title: A lineage commitment checkpoint in early ILC development [single cell RNA-seq]

status: Public on Apr 22 2019

city: Bethesda

first: Margaret

last: Cam

state: MD

institute: NIH

summary: Understanding how cellular function is imprinted during development requires the identification of factors controlling lineage specification and commitment, and the intermediate progenitors in which they act. Using population level and single cell approaches, we examine transcriptional and functional heterogeneity within early innate lymphoid cells (ILC) progenitors. We identify a developmental bifurcation toward dendritic cell fate that reveals the uncommitted state of early specified ILC progenitors. We subsequently characterize an ILC-commitment checkpoint controlled by the transcription factor TCF-1. The present study reveals unexpected heterogeneity within early innate progenitor populations, and characterizes lineage infidelity that accompanies early ILC specification prior to commitment.

overall_design: transcriptional profiling of early ILC progenitors (EILP, ILCP), and common lymphoid progenitors (ALP) from WT or Tcf7 null mice was performed by RNA sequencing

first: Christelle

last: Harly

first: Maggie

first: Devin

last: Kenney

first: Tobias

last: Raabe

first: Qi

last: Yang

first: Hai-Hui

last: Xue

first: Avinash

last: bhandoola


title: Gene expression comparison of splenic virus-specific CD8 T cells after immunization with LCMV vector and treatment with IgG or aIFNAR1

city: Chicago

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: Acute, transient IFNAR1 blockade induces a compensatory IFN-I response during the effector phase (day 7)

overall_design: We MACS-purified splenic CD8 T cells by negative selection. Then, we FACS-sorted DbGP33+ CD8 T cells.

last: Penaloza-MacMaster


title: Quiescent glioblastoma cells shift to an epithelial-mesenchymal transition-like gene program

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Quiescent stem cells of glioblastoma (GBM), a malignant primary brain tumor, are potential sources for recurrence after therapy. However, the gene expression program underlying the physiology of GBM stem cells remains unclear. We have isolated quiescent GBM cells by engineering them with a knock-in H2B-GFP proliferation reporter and expanding them in a 3D tumor organoid model that mimics tumor heterogeneity. H2B-GFP label retaining quiescent cells were subjected to stem cell assays and RNA-Seq gene expression analysis. While quiescent GBM cells were similar in clonal culture assays to their proliferative counterparts, they displayed higher therapy resistance. Interestingly, quiescent GBM cells upregulated epithelial-mesenchymal transition (EMT) genes and genes of extracellular matrix components. Our findings connect quiescent GBM cells with an EMT-like shift, possibly explaining how GBM stem cells achieve high therapy resistance and invasiveness, and suggest new targets to abrogate GBM.

overall_design: Glioblastoma cancer cells in 3D organoid culture were pulsed for 2 weeks with H2B-GFP, then chased either 2 or 4 weeks. Label-retaining GFP-high cells (quiescent) were separated from bulk population, and both populations were analyzed by RNA-Seq.

first: Rut

last: Tejero

first: Yong

last: Huang

first: Igor

last: Katsyv

first: Michael

last: Kluge

first: Caroline

middle: C

last: Friedel

first: Jung-Yi

last: Lin

first: Nicolas

last: Daviaud

first: Hongyan

last: Zou

first: Roland

middle: H


title: Combined MEKi (GDC-0973) and WNT (G007-LK) treatment in APC and KRAS mutant HCT-15 cell line

city: Oslo

first: Martin

middle: Frank

last: Strand

address: Prinsensgate 7

country: Norway

institute: Høyskolen Kristiania

summary: We report RNAseq data from HCT-15 cells were treated wih control(DMSO), GDC-0973, G007-LK and combined GDC-0973 and G007-LK treatmetn for 24 hours.

overall_design: Three biological replicates of cultured HCT-15 cells treated with DMSO (0.02%), G007-LK (1µM), GDC-0973 (1µM) or G007-LK and GDC-0973 for 24 hours before Rna extraction

first: Nina

middle: T

last: Solberg

first: Maria

last: Melheim

middle: F

first: Petter

middle: A

last: Olsen

first: Stefan

last: Krauss


title: Deletion of the KH1 domain coding sequence of Fmr1 leads to transcriptional alterations and attentional deficits in rats

status: Public on Apr 23 2019

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: We found that the previously published Fmr1 knockout rat model of FXS expresses an Fmr1 transcript with an in-frame deletion of exon 8, which encodes for the K-homology (KH) RNA-binding domain, KH1. We observed that the deletion of exon 8 in 10 male rats within the medial prefrontal cortex (mPFC) led to transcriptional alterations compared to 12 WT rats using RNAseq. Additionally, we used weighted gene co-expression network analysis to generate 23 modules specific to the mPFC with tissue from 35 WT rat samples.

overall_design: RNAseq using WT and Fmr1 delta exon 8 mPFC samples

first: Carla

middle: E

last: Golden

first: Lacin

last: Koro

first: Sankalp

last: Sonar

first: Kristi

last: Niblo

first: Andrew

last: Browne

first: Natalie

last: Burlant

first: Daniele

last: Di Marino

first: Silvia

last: De Rubeis

first: Mark

middle: G

last: Baxter

first: Joseph

middle: D

last: Buxbaum

first: Hala

last: Harony-Nicolas


title: Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration

city: University Park

first: William

middle: J.

last: Horton

state: PA

address: 324 Henning Bldg

department: Animal Science

institute: Pennsylvania State University

summary: Most migrating passerine birds undertake their long biannual voyages during the night. During these times of the year birds are in a continuous state of severe sleep restriction, yet curiously they perform as well, or better, on tests of physical and cognitive performance than during non-migrating times of the year. This inherent physiological protection, a component of the endogenous circannual program regulating this crucial life history stage, disappears when birds are forced to stay awake at other times of the year, demonstrating that these protective changes are only associated with the nocturnal migratory state. The goal of the current  study was to identify the physiological mechanisms that confer protection against the usually negative consequences of sleep loss while simultaneously allowing for the increased metabolic and cardiovascular output required for migration. To that end, we performed an RNA-seq analysis of heart and Liver collected from birds at different times of day under different migratory states and analyzed these data using differential expression, Ingenuity Pathway Analysis and Weighted Gene Co-expression Network Analysis. We identified numerous changes in gene expression networks implicating the involvement of multiple systems and pathways. These pathways regulate many aspects of metabolism, immune function, extracellular matrix wound repair, and protection of multiple organ systems in the body. Consequently, the circannual program controlling the appearance of the migratory phenotype involves the complex regulation of diverse gene networks associated with the physical demands of migration.

overall_design: Examination of transcriptome in two tissues from white-throated sparrows (heart & liver), at two time points (ZT6 & ZT18), under two phenotypic conditions (migratory and non-migratory), with n=5/group, sequenced to ~40 million reads/sample, 100bp, single-end reads for quantification

middle: J

first: Matthew

last: Jensen

first: Aswathy

last: Sebastian

first: Craig

last: Praul

first: Istvan

last: Albert

first: Paul

last: Bartell


title: Changes in the level of expression of genes involved in the pathogenic mechanisms in rare, inherited metabolic diseases.

city: Warsaw

first: Agnieszka

last: Lugowska

address: Al. Sobieskiego 9

department: Department of Genetics

country: Poland

institute: Institute of Psychiatry and Neurology

summary: Inherited metabolic diseases belong to the group of rare diseases (so called ‘orphan diseases’) whose incidence is less than 1: 5 000 live births. Among these diseases the lysosomal storage diseases (LSD) are also distinguished, which are caused by disorders in the lysosomal system resulting from the mutations in the genes coding for lysosomal hydrolases, cofactors, enzymes involved in the posttranslational processing, and proteins present in the lysosomal membrane.  Although about 70 LSD are recognized so far, their pathomechanism is almost unknown. Hitherto existing results of scientific investigations indicate that different cellular pathways and events are involved in the pathogenic processes: autophagy, apoptosis, toxic action of lyso- derivatives of lipid compounds, disordered  Ca2+ ions intracellular homeostasis, secondary storage of macromolecular compounds, signal transduction, inflammatory processes, deficient by-products and many more. We are especially interested in the explanation of pathomechanisms of Gaucher disease and Niemann-Pick type C disease (for the latter disease there is no therapy officially accepted). In this project we aim to experimentally explain:  - which cellular pathways and mechanisms are activated and inactivated in cells originating from patients with different LSD and healthy individuals  - are there differences in genes expression in different diseases  - are gene expression changes related to known and observed biochemical and clinical changes.

overall_design: Material for the study consists of RNA samples isolated from cultured skin fibroblasts obtained from 20 individuals, in whom no LSD was diagnosed (healthy persons), 20 patients in whom Niemann-Pick type C disease has been diagnosed, and 5 patients with Gaucher disease. Changes in genes expression were investigated by means of microarray analysis with the use of the Illumina technology, which enables the tracking of changes in the whole human genome. Results of microarray analysis were verified by quantitative RT-PCR technique.

last: Ługowska

first: Roksana

middle: M

last: Iwanicka-Nowicka

first: Rafał

last: Płoski

first: Marta

middle: K

last: Koblowska

first: Anna

last: Fogtman

first: Paweł

last: Włodarski


title: Bulk RNA sequencing of VE-Cadherin+GFP+, VE-Cadherin- GFP+ and VE-Cadherin+GFP- populations from E11.5 miR144/451+/GFP mouse yolk sac.

status: Public on Apr 20 2019

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

summary: The aim of the experiment was to compare a newly defined population VE-Cadherin+GFP+ to control populations, VE-Cadherin- GFP+ and VE-Cadherin+GFP-.

overall_design: Yolk sacs from E11.5 miR144/451+/GFP mouse embryos were isolated and single cell suspensions were generated. Cells were stained with the anti-VE-Cadherin antibody and 24 VE-Cadherin+GFP+ cells (n=2), 25 VE-Cadherin- GFP+ cells (n=3) and 25 VE-Cadherin+GFP- cells (n=3) were sorted by flow cytometry. The SMART-Seq 2 method was then used to produce cDNA from these eight samples. Sequencing libraries were generated and were later sequenced together on the Illumina Next Seq 500 sequencer.

first: Kerstin

last: Ganter


title: Deciphering the mammary stem cell niche: a role for laminin-binding integrins

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Integrin dimers a3/b1, a6/b1 and a6/b4 are the receptors of mammary epithelial cells for Laminin, major component of the mammary basement membrane. Antibodies against a6 and a3 integrin chains serve to isolate stem cell enriched populations from mammary epithelium, however, role of integrin dimers comprising these chains in the control of mammary stem cell activity are not known. To investigate the role of Laminin-binding integrins in the control of mammary stem cell function, a3 and a6 chains were deleted from mammary basal cells in vitro using Cre-recombinase carrying adenovirus. We found that deletion of single integrin chain (either a3, or a6) did not significantly affect stem cell potential as evaluated by transplantation and mammosphere assays, whereas basal cells depleted of both a3 and a6 integrin chains (a3a6KO) presented severely diminished stem cell activity. In this study the transcriptional profiles of a3a6KO were analysed and compared to those of control cells.

overall_design: Ctrl basal cells/a3a6KO basal cells - 4 biological replicates each

first: Marisa

last: Faraldo

first: Mathilde

last: Romagnoli

last: delaGrange

first: Sylvain

last: Baulande

first: Marina

last: Glukhova


title: Diverse Compounds from Pleuromutilin Lead to a Thioredoxin Inhibitor and Inducer of Ferroptosis

city: Urbana

last: Hergenrother

state: IL

address: 600 S. Mathews

institute: University of Illinois

summary: The chemical diversification of natural products provides a robust and general method for creation of stereochemically rich and structurally diverse small molecules. The resulting compounds have physicochemical traits different from those in most screening collections, and as such are an excellent source for biological discovery. Herein, we subject the diterpene natural product pleuromutilin to reaction sequences focused on creating ring system diversity in few synthetic steps. This effort resulted in a collection of compounds with previously unreported ring systems, providing a novel set of structurally diverse and highly complex compounds suitable for screening in a variety of different settings. Biological evaluation identified the novel compound ferroptocide, a small molecule that rapidly and robustly induces ferroptotic death of cancer cells. Target identification efforts and CRISPR knockout studies reveal that ferroptocide is an inhibitor of thioredoxin, a key component of the antioxidant system in the cell.  Ferroptocide positively modulates the immune system in a murine model of breast cancer and will be a useful tool to study the utility of pro-ferroptotic agents for treatment of cancer.

overall_design: 2 cell lines (HT29 and A549) X 2 treatments (DMSO and ferroptocide) X 2 replicates = 8 samples

first: Evijola

last: Llabani

first: Robert

middle: W

last: Hicklin

first: Hyang

middle: Y

last: Lee

first: Stephen

last: Motika

first: Lisa

last: Crawford

first: Eranthie

last: Weerapana


title: Dynamic changes in the epigenetic landscape are mandatory for acinar cell reprogramming and pancreatic carcinogenesis [ChIP-seq]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pancreatic acinar cell reprogramming is described as a common hallmark in pancreatic regeneration and carcinogenesis, although the regulatory mechanisms are barely understood. To overcome limitations of cellular diversity posed by heterogeneous cell compositions and high stroma density in pathogenic tissue specimens, we have established a pure in vitro system mimicking the pancreatic carcinogenic sequence. With this model, we globally profiled for epigenetic and transcriptional alterations and demonstrate that regulatory key players and structural genes are extensively regulated by epigenetic mechanisms. A conditional knockout of the epigenetic repressor Ring1b showed that particularly the epigenetic silencing of acinar differentiation genes is a crucial step in acinar cell reprogramming and pancreatic cancer development. Moreover, a persistent epigenetic repression of these genes manifests tumor cell malignancy. Depletion or drug-dependent inhibition of Ring1b promoted tumor cell reprogramming towards a less aggressive phenotype offering new options for therapeutic intervention.

overall_design: ChIP-Seq of H3K4me3, H3K3K27me3, and H2AK199ub in in different pancreatic tissues

first: Simone

last: Benitz

first: Ujjwal

last: Mahajan

first: Stefan

last: Czemmel

first: Tatjana

last: Unruh

first: Britta

last: Wingerath

first: Sabrina

last: Deubler

first: Tao

last: Cheng

first: Sven

last: Nahnsen

first: Philipp

last: Bruns

first: Bo

last: Kong

first: Susanne

last: Raufels

first: Güralp

last: Ceyhan

first: Julia

last: Mayerle

first: Katja

last: Steiger

first: Irene

last: Esposito

first: Jörg

last: Kleeff

first: Christoph

last: Michalski

first: Ivonne

last: Regel


title: Gene expression profiling of B-cell depleted tonsil fractions

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Tonsil specimens were freshly obtained from children undergoing elective tonsillectomy, trimmed of adjacent mucosa and skeletal muscle, disaggregated into single-cell suspensions, and viably cryopreserved. Thawed suspensions were magnetically sorted to deplete cells expressing CD19+ and/or CD20+. Total RNA was extracted for gene expression profiling (GEP).

overall_design: GEP data were used for comparison to similarly-prepared B-cell depleted fractions of follicular lymphoma samples.

first: Min

last: Zhang

first: Jason

last: Westin

first: Zhiqiang

last: Wang

first: Larry

last: Kwak

first: Sattva

last: Neelapu

first: R

last: Davis


title: Dynamic changes in the epigenetic landscape are mandatory for acinar cell reprogramming and pancreatic carcinogenesis [microarray]

first: Tobias

last: Straub

summary:
Pancreatic acinar cell reprogramming is described as a common hallmark in pancreatic regeneration and carcinogenesis, although the regulatory mechanisms are barely understood. To overcome limitations of cellular diversity posed by heterogeneous cell compositions and high stroma density in pathogenic tissue specimens, we have established a pure in vitro system mimicking the pancreatic carcinogenic sequence. With this model, we globally profiled for epigenetic and transcriptional alterations and demonstrate that regulatory key players and structural genes are extensively regulated by epigenetic mechanisms. A conditional knockout of the epigenetic repressor Ring1b showed that particularly the epigenetic silencing of acinar differentiation genes is a crucial step in acinar cell reprogramming and pancreatic cancer development. Moreover, a persistent epigenetic repression of these genes manifests tumor cell malignancy. Depletion or drug-dependent inhibition of Ring1b promoted tumor cell reprogramming towards a less aggressive phenotype offering new options for therapeutic intervention.
Simone,Benitz

overall_design: Total RNA isolated from different pancreatic tissues.

first: Ujjwal

last: Mahajan

first: Stefan

last: Czemmel

first: Tatjana

last: Unruh

first: Britta

last: Wingerath

first: Sabrina

last: Deubler

first: Tao

last: Cheng

first: Sven

last: Nahnsen

first: Philipp

last: Bruns


title: MULTIPLE SCN5A ENHANCERS MODULATE CARDIAC GENE EXPRESSION AND QT INTERVAL VARIATION

first: Ashish

last: Kapoor

state: TX

address: 1825 Pressler St. Rm SRB 530C

institute: University of Texas Health Science Center at Houston

summary: Genome-wide association studies (GWAS) have suggested that sequence variation in cis-regulatory elements (CREs) modulate common disease risk and trait variation. However, identification of the majority of these causal variants and their mechanism of action have remained significant challenges. We used reporter assays for all common variants at the QT interval associated SCN5A GWAS locus with the goal of identifying causal variants for the association. A target region of ~500kb containing SCN5A was defined based on recombination hotspots (rate>10cM/Mb; estimated from HapMap) flanking the 5 independent QT interval GWAS hits. Within this region, all common variants (minor allele frequency >5%), from the 1000 Genomes European ancestry populations, in moderate linkage disequilibrium (LD; r2>0.3) with any of the 5 sentinel hits, were selected for analyses. Of a total 121 variants selected, 112 variants in 104 amplicons passed primer design (amplicon size 256-617bp; median 397bp), with both alleles of 106 variants successfully cloned along with flanking sequences into 98 amplicons upstream of a minimal promoter-driven firefly luciferase gene in pGL4.23. Cardiomyocyte cells, AC16 (human) and HL1 (mouse), were transfected with test constructs and Renilla luciferase vector (for transfection normalization) in triplicate; luciferase assays were performed 24h later. All cloning and reporter assays were performed in 96- and 24-well plates. In reporter assays across the two cell lines, compared to empty vector, 37 amplicons showed enhancer activity (z-score>99 %tile), with a concordance rate of ~70%. Of these 37 enhancer CREs, 9 overlapped open chromatin regions (DNase-seq peaks) observed in adult human heart tissue, largest among all human tissues evaluated by the RoadMap Epigenomics project. Of these 37 enhancer CREs, 12 showed allelic difference in reporter activity (P<0.05), thus identifying at least one enhancer CRE variant in high-to-moderate LD with each of the 5 sentinel hits. Using GTEx heart left ventricle (n=190) gene expression data, we showed correlation between SCN5A expression and the number of QT interval prolonging alleles across the 5 index SNPs. We are currently assessing the binding of cardiac nuclear factors at the 12 enhancer CRE variants by gel-shift assays and the effect of CRISPR-Cas9 mediated CRE deletion on SCN5A expression in AC16 and HL1 cells, an analyses helped by evaluation of AC16 and HL1 cells by RNA-seq, ATAC-seq and karyotyping. Thus, independent of the publicly available epigenomic data, which are of limited cell-type relevance, an unbiased in vitro reporter screen for CREs overlapping all common variants associated with QT interval at the SCN5A GWAS locus identified 12 common cis-regulatory variants that map to cardiac open chromatin regions and correlate with SCN5A cardiac expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq and ATAC-seq in AC16 and HL1 cell lines

first: Dongwon

last: Lee

first: Aravinda

last: Chakravarti


title: A lineage commitment checkpoint in early ILC development [bulk RNA-seq]

first: Margaret

last: Cam

first: Christelle

last: Harly

first: Maggie

first: Devin

last: Kenney

last: Raabe

first: Qi

last: Yang

first: Hai-Hui

last: Xue

first: Avinash

last: bhandoola


title: The histone methyltransferases Suv420h regulate PPAR-γ and energy expenditure in response to environmental stimuli

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary:
The rising prevalence of obesity and its associated metabolic abnormalities have become global diseases that carry considerable morbidity and mortality. While there is certainly an important genetic component, extensive human epidemiologic and animal model data suggest an epigenetic component to obesity. Nevertheless, the cellular and molecular underpinnings of these pathways and how they contribute to the development of obesity remain to be elucidated.
Suv420h1 and h2 are histone methyltransferases responsible for chromatin compaction and gene repression. Through in vivo, ex-vivo and in vitro studies, we found that Suv420h1 and h2 respond to environmental stimuli and regulate metabolism by downregulating PPAR-γ, a master transcriptional regulator of lipid storage and glucose metabolism. Accordingly, mice lacking Suv420h proteins activate PPAR-γ target genes in brown adipose tissue to increase mitochondria respiration, improve glucose tolerance and reduce adipose tissue to fight obesity.
We conclude that Suv420h proteins are key epigenetic regulator of PPAR-γ and the pathways controlling metabolism and weight balance in response to environmental stimuli.

overall_design:
For experiment 1, total RNA was isolated from males and females control- and Suv420h dKO-derived BAT.
For experiment 2, total RNA was isolated from BAT collected from females control and Suv420h dKO mice after both diet regimes (nd = normal diet, hfd = high fat diet).

first: Simona

last: Pedrotti

first: Ivan

last: Molineris

first: Davide

last: Gabellini


title: Transcriptomic study revealing the effect of thiamin on the morphology of Yarrowia lipolytica

city: Thiverval Grignon

first: Reine

last: Malek

address: Avenue Lucien Brétignières

institute: INRA, UMR 1319 MICALIS

summary:
A comparison between Y. lipolytica growth in a Synthetic agar Medium not containing THiamin (SM TH-) to its growth in a Synthetic agar Medium supplemented with THiamin (SMTH+) at day 8 of the culture. This study allowed us to discover the effect of thiamin on the growth and the morphology of Y. lipolytica
The transcriptomic study was carried out using Agilent 8X15k slides with a custom oligoset designed by V. Loux using the Yarrowia lipolytica ORFeome extracted from genolevures database

overall_design: Two conditions experiment: growth of Y. lipolytica in SM TH- versus growth of Y. lipolytica in SM TH+ at day 8 of culture. Dye switches were done using four biological replicates for both conditions.

first: Pascale

last: Frey-Klett

first: Djamila

last: Onésime

first: Dominique

last: Swennen

first: Pascal

last: Bonnarme

first: Françoise

last: Irlinger

first: Julie

last: Aubert

first: Jean-Marie

last: Beckerich


title: Expression data from WT and Tbx21-/- in vivo TFH cells versus TH1 cells

city: Chongqing

first: Pengcheng

last: Wang

state: chongqing

address: gaotanyan street

department: Institute of Immunology

country: China

institute: Army Medical University

summary: Follicular helper T cells (TFH), known as the primary helpers of the germinal center (GC) reaction, promote the humoral immune response to defend against various pathogens. Under conditions of infection by different types of pathogens, many shared transcription factors (TFs), such as Bcl-6, TCF-1 and Maf, are broadly expressed in TFH cells, orchesting TFH cell differentiation and function. In addtion, TFH cells also coexpress environmentally specific TFs as their conventional T cell counterparts (such as T-bet, GATA-3 or ROR-γt, which are expressed in Th1, Th2 or Th17 cells, respectively). This phenomenon indicates the complexity and environmental adaptivity of the TFH cell response. However, the extent to which the TFH cell response relies on these environmentally specific TFs is not completely understood. Here, we found that transcription factor T-bet was specifically expressed in type I but not type II TFH cells and that the T-bet-IFN-γ axis was essential for the maintenance of TFH cells, promoting their proliferation and inhibiting their apoptosis during acute viral infection. Microarray analysis showed both similarities and differences in transcriptome dependency on T-bet in TFH and Th1 cells, suggesting the distinctive role of T-bet in TFH cells. Collectively, our findings reveal an important and specific supporting role for T-bet in type I TFH cell response, which can help us gain a depper understanding of TFH cell subsets.

overall_design: analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) WT and Tbx21-/- TFH cells, versus TH1 cells, six days after viral infection. Cells were sorted for RNA extraction and hybridization on Affymetrix microarrays.


title: BCR repertoire profiling of murine ABC-DLBCL-like tumors [targeted RNA-seq]

status: Public on Apr 19 2019

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

summary: We have developed a novel immunocompetent multi-lesion mouse model of activated B cell diffuse large B-cell lymphoma (ABC-DLBCL; the pBIC mice) that recapitulates relatively fast the molecular, cellular and tumor microenvironment of aggressive human ABC-DLBCL. We demonstrate that perturbed p53 signaling cooperates with constitutive NF-kB activation in GC-experienced plasmablasts with blocked terminal differentiation to promote lymphomagenesis and tumor progression through triggering downstream intracellular molecular addictions (e.g. deregulating Foxp1 and AID pathways) and intercellular immunosuppressive signals for evading anti-tumoral responses (e.g. MHC-II antigen presentation and deregulating PD-L1/PD-1 immune checkpoint). Our immunocompetent ABC-DLBCL murine model provides in vivo evidence that PD-1 blockade cooperates with anti-CD20-based current standard-of-care therapy to reshape the immunosuppressive TME and facilitate long-term anti-tumoral responses. Therefore, our results support that immune checkpoints may hold promising therapeutic potential in ABC-DLBCL.

overall_design: IgH VDJC-sequencing of FACS-sorted naïve (N=4) or, GC (N=4) B cells from YC control mice and lymphoma B cells from BIC (N=2) or pBIC (N=2) mice.

first: Marien

last: Pascual

first: Maria

last: Mena-Varas

first: Eloy

last: Robles

last: Garcia-Barchino

first: Carlos

last: Panizo

first: Sandra

last: Hervas-Stubbs

first: Diego

last: Alignani

first: Ainara

last: Sagardoy

middle: I

last: Martinez-Ferrandis

first: Karen

last: Bunting

first: Stephen

last: Meier

first: Xavier

last: Sagaert

last: Bagnara

first: Elizabeth

last: Guruceaga Martinez

first: Oscar

last: Blanco

first: Jon

last: Celay

first: Alvaro

last: Martinez Baztan

first: Noelia

last: Casares

first: Juan

last: Lasarte

first: Thomas

last: MacCarthy

first: Ari

last: Melnick

last: Martinez-Climent

first: Sergio

last: Roa


title: Transcriptional profiling of murine ABC-DLBCL-like tumors [RNA-seq]

first: SERGIO

last: ROA

overall_design: RNAseq profiling of FACS-sorted reporter positive splenic B cells (B220+GFP+/YFP+) from two ABC-DLBCL lymphoma murine models (3 BIC and 6 pBIC mice) compared to normal controls (3 YC mice).

first: Marien

last: Pascual

first: Maria

last: Mena-Varas

first: Eloy

last: Robles

last: Garcia-Barchino

last: Panizo

last: Hervas-Stubbs

last: Alignani

first: Jose

first: Davide

last: Guruceaga


title: Expression data from HCT116 cell transduced with lentivirus encoding PNO1 shRNA (sh-PNO1) or Control shRNA (sh-Ctrl)

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: To further explore the underlying mechanism of PNO1 knockdown on suppression of CRC cell growth in vivo and in vitro, Affymetrix human GeneChip primeview arrays  were performed to determine the global gene expression in HCT116 cells after transduction lentivirus encoding PNO1 shRNA (n=3) or control shRNA (n=3).

overall_design: HCT116 cells were transduced with lentivirus encoding PNO1 shRNA (n=3) or Control shRNA (n=3) for 72 h, and the samples were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Aling

last: Shen


title: Expression data of GTSE1-knockdown hepatoma cell line Bel-7404

city: Beijing

first: Jingyu

last: Wang

state: Select State

address: 4204, Biotechnology Building, Tsinghua University

department: Medical School

institute: Tsinghua University

summary:
Liver cancer is the fourth deadliest cancer worldwide and is in lack of prognostic indicators. As a p53 inducible gene, GTSE1 (G2 and S phase-expressed-1) showed widely correlation with tumor progress and prognosis in clinical, while its potency as a prognosis indicator or molecular mechanism in regulating cell cycle remain little known. This study aimed to elucidate clinical values and potential functions of GTSE1 in liver cancer.
In study of GTSE1 functions, Bel-7404 cell, a human hepatoma cell line, was induced GTSE1-knockdown using lentiviral-mediated RNAi and performed RNA microarray analysis.

overall_design: Bel-7404 was induced GTSE1-knockdown using lentiviral-mediated RNAi and performed RNA microarray analysis

first: Yang

last: Chen


title: Implications of epigenetic drift in colorectal neoplasia

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

type: Methylation profiling by genome tiling array

summary: Many normal tissues undergo age-related DNA methylation drift  providing a quantitative measure of tissue age. However  this drift has not been demonstrated in neoplastic tissues. Here we identify and validate 781 CpG-islands (CGIs) that undergo significant methylomic drift in normal colorectal tissues  continue to drift in neoplasia and remain significantly correlated with one another across tissue samples. However  compared with normal colon  this drift advances (~3-4 fold) faster in neoplasia consistent with increased cell proliferation during neoplastic progression. Furthermore  we show that the observed drift patterns are broadly consistent with modeled adenoma-carcinoma sojourn time distributions from colorectal cancer (CRC) incidence data. These results support the hypothesis that  beginning with the founder premalignant cell  cancer precursors frequently sojourn for decades before turning into cancer which implies that the founder cell typically arises early in life. We estimate that at least 77-89% of the observed drift variance in distal and rectal tumors is explained by stochastic variability associated with neoplastic progression  while only 55% of the variance is explained for proximal tumors. However  >50%  of identified gene-CGI pairs in the proximal colon that undergo drift are significantly and mainly negatively correlated with cancer gene expression  suggesting that methylomic drift participates in the clonal evolution of CRCs.  Significance:  Methylomic drift advances in colorectal neoplasia consistent with extended sojourn time distributions explaining a significant fraction of epigenetic heterogeneity in CRCs. Importantly  the estimated long-duration premalignant sojourn times suggest that early dietary and lifestyle interventions may be more effective than later changes in reducing CRC incidence.

overall_design: We evaluated methylation levels at  CpG probes using the Illumina HM450 beadchip array (HM450) in a total of 675 colorectal tissue samples. Of particular interest were site and sex differences in methylomic drift  inter-individual heterogeneity  and whether drift patterns at the probe and CGI level reflect the expected variance of tissue sojourn times in the adenoma-to-carcinoma sequence.

first: Georg

last: Luebeck

first: William

last: Hazelton

first: Kit

last: Curtius

first: Ming

last: Yu

first: Kelly

last: Carter

first: Wynn

last: Burke

first: Paul

last: Lampe

first: Christopher

last: Li

first: Cornelia

last: Ulrich

first: Polly

last: Newcombe

last: Westerhoff

first: Andrew

last: Kaz

first: Yanxin

last: Luo

first: John

last: Inadomi

last: Grady


title: Expression of defense related genes in resistance and susceptible tobacco (Nicotiana tabacum) in response to Ralstonia solanacearum infection

city: Changsha

first: Yongting

address: No 348, Xianjiahu West Rd.

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

summary: Comparative transcriptome analysis was performed to study gene expression profiles in resistant (Yanyan 97, YY97, 25) and susceptible (Huanghuadajinyuan, HD, 36) tobacco in responding to Ralstonia solanacearum infection. Illumina sequencing yielded a total of 67,619,833,668 bases data, and about 223.99 M and 223.82 M raw reads for Hd and Yy97 plants, respectively. About 209.73 M and 209.18 M clean reads of Hd and Yy97 were mapped to reference genome via Hisat2, respectively. The ratio of mapped clean reads for eight libraries ranged from 93.92% to 96.67% (average: 95.9%). By comparing gene expression levels in Rs infected and control tobacco stems, we identified 15374 DEGs in Hd plants after Rs infection, which included 7220 up-regulated and 8154 down-regulated DEGs. We identified 2120 DEGs in Yy97 plants after Rs infection, which included 1794 up-regulated and 326 down-regulated DEGs.

overall_design: Stem samples of Ralstonia solanacearum infested(tm) and un-infested (ck) tobacco were RNA-Seq sequenced to compare differentially expressed genes.

first: Yihuan

last: Zhang

first: Bing

last: Guo


title: Comparison of gene expression profiles between MC3T3-E1 without osteoblastic induction and with 14 days of ostoblastic induction

status: Public on Apr 21 2019

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

summary: Microarray study revealed 1324 genes that were up-regulated and 1550 genes that were down-regulated more than 1.5 fold change (corrected p<0.05) in MC3T3-E1-derived-mature Osteoblasts compared to control MC3T3-E1.

overall_design: 6 samples were analyzed. Among the 6 samples, 3 independent replicates for MC3T3-E1 cell line without osteoblast induction and 3 independent replicates for MC3T3-E1 underwent for 14 days of osteoblast differentiation

first: C

last: Swindle

first: Chao

last: Wan

first: Robert

last: Flynn

first: Dongquan

last: Chen

last: Klug


title: A NOTCH feed-forward loop drives reprogramming from adrenergic to mesenchymal state in neuroblastoma.

status: Public on Apr 18 2019

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Transition between differentiation states in development occurs swift but the mechanisms leading to epigenetic and transcriptional reprogramming are poorly understood. The pediatric cancer neuroblastoma includes adrenergic (ADRN) and mesenchymal (MES) tumor cell types, which differ in phenotype, super-enhancers (SEs) and core regulatory circuitries. These cell types can spontaneously interconvert, but the mechanism remains largely unknown. Here, we unravel how a NOTCH3 intracellular domain reprogrammed the ADRN transcriptional landscape towards a MES state. A transcriptional feed-forward circuitry of NOTCH-family transcription factors amplifies the NOTCH signaling levels, explaining the swift transition between two semi-stable cellular states. This transition induces genome-wide remodeling of the H3K27ac landscape and a switch from ADRN SEs to MES SEs. Once established, the NOTCH feed-forward loop maintains the induced MES state. In vivo reprogramming of ADRN cells shows that MES and ADRN cells are equally oncogenic. Our results elucidate a swift transdifferentiation between two semi-stable epigenetic cellular states.

overall_design: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam) .  De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the 5500W Flowchip v2 kit  (Life Technologies) and sequenced on the SOLiD Wildfire (Illumina) resulting in 50 bp reads. Alternatively, the libraries were sequenced using the HiSeq PE cluster kit v4 (Illumina) with the HiSeq2500 (Illumina) resulting in 125 bp reads.

first: Johan

last: van Nes

first: J

last: Koster

first: D

last: Zwijnenburg

first: R

last: Versteeg


title: Comparative transcriptome analysis of Ogataea parapolymorpha wild-type and met4 mutant under sulfur limitation

city: Seoul

first: Su Jin

last: Yoo

address: Heukseok-ro

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: We analyze the transcriptome of Ogataea parapolymorpha wild-type and met4 mutant under sulfur limited condition to investigate the function of Met4 protein in this yeast in the absence of any sulfur source. By sequencing the mRNAs of the wild-type and mutant grown in sulfur-limited B minimal medium with or without cysteine as a sole sulfur source, we find the role of OpMet4p as a master regulator for cell homeostasis under sulfur limitation.

overall_design: Examination of transcriptome in Ogataea parapolymorpha wild-type and met4 mutant in the absence or presence of sulfur source

first: SuJin

first: MinJeong

last: Sohn

first: HyunAh

last: Kang


title: Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome

city: Riversidy

first: Giovanna

last: Pozuelos

state: California

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: The purpose of this study was to evaluate gene expression changes in the nasal epithelium of non-smoking human females following acute inhalation THS compared to harmless clean air.

overall_design: Four non-smoker females were first exposed to clean air for ~3 hours. At least 21 days later, the same individuals were exposed to THS using the same laboratory conditions. Nasal scrapes were collected before and after each exposure.

middle: L

first: Meenakshi

last: Kagda

first: Suzaynn

last: Schick

first: Thomas

last: Girke

first: David

middle: C

last: Volz

first: Prue

last: Talbot


title: Gene expression profiling of B-cell and non-B-cell fractions of follicular lymphoma

first: Wencai

last: Ma

summary: Excisional biopsies of lymph nodes involved by follicular lymphoma (FL) were obtained from previously-untreated, advanced-stage patients to generate heterohybridomas and idiotype vaccine for a clinical trial (PMID: 21632504). Residual, viably-cryopreserved suspensions of disaggregated cells were magnetically sorted by negative selection into nominal B (CD3-depleted) and non-B (NB; CD19- and CD20-depleted) fractions. Total RNA was extracted from each fraction for separate gene expression profiling (GEP). Technically-satisfactory GEP results were obtained from both fractions for 43 patients.

overall_design:
GEP data from the NB fraction were used to identify signatures of immune cell types and biological processes in the NB fraction, through the technique of correlation matrix analysis (CMA). B and NB fraction data were also cross-correlated, by CMA and other means, to implicate immune cell types, genes, and biological processes involved in interactions between tumor B cells and the immune microenvironment in FL.
Negatively-enriched B or non-B cells, as indicated, from untreated follicular lymphoma. 7-digit number is the unique patient identifier. Suffix number, when present, indicates which one of the duplicate arrays that were used for the same patient.

first: Min

last: Zhang

first: Jason

last: Westin

first: Zhiqiang

last: Wang

first: Larry

last: Kwak

first: Sattva

last: Neelapu

last: Davis


title: Lnc-ITSN1-2 promotes rheumatoid arthritis fibroblast-like synoviocytesproliferation and inflammation while represses apoptosis via positive regulation of IL-23R/JAK/STAT pathway, and correlates with increased disease risk and activity

city: Shanghai

first: Tao

last: Yue

address: 540 Xinhua Road

department: Department of Rheumatology

institute: ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine

summary: This study aimed to investigate the effect of lnc-ITSN1-2 on cell proliferation, apoptosis and inflammation as well as its possible regulatory network and molecular mechanisms in rheumatoid arthritis (RA).

overall_design: Lnc-ITSN1-2 overexpression and ShRNA were transfected into RA fibroblast-like synoviocytes (FLS) followed by measurement of cell proliferation, apoptosis, inflammatory cytokines and mRNA sequencing.

first: Lianbo

last: Xiao


title: Analysis of mouse lymph node fibroblastic reticular cells (FRC) gene signature during autoimmune inflammation (EAE)

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

summary: We determined differentially regulated gene expression profile in WT and Il17RA-/- FRC during EAE. gene signature in FRC during EAE.

overall_design: FRC were isolated from skin draining lymph nodes of WT and IL17RA-/- mice day 12 post immunization with CFA and MOG peptide

first: Saikat

last: Majumder

first: Mandy

last: McGeachy

first: Natalie

last: Rittenhouse


title: Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain stuied at single-cell resolution

city: Baltimore

first: Jacob

last: Heng

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: The mammalian central nervous system (CNS) is capable of tolerating chronic hypoxia, but cell type-specific responses to this stress have not been systematically characterized.  In the Norrin-knockout (NdpKO) mouse, a model of familial exudative vitreoretinopathy (FEVR), developmental hypovascularization of the retina produces chronic hypoxia of inner nuclear layer (INL) neurons and Muller glia.  We have used single-cell RNA sequencing, untargeted metabolomics, and metabolite labeling from 13C-glucose to compare wild type and NdpKO retinas.  In NdpKO retinas, we observe gene expression responses consistent with hypoxia in Muller glia and retinal neurons, and we find a metabolic shift that combines reduced flux through the tricarboxylic acid cycle with increased synthesis of serine, glycine, and glutathione.  We also used single-cell RNA sequencing to compare the responses of individual cell types in NdpKO retinas to those in the hypoxic cerebral cortex of mice that were housed for one week in a reduced oxygen environment (7.5% oxygen).  In the hypoxic cerebral cortex, glial transcriptome responses most closely resemble the response of Muller glia in the NdpKO retina.  In both retina and brain, vascular endothelial cells activate a previously dormant tip cell gene expression program, which likely underlies the adaptive neo-angiogenic response to chronic hypoxia.  These analyses of retina and brain transcriptomes at single-cell resolution reveal both shared and cell-type-specific changes in gene expression in response to chronic hypoxia, implying both shared and distinct cell type-specific physiologic responses.

overall_design: Single-cell RNAseq of NdpKO and WT retinas as well as normoxic and hypoxic cerebral cortices; Ribotag RNA-seq of NdpKO and WT retinas; RNA-seq of normoxic and hypoxic whole brains.

first: Amir

last: Rattner

first: Genevieve

last: Stein-O'Brien

first: Briana

last: Winer

first: Bryan

last: Jones

first: Hilary

last: Vernon

first: Loyal

last: Goff

first: Jeremy

last: Nathans


title: Transcriptomic analysis of human macrophages in 3D

city: La Tronche

first: arnaud

last: MILLET

address: Allée des Alpes

institute: Institute for Advanced Studies

summary: Macrophages are involved in a large number of tissue functions in homeostasis and various pathological situations. These cells present a high degree of phenotypic plasticity that is grasped by the concept of polarization. One goal of the macrophage’s biology field is to obtain molecular signatures of these polarizations. To achieve this task, it is necessary to integrate how physical environment signals are interpreted by macrophages under immune stimulation. In this work, we have studied how a 3D collagen scaffold modulates the polarizations of human macrophages and revealed that some traditionally used markers should be reassessed.To perform this task we conducted a RNAseq analysis.

overall_design: Human macrophages were polarized in 3D collagen scaffolds and their transcriptome were analyzed

first: Magali

last: Court

first: Marie

last: Malier

first: Arnaud

last: Millet


title: BRCA1 Mutations Attenuate Super-Enhancer Function and Chromatin Looping in Haploinsufficient Human Breast Epithelial Cells

city: San Antonio

first: Rong

last: Li

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: BRCA1 functions in multiple biological processes, including double-strand break repair, replication stress suppression, transcriptional regulation, and chromatin reorganization. While non-malignant cells carrying cancer-predisposing BRCA1 mutations exhibit increased genomic instability, it remains unclear whether BRCA1 haploinsufficiency affects transcription and chromatin dynamics. Here we show that primary mammary epithelial cells from women with BRCA1 mutations (BRCA1mut/+) display significant loss of H3K27ac-associated super-enhancers.

overall_design: Primary human mammary epithelial cells (HMECs) were isolated from fresh cancer-free breast tissues of BRCA1 mutation carriers (BRCA1mut/+, n = 3) and non-carriers (BRCA1+/+, n = 3), who underwent prophylactic mastectomy and reduction mammoplasty, respectively. H3K27ac chromatin immunoprecipitation with deep-sequencing (ChIP-seq) was performed.

first: Xiaowen

last: Zhang

first: Yao

last: Wang

first: Huai-Chin

last: Chiang


title: Genome-wide identification of mRNA 5-methylcytosine in mammals

city: Guangzhou

first: Rui

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing of myeloid cell subsets in brain trauma links targeting Ccr2-dependent macrophages with both improved functional outcomes and a reduction in type I IFN responses from TBI microglia subsets

city: Cambridge

first: Chris

last: Roberts

state: Massachusetts

address: 301 Binney St.

institute: Biogen

summary: Traumatic brain injury (TBI) induces neuroinflammatory innate immune responses that plays roles in both worsening brain damage and facilitating functional recovery. A major goal is to understand the heterogeneity of the immune responses to TBI, and to precisely identify key components that impact functional outcomes.  We previously demonstrated that genetically targeting Ccr2 in a mouse model of controlled cortical impact led to neuroprotection in TBI. Our current studies of TBI use single cell RNA sequencing of over 10,000 TBI ipsilateral brain leukocytes to examine the mechanisms associated with the observed benefit in Ccr2-/- mice by comparing gene expression in leukocyte subsets from Ccr2-/- mice to gene expression in C57BL/6 wild type mice. Unbiased clustering identified two monocyte subsets, Chil3hi Ly6Chi classical monocytes and Gpnmbhi Ly6Clo nonclassical monocytes, and nine microglia states in the ipsilateral TBI brain.  Comparative analysis between the genotypes revealed that Ccr2-/- TBI mice contained reduced numbers of inflammatory macrophages. In TBI, we observed a subset of microglia highly expressing several type I interferon-stimulated genes (ISGs) and is designated as Irf7hi microglia.  Notably, unbiased differential expression analysis detected a two-fold reduction in the type I interferon response in multiple Ccr2-/- TBI microglia subsets compared to wild type TBI microglia.   Treatment post-injury with a human CCR2 (hCCR2) inhibitor, CCX872, in hCcr2 knock-in mice improved cognitive function post-TBI, and also correlated with reduced expression of a key ISG, Irf7.  We identified and characterized macrophage and microglia subsets during acute TBI. Our data showed that a reduction in macrophage expansion in TBI by both genetic and pharmacological methods, improved TBI and correlated with a reduction in the type I IFN response.  These data indicate that macrophage expansion co-directs a type IFN response in microglia, and that targeting macrophage expansion in the brain can alter the profile of microglia subsets and lead towards improved functional outcomes.

overall_design: Contralateral or ipsilateral brain hemisphere samples were analyzed by RNA-Seq from either Controlled Cortical Injury (CCI) or sham-treated animals.  13 total samples were analyzed, from 4 groups: 1) sham-treated, contralateral (3 samples); 2) sham-treated, ipsilateral (2 samples); 3) CCI-treated, contralateral (4 samples); 4) CCI-treated, ipsilateral (4 samples).

first: Walter

last: Eckalbar

first: Kerri

last: Somebang

first: Isabella

last: Imhof

first: Luyi

first: Erene

last: Niemi

first: Michael

last: Gill

first: Judy

last: Shigenaga

first: Huy

last: Tran

first: Brian

last: Zabel

first: James

last: Campbell

first: Timothy

last: Sullivan

first: Rajinder

last: Singh

last: Wipke

first: Davide

last: Gianni

first: Marianna

last: Foos

first: Mary

last: Nakamura

first: Christine

last: Hsieh


title: Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity

city: Rehovot

first: yitzhak

last: Pilpel

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

type: Non-coding RNA profiling by high throughput sequencing

summary: The protein translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology, fitness and protein evolution. Mapping translation errors in proteomes and understanding their causes was hindered by lack of a proteome-wide experimental methodology. Here, we present the first methodology for systematic detection and quantification of errors in entire proteomes. Following proteome mass-spectrometry, we identify in E. coli and S. cerevisiae peptides whose mass indicates specific amino acid substitutions. Most substitutions occur due to codon-anticodon mispairing within the ribosome. we performed a deep RNA sequencing of the bacterial tRNA pool at the same time points in which we measured the proteome during E. coli culture growth. We compared ratio of abundances between congate and near-cognate tRNAs and found the changes corespond with changes in translation errors.

sample_organism:
Escherichia coli
Escherichia coli BW25113

overall_design: tRNA-sequencing of E.coli in stages along culture growth

first: Ernest

last: Mordret

first: Orna

last: Dahan

first: Omer

last: Asraf

first: Roni

last: Rak

first: Avia

last: Yehonadav

first: Georgina

last: Barnabas

first: Jürgen

last: Cox

first: Tamar

last: Geiger

first: Ariel

middle: B

last: Lindner

first: Yitzhak


title: Gene expression profiling of follicular lymphoma and tonsils

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center


title: DNA microarray analysis of R1-9 ES cells

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: We have studied protein expression in mouse embryonic stem (mES) cells- R1-9 and identified the largest complement of proteins reported thus far for mES cells, using on-line LC-MS/MS analysis. With support from a transcriptome profile of the same mES cell line, we arrived at an integrated dataset of 9,370 protein expressions that may be useful to understand the stem cell dynamics. 6,278 protein identifications (IDs) were based on two or more peptide signatures and 3,092 with single peptide signatures. These single peptide-based protein IDs were also supported by transcriptome data. The proteomic analysis demonstrated the expression of 1,369 genes (among 9,370) that were not seen in RNA transcripts. Pathway analysis of the protein IDs in our dataset, using KEGG and BioCarta and their gene ontology classification, revealed high representation of the proteins belonging to many regulatory pathways and showed enrichment for protein IDs involved in transcription regulation, signal transduction, cell-cycle, and differentiation. Interestingly, the data support the expression of 1,299 putative open reading frames. In silico domain comparisons of some of these sequences matched with regulatory proteins such as transcription factors or signal transduction molecules. Over 60% of the transcript complement is represented in our protein dataset implying a corresponding richness of the dynamic network of proteins in a pluripotent mES cells.have thus arrived at a dataset of 10428 expressed proteins with high confidence which was also verified by microarray analysis of the expressed mRNAs R1-9 ES cells.  Pathway analysis of these expressed proteins was carried out using KEGG, IPA and their gene ontology classification revealed the presence of large number of transcription regulators, signal transducers, cell cycle and differentiation molecules along with other general classes of proteins belonging to a number of regulatory pathways. The database also includes IDs of proteins corresponding to many still unidentified / unannotated ORFs from the mouse genome and with putative regulatory functions. Our study thus represents the largest database of expressed proteins in mouse ES cells that would be a valuable molecular resource for experimental designs in targeted proteomics investigations using mES cell lines.

overall_design: microarrays of 2-replication R1-9 ES cells were done with the same universal reference on channel 2.

first: K

last: Rakesh

first: Dawood

last: Dudekula

first: Ramaiah

last: Nagaraja

first: Yulan

last: Piao

first: David

last: Schlessinger

first: Ramamoorthy

last: Kalidoss

first: Ravi

last: Sirdeshmukh


title: Combined Developmental Effects of Environmental Stressors and Polycyclic Aromatic Hydrocarbons on Fundulus grandis Larvae

city: West Lafayette

first: Maria

last: Sepulveda

state: Indiana

address: 195 Marsteller St.

department: Forestry and Natural Resources

institute: Purdue University

summary: Oil spills have polluted the marine environment for decades and continue to be a major source of polycyclic aromatic hydrocarbons (PAHs) to marine ecosystems around the globe. Although the toxicity of PAHs to fish has been well studied, the combined effects of extreme abiotic factors and oil are poorly understood. Gulf of Mexico killifish Fundulus grandis larvae (< 24 hours post hatch) were exposed to varying environmental conditions (dissolved oxygen 2, 6 ppm; temperature 20, 25, 30°C; and salinity 3, 10, 30 ppt) combined with varying concentrations of high energy water accommodated fractions (HEWAF) (total PAHs 0 – ~ 125 ppb) for a total of 48 h. Larvae survival and development were negatively affected by PAHs, starting with the lowest concentration tested (~15 ppb). High temperature + hypoxia + PAHs resulted in the lowest survival with salinity having little impact on any of the endpoints tested. Expression of the hepatic detoxifying gene cyp1a was highly induced in PAH-exposed larvae, but only under normoxic conditions. A lack of cyp1a induction under hypoxia and PAH exposure could explain the enhanced toxicity observed. This work highlights the need for more studies examining the combined impact of suboptimal water quality parameters in the presence of pollution in fish early life-stages.

first: Jennifer

last: Serafin

first: Thijs

last: Bosker

first: Sylvain

last: DeGuise

first: Robert

last: Griffitt


title: Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [RNA-Seq]

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

summary: Early mammalian development is accompanied by a profound global remodeling of chromatin-based regulation. The Zdbf2 locus provides a valuable model to uncover the effect of dynamic chromatin transition, as it is polycomb silenced in embryonic stem cells (ESCs) and only becomes activated after Long isoform of Zdbf2 (Liz) transcription-dependent de novo DNA methylation during differentiation. Here we show that four enhancers contribute to the Liz-to-Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. CTCF plays a key role in partitioning the locus in ESCs, when Liz is active and Zdbf2 is silenced.  The partition is relieved when Zdbf2 becomes DNA methylated and active. Mutant ESCs that lack the partition fail to properly activate Zdbf2. Notably, the CTCF-based regulation occurs independently of the polycomb and DNA methylation pathways, suggesting a multi-layered regulatory framework that ensures proper epigenetic programming of a developmentally important gene.

overall_design: RNA-seq in mouse ESCs and EpiLCs in WT and mutant backgrounds

first: Maxim

middle: V

last: Greenberg

first: Aurelie

last: Teissandier


title: Microarray analysis of molecular pathways and candidate genes between dorsal and leg Skin in Chicken

status: Public on Apr 26 2019

city: Yangzhou

first: gaige

last: ji

address: no.58, Cang jie Road

institute: Jiangsu Institute of Poultry Science

summary:
The dorsal and leg skin showed significant difference in skin thickness, feather follicle density and size.These traits are important characters of slaughtered chicken appearance. Global gene expression profiling was conducted in dorsal and leg skin of chickens, using the Agilent Chicken Gene Expression Chip.
A total of 676 differentially expressed genes (DEGs) with at least 2-fold differences were identified (P < 0.05).GO analysis showed that DEGs were significantly involved in cell proliferation, differentiation, apoptotic, cell-cell adhesion and Wnt signaling pathway; KEGG pathway analyses found that DEGs were significantly mapped into ECM-receptor interaction, focal adhesion, Cell adhesion molecules (CAMs), regulation of actin cytoskeleton and Hedgehog signaling pathway.

overall_design: Four Chickens were randomly selected and killed  at 9 weeks of age (marketing age). The right dorsal and leg skin samples  were  used in this experiment.

first: Gai-ge

last: Ji

first: Jing-ting

last: Shu


title: Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [bisulfite-seq]

overall_design: Circular  chromosome conformation capture followed by sequencing (4C-seq) in mouse ESCs and EpiLCs in WT and mutant backgrounds


title: Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [4C-Seq]


title: Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming


title: Transcriptome profiling of macrophages exposed to extracellular vesicles containing miR-17 family.

city: Boston

first: Yang

last: Jin

state: MA

address: 72 E Concord St, R304

institute: Boston University Medical Campus

summary:
Purpose: The goal of this study is to generate NGS-derived transcriptome profiles (RNA-seq) from bone marrow-derived macrophages (BMDMs) exposed to extracellular vesicles (EVs) containing the miR-17 family (miR-17 and miR-93).
Methods: BMDMs were isolated from mouse bone and were exposed to lung epithelial Beas2B cell-derived EVs transfected with scrambled control RNAs, miR-17 mimics or miR-93 mimics. Whole transcriptome profiles of the exposed BMDMs (n = 4 biological replicates were pooled) were then generated using the Ion Proton™ System.
Results: A wide range of transcript expressions were regulated by the EV-containing miR-17 and/or miR-93 in BMDMs. AC118255.2, Phox2a, 1700066J24Rik, and Gm20412 were effectively downregulated by both MV-miR-17 and MV-miR-93.
Conclusions: Our study provides potential target transcripts of EV-containing miR-17/93 in macrophages.

overall_design: Examination of BMDM transcriptome profiles modulated by EV-containing miR-17 and/or -93.

first: Heedoo

last: Lee


title: Transcriptional profiling of human OCI-Ly1 DLBCL cells after siRNA-mediated silencing of FOXP1 [array]

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

institute: University of Navarra

summary: We have developed a novel immunocompetent multi-lesion mouse model of activated B cell diffuse large B-cell lymphoma (ABC-DLBCL; the pBIC mice) that recapitulates relatively fast the molecular, cellular and tumor microenvironment of aggressive human ABC-DLBCL. We demonstrate that perturbed p53 signaling cooperates with constitutive NF-kB activation in GC-experienced plasmablasts with blocked terminal differentiation to promote lymphomagenesis and tumor progression through triggering downstream intracellular molecular addictions (e.g. deregulating Foxp1 and AID pathways) and intercellular immunosuppressive signals for evading anti-tumoral responses (e.g. MHC-II antigen presentation and deregulating PD-L1/PD-1 immune checkpoint). Our immunocompetent ABC-DLBCL murine model provides in vivo evidence that PD-1 blockade cooperates with anti-CD20-based current standard-of-care therapy to reshape the immunosuppressive TME and facilitate long-term anti-tumoral responses. Therefore, our results support that immune checkpoints may hold promising therapeutic potential in ABC-DLBCL.

overall_design: Triplicate RNA samples from OCI-Ly1 DLBCL cells after FOXP1 silencing by two different siRNAs and one scramble control were profiled by NimbleGen Expression Arrays.

first: Marien

last: Pascual

last: Mena-Varas

first: Eloy

middle: F

last: Robles

first: Mari

last: Garcia Barchino

first: Carlos

last: Panizo

first: Sandra

last: Hervas-Stubbs

first: Diego

last: Alignani

first: Ainara

last: Sagardoy

first: Jose

last: Martinez-Ferrandis

first: Karen

last: Bunting

first: Stephen

last: Meier

first: Xavier

last: Sagaert

first: Davide

last: Bagnara

first: Elizabeth

last: Guruceaga Martinez

first: Oscar

last: Blanco

first: Jon

last: Celay

first: Alvaro

last: Martinez Baztan

first: Noelia

last: Casares

first: Juan

last: Lasarte

first: Thomas

last: MacCarthy

first: Ari

last: Melnick

first: Jos

middle: A

last: Martinez-Climent

first: Sergio

last: Roa


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ATAC-seq data sets)

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Remodelers define nucleosome composition, presence and position. Mammalian imitation-switch-type (ISWI) comprise one class, mostly relying on the ATPase Snf2h for activity. We show that embryonic stem cells are viable without Snf2h, enabling to study its function and contrast it to Brg1, the ATPase of SWI/SNF. Loss of Snf2h specifically affects nucleosomal positioning and increases linker lengths genome-wide providing in vivo evidence for ISWI function in ruling nucleosomal spacing. Systematic analysis of transcription factor binding reveals selective requirement on either remodeling activity. One group, containing the transcriptional repressor REST depend on BRG1, while a non-overlapping set including the insulator protein CTCF, relies on Snf2h. Importantly localized reduction in CTCF binding decreases long-range interactions. Collectively, this links mammalian ISWI to nuclear organization, demonstrates its cellular role for nucleosomal periodicity and reveals that transcription factors rely on specific remodeling pathways for proper genomic binding.

overall_design: ATAC-seq (14, 2 or 3 replicates per condition), Bis-seq (4, single replicate per condition), ChIP-seq (18 CTCF and 20 REST, 1 or 2 replicates per condition), HiC-seq (8, two replicates per condition), MNase-seq (8, 2 replicates per condition) and RNA-seq (18, 2 to 5 replicates per condition) profiling of mouse embryonic stem cells of wildtype, Snf2h ko, Snf2h ko/add-back (wildtype and mutant) and Brg1 ko genotypes.

first: Darko

last: Barisic

first: Michael

last: Stadler

first: Mario

last: Iurlaro

last: Schübeler


title: Transcriptional profiling elucidates the essential role of glycogen synthase kinase 3 to fruiting body formation in Coprinopsis cinerea

city: Hong Kong

first: Kathy

last: Chan

address: 386, South Block, Science Center, The Chinese University of Hong Kong, Sha Tin

department: School of Life Sciences

institute: The Chinese University of Hong Kong

summary: We used high-throughput RNA sequencing (RNA-Seq) to reveal the transcriptional response of C. cinerea on fruiting body formation and development with GSK3 inhibited by the addition of LiCl. The transcriptional profile revealed could elucidate the role of GSK3 activity in fruiting body development.

overall_design: Examination of control and treated samples in two time points- mycelium stage and hyphal knots stage, in triplicate, using Illumina HiSeq 2000

middle: P


title: Gene expression profile in human ovarian granulosa cells during long-term in vitro culture

status: Public on Apr 17 2019

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

institute: Poznań University of Medical Sciences

summary:
Granulosa cells (GCs) have many endocrine functions. However, in long-term in vitro culture GCs can change their properties. GCs were collected from hyper-stimulated ovarian follicles from woman during IVF procedures. They were cultured in in vitro long-term culture. RNA was collected after 1, 7, 15 and 30 days of culture. Expression microarrays were used for analysis, which allowed to identify groups of genes characteristic for particular cellular processes.
In this study, we demonstrated the gene expression profile of long time primary cultured human ovarian granulosa cells.

overall_design: Human ovarian granulosa cells were obtained from patients, aged 18-40 years, with diagnosed infertility. The cells were harvested after 24h, 7 days, 15 days and 30 days after beginning of culture and submitted to RNA isolation and microarray analysis.

first: Wiesława

last: Kranc

first: Maciej

last: Brązert

first: Piotr

last: Celichowski

first: Joanna

last: Budna-Tukan

first: Leszek

last: Pawelczyk

first: Małgorzata

last: Bruska

first: Bartosz

last: Kempisty


title: Human tumor cell lines treated with 5AZA-dC vs control untreated cells.

city: São Paulo

first: Erico

middle: T

last: Costa

address: R. Prof. Daher Cutait, 69

department: Instituto Sírio-Libanês de Ensino e Pesquisa

country: Brazil

institute: Hospital Sírio-Libanês

summary:
Equal amounts of test and reference cDNA Cy-labeled mRNA targets were competitively hybridized against a customized cDNA platform with 4,608 ORESTES (open reading frame expressed sequences tags) representing human genes.
With this microarray experiment, we found that N-Myc downstream-regulated gene 4 (NDRG4) is silenced in tumor cells and acts as a mechanistic biomarker of metastasis in ductal invasive breast tumors. While aberrant NDRG4 silencing, by DNA hypermethylation, is significantly associated with the development of metastatic disease, downregulation of NDRG4 transcription and protein expression is functionally associated with enhanced lymph node adhesion and cell mobility. Based on following functional assays, we show that silencing of NDRG4 modulates integrin signaling by assembling β1-integrins into large punctate clusters at the leading edge of tumor cells to promote an “adhesive switch,” decreasing cell adhesion to fibronectin and increasing cell adhesion and migration towards vitronectin, an important component of human lymph nodes.

overall_design:
Two condition experiments: untreated (Mock) vs 5Aza-dC treated cells (T1) (1uM, 6 days). Three tested human tumor cell lines: MCF-7 (breast cancer), MDA-MB231 (breast cancer) and MDA-MB435 (melanoma) and one cell line used as reference: non-tumor human mammary epithelial cell line HB4a. Two replicates per array.
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The author is unable to extract data from the TIFF files thus this record is incomplete.

first: D

last: Carraro

first: H

last: Brentani

first: E


title: BCL6 de-repression induces the fasting transcriptome and protects from steatosis (ChIP-Seq II)

city: Chicago

first: Grant

middle: D.

last: Barish

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary: Here, we find that the B cell lymphoma 6 (BCL6) repressor is enriched upon feeding and converges genome-wide with PPARs to opposingly control lipid metabolism.

overall_design: Identification of BCL6, PPARa, PPARd, SMRT, NCoR, HDAC3 and H3K27ac binding sites in fasted and fed livers.

first: Meredith

last: Sommars

middle: D


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors

first: Dirk

last: Schuebeler


title: Genome-wide identification of mRNA 5-methylcytosine in mammals [RIP_seq]

first: Rui

last: Zhang

summary: We report a robust experimental and computational framework to identify mRNA m5C sites with high specificity. A quantitative atlas of RNA m5C in mammals with five thousand high-confidence exonic m5C sites has been developed based on our framework.

overall_design:
RNA BS-seq of mRNA from human cell lines, multiple human and mouse tissues. Replicate of each seq is also included. m5C RIP-seq from human cell lines.
RIP_seq

first: Wanying

last: Chen

first: Tao

last: Huang

first: Jianheng

last: Liu


title: PD-1/PD-L1 immune checkpoint and p53 loss facilitate tumor progression in activated B cell diffuse large B-cell lymphomas

first: SERGIO

last: ROA

department: Biochemistry and Genetics


title: Transcriptome profiling of Plasmodium vivax in Saimiri monkeys identifies potential ligands for invasion

city: Hamilton

first: Sarah

last: Anzick

state: MT

address: 903 South 4th Street

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Unlike in Asia and Latin America, Plasmodium vivax infections were rare in Sub-Saharan Africa due to the absence of the Duffy blood group antigen (Duffy Antigen), the only known erythrocyte receptor for the P. vivax merozoite invasion ligand, Duffy Binding Protein 1 (DBP1).  However, P. vivax infections have been documented in Duffy-negative individuals throughout Africa, suggesting that P. vivax may use ligands other than DBP1 to invade Duffy-negative erythrocytes through other receptors. To identify potential P. vivax ligands, we compared parasite gene expression in Saimiri and Aotus monkey erythrocytes infected with P. vivax Salvador I (Sal I). DBP1 binds Aotus but does not bind to Saimiri erythrocytes, and thus P. vivax Sal I must invade Saimiri erythrocytes independently of DBP1. Comparing RNA sequencing (RNAseq) data for late stage infections in Saimiri and Aotus erythrocytes when invasion ligands are expressed, we identified genes that belong to tryptophan-rich antigen and MSP3 families that were more abundantly expressed in Saimiri infections as compared to Aotus infections. These genes may encode potential ligands responsible for P. vivax infections of Duffy-negative Africans.

overall_design: Differential expression analysis of Plasmodium vivax from two Aotus and two Saimiri P. vivax-infected monkeys using high throughput RNA sequencing.

first: Karthigayan

last: Gunalan

first: Juliana

middle: M

last: Sá

first: Roberto

middle: R

last: de Moraes Barros

first: Ramoncito

last: Caleon

first: J

last: Mershon

first: Kishore

last: Kanakabandi

first: Monica

last: Paneru

first: Kimmo

last: Virtaneva

first: Craig

last: Martens

first: John

last: Barnwell

first: Jose

last: Ribeiro

first: Louis

middle: H

last: Miller


title: A functional unfolded protein response is required for normal vegetative development in Arabidopsis

city: East Lansing

first: Yan

last: Bao

address: 603 Wilson Road

institute: MIchigan State University

summary: The Unfolded Protein Response (UPR) is activated in plants in response to ER stress and plays an important role in mitigating stress damage.  We have analyzed an ire1a ire1b bzip17 triple mutant in Arabidopsis with defects in stress signaling and found that the mutant is also impaired in vegetative plant growth under conditions without externally applied stress. This raises the question as to whether the UPR functions in plant development in same manner as it does in responding to stress. bZIP17 is an ER-associated membrane transcription factor that is mobilized to the nucleus in response to stress.   Through the analysis of a mobilization defective bZIP17 mutant, we found that bZIP17 must be capable of mobilization to support normal plant development.  Likewise, through the analysis of ire1 mutants, we found that protein kinase and ribonuclease activities of IRE1 must be functional to support normal development.  These findings demonstrate that the UPR is active, albeit at low levels, during unstressed conditions, and that these activities are required for normal development.

overall_design: We examined gene expression by RNA-seq in Arabidopsis wide-type and mutant 17ab

first: Diane

last: Bassham

first: Stephen

last: Howell


title: Identification of CITED2 and PU.1 target genes in human CB

city: Groningen

first: Hein

last: Schepers

state: Groningen

address: Hanzeplein 1

department: Internal Medicine

institute: University Medical Center Groningen

summary: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 12 hrs. Cells were transduced with control, CITED2 overexpression lentivectors, shRNA PU.1 lentivectors or both,  in two rounds over 48 hrs. Transduced cells were sorted after which RNA was isolated for Illumina beadchip arrays HT12 v4


title: Usefulness of serum microRNA as a predictive marker of recurrence and prognosis in biliary tract cancer after radical surgery

city: Fukui

first: Yu

last: Akazawa

address: 23-3 Eiheiji-cho

department: Faculty of Medical Sciences

country: Japan

institute: University of Fukui

summary: Our results provide compelling evidence for the potential usefulness of specific serum miRNAs as an effective predictive tool of recurrence and prognostic in BTC patients with radical surgery.

overall_design: Serum microRNA profiles of 66 samples from 22 BTC patients (recurrence group; 13, non-recurrence group; 9) who underwent radical surgery at three time points; before surgery, after surgery, recurrence or last observation period (in case of non-relapse).


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (MNase-seq data sets)

first: Dirk

last: Schuebeler

first: Darko

last: Barisic

first: Michael

last: Stadler

first: Mario

last: Iurlaro

last: Schübeler


title: Differential effects, on Oncogenic Pathway Signaling, by Derivatives of the HNF4alpha Inhibitor BI6015

city: Incheon

first: Seungyoon

last: Nam

state: Incheon

address: Namdong-gu, Namdongdae-ro 774-21

institute: Gachon University Colleage of Medicine

summary: Gastric cancer (GC) is a highly heterogeneous disease, having few “targeted” therapeutic drugs. Previously, we demonstrated involvement of HNF4α and WNT5A, as a prognostic GC biomarker. One previously discovered HNF4α antagonist, BI6015, demonstrated potent in vitro and in vivo hepatocellular cancer models. We extensively characterized the antineoplastic activity of derivatives of BI6015, including transfer of a nitro group from a para position to the ortho- and meta-positions. Biologic activity was assessed by treatment efficacy against a panel of GC cell lines, including pathway and functional analysis. The para positioned BI6105 compound was found substantially more growth-inhibitory, and effective in downregulating numerous oncogenic signal pathways, including the embryonic cascade WNT, and suggested WNT5A as a possible therapeutic biomarker. Here, we present a strategy for identifying effective transcription factor inhibitors and their impact on specific signaling pathways, which may provide prognostic and therapeutic biomarkers.

overall_design: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit. Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

first: Jin-Hee

last: Kim

first: Hyo

middle: J

last: Eom

first: GyuTae

last: Lim

first: Sungjin

last: Park

first: Jinhyuk

last: Lee

first: Yon

first: Jin-Hyun

last: Jeong


title: The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis

city: San Diego

first: Bing

last: Zhou

state: CALIFORNIA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Leaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent manner. We found that JMJ16, an Arabidopsis JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence. The histone demethylase activity and the JmjN, JmjC, and FYR domains of JMJ16, but not the zf-C5HC2 domain, are essential for JMJ16 function in the regulation of leaf senescence. Genome-wide analysis revealed a widespread coordinated up-regulation of H3K4me3 and gene expression associated with leaf senescence in the loss-of-function jmj16 mutant compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence at least partly through repressing the expression of WRKY53 and SAG201, two known positive regulators of leaf senescence. Further analyses demonstrated that JMJ16 associates with WRKY53 and SAG201, and represses precocious expression of WRKY53 and SAG201 in mature leaves by reducing H3K4me3 levels at these loci. Moreover, association of JMJ16 on WRKY53 and SAG201 loci increased at mature stage but decreased at later stage, suggesting that the age-dependent dynamic chromatin association of JMJ16 is required for precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at senescence-associated genes in an age-dependent manner.

overall_design: Examination of the difference of transcriptomes, H3K4me3 modifications and JMJ16 binding in Col and jmj16 KO Arabidopsis.

first: Peng

last: Liu

first: Shuaibin

last: Zhang

first: Xi

last: Luo

first: Xiao

first: Bin

last: Cai

first: Yin

last: Jin

first: Jinxing

last: Lin

first: Xiaofeng

last: Cao

first: Jing


title: Modulation of the ATM/autophagy pathway tips the balance between senescence and apoptosis in response to 20A ligand

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

institute: University of Bordeaux

summary: G-quadruplex ligands (G4L) exert their anti-proliferative effect through telomere-dependent and -independent mechanisms, but the inter-relationship between autophagy, cell growth arrest and cell death induced by these ligands remains largely unexplored. 20A is a 2,4,6-triarylpyridine derivative that binds to G4-DNA with fair to excellent selectivity. Here, we demonstrate that this compound impairs cancer cell viability through induction of senescence and apoptotic cell death in a p53-independent manner. In vivo results corroborate those obtained in in vitro, showing that 20A elicits an important tumor growth inhibition in HeLa-xenografted tumor model. The transcriptomic and proteomic analyses reveal the functional enrichment in the growth arrest, DDR and lysosomal pathways upon 20A treatment. More particularly, we find that ATM and autophagy are activated upon 20A treatment. Genetic inhibition of ATM following 20A treatment inhibits both autophagy and senescence and directs cells to apoptosis. Moreover, loss of autophagy by deletion of two essential autophagy genes ATG5 and ATG7 leads to failure of CHK1 activation and increased cell death triggered by 20A. Our results therefore identify ATM as a critical determinant in the balance between senescence and apoptosis and uncover autophagy as one of the key mediators of such regulation. Thus, targeting the ATM/autophagy pathway might be a promising strategy to achieve the maximal therapeutic effect of the 20A G4-ligand.

overall_design: Hela cells were treated or left treated  with the  G4 ligand 20A . At time points 6 hand 16h, total RNA were extracted for microarray experiment. Three replicates were performed at each time point of treatment and at 6h of control.

first: Jennifer

last: Beauvarlet

first: Paul

last: Sadoun

first: Elodie

first: Gaelle

last: Labrunie

first: Benoît

last: Rousseau

last: Richard

first: Rabindra

middle: N

last: Das

first: Guillaume

last: Robert

first: Jean-William

last: Dupuy

first: Francois

last: Orange

first: Sabrina

last: Croce

first: Valerie

last: Valesco

first: Pierre

last: Soubeyran

first: Kevin

last: Ryan

first: Jean-Louis

last: Mergny

first: Mojgan

last: Djavaheri-Mergny


title: In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. [RRBS]

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Developmental exposure to particulate matter air pollution is harmful to cardiovascular health, but the mechanisms by which this exposure mediates susceptibility to heart disease is poorly understood. We have previously shown, in a mouse model, that gestational exposure to diesel exhaust results in increased cardiac hypertrophy, fibrosis and susceptibility to heart failure in the adult offspring following transverse aortic constriction. In this study we have found hypomethylation of DNA in neonatal cardiomyocytes isolated from in utero DE exposed neonates. We have demonstrated that in utero exposure to diesel exhaust alters the neonatal cardiomyocyte transcriptional and epigenetic landscapes, as well as the metabolic capability of these cells. Understanding how exposure alters the developing heart through dysregulation of gene expression, metabolism and DNA methylation is vital for identifying therapeutic interventions for air pollution-related heart failure.

overall_design: Female mice were paired with male mice for timed mating in FA. After observation of a vaginal plug, pregnant mice were put into FA or DE with exposures beginning at E0.5 and lasting until E17.5, at which point pregnant mice were transferred from the Northlake facility to the UW Medicine South Lake Union SPF vivarium for neonatal sample collection or weaned and kept until 11-12 weeks for adult sample collection. Upon birth, neonatal hearts were harvested, trimmed of surrounding vascular and atrial tissue, and dissociated as previously described. Dissociation was performed using 1mg/mL Liberase TH (Roche; Pleasanton, CA, USA) in 1X HBSS by incubating hearts at 37 degrees for 5 minutes in solution, with pipetting to release cells after incubation. Media containing released neonatal carciomyocytes (NCMs) was adjusted to 20% FBS-DMEM, and cellular dissociation was continued until the majority of cells were released. Cells were then filtered using a 70um sieve, re-eluted in 20% FBS-DMEM with 20uM Ara-C and incubated at 37 degrees for 1 hour to allow fibroblasts to attach onto the plate. After incubation, media with suspended cardiomyocytes was carefully removed, spun and purified cardiomyocyte pellets were collected and frozen at -80°C.

first: Jamie

last: Goodson

middle: W

first: Theo

middle: K

last: Bammler

first: Wei-Ming

last: Chien

first: Michael

last: Chin


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Bis-seq data sets)

first: Dirk

last: Schuebeler

first: Darko

last: Barisic

last: Stadler

first: Mario

last: Iurlaro

last: Schübeler


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (RNA-seq data sets)


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (HiC-seq data sets)


title: H3K4me3 and H3K27me3 modification profiling in early zebrafish embryo

city: Beijing

first: Wei

last: Zhu

address: No.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: Multicellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and find out that patterns in gene promoter regions have been largely set to either bivalent or active states in gametes and then passed on to zygote. Bivalent states are partially maintained and active states are restored to match sperm’s pattern. But repressive H3K27me3 modifications as well as stage specific modifications in promoter regions are discarded. Prior to zygotic genome activation, patterns of genes that initialize ZGA have been converted to non-repressive states to coordinate gene expression. Histone modification in hyper methylated promoter peaks are erased independent of DNA methylome reprogramming. Comparative analysis revealed that functions of bivalent and active genes passed on from gametes are conserved in vertebrates and gene age preferences by bivalent and active histone modifications are also confirmed in vertebrates.

overall_design: H3K4me3 and H3K27me3 ChIP-seq with two replicates were performed for sperm/oocyte,2-cell, 16-cell, 128-cell and 1K-cell in zebrafish

first: Jiang

last: Liu


title: Genome-wide identification of mRNA 5-methylcytosine in mammals [human_BS]

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

overall_design:
RNA BS-seq of mRNA from human cell lines, multiple human and mouse tissues. Replicate of each seq is also included. m5C RIP-seq from human cell lines.
human_BS

first: Wanying

last: Chen

first: Tao

last: Huang

first: Jianheng


title: Expression data from human neutrophils isolated from the peripheral blood of psoriasis patients and healthy controls

city: Xi’an

first: Shuai

last: Shao

address: No. 127 of West Changle Road

department: Department of Dermatology

institute: Xijing Hospital, Fourth Military Medical University

summary: In psoriasis, neutrophils accumulate in the epidermis or scatter in the dermis, which may contribute to the inflammation by releasing a variety of cytokines, chemokines, as well as various enzymes and antimicrobe proteins (AMPs). However, the exact role of neutrophils needs to be further illustrated. To identify the differences between psoriasis neutrophils and healthy ones, we analyzed microarray expression data from 3 peripheral neutrophil samples of psoriasis patients and 3 samples of healthy controls. This study identifies that neutrophils are activated and regulated in psoriasis, and these DEGs may contribute to the development of psoriasis.

overall_design: We empolyed CD15 microbeads to isolate peripheral neutrophils of psoriasis patients and healthy controls (n = 3 for each group), and total RNA containing small RNA was extracted


title: Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [ATAC-Seq]

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

summary: Early mammalian development is accompanied by a profound global remodeling of chromatin-based regulation. The Zdbf2 locus provides a valuable model to uncover the effect of dynamic chromatin transition, as it is polycomb silenced in embryonic stem cells (ESCs) and only becomes activated after Long isoform of Zdbf2 (Liz) transcription-dependent de novo DNA methylation during differentiation. Here we show that four enhancers contribute to the Liz-to-Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. CTCF plays a key role in partitioning the locus in ESCs, when Liz is active and Zdbf2 is silenced.  The partition is relieved when Zdbf2 becomes DNA methylated and active. Mutant ESCs that lack the partition fail to properly activate Zdbf2. Notably, the CTCF-based regulation occurs independently of the polycomb and DNA methylation pathways, suggesting a multi-layered regulatory framework that ensures proper epigenetic programming of a developmentally important gene.

overall_design: Circular  chromosome conformation capture followed by sequencing (4C-seq) in mouse ESCs and EpiLCs in WT and mutant backgrounds

first: Maxim

last: Greenberg

first: Aurelie

last: Teissandier


title: Genome-wide identification of mRNA 5-methylcytosine in mammals [mouse_BS]

overall_design:
RNA BS-seq of mRNA from human cell lines, multiple human and mouse tissues. Replicate of each seq is also included. m5C RIP-seq from human cell lines.
mouse_BS


title: Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ChIP-seq data sets)

city: Basel

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: Remodelers define nucleosome composition, presence and position. Mammalian imitation-switch-type (ISWI) comprise one class, mostly relying on the ATPase Snf2h for activity. We show that embryonic stem cells are viable without Snf2h, enabling to study its function and contrast it to Brg1, the ATPase of SWI/SNF. Loss of Snf2h specifically affects nucleosomal positioning and increases linker lengths genome-wide providing in vivo evidence for ISWI function in ruling nucleosomal spacing. Systematic analysis of transcription factor binding reveals selective requirement on either remodeling activity. One group, containing the transcriptional repressor REST depend on BRG1, while a non-overlapping set including the insulator protein CTCF, relies on Snf2h. Importantly localized reduction in CTCF binding decreases long-range interactions. Collectively, this links mammalian ISWI to nuclear organization, demonstrates its cellular role for nucleosomal periodicity and reveals that transcription factors rely on specific remodeling pathways for proper genomic binding.

overall_design: ATAC-seq (14, 2 or 3 replicates per condition), Bis-seq (4, single replicate per condition), ChIP-seq (18 CTCF and 20 REST, 1 or 2 replicates per condition), HiC-seq (8, two replicates per condition), MNase-seq (8, 2 replicates per condition) and RNA-seq (18, 2 to 5 replicates per condition) profiling of mouse embryonic stem cells of wildtype, Snf2h ko, Snf2h ko/add-back (wildtype and mutant) and Brg1 ko genotypes.


title: Transcriptional response of HT-29 intestinal epithelial cells to bovine colostrum fraction and 3'-Siallylactose.

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

summary: We have employed whole genome microarray analysis to determine the transcriptional response of intestinal epithelial cells following treatment with bovine colostrum fraction and 3'-Siallylactose.

overall_design: HT-29 intestinal epithelial cells were exposed to Bovine colostrum fraction or 3'-Siallylactose for 24 hours after which the cells were harvested for RNA extraction. Three independent biological replicates were performed for each exposure.

first: Jonathan

last: Lane

first: John

last: O'Callaghan

first: Sinead

last: Morrin

first: Stephen

last: Carrington