title: miRNA expression in Anopheles gambiae tissues

city: Berlin

first: Lena

last: Lampe

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Anopheles gambiae mosquitoes transmit the human malaria parasite Plasmodium falciparum, which causes the majority of fatal malaria cases worldwide. The hematophagous life style defines the mosquito reproductive biology and is exploited by P. falciparum for its own sexual reproduction and transmission. The two main phases of the mosquito reproductive cycle, pre-vitellogenic (PV) and post-blood meal (PBM) shape its capacity to transmit malaria. Transition between these phases is tightly coordinated to ensure homeostasis between mosquito tissues and successful reproduction. One layer of control is provided by microRNAs, well-known regulators of blood meal digestion and egg development in mosquitoes. Here, we report a global overview of tissue-specific miRNA expression during the PV and PBM phases and identify miRNAs regulated during PV to PBM transition. The observed coordinated changes in the expression levels of a set of miRNAs in the energy-storing tissues suggest a role in the regulation of blood meal-induced metabolic changes.

platform_organism:
Tribolium castaneum
Bombyx mori
Aedes aegypti
Anopheles gambiae
Culex quinquefasciatus
Drosophila melanogaster
Apis mellifera

overall_design: 40 samples were analyzed.

first: Elena

last: Levashina


title: The TNF receptor super family - NF-κB axis is critical to maintain effector regulatory T cells in lymphoid and non-lymphoid tissues [RNA-seq]

status: Public on Aug 28 2017

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

type: Expression profiling by high throughput sequencing

summary: After exiting the thymus, Foxp3+ regulatory T (Treg) cells undergo further differentiation in the periphery resulting in the generation of effector (e)Treg cells, a process dependent on TCR signaling and the transcription factor IRF4. Here we show tumor necrosis factor receptor super family (TNFRSF) signaling plays a crucial role in the development and maintenance of eTreg cells. TNFRSF signaling activated the NF-κB transcription factor RelA and induced expansion and survival of eTreg cells in lymphoid and non-lymphoid tissues, including RORγt+ resident Treg cells in the small intestine. RelA regulated basic cellular processes in Treg cells, including cell survival and proliferation in response to TNFRSF signaling, but was not required for IRF4 expression or DNA binding, indicating that both pathways operate independently. Importantly, a similar pathway appeared to be active in humans, as patients with a point mutation in NF-κB1, a binding partner of RelA, had severely compromised Treg cells. Therefore, although TCR signaling is essential for eTreg cell differentiation, the TNFRSF-NF-κB axis was additionally required in a non-redundant manner to maintain the pool of eTreg cells.

overall_design: Transcriptional profiling of WT and RelA/p65-deficient Treg cells (from steady state mice).

first: Ajith

last: Vasanthakumar

first: Yang

last: Liao

first: Axel

last: Kallies


title: Cisplatin-induced gene expression changes in triple-negative breast cancer (TNBC) cells

status: Public on Aug 26 2017

city: Groningen

first: Anne Margriet

last: Heijink

state: Groningen

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

summary: Breast cancers lacking receptors for estrogen, progesterone or HER2 on their cell surface are called triple-negative breast cancers (TNBCs). TNBCs account for ~15-20% of all invasive breast cancers and do not benefit from anti-hormonal or anti-HER2 treatments. Although patients with TNBC can initially respond to chemotherapy, they do have worse overall prognosis compared to other breast cancer subtypes. Unfortunately, TNBCs lack clear targetable ‘driver’ oncogenes. Thus, there is an unmet need for strategies to improve the therapeutic options for these patients.  We used microarrays to assess differences in gene expression in triple-negative breast cancer cells in response to the platinum-based chemotherapeutic agent cisplatin. The purpose was to find drug induced changes in gene expression level that could differentiate cisplatin sensitive from cisplatin resistant TNBC cell lines.

overall_design: Four triple-negative breast cancer cell lines, MDA-MB-231, MDA-MB-157, BT549 and HCC38, were treated with 2 µM cisplatin for 0, 24 or 72 hours. Two independent replicates were collected for each cell line.

first: Anne

middle: M

first: Marcel

last: van Vugt


title: Human Adult Sorted Live Cell Erythroblasts transduced with Sigma shRNA Clone TRCN0000005418 targeting RIOK3 with puromycin selection RNAseq

city: Bethesda

first: Jeffery

middle: L.

last: Miller

state: MD

address: 10 Center Drive Room 9N311

department: NIDDK

country: USA

institute: NIH

summary: Erythroblasts cultured from mobilized CD34+ cells from healthy adult human donors were used to generate an erythroblast transcriptome transduced with Sigma shRNA Clone TRCN0000005418 targeting RIOK3 gene. Cellular maturation was maintained including enucleation.  On culture day 14 total RNA was isolated (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter). Preliminary screening data demonstrated a robust increase in fetal hemoglobin that may be due to off-target effects from this shRNA clone. A non-targeting shRNA dataset was used for control. These samples were originally published in GSE94147 and are included in this series as well.

overall_design:
Human CD34+ cells from health donor transduced with lentivirus expressing Sigma shRNA Clone TRCN0000005418 to knockdown RIOK3 gene expression in serum free culture.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.

We would like to thank Gerard Bouffard and the National Human Genome Research Institute for their expertise and assistance with RNA-seq.

middle: L

first: Y

middle: T

last: Lee

first: Colleen

last: Byrnes


title: Gene expression assessed by genome wide hybridization bead array in T84 polarized tight monolayers after challenge with celiac disease-associated bacteria [CTR 22 28 27]

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

summary: Analysis of the influence of celiac disease-associated bacteria on intestinal epithelial cells

overall_design: Stimulation with CD-associated bacteria was done from the apical side of polarized tight monolayers of T84 cells by replacing the medium in the upper chamber with 0.5 mL challenge medium containing 5x10^7 bacteria. For each stimulant three parallel wells were used to carry out the experiment and wells treated with challenge medium only served as experimental controls. The challenge was done under anaerobic condition and at 37°C for four hours. T84 tight monolayers were challenged with two isolates of Prevotella jejuni (CD3:27 and CD3:28) and Lachnoanaerobaculum umeaense.

first: Grzegorz

last: Pietz


title: Inflammatory Memory in Epidermal Stem Cells Accelerates Tissue Damage Responses

city: New York

first: Nicholas

last: Gomez

state: NY

address: 1230 York Ave

institute: Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The body’s first line of defense against environmental assaults, the skin’s barrier, is maintained by epidermal stem cells (EpdSCs). Despite EpdSC’s vulnerability to inflammatory pressures, neither their primary response nor its enduring consequences are understood. Here, we unearth a prolonged memory to acute inflammation that enables EpdSCs to hasten barrier restoration following subsequent tissue damage. This functional adaptation does not require resident skin T cells. Rather, EpdSCs maintain chromosomal accessibility at key regions activated by the primary stimulus. Upon secondary challenge, genes regulated by these domains are rapidly transcribed. Aim2, encoding an activator of the inflammasome, is at the crux of this memory as blocking the AIM2 effector Caspase-1 erases inflammation-exposed EpdSC’s recollection. The inflammatory tuning of EpdSCs has significant therapeutic implications: while enabling EpdSCs to cope with recurrent stress by  enhancing their barrier repair capabilities, it may also render them more susceptible to autoimmune and hyperproliferative disorders, including cancer.

overall_design: mRNA (RNA-seq, 16 samples) and chromasomal accessibility (ATAC-seq, 8 samples) profiles from fluorescence-activated cell sorted (FACS) EpdSCs from adult normal, imiquimod inflamed, and wounded skin.

first: Shruti

last: Naik

first: Samantha

last: Larsen

first: Elaine

last: Fuchs


title: Expression of angiogenic and inflammatory factors in CNV-derived RPE

status: Public on Aug 25 2017

city: Freiburg

first: Gottfried

last: Martin

address: Killianstr. 5

department: Klinik für Augenheilkunde

country: Germany

institute: Universitätsklinikum Freiburg

summary:
Purpose: Anti-angiogenic treatment is well established in the management of exudative AMD, but not sufficient in all patients. Characterization of factors driving this chronic disease could serve to identify additional treatment options. The purpose of this study was to assess gene expression patterns and distinct changes in cells derived from surgically extracted CNV (chorioidal neovascularization) membranes.
Materials and Methods: Expression of >11.000 genes was analyzed by means of a microarray in cells cultured from two late-stage CNV membranes, compared to primary human RPE and ARPE-19 cells. A pathway analysis was performed to identify gene expression patterns associated with exudative AMD.
Results: The analysis revealed significant alterations in gene sets associated with inflammatory processes in CNV-derived cells, involving up-regulation of pro-inflammatory factors IL6, C3, and C5 and downregulation of anti-inflammatory CFB and CFI. Factors associated with angiogenesis, such as VEGFA or ANGPT2, were not significantly regulated in the two RPE-derived cell lines.
Conclusion: In late-stage CNV membrane-derived RPE, gene expression was shifted towards a pro-inflammatory state. Angiogenesis-associated factors were regulated differently in the two CNV-derived RPE membranes.  While inflammation seems to be continuously stimulated by RPE associated with late exudative AMD, this seems not the case with regard to angioregulatory mechanisms.

overall_design: The surgical extraction of CNV membranes was a therapeutical option for patients with advanced neovascular AMD before the availability of anti-VEGF agents for intravitreal injection. Patients underwent a standard 20 gauge vitrectomy after signing informed consent. CNV membranes were removed from the subretinal space after a retinotomy. The retinotomy was secured by a laser retinopexy and gas endotamponade. The extracted CNV membranes were cultured in DMEM / Ham’s F-12 medium and characterized for RPE features, such as expression of RPE markers cytokeratine 18, vimentin, CRALBP and RPE65, as well as absence of glial fibrillary acidic protein (GFAP) or alpha smooth muscle actin (SMA). hRPE cells were obtained from ScienCell Research Laboratories (HRPEpiC, Cat. No 6540, Lot No. 0562, Carlsbad, CA, USA) at passage one. ARPE-19 is a widely used immortalized cell line obtained from ATCC (#CRL-2302).


title: Expression data after Dmrt2a brief overexpression at bud-stage zebrafish embryos

city: Lisboa

first: Rita

last: Pinto

state: Lisboa

address: Faculdade de Medicina da Universidade de Lisboa Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary:
We used the Dmrt2a inducible transgenic line Tg(hsp70:HA-dmrt2a) to do a brief dmrt2a overexpression at bud-stage in order to identify Dmrt2a immediate targets and understand its mechanism of action. Both wildtype and transgenic embryos received the same treatment.
Zebrafish embryos were collected between 2 hours and 2 hours 30 minutes after heat-shock (Dmrt2a overexpression) and were microdissected in two regions: Region 1 (contains the somites and all associated tissues) and Region 2 (contains the tailbud, Kupffer's Vesicle and all associated tissues)

overall_design: We selected 100 pieces from Region 1 and 100 pieces from Region 2. We used three biological replicates. We compared the transgenics samples with control samples within Region 1 and within Region 2, in separate. We selected genes with a fold change higer than 2 or lower than -2. We selected p-values lower than 5% and FDR lower than 5%.

first: R

middle: A

first: L

last: Saude


title: The function of morphogen Indian Hedgehog in the colon

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

institute: Academic Medical Center

summary:
The morphogen Indian Hedgehog plays a very important role during intestinal embryogenesis, but also maintains homeostasis of the adult gut. Intestinal Indian Hedgehog is expressed by the intestinal epithelium and signals in paracrine manner
to fibroblasts in the stromal compartment. Unresolved deletion of Ihh from the intestinal epithelium leads to a severe enterocolitis. We studied the short term changes in the colon upon deletion of Ihh from the epithelial layer.

overall_design: By using VillinCreERT2-IHH fl/fl mice we specifically deleted Indian Hedgehog from the intestinal epithelium (Villin is expressed by the intestinal epithelial layer). 7 days after the start of induction with tamoxifen colons were isolated.

first: B

middle: F

first: G

middle: R

last: van den Brink


title: RNA-seq analysis of melanoma and carcinoma cells expressing FOXQ1

city: Boston

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

institute: Dana-Farber Cancer Institute

summary: We report the genome wide RNA sequencing for high-throughput profiling of FOXQ1 target genes in melanoma and carcinoma cells. We generated melanoma (SK-Mel-147) and ovarian carcinoma cells (SCOV3) ectopically expressing FOXQ1. We find that FOXQ1 differentially regulates the expression of several genes in melanoma cells as compared to carcinoma cells. Specifically, FOXQ1 induces the expression of several genes in ovarian carcinoma cells SCOV3 and suppresses the expression of the same genes in melanom cells.  We show that this differentialy regulation of the same target gene depends upon the nuclear levels of beta-catenin. High levels of active nuclear beta-catenin promote FOXQ1 mediated transcriptional activation of genes whereas low levels contribute to TLE/Groucho- mediated repression. This study provides a framework for understanding the lineage specific pattern of transcriptional regulation by FOXQ1 and its contextual determinants.

overall_design: Examination of FOXQ1 target genes in 2 cell lineages

first: Mikhail

last: Nikiforov


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies I

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

institute: National Cancer Institute

summary:
Purpose:  This study uses a high-throughput glycan microarray to evaluate the immunological evolution of antibodies to the glyco-antigen GD2.  The goal is to determine germline and affinity mature antibody specificity and affinities/
Results:  Affinity mature anti-GD2 antibodies 3F8 and ch14.18 had high affinity and were highly specific for the target GD2.  Germline antibodies were also hihgly specific and had surprisingly high affinity.
Conclusion: Antibodies to GD2 evolved from highly specific germlines.  Highly specific germlines may be critical in evading autoimmunity issues.

sample_organism:
Homo sapiens
Mus musculus
unidentified

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Sus scrofa domesticus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design: Germline variable regions of 3F8 and ch14.18 were determined.  Germline and affinity mature antibody DNA were synthesized and transfected into HEK293 cell lines.  Secreted antibodies were purified from supernatant using affinity chromatography.  Antibodies were evaluated on multiple assay platforms, including glycan microarrays, protein microarrays, and cell binding assays.

first: Eric

last: Sterner

first: Megan

last: Peach

first: Marc

middle: C

last: Nicklaus

first: Jeffrey


title: Expression data from differentiated macrophages-Various conditions-PMA only stimulated, 1 min and 3 min plasma stimulated

city: Seoul

first: Nagendra

middle: Kumar

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

country: South Korea

institute: Kwangwoon University

summary:
Macrophage polarization factors to direct digit number and identity in the treated macrophages. We have characterized the macrophage-dependent regulatory genes network through a combination of whole genome RNA sequencing and transcriptional profiling in the phorbol and non-thermal plasma treated THP-1 monocytes.
In this dataset, we include the expression data obtained from differentiated macrophages (THP-1) using a very lose doses of non-thermal plasma, as well as THP-1 which were treated only with phorbol (PMA). These data are used to obtain genes that are differentially expressed in response to macrophage polarization by plasma treatments.

overall_design: 4 total samples were analyzed. We generated the following comparisons: con1 vs. cont2, 1min vs. cont2; 3min vs. cont2. Genes with a fold-change ≥2 were selected.

first: Neha


title: A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture

city: Vienna

first: Johanna

last: Gassler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute for Molecular Biotechnology

summary: Fertilization triggers assembly of higher-order chromatin structure from a nucleosomal state to generate a totipotent embryo. Chromatin loops and domains are detected in mouse zygotes by single-nucleus Hi-C (snHi-C) but not bulk Hi-C; both are absent in Drosophila embryos. We investigated whether zygotic chromatin structures are generated by cohesin-dependent loop extrusion. Using snHi-C of mouse knockout embryos, we demonstrate the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and are regulated in size by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting loop extrusion dynamics and reprogramming states. Polymer simulations based on snHi-C are consistent with a model where cohesin locally compacts chromatin and restricts inter-chromosomal interactions by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onwards.

overall_design: We generated 144 Hi-C libraries from pronuclei of zygotes of Scc1 and Wapl knockout mice and wild-type G2 zygotes (31 Scc1flox, 45 Scc1D(m)/+(p), 18 Waplflox, 18 WaplD(m)/+(p), 32 G2).

first: Hugo

middle: B

last: Brandão

first: Maxim

last: Imakaev

first: Ilya

last: Flyamer

first: Sabrina

last: Ladstätter

first: Wendy

last: Bickmore

first: Jan-Michael

last: Peters

first: Leonid

last: Mirny

first: Kikuë

last: Tachibana-Konwalski


title: Transcriptome Landscape of Mycobacterium smegmatis

status: Public on Aug 29 2017

city: Wuhan

first: Xinfeng

last: Li

address: Shi zi shan street

country: China

institute: Huazhong Agricultural University

summary: The non-pathogenic bacterium Mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Here we report the transcriptome, expression profiles and transcriptional structures through growth-phase-dependent RNA sequencing (RNA-seq) as well as other related experiments. We found: (1) 2,139 transcriptional start sites (TSSs) in the genome-wide scale, of which eight samples were randomly selected and further verified by 5'-RACE; (2) 2,233 independent monocistronic or polycistronic mRNAs in the transcriptome within the operon/sub-operon structures which are classified into five groups; (3) 47.50% (1016/2139) genes were transcribed into leaderless mRNAs, with the TSSs of 41.3% (883/2139) mRNAs overlapping with the first base of the annotated start codon. Initial amino acids of MSMEG_4921 and MSMEG_6422 proteins were identified by Edman degradation, indicating the presence of distinctive widespread leaderless features in M. smegmatis mc2155. (4) 150 genes with potentially wrong structural annotation, of which 124 proposed genes have been corrected; (5) eight highly active promoters, with their activities further determined by β-galactosidase assays. These data integrated the transcriptional landscape to genome information of model organism mc2155 and lay a solid foundation for further works in Mycobacterium.

overall_design: Mid-exponential (16 h), stationary (26 h) and mid-stationary growth phase (39 h) samples were sequenced, each with two repetitions.

first: Jin

last: He


title: Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity [mouse]

city: Osaka

first: Tomotsugu

last: Takano

address: 3-1 Yamadaoka, Suita

department: Research Institute for Microbial Diseases

country: Japan

institute: Osaka University

summary:
C-type lectin receptors (CLRs) are a large family of immunoreceptors that recognizes polysaccharides exposed on pathogens and triggers innate immune responses. However, the ligand spectrums of the whole members have not been fully understood. In this study, we found that seaweed-derived fucan activates cells expressing human Dectin-1 but not mouse Dectin-1. In fucan, low-valency β-glucan appeared to represent this activity, as the ligand activity was eliminated by the treatment of westase, a β-glucanase. Another low-valency β-glucan, laminarin, also acts as an agonist on human Dectin-1 but not for mouse Dectin-1, whereas high-valency β-glucan curdlan activated both human and mouse Dectin-1.
Reciprocal mutagenesis analysis revealed that the ligand-binding domain of human Dectin-1 did not determine its unique sensitivity to low-valency β-glucan. Rather, its intracellular domain contributes to render human Dectin-1 reactive to low-valency β-glucan. Within the hDectin-1 intracellular domain, only two amino acids, Glu2 and Pro5, were sufficient to confer sensitivity on mouse Dectin-1. Conversely, the introduction of mouse-type amino acids, Lys2 and Ser5, to human Dectin-1 reduced the reactivity. These results suggest that the intracellular domain, but not the ligand binding domain, of Dectin-1 modulate their functions which determine the ligand spectrum.

overall_design: To confirm the hDectin-1 specific phenomenon using primary cells, we stimulated human monocyte-derived dendritic cells (hMoDCs) and mouse bone marrow-derived dendritic cells (mBMDCs) with laminarin, and compare the gene expression.

first: Chihiro

last: Motozono

first: Sho

last: Yamasaki


title: Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies

first: Jeff

last: Gildersleeve


title: Gene expression assessed by genome wide hybridization bead array in intraepithelial lymphocytes (IELs) isolated from small intestinal biopsies of celiac disease  patients with active disease and clinical controls

status: Public on Aug 24 2017

first: Marie-Louise

last: Hammarström

summary: Analysis of role of small intestinal intraepithelial lymphocytes (IELs) in the immunopathology of celiac disease

overall_design: Five samples of purified IELs from duodenal mucosa of CD patients with active disease, 3  samples of purified IELs of clinical controls were individually subjected to genome-wide hybridization bead array analysis for gene expression.

first: Grzegorz

last: Pietz


title: BMS_SLE_cytotoxicity_study

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

summary: The goal of these studies is to define the molecular signatures of SLE.

overall_design: Total RNA from patients with the disease, under standard of care, were collected over the course of 18 months from a single clinical center.

first: Nataly

last: Manjarrez-Orduno


title: Microarray whole transcriptome profiling of LPS (Escherichia coli O111:B4) treated BV-2 Cells

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

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

summary: A common in vitro model for evaluating anti-inflammatory agents is use of lipopolysaccharide (LPS) , a cell wall endotoxic component from gram negative bacteria which evokes a deadly cytokine storm associated with septicemia, septic shock and multi organ failure. In this study , we investigate whole transcriptome changes occurring at 24 hours of incubation with LPS (1ug/ml) in BV2 murine microglia cells. Microarrays were acquired for mRNAs and long intergenic non-coding RNA transcripts using the GeneChip™ MOGENE 2.1ST ARRAY Arrays by Affymetrix Inc.

overall_design: BV-2 Cells treated with LPS or control

first: Aisha

last: Jemenez

first: Karam

last: Soliman


title: Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity [human]


title: ZIC2 ChIP-Seq in KSHV latent and lytic reactivated BCBL-1 cells

city: sacramento

first: Yoshihiro

last: Izumiya

address: 4645 Second Avenue

institute: UC Davis Medical Center

summary: ZIC2 is required for the maintenance of KSHV latency in human host cells. To understand the molecular action of ZIC2, we map ZIC2 binding sites across the KSHV genome in BCBL-1 cells using ChIP-Seq analysis.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Examination of ZIC2 binding in KSHV latent and lytic reactivated cells

first: Yuanzhi

last: Lyu


title: C57BL/6J WT mice liver and adipose: normal diet (ND) vs.  high-fat diet (HFD)

first: Sung-Joon

middle: Joon

last: Lee

address: 145 Anam-Ro, Rm410, East Bldg., College of Life Sci&Biotechnol. Korea University

department: Biotechnology

institute: Korea University

summary: Transcriptional profiling for screening olfactory receptor expressions in C57BL/6J mouse liver and adipose tissue under either ND and HFD

overall_design: Two-condition experiment, Liver ND vs. HFD and Adipose ND vs. HFD. RNA samples from 10 mouse livers and 10 mouse adipose tissues were pooled from both ND and HFD and single microarray experiments were performed.

first: Chunyan

last: Wu

first: Sunwoo


title: Lenalidomide-mediated erythroid improvement in non-del(5q) myelodysplastic syndromes is associated with bone marrow immuno-remodeling [Affymetrix]

city: Paris

first: Olivier

last: KOSMIDER

address: 27 Rue du faubourg Saint Jacques

country: France

institute: Institut Cochin

summary:
In the field of MDS and on bone marrow mononuclear cells , we search for a signature which predict the response to Lenalidomide treatment.
This transcriptome study appended to the GFM-LEN-EPO-2008 clinical trial reports a predictive signature of response to lenalidomide and a unique immune response signature after treatment.

overall_design: Examination of expression data before and after treatment by Len in non del(5q) MDS

first: O

first: G

last: KERDIVEL

first: V

last: CHESNAIS

first: E

last: BECHT

first: F

last: DUMONT

first: M

last: FONTENAY

first: H

last: FRIDMAN


title: The different miRNA expression between cervical cancer tissues with or without lymph-node metastasis.

city: Shanghai

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

summary: To investigate the differences in miRNA profiles specially related to lymph node metastasis in cervical cancer, six primary cervical cancer tissues derived from stage І-ІІ patients with (n=3) or without (n=3) lymph node metastasis were collected. The differential expression of seven representative miRNAs (top seven miRNAs included: miR-135-5p, miR-221-3p, miR-25-3p, miR-96-5p, miR-182-5p, miR-183-5p, and miR-144-3p) was verified using qRT-PCR in the same tissues used for microarray analysis.

overall_design: Six cervical cancer tissues derived from stage I and II patients with (n=3) or without (n=3) lymph node metastasis collected.

first: Wang

last: Wei


title: Expression data from A549 cells infected with H1N1 virus

city: Beijing

first: Keyu

last: Wang

address: Fengtai DONG DA Street NO.20

institute: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary:
Fibroblast growth factor (FGF) 2 (FGF2 or basic FGF) mediates a wide range of biological functions, such as regulating proliferation, angiogenesis, migration, differentiation and injury repair. However, the roles of FGF2 and the underlying mechanisms of action in influenza virus (IAV) -induced lung injury remain largely unexplored. In this study, we firstly report miR-194 expression is significantly decreased in A549 cells following influenza virus A/Beijing/501/2009 (BJ501) infection. MiR-194 directly targeting FGF2, a novel antiviral regulator, could suppress FGF2 expression both in mRNA and protein levels. Overexpression miR-194 facilitate IAV replication via negatively regulating type I IFN production, and reintroduction of FGF2 abrogates miR-194-induced effects on promoting IAV replication. On the contrary, inhibition of miR-194 alleviate IAV induced lung injury via promoting type I IFNs antiviral activities in vivo. Importantly, contrary to FGF2 activated RIG-I signaling pathway, miR-194 suppressed TBK1 and IRF3 phosphorylation. Taken together, our findings demonstrated that miR-194-FGF2 axis play a vital role in IAV-induced lung injury, and miR-194 antagonism might be as a potential therapeutic target during IAV infection.
Fibroblast growth factor (FGF) 2 (FGF2 or basic FGF) mediates a wide range of biological functions, such as regulating proliferation, angiogenesis, migration, differentiation and injury repair. However, the roles of FGF2 and the underlying mechanisms of action in influenza virus (IAV) -induced lung injury remain largely unexplored. In this study, we firstly report miR-194 expression is significantly decreased in A549 cells following influenza virus A/Beijing/501/2009 (BJ501) infection. MiR-194 directly targeting FGF2, a novel antiviral regulator, could suppress FGF2 expression both in mRNA and protein levels. Overexpression miR-194 facilitate IAV replication via negatively regulating type I IFN production, and reintroduction of FGF2 abrogates miR-194-induced effects on promoting IAV replication. On the contrary, inhibition of miR-194 alleviate IAV induced lung injury via promoting type I IFNs antiviral activities in vivo. Importantly, contrary to FGF2 activated RIG-I signaling pathway, miR-194 suppressed TBK1 and IRF3 phosphorylation. Taken together, our findings demonstrated that miR-194-FGF2 axis play a vital role in IAV-induced lung injury, and miR-194 antagonism might be as a potential therapeutic target during IAV infection.

overall_design: A549 cells were selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain miRNA expression at different stage of influenza H1N1 virus infection in order to increase the temporal resolution of expression profiles. To that end, we selected infected A549 at four time-points: non-infected A549, A549 of 24h post infection, A549 of 48h post infection, A549 of 72h post infection.


title: ChIP-seq analysis of BRD4 and RNAPII in K562 cells treated with DMSO or JQ1, NUP98 and NUP153 in K562 cells, and H3K27ac in mouse KH2 undifferentiated embryonic stem cells (ESCs) or differentiated embryonic bodies (EBs)

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

overall_design: ChIP-seq was performed to determine the BRD4 and RNAPII chromatin occupancy in K562 cells treated with BRD4 inhibitor (JQ1) or vehicle control (DMSO) for 2 or 6 hours, the NUP98 and NUP153 chromatin occupancy in K562 cells, and the H3K27ac mark in mouse KH2 ESCs or differentiated EBs

first: Xin

last: Liu

first: Yuannyu

last: Zhang


title: OXYGEN-LIMITED METABOLISM IN THE METHANOTROPH METHYLOMICROBIUM BURYATENSE 5GB1C

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

summary: The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon.  One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation.   We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1C .  Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1C, formate and acetate are excreted in response to redox imbalance, and the resulting metabolic state represents a combination of fermentation and respiration metabolism.

overall_design: RNA-seq analysis of gene expression of M. buryatense 5GB1 grown in continuous bioreactor culture. Several conditions were used to isolate the effects of O2 limitation on 5GB1 metabolism: O2 limitation at slow growth, O2 limitation with fast growth, CH4 limitation with fast growth, and a terminal oxidase knockout mutant. Each condition had two biological replicates, and between 1 and 4 technical replicates.

first: Alexey

last: Gilman

first: Yanfen

last: Fu

first: Melissa

last: Hendershott

first: Frances

last: Chu

first: Aaron

middle: W

last: Puri

first: Amanda

last: Smith

first: Rose

last: Lieberman

first: David

last: Beck

first: Mary

middle: E

last: Lidstrom


title: ATAC-seq analysis in K562 cells with or without HBD-1k region knockout, mouse KH2 embryonic stem cells (ESCs) and differentiated KH2 Embryoid bodies (EBs)

overall_design: ATAC-seq was performed to determine the chromatin accessibility in HBD-1kb intergenic region wildtype or knockout K562 cells, and in mouse KH2 ESCs or differentiated EBs


title: ChIP-seq analysis of dCas9 chromatin occupancy by dCas9/sgRNA-mediated CAPTURE

overall_design: ChIP-seq was performed to determine the chromatin occupancy of biotinylated dCas9 in cells expressing target-specific sgRNAs or the non-targeting sgRNA (sgGal4).


title: In situ CAPTURE of chromatin interactions by biotinylated dCas9


title: Glioblastoma stem cells infected by ZIKA virus

status: Public on Aug 23 2017

city: Cleveland

first: Zhe

last: Zhu

state: OH

address: 9500 Euclid Avenue NE3-201

department: Stem cell biology

institute: Cleveland clinic foundation

summary: We repoted the Glioblastoma stem cells(GSCs) infected by two strains of ZIKA virus, the Brazil and Dakar strains. The ZIKV was added into the medium of GSCs for 48 hours, the RNA was harvested after ZIKV infection. We found that the GSCs up-regulated the Type 1&2 interferons after infected by ZIKV

overall_design: 3 GSCs in two status(GSCs vs DGCs) were infected by ZIKV-Brazil and Dakar strains for 48 hours

first: Eric

last: Tycksen

first: Milan

middle: G

last: Chheda


title: NaMYB8 regulates distinct, optimally distributed herbivore defense traits

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identifying whether NaMYB8 regulated genes in Nicotiana attenuata

overall_design: Gene expression in leaves of Nicotiana attenuata wild type and ir-MYB8 plants was measured at 1 h and 5 h after elicitation with Manduca sexta oral secretions and control (not treated). Three biological replicates were performed with both wild type and  ir-MYB8 plants. For each replicate, leaves from two samples were pooled. In total 24 microarraies were hybridized.

first: Martin

last: Schaefer

first: Christoph

last: Bruetting

first: Shuqing


title: DNA methylation profiles in the retina of AMD patients

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

summary: Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies  have linked both common and rare variants in genes involved in regulation of the complement system to increased risk  of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of  developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part,  the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to  AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential  methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWASdefined  AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of  neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially  associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the  genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide  DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a  consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These  methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute  to AMD development and progression.

overall_design: We profiled DNA methylation profiles of 9 control eyes and 9 AMD eyes

first: Verity

last: Oliver

first: Andrew

last: Jaffe

first: Jiang

last: Qian

first: Shannath

last: Merbs


title: Developing human radiation biodosimetry models: Testing cross-species conversion approaches using an ex vivo model system

city: Tempe

first: Jia

last: Zeng

state: AZ

address: 1001 S McAllister Ave

department: The Biodesign Institute

institute: Arizona State University

summary: In the event of a large-scale radiation exposure incident, accurate and quick assessment of radiation dose would be critical for triage and medical treatment of large numbers of potentially exposed individuals. Current methods of biodosimetry, such as the dicentric chromosome assay, are time consuming and require sophisticated equipment and highly trained personnel. Therefore, scalable biodosimetry approaches, including gene expression profiles in peripheral blood cells, are being investigated.  Due to limited availability of appropriate human samples, however, biodosimetry development has relied heavily on mouse models, which are not directly applicable to human response. Therefore, to explore the feasibility of using non-human primate models to build and test a biodosimetry algorithm for use in humans, we ex vivo-irradiated peripheral blood samples from both humans and rhesus macaques to 0, 2, 5, 6, and 7 Gy, and compared the gene expression profiles 24 hours later using Agilent human microarrays. Among the dose-responsive genes in human and using non-human primate, 52 genes showed highly correlated expression patterns between the species, and were enriched in p53/DNA damage response, apoptosis, and cell cycle-related genes. When these interspecies-correlated genes were used to build biodosimetry models with using non-human primate data, the mean prediction accuracy on non-human primate samples was about 90% within 1 Gy of delivered dose in leave-one-out cross-validation. However, tests on human samples suggested that human gene expression values may need to be adjusted prior to application of the non-human primate model. A ‘multi-gene’ approach utilizing all gene values for cross-species conversion and applying the converted values on the non-human primate biodosimetry models, gave a leave-one-out cross-validation prediction accuracy for human samples highly comparable (up to 94%) to that for non-human primate. Overall, this study demonstrates that a robust NHP biodosimetry model can be built using interspecies-correlated genes, and that, by using multiple regression-based cross-species conversion of expression values, absorbed dose in human samples can be accurately predicted by the non-human primate model.

sample_organism:
Macaca mulatta
Homo sapiens

overall_design: Twenty-four (24) hours after ex vivo irradiation ranging from 0, 2, 5, 6 and 7 Gy G-rays, gene expression was measured in peripheral blood samples from 9 healthy male and 5 female Chinese rhesus macaques, as well as 10 male and 10 female human volunteers.

first: Jin

last: Park

first: Sunirmal

last: Paul

first: Natalia

last: Briones

first: Kristin

last: Gillis

first: Garrick

last: Wallstrom

first: Joshua

last: LaBaer

first: Sally

last: Amundson


title: Gene expression assessed by genome wide hybridization bead array in intestinal epithelial cells (IECs) isolated from small intestinal biopsies of celiac disease  patients with active disease and clinical controls

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

institute: Umeå universitet

summary: Analysis of role of small intestinal epithelial cells (IECs) in the immunopathology of celiac disease

overall_design: Four samples of purified IECs from duodenal mucosa of CD patients with active disease, 4 samples of purified IECs of clinical controls were individually subjected to genome-wide hybridization bead array analysis for gene expression.

first: Grzegorz

last: Pietz


title: Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression [array]

city: Stockholm

first: Johan

last: Holmberg

address: Nobels väg 3

department: Department of Cell- and Molecular Biology, Ludwig Institute for Cancer Research

institute: Karolinska Institute

type: Methylation profiling by genome tiling array

summary: Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regression to life-threatening progression. High-risk neuroblastoma patients receive myeloablative chemotherapy with hematopoietic stem-cell transplant followed by adjuvant retinoid differentiation treatment. However, the overall survival remains low; hence, there is an urgent need for alternative therapeutic approaches. One feature of high-risk neuroblastoma is the high level of DNA methylation of putative tumor suppressors. Combining the reversibility of DNA methylation with the differentiation-promoting activity of retinoic acid (RA) could provide an alternative strategy to treat high-risk neuroblastoma. Here we show that treatment with the DNAdemethylating drug 5-Aza-deoxycytidine (AZA) restores high-risk neuroblastoma sensitivity to RA. Combined systemic distribution of AZA and RA impedes tumor growth and prolongs survival. Genomewide analysis of treated tumors reveals that this combined treatment rapidly induces a HIF2α-associated hypoxia-like transcriptional response followed by an increase in neuronal gene expression and a decrease in cell-cycle gene expression. A small-molecule inhibitor of HIF2α activity diminishes the tumor response to AZA+RA treatment, indicating that the increase in HIF2α levels is a key component in tumor response to AZA+RA. The link between increased HIF2α levels and inhibited tumor growth is reflected in large neuroblastoma patient datasets. Therein, high levels of HIF2α, but not HIF1α, significantly correlate with expression of neuronal differentiation genes and better prognosis but negatively correlate with key features of high-risk tumors, such as MYCN amplification. Thus, contrary to previous studies, our findings indicate an unanticipated tumor-suppressive role for HIF2α in neuroblastoma.

overall_design: 12 samples, 3 samples per group, 4st treatment molecules; Ctrl (DMSO), Retinoic acid (RA), 5-Aza-deoxycytidine (AZA) and RA+AZA. 2x10^6 cells were injected, treatment start day 8 and tumors were collected at EP (1000m3).

first: Isabele

last: Westerlund

first: Yao

last: Shi

first: Konstantinos

last: Toskas

first: Stuart

middle: M

last: Fell

first: Shuijie

last: Li

first: Olga

last: Surova

first: Erik

last: Södersten

first: Per

last: Kogner

first: Ulrika

last: Nyman

first: Susanne

last: Schlisio


title: Peripheral blood transcriptomics following immunization with TLR-adjuvanted nanoparticle vaccine in rhesus macaques

first: Elizabeth

middle: Anne

last: Thompson

department: Department of Medicine, Solna

institute: Karolinska Institutet

summary: Transmission-blocking vaccines (TBVs) aim to disrupt malaria parasite development by targeting antigens expressed in the mosquito midgut and are considered an integral element of malaria eradication efforts. Here, we used non-human primates to demonstrate that immune responses to Pfs25, the leading TBV candidate, can be improved using unconjugated Pfs25 encapsulated in PLGA-based synthetic vaccine particles (SVP[Pfs25]) delivered subcutaneously, compared to the multimeric form, Pfs25-EPA administered intramuscularly. Pfs25-EPA given with the toll-like receptor (TLR)-based adjuvant GLA-LSQ induced robust Ab responses, but SVP[Pfs25] adjuvanted with GLA-LSQ or SVPs containing CpG or R848 increased Ab titers, Pfs25-specific plasmablasts, circulating memory B cells, and plasma cells in the bone marrow. Animals receiving R848 or CpG showed particularly strong type I IFN polarized innate activation, which correlated with increased Ab half-life. Only SVP[Pfs25] induced detectable Pfs25-specific CD4 Th1 and Tfh cells, correlating with improved Ab avidity. Collectively, multiple aspects of the responses elicited to Pfs25 indicate that the nanoparticle technology combined with TLR agonists is a promising platform for TBVs.

overall_design: Four groups of rhesus macaques (n=6/group) were immunized with nanoparticles adjuvanted with nanoparticles containing CpG or R848 or the liposomal adjuvant GLA-LSQ. Whole blood was collected prior to and 24 hours after immunization and gene expression profiles were compared to cellular activation as determined by flow cytometry and cytokine production in plasma.

first: Karin

last: Loré


title: speG affects intracellular replication, polyamine metabolism, and transcriptomes of Salmonella

status: Public on Aug 22 2017

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

summary: The speG gene has been reported to regulate polyamine metabolism in Escherichia coli and Shigella, but its role in Salmonella remains unknown. Our preliminary studies have revealed that speG widely affects the transcriptomes of infected in vitro M and Caco-2 cells and that it is required for the intracellular replication of Salmonella enterica serovar Typhimurium (S. Typhimurium) in HeLa cells. In this study, we demonstrated that speG plays a time-dependent and cell type-independent role in the intracellular replication of S. Typhimurium. Moreover, high-performance liquid chromatography of four major polyamines demonstrated putrescine, spermine, and cadaverine as the leading polyamines in S. Typhimurium. The deletion of speG significantly increased the levels of the three polyamines in intracellular S. Typhimurium, suggesting the inhibitory effect of speG on the biosynthesis of these polyamines. The deletion of speG was associated with elevated levels of these polyamines in the attenuated intracellular replication of S. Typhimurium in host cells, which was subsequently validated by the dose-dependent suppression of intracellular proliferation after the addition of the polyamines. Furthermore, our RNA transcriptome analysis of S. Typhimurium SL1344 and its speG mutant outside and inside Caco-2 cells revealed that speG regulates the genes with documented virulence in flagellar biosynthesis, fimbrial expression, and functions of types III and I secretion systems. speG also affects the expression of genes that have been rarely reported to correlate with polyamine metabolism, including those associated with the periplasmic nitrate reductase system, glucarate metabolism, the phosphotransferase system, cytochromes, and the succinate reductase complex in S. Typhimurium in the mid-log growth phase, as well as those in the ilv–leu and histidine operons of intracellular S. Typhimurium after invasion in Caco-2 cells. In the present study, we characterized the phenotypes and transcriptome effects of speG in S. Typhimurium and reviewed the relevant literature to facilitate a more comprehensive understanding of the key role of speG in the polyamine metabolism and virulence regulation of Salmonella.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: In this study, we examined whether the deletion of speG affects the intracellular proliferation of S. Typhimurium in various human cells. Subsequently, we studied the polyamine metabolism of S. Typhimurium and the effect of speG by quantifying the four major polyamines in extracellular and intracellular wild-type and speG-deleted strains. We verified whether the accumulation of polyamines suppresses the intracellular proliferation of S. Typhimurium. Moreover, we investigated how speG regulates the transcriptome of S. Typhimurium before and after invasion in human intestinal epithelium.

first: Shiuh-Bin

last: Fang

first: Ching-Jou

last: Huang

first: Chih-Hung

first: Nai-Wen

last: Chang

first: Hung-Yin

last: Pan

first: Hsu-Wei

first: Ming-Te

first: Ching-Kuo

last: Chen


title: Expression data from parental B16F0 cells and B16F0 exosomes

city: Morgantown

first: David

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression

first: Johan

last: Holmberg


title: Transcription elongation has a tissue-specific impact in alternative cleavage and polyadenylation in Drosophila melanogaster

city: Newark

first: Bin

last: Tian

state: NEW JERSEY

address: 205 South Orange Ave., CC-F1230

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

summary: Alternative cleavage and polyadenylation (APA) is a mechanism generating multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here we used 3' Region Extraction And Deep Sequencing (3'READS) to systematically map cleavage and polyadenylation sites (PAS) in Drosophila and analyzsed APA in the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate. We found that about two thirds of mRNA genes in fly undergo APA and cis element analysis indicates that fly PASs are associated with downstream UGUG elements to a lesser degree than mammalian PASs. The head tissue tends to use distal PASs compared to the body, leading to preferential expression of long 3'UTR isoforms and transcripts using distal terminal exons. Gene Ontology analysis correlates brain-specific APA events with neuronal functions, indicating their functional relevance. We also found that the distance between the proximal and distal PASs and intron locations might play important roles for brain APA. Analysis of the RpII215 C4 mutant strain, reveals that a 50% decrease in transcriptional elongation rate leads to shortened 3'UTRs in the fly body, but not in the head. This correlates with an upregulation of Ssu72 specifically in RpII215 C4 bodies, suggesting that the mechanism underlying those observations involves another layer of regulation by RNAPII termination factors. By contrast, more significant activation of intronic PASs was observed in the head compared to the body when RNAPII speed is slow. Together, our results reveal that in Drosophila RNAPII elongation impacts on PAS choice in a context-specific manner.

overall_design:
Fly samples. Fly strains were obtained from the Bloomington Stock Centre and grown at 25ºC using standard culture conditions and media. w1118 flies were used as a wild-type strain and the RpII215 flies, carrying the RNA Pol II 215 C4 allele (Chen et al. 1993), as the mutant fly strain. Heads and bodies were dissected from adult flies using standard procedures.

3'READS and PAS identification. Total RNA was extracted and purified from different strains of Drosophila using Trizol reagent (Invitrogen). The 3' region extraction and deep sequencing (3'READS) and 3'READS+ methods were previously described in (Hoque et al. 2014) and in (Zheng, 2016), respectively. Briefly, 25 ug of input total RNA from each sample was used and poly(A)+RNA was selected using oligo d(T)25 magnetic beads (NEB), followed by on-bead fragmentation using RNase III (NEB). Poly(A)+RNA fragments were then selected using the chimeric U5 and T45 (CU5T45) oligo conjugated on streptavidin beads, followed by RNase H (NEB) digestion. Eluted RNA fragments were ligated with 5' and 3' adapters, followed by reverse transcription and PCR (15x) to obtain cDNA libraries for sequencing on the Illumina platform.

first: Xiaochuan

last: Liu

first: Jaime

last: Freitas

first: Dinghai

last: Zheng

first: Mainul

last: Hoque

first: Torcato

last: Martins

first: Telmo

last: Henriques

first: Alexandra

last: Moreira


title: Myocardial gene expression in mice with cardiac-restricted knockout of COP9 signalosome subunit 8 (CSN8)

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Background: The COP9 signalosome (CSN) consisting of 8 protein subunits (CSN1 through CSN8) is a deneddylase for Cullin-RING ligases (CRLs), essential to the functioning of the ubiquitin-proteasome system.  CSN8 is encoded by the Cops8 gene. We have shown that CSN8 plays a key role in the regulation of cardiac protein quality control (PQC), and cardiomyocyte-restricted Cops8 knockout (CSN8-CKO) in perinatal and adult mice causes massive cardiomyocyte necrosis and acute heart failure in mice. Objective:  To identify the underlying mechanisms at the transcriptional level, we examined the impact of perinatal CSN8-CKO on myocardial gene expression.  Design:  Whole mouse genome DNA microarrays (CodeLink) were used to assess myocardial gene expression profiles in Control (CTL), heterozygous (Het-CKO), and homozygous (Hom-CKO) cardiac Cops8 knockout littermate mice at 2- and 3-weeks-of-age. GeneSpring GS software (v.12.5) was used to analyze differentially expressed genes (DEGs). DEGs were analyzed using the GeneGo MetaCore Analytical Suite (http://genego.com; GeneGo, St. Joseph, MI) to identify significantly enriched pathways. Network analysis was performed using R package WGCNA on the expression profiles of DEGs. IPA analysis was also performed.  Results: The microarray data revealed 521 DEGs at 3-weeks-of-age with cut-off log2 |fold change|≧1. Among these genes, 271 genes were upregulated and 250 were downregulated. Similarly, at 2-weeks-of-age, out of 78 DEG, 35 genes were upregulated and 43 were downregulated. The transcript levels of many substrate receptors of CRLs (Fbxo14, Fbxo31, Klhdc1, Klhdc7a, Klh31, Klh41) were significantly down-regulated by CSN8-CKO. Consistent with cardiac pathology and prior RNA dot blot analysis results, the microarray analysis revealed significant upregulation of fetal genes (e.g., Nppa, Nppb, Acta1) and down-regulation of many postnatal genes (Actc1, Atp2a2,  Pln, Tpm1). Our results suggest that CSN8-CKO-induced decrease in cardiac contractility could be due to decreased transcription of cacna1s, ptgfr and mylk2 genes. Pathways related to cellular stress particularly oxidative stress and vesicular trafficking were also observed to be enriched following CSN8 deficiency in cardiomyocytes. Enrichment of DEGs in chromatin remodeling pathway corroborates the involvement of CSN8 in gene expression regulation.  Conclusions: Myocardial gene expression profiles are dynamically affected by CSN8-CKO in mice. Our data strongly suggest that CSN8 is involved in the regulation of myocardial gene expression programs that regulate ubiquitination, chromatin remodeling, and vesicle trafficking in cardiomyocytes.

overall_design: The goal of this experiment was to examine myocardial differential gene expression in mice with perinatal conditional cardiac-restricted knockout of COP9 signalosome subunit 8 (CSN8). 18 total samples were analyzed; each sample comprised ventricular cardiac tissue from one animal. 9 of the samples were obtained from mice at two weeks of age and 9 from mice at three weeks of age. At each time point there were 3 control animals (Csn8flox/flox::Myh6-CreNTG), 3 homozygous Csn8 cardiac knockout animals (Csn8flox/flox::Myh6-CreTG or Hom-CKO), and 3 heterozygous Csn8 cardiac knockout animals (Csn8flox/+::Myh6-CreTG or Het-CKO).

first: Ammara

last: Abdullah

first: Travis

last: Bjordahl

first: Peng

last: Ziao

first: Erliang

last: Zeng

first: Xuejun


title: Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation [ChIP-seq]

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

summary: Over-expression of the Myc transcription factor causes its widespread interaction with regulatory domains in the genome, but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following Myc activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing and mathematical modeling. Transcriptional activation correlated with the highest increases in Myc binding at promoters. Repression followed a reciprocal scenario, with the lowest gains in Myc binding. Altogether, the relative abundance (henceforth, “share”) of Myc at promoters was the strongest predictor of transcriptional responses in diverse cell types, predominating over Myc’s association with the co-repressor Miz1. Myc activation elicited immediate loading of RNAPII at activated promoters, followed by increases in pause-release5, while repressed promoters showed opposite effects. Gains and losses in RNAPII loading were proportional to the changes in the Myc share, suggesting that repression by Myc may be largely indirect, owing - at least in part - to competition for limiting amounts of RNAPII. Secondary to the changes in RNAPII loading, the dynamics of elongation and pre-mRNA processing were also rapidly altered at Myc regulated genes, leading to the transient accumulation of partially or aberrantly processed mRNAs. Altogether, our results shed light on how over-expressed Myc alters the various phases of the RNAPII cycle and the resulting transcriptional response.

overall_design: Time course profiling of Myc binding, RNAPII binding upon Myc activation in 3T9-MycER mouse fibroblasts and Miz1 binding in non-activated 3T9-MycER mouse fibroblasts and Primary B-cells

first: Theresia

last: Kress

first: Bruno

last: Amati

first: Mattia

last: Pelizzola


title: Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation

overall_design: Time course profiling of Myc binding, RNAPII binding, 4sU-labeled and total RNA upon Myc activation in 3T9-MycER mouse fibroblasts and Miz1 binding in non-activated 3T9-MycER mouse fibroblasts and Primary B-cells


title: An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.

overall_design: 3'READS of siMtr4, siRBM7, siZCCHC8 and siControl samples in HeLa cells

first: Koichi

last: Ogami

first: Patricia

last: Richard

first: Yaqiong

last: Chen

first: James

middle: J

last: Moresco

first: John

last: Yates

middle: L

last: Manley

first: Bin

last: Tian


title: Transcriptomic profiling of MDA-MB-231 cells treated with Boswellia Serrata Extract or 3-O-Acetyl-β-boswellic acid; ER/UPR mediated programmed cell death.

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

address: 1515 MLK Blvd

institute: Florida Agricultural & Mechanical University

summary: The effects of BSE and 3-OAβBA on MDA-MB-231 cells were evaluated for effects on the whole transcriptome: including mRNAs and long intergenic non-coding RNA transcripts (lincRNA) using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc.

overall_design: 9 Samples

first: Karam

last: Soliman


title: Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

summary:
Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria.
We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements.   One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, the transcript of the cyanobacterial homolog of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658  disruption mutants. pgr5 transcript in the slr1658 retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that is most probably involved in regulating alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.

overall_design: Cultures of Dslr0242_slr1658m and Dslr0242_slr1658c were sampled 1h before (-1h) and 3, 6, and 24h after iron repletion. Samples were taken in biological replicates

first: Hagit

last: Zer

first: Ketty

last: Margulis

first: Yoram

last: Shotland

first: Gergana

last: Kostova

first: Laure

last: Sultan

first: Wolfgang

last: Hess

first: Nir

last: Keren


title: The function of the Hedgehog signaling pathway in the colon

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

address: Meibergdreef 69-71

institute: Academic Medical Center

summary: The morphogen Indian Hedgehog plays a very important role during intestinal embryogenesis, but also maintains homeostasis in the adult gut. Intestinal Hedgehog is expressed by the intestinal epithelium and signals in paracrine manner to fibroblasts in the stromal compartment. We studied the colonic changes upon activation of the Hedgehog pathway by deleting the Hedgehog receptor Patched1 in order to alleviate its repressive function.

overall_design: By using Rosa26CreERT2-Ptch1 fl/fl mice we deleted exon 8 and 9 of the Patched1 receptor in a body-wide fashion to activate the Hedgehog pathway. 12 days after the start of the induction with tamoxifen, colons were isolated.

first: B

middle: F

first: G

last: van den Brink


title: Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: VHL loss is the most common genetic alteration event in ccRCC, but its effect on epigenetic landscape has not been elucidated previously. We describe the genome-wide cis-regulatory landscapes of VHL-deficient ccRCC tumors by comparing the epigenetic changes in terms of histone modifications (H3K27ac, H3K4me1, H3K4me3)  with the transcriptomics profiles in 10 pairs of normal kidney and ccRCC tissues.

overall_design: RNA-seq profiles of 10 patient-matched normal kidney and ccRCC pairs

first: Patrick

last: Tan


title: Effects of blackcurrant extract on gene expression on TIG113.

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: To investigate new health functions by blackcurrant extract (BCE), we compare altered of the genes expression before and after BCE (1.0μg/ml) treatment in TIG113.

overall_design: TIG113 cells were seeded in culture dish and maintain to confluent. Then medium replace with phenol-red-serum-free DMEM medium with or without BCE (1.0μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.


title: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RRBS]

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

type: Methylation profiling by high throughput sequencing

summary: We demonstrate that dCas9-SunTag-DNMT3A dramatically increased CpG methylation at the HOXA5 locus in human embryonic kidney 293T cells (HEK293T). Furthermore, using a single sgRNA, dCas9-SunTag-DNMT3A was able to methylate a 4.5 kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing (RRBS) and RNA-seq showed that dCas9-SunTag-DNMT3A methylated regions of interest with minimal impact on the global DNA methylome and transcriptome.

overall_design: I)PCR amplicon deep sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples  using Illumina Nextseq sequencing system. II) Reduced representation bisulfited sequencing (RRBS) of plasmid transfected HEK 293T cells using Illumina Hiseq2000 sequencing system. III)  Whole genome bisulfite sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples. IV) RNA sequencing of dCas9-SunTag-DNMT3A treated HEK2937 samples

first: Yung-Hsin

last: Huang

first: Wei

last: Li

first: Margaret

last: Goodell


title: VHL/HIF2a axis alters transcriptomic profiles in ccRCC

summary: VHL loss is the most common genetic alteration event in ccRCC. VHL loss stabilizes hypoxia-inducible factor-2 alpha (HIF2a). We compared the changes in transcriptomics profiles after VHL restoration or HIF2a siRNA knockdown in 786-O cells.

overall_design: RNA-seq profiles of ccRCC cell line 786-O with and without wild-type VHL restoration, with non-targeting control or pooled siRNA against HIF2a


title: Mediator subunit MED23 links pigmentation and DNA repair through the transcription factor MITF (ChIP-Seq)

city: Shanghai

first: Min

last: Xia

address: 320 YueYang Road

institute: SIBCB

summary: ChIP-seq of transcriptional Pol II and histone modifications in melanoma cell line

overall_design: Pol II and H3K27 ChIP

first: Gang

last: Wang


title: CG-dinucleotide suppression enables antiviral defense targeting non-self RNA

city: New York

first: Matthew

last: Takata

state: NY

address: 1230 York Ave

institute: The Rockefeller Univeristy

summary: Vertebrate genomes exhibit marked CG-suppression, that is lower than expected numbers of 5’-CG-3’ dinucleotides1. This feature is likely due to C-to-T mutations that have accumulated over hundreds of millions of years, driven by CG-specific DNA methyl transferases and spontaneous methyl-cytosine deamination. Remarkably, many RNA viruses of vertebrates that are not substrates for DNA methyl transferases mimic the CG-suppression of their hosts2-4. This striking property of viral genomes is unexplained4-6. In a synonymous mutagenesis experiment, we found that CG-suppression is essential for HIV-1 replication. The deleterious effect of CG dinucleotides on HIV-1 replication was cumulative, evident as cytoplasmic RNA depletion, and exerted by CG dinucleotides in both translated and non-translated exonic RNA sequences. A focused siRNA screen revealed that zinc finger antiviral protein (ZAP)7 inhibited virion production by cells infected with CG-enriched HIV-1. Crucially, HIV-1 mutants containing segments whose CG-content mimicked random sequence were defective in unmanipulated cells, but replicated normally in ZAP-deficient cells. Crosslinking-immunoprecipitation-sequencing assays demonstrated that ZAP binds directly and selectively to RNA sequences containing CG dinucleotides. These findings suggest that ZAP exploits host CG-suppression to discriminate non-self RNA. The dinucleotide composition of HIV-1, and perhaps other RNA viruses, appears to have adapted to evade this host defense.

overall_design: PAR-CLIP data sets from 293T cells

first: Paul

middle: D

last: Bieniasz


title: Mediator subunit MED23 links pigmentation and DNA repair through the transcription factor MITF


title: Cooperative and Antagonistic effects on SWI/SNF occupancy following BRG1 loss [ChIP-seq]

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: We monitored changes to genomic binding of BRG1 andBRM  following BRG1 or BRM loss to understand how disuprtion of one member of the SWI/SNF complex affected remaining forms of the complex present in the cell.

overall_design: ChIP-seq was performed for BRG1 and BRM in HepG2 cells treated with non-targeting, BRG1 shRNA , or BRM shRNA


title: The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin Remodeling Complexes

status: Public on Aug 21 2017

city: San Francisco

first: Melanie

last: Ott

state: CA

address: 1650 Owens St.

institute: Gladstone Institutes

summary: BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a novel corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells and was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BAF, a SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromo- and ET domains and was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using ChIP-seq combined with ATAC-seq data, we found that the latent HIV-1 promoter phenotypically resembles endogenous LTR sequences, pointing to a select role of BRD4S:BRG1 complexes in genomic silencing of invasive retroelements.

overall_design: ChIP-seq of BRD4, BRG1, and Pol II +/- JQ1, ATAC-seq +/- JQ1, RNA-seq of selective BRD4 isoform knockdown cells in a Jurkat derived model of HIV-1 latency

first: Ryan

last: Conrad


title: p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics

city: Boston

first: Antonina

last: Hafner

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

summary: Investigation of mechanism of gene regulation in response to pulses in p53 protein level induced by gamma irradiation. To directly connect p53 pulses with gene expression, we collected time-course ChIP-Seq and RNA-Seq data.

overall_design: Time course p53, H3K27ac ChIP-Seq and RNA-Seq data in MCF7 cells treated with 10Gy gamma irradiation. As well as time course RNA-Seq data in MCF7 cells expressing p53shRNA.

first: Galit

last: Lahav


title: Reduced representation bisulfite-sequencing of human leukemia cells and mouse hematopoietic progenitors

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Human leukemia cells treated with vitamin C for 12 and 72hrs and mouse hematopoietic progenitor cells with knockdown and Tet2 restoration

overall_design: examination of 2 mouse hematopietic progenitor cell lines and 2 human leukemia cell lines

first: Luisa

last: Cimmino

first: Iannis

last: Aifantis


title: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A

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

overall_design: Refer to individual Series


title: VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell carcinoma

first: Xiaosai

last: Yao


title: VHL restoration alters cis-regulatory landscape

summary: VHL loss is the most common genetic alteration event in ccRCC. By profiling histone modifications from VHL-deficient ccRCC primary tumors and cell lines, we identifed tumor-associated promoters and enhancers. We next investigate whether VHL restoration alters tumor associated promoters and enhancers. We compared H3K27ac ChIP-seq with and without VHL restoration in 786-O cells. Restoration of wild-type VHL significantly altered a subset of tumor enhancers but affected promoters to a less extent.

overall_design: H3K27ac ChIP-Seq in ccRCC cell line, 786-O, with wild-type VHL restoration

first: Patrick

last: Tan


title: Human iPSC-derived dopaminergic neurons function in primate Parkinson’s disease models

city: Kyoto

first: Tetsuhiro

last: Kikuchi

state: Kyoto

address: 53 Kawahara-cho Shogoin Sakyo-ku

institute: Kyoto University

summary: Induced pluripotent stem cells (iPSCs) are a promising source for cell-based therapy to treat Parkinson's disease (PD), in which midbrain dopaminegic (DA) neurons progressively degenerate. However, long-term analysis of human iPSC-derived DA neurons in primate PD models has never been performed. Here we show that DA progenitor cells derived from iPSCs of both healthy individuals and PD patients survived well in the brains of PD model primates and improved animal behavior. Magnetic resonance and positron emission tomography were useful to monitor the survival and function of the DA neurons. Score-based and video-recording analyses revealed an increase in spontaneous movement of the monkeys after transplantation. Histological studies showed that the mature DA neurons extended dense neurites into the host striatum. In addition, we never observed tumor formation for two years. Thus, this preclinical study using primate models indicates that human iPSC-derived DA progenitors are clinically applicable to treat PD patients.

overall_design: 8 human iPSC-derived dopaminergic neuron progenitors, 2 undifferentiated human iPSCs, human fetal ventral mesencephalon, dorsal mesencephalon, adult whole brain and adult substantia nigra were subjected to RNA extraction and hybrdization on Affymetrix microarrays.

first: Jun

last: Takahashi


title: Shelterin Mediates Genome Reorganization in Response to Replication Stress

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome variation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart [4C-seq]

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

summary: Analysis of chromatin architecture suggests that the 3D structure of the genome plays a major role in regulating gene expression, orchestrating the compartmentalization of chromatin and facilitating specific enhancer-promoter interactions. However, the mechanisms that control this structuring of the genome are not fully understood. We have addressed this issue by analyzing the role of CTCF, a major architectural factor in chromatin structure, in the embryonic heart. Loss of CTCF triggered an overall downregulation of the cardiac developmental program, suggesting that CTCF facilitates enhancer-promoter interactions in the developing heart. Detailed analysis of the IrxA gene cluster showed that CTCF loss leads to disruption of the heart-specific regulatory domain that surrounds Irx4, resulting in changes in expression of IrxA cluster genes and neighboring genes. In contrast to the critical role proposed for CTCF in organizing large-scale chromatin domains, our results show that CTCF preferentially mediates local regulatory interactions.

overall_design: 4C-seq of E11.5 mouse embryonic hearts using Irx4 and Ndufs6 promoters and a CTCF binding site as as viewpoints. We have two conditions: control and Ctcf heart Knockout

first: Melisa

last: Gómez-Velázquez

first: Juan

last: Tena

first: Carlos

last: Torroja

first: Caludio

last: Badía


title: hMeDIP sequencing of human leukemia cells

summary: Human leukemia cells treated with vitamin C for 72hrs.

overall_design: Examination of human leukemia cell line.


title: Transcription factors enriched in tumor-associated enhancers in VHL-deficient ccRCC

summary: VHL loss is the most common genetic alteration event in ccRCC. We profiled histone modifications from VHL-deficient ccRCC primary tumors and cell lines. We show that ccRCCs exhibit a pervasive gain of enhancers around hypoxic and metabolic transcriptional targets. Motif analysis using HOMER revealed significant enrichment of AP-1, ETS, NFĸB and HIFα in tumor enhancers. We generated ChIP-seq binding data for c-Jun, ETS1, NFĸB, and P300, a histone acetyltransferase, in 786-O cells. ChIP-seq profiles of HIF2α and HIF1β in 786-O were already generated previously (GSE34871)

overall_design: Transcription factor ChIP-Seq in ccRCC cell lines


title: The gene expression profiles in BALB/3T3 cells during ECTV infection

city: Lanzhou

first: Wenyu

last: Cheng

state: Gansu

department: State Key Laboratory of Veterinary Etiological Biology

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary:
Ectromelia virus (ECTV) has emerged as a valuable model for investigating the host-orthopoxvirus relationship as it relates to pathogenesis and the immune response. We analyzed the transcriptional signatures of BALB/3T3 cells at different times after infection with Ectromelia virus. Mouse Genome 430 2.0 arrays were used to analyze global changes in gene transcripts to generate a pool of genes that was a fold change cut-off of ≥ 1.5 or ≤ 0.5 in infected samples versus non-infected samples.
Gene ontology and KEGG pathway analysis showed that the DEGs were involved mainly in immunity, apoptosis, spliceosomes, MAPK signaling and cancer-related pathways.

overall_design: 5×10^5 BALB/3T3 cells were seeded in each well of a 6-well plate and infected in triplicate with ECTV at a multiplicity of infection (MOI) of 1. Control cells were mock infected with virus-free DMEM. All infected and control cells were incubated in complete DMEM at 37 °C in 5% CO2 and harvested for total RNA extraction at 6 (BT6), 12 (BT12), 24 (BT24), 48 (BT48), and 96 (BT96) h post infection (hpi). The non-infected at 0 hour (BT0) biological condition were used as an additional control.

first: Huaijie

last: Jia

first: Xiaobing

last: He

first: Xiaoxia

last: Wang

first: Zhizhong

last: Jing


title: DNA replication-coupled histone modification maintains Polycomb gene silencing in plants

status: Public on Aug 20 2017

city: Beijing

first: Danhua

last: Jiang

address: No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology

sample_organism:
Arabidopsis thaliana
Homo sapiens

platform_organism:
Arabidopsis thaliana
Homo sapiens


title: Pneumococci in the heart subvert the host response through biofilm-mediated macrophage killing

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: For over 130 years, invasive pneumococcal disease has been associated with the presence of extracellular diplococci or short chains in affected tissues. Herein, we show that Streptococcus pneumoniae that invade the myocardium from the bloodstream replicate within cellular vesicles and transition into non-purulent biofilms. Pneumococci within cardiac microlesions exhibited salient biofilm properties including intrinsic resistance to antibiotic killing and the presence of an extracellular matrix. Dual RNA-seq data generated from heart- and blood-isolated pneumococci confirmed the biofilm phenotype in vivo and revealed stark anatomical site-specific differences in virulence gene expression; the latter having major implications on vaccine antigen selection. Genes within three genomic islands were identified as exclusively expressed in vivo. Deletion of one such island, i.e. Region of Diversity 12, resulted in a biofilm-deficient and highly inflammogenic phenotype, suggesting a link between the ability to form biofilms and a dampened host-response. We subsequently determined that biofilm pneumococci subvert cytokine/chemokine production and myocardial neutrophil infiltration by rapidly killing cardiac macrophages in a pneumolysin dependent manner. Our findings contradict the emerging notion that biofilm pneumococci are immunoquiescent and instead show that biofilm S. pneumoniae actively suppress the host response through pneumolysin-mediated immune cell killing.

sample_organism:
Mus musculus
Streptococcus pneumoniae TIGR4

overall_design: 14 mRNA profiles of Streptococcus pneumoniae samples that were grown under different conditions were generated using deep sequencing (3 planktonic, 3 biofilm, 3 infected mouse hearts, 2 infected mouse blood and 3 uninfected mouse hearts).

first: Anukul

middle: T

last: Shenoy

first: Ryan

middle: P

last: Gilley

first: Nikhil

last: Kumar

first: Whitney

last: Hinkle

first: Norberto

last: Gonzalez-Juarbe

first: Yong

first: Terry

last: Brissac

first: Sean

middle: C

last: Daugherty

first: Amol

last: Shetty

first: Sandra

last: Ott

first: Luke

last: Tallon

first: Jessy

last: Deshane

first: Hervé

last: Tettelin

last: Orihuela


title: CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart

first: Miguel

last: Manzanares


title: Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia

first: Igor

last: Dolgalev


title: Expression profiling macrophage subsets [P2538]

status: Public on Aug 19 2017

city: St. Louis

first: DAvid

last: DeNardo

state: Mo

address: 660 S. Euclid Ave

department: Medicine

institute: Washington University

summary:
Experiments expression profile several FACS-sorted pancreas tumor-associated macrophages.
Tumor-associated macrophages (TAMs) are essential components of the cancer microenvironment and play critical roles in the regulation of tumor progression. Optimal therapeutic intervention requires in-depth understanding of the sources that sustain macrophages in malignant tissues. In this study, we investigated the ontogeny of TAMs in murine pancreatic ductal adenocarcinoma (PDAC) models. We identified both inflammatory monocytes and tissue-resident macrophages as sources of TAMs. Unexpectedly, significant portions of pancreas-resident macrophages originate during embryonic development and expand through in situ proliferation during tumor progression. While monocyte-derived TAMs play more potent roles in antigen presentation, embryonically derived TAMs exhibit a pro-fibrotic transcriptional profile, indicative of their role in producing and remodeling extracellular matrix molecules. Collectively, these findings uncover the heterogeneity of TAM origin and functions, and could provide therapeutic insight for PDAC treatment.

overall_design: Macrophages were either sorted from the normal pancreas or PDAC tissues of wild-type, or KPC or FLT3-CRE/LSL-YFP mice.

first: Yu

last: Zhu

first: Brett

last: Knolhoff

first: David


title: Co-regulation of transcription by BRG1 and Brm, two mutually exclusive SWI/SNF ATPase subunits

first: Jesse

last: Raab


title: Expresion data for LNA, GLA and DGLA treated C. elegans

city: Pamplona

last: Navarro-Herrera

state: Navarra

address: C/ Irunlarrea s/n, Ed. Investigación

department: Biochemistry & Genetics

institute: University of Navarra

summary:
Bioactive compounds, including some fatty acids (FAs), can induce beneficial effects on body fat-content and metabolism. In this work, we have used C. elegans as a model to examine the effects of several FAs on body fat accumulation. Both omega-3 and omega-6 fatty acids induced a reduction of fat content in C. elegans, with linoleic, gamma-linolenic and dihomo-gamma-linolenic acids being the most effective ones. These three FAs are sequential metabolites in PUFA synthesis pathway and the effects seem to be primarily due to dihomo-gamma-linolenic acid, being independent of transformation into omega-3 or arachidonic acid. Gene expression analyses show that peroxisomal beta oxidation is the main mechanism involved in this fat-loss. All these results point out the importance of further analysis of the activity of these omega-6 FAs, due to their potential application in obesity and related diseases.
In order to elucidate the mechanisms underlying the fat loss induced by the omega-6 FAs LNA, GLA and DGLA, we analyzed the whole-transcriptome expression profiling in response to LNA, GLA and DGLA treatments in wild-type worms using Affymetrix C. elegans expression arrays.

overall_design: Age-synchronous wild-type N2 worms were exposed to 1000 µM of each FA. Three biological replicates were analyzed from C. elegans grown in each condition (3 x LNA treated C. elegans, 3 x GLA treated C. elegans, 3 x DGLA treated C. elegans and 3 x NGM reference samples of worms grown un NGM without treatment).

first: Jose

last: Vizmanos

first: Carlos

last: González-Navarro


title: Expression profiling macrophage subsets [P1991]


title: Generation and characterization of a mouse line for monitoring translation in dopaminergic neurons.

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

type:
Expression profiling by array
Other

summary: We developed a mouse line targeting midbrain dopamine neurons for Translating Ribosome Affinity Purification (TRAP).  Here, we briefly report on the basic characterization of this mouse line including confirmation of expression of the transgene in midbrain dopamine neurons and validation of its effectiveness in capturing mRNA from these cells.  We also report a translational profile of these neurons which may be of use to investigators studying the gene expression of these cells.  Finally, we have donated the line to Jackson Laboratories for distribution and use in future studies.

overall_design: Replicate pools of 5 mixed sex adult mice from the Slc6a3 JD1640 TRAP line were analyzed.


title: DNA replication-coupled histone modification maintains Polycomb gene silencing in plants [RNA-seq]

first: Danhua

last: Jiang

summary: Propagation of patterns of gene expression through the cell cycle requires prompt restoration of epigenetic marks after the twofold dilution caused by DNA replication. Here, we show that the transcriptional repressive mark histone H3K27 trimethylation (H3K27me3) is restored in replicating plant cells through DNA replication-coupled modification of histone variant H3.1. Plants evolved a mechanism for efficient K27 trimethylation on H3.1, which is essential for inheritance of the silencing memory from mother to daughter cells. We illustrate how this mechanism establishes H3K27me3 mediated silencing during the developmental transition to flowering. Our study reveals transmission of H3K27me3 in plant cells through cell divisions, enabling H3K27me3 to function as an epigenetic mark.

overall_design: Comparison of gene expression between Col and h3.1kd lines.

first: Frédéric

last: Berger


title: Expression profiling macrophage subsets [P1301]


title: Mechanistic Implications of Enhanced Editing by a HyperTRIBE RNA-binding protein

city: Waltham

first: Weijin

last: Xu

address: 415 South st.

institute: Brandeis University

summary: Most current methods to identify cell-specific RNA binding protein (RBP) targets require analyzing an extract, a strategy that is problematic with small amounts of material. We previously addressed this issue by developing TRIBE, a method that expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR. TRIBE performs Adenosine-to-Inosine editing on candidate RNA targets of the RBP. However, target identification is limited by the efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites than TRIBE, many of which are also edited by TRIBE but at a much lower editing frequency. The data have mechanistic implications for the enhanced editing activity of the HyperADARcd as part of a RBP fusion protein and also indicate that HyperTRIBE more faithfully recapitulates the known binding specificity of its RBP than TRIBE.

overall_design: E488Q mutation has been reported to increase ADAR editing efficiency. We adopted this mutation in TRIBE technique to address its false negative problem

first: Michael

last: Rosbash


title: DNA replication-coupled histone modification maintains Polycomb gene silencing in plants [ChIP-Rx]

overall_design: Comparison of H3K27me3 profiles between Col and h3.1kd lines using ChIP-Rx.


title: Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide

status: Public on Aug 18 2017

city: Ithaca

first: Ji

last: Wan

address: 303 Biotech 526 Campus Road

institute: Cornell University

summary: The goal of this study is to evaluate the competition between eIF5 and 5MP in utilizing non-AUG translation initiation sites

overall_design: Investigating the role of eIF5 and 5MP in controlling translation initiation

first: Leiming

last: Tang

first: Jacob

last: Morris

first: Chelsea

last: Moore

first: Yoshihiko

last: Fujita

first: Sarah

last: Gilaspie

first: Eric

last: Aube

first: Jagpreet

last: Nanda

first: Maud

last: Marques

first: Maika

last: Jangal

first: Abbey

last: Anderson

first: Christian

last: Cox

first: Hiroyuki

last: Hiraishi

last: Dong

first: Chingakham

middle: R

last: Singh

last: Witcher

first: Ivan

last: Topisirovic

first: Shu-Bing

last: Qian

first: Katsura

last: Asano


title: Effect of CBL0137 on gene expression in FACT positive and negative organs of mice

city: Buffalo

first: Katerina

last: Gurova

address: Elm and Carlton Str

department: Cell Stress Biology

institute: Roswell Park Cancer Institute

summary: CBL0137 is chromatin destabilizing agent, which causing trapping of FACT histone chaperone in chromatin (Gasparian et all, Science TM, 2011, Safina et all, NAR, 2017). We compared effect of CBL0137 on gene expression in mouse organs, expressing FACT (testes, spleen ) or not (lung, liver) to figure out what effects of CBL0137 is due to the inhibition of FACT and which are independent of FACT.

overall_design: NIH Swiss mice, male, 7 weeks old were treated with three doses of CBL0137, once via IV, 30, 60 and 90 mg/kg. Vehicle was 5% dextrose. Organs were collected 24 hours after treatment, n=2.


title: Effect of CBL0137 on gene expression in mouse cells and tissues

summary: We analyzed changes in abundance of RNAs in mouse embryonic fibroblasts (MEF) from wild type and p53 knockout mice and in lungs of NIH Swiss mice upon treatment with 1microM (cells) or 60mg/kg IV (mice) of curaxin CBL0137 for 24 hours. CBL0137 is chromatin destabilizing agent.

overall_design: MEF were from C57BL/6J mice (wild type) or Trp53tm1Tyj (p53-/-) mice. Mice were male NIH Swiss, 7 weeks old. CBL0137 was dissolved in DMSO for in vitro experiment and in 5% dextrose for in vivo. Control cells were untreated, control mice received IV injection of 5% dextrose. Two replicates of wild type and one replicate of p53 knockout MEFs were used. Two mice per group were used. All treatments were for 24 hours. In vitro - 1microM of CBL0137 were used, in vivo - 60mg/kg.

first: K