KO cells treated with RIG-I ligand or CT DNA for 6 hours.

overall_design:
Total RNA was isolated from wild-type and RNase L KO BMDMs 6 hours following transfection of cells with either RIG-I ligand, CT DNA or left untreated. Each sample was
treated and analyzed in triplicate.

last: Clingan

first: Sterling

last: Eckard


title: Cold acclimation responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed  where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. Expression patterns were compared between treatments, accessions and species.

sample_organism:
Arabidopsis thaliana
Eutrema salsugineum

overall_design: In total, 36 samples were hybridized. They were derived from three independent biological experiments (replicate_1 to replicate_3).

first: Yang

last: Lee

first: Dirk

last: Hincha