title: Identification of ADPKD-related Genes and Pathways in the Cells Overexpressing PKD2

city: 杭州

first: Zhe

last: Zhang

state: 浙江

address: Yuhangtang Road 866

institute: Zhe Jiang University

summary: Based on the dosage effect hypothesis, renal cysts could arise in transgenic murine models overexpressing either PKD1 or PKD2, which are causal genes responsible for autosomal dominant polycystic kidney disease (ADPKD). To prove whether PKD genes overexpression is a universal mechanism driving cystogenesis or is merely restricted to rodents, other animal models are required. Previously, we failed to observe any renal cysts in a PKD2 overexpression transgenic pig model partially due to epigenetic silencing of transgene. Thus, to explore the feasibility of pig models and identification potential affected genes/pathways related to ADPKD, LLC-PK1 cells with high PKD2 expression were generated. RNA-seq was performed and MYC, IER3, ADM were found to be commonly upregulated genes in different PKD2 overexpression cell models. MYC is a well-characterized factor contributing to cystogenesis, and ADM is a biomarker for chronic kidney disease. Thus, theses genes might be indicators of disease progression. Additionally, some ADPKD associated pathways, e.g., MAPK, were also enriched in the cells. Besides, GO analysis demonstrated proliferation, apoptosis, cell cycle regulation, which are hall marks of ADPKD were disturbed. Therefore, our experiment not only identified some biomarkers or indictors regarding ADPKD, but also demonstrated high PKD2 expression would like to drive cystogenesis in future porcine models.

overall_design:
Four different genotypes of PKD2 gene (Tg1 Tg2 Tg3 and WT (wild type)) and NC (control) with 3 replicates for each genotype and NC
Tg1 = FLAG-floxP-neo-pH11 with mutant PKD2 (c.A1532T/p.D511V-3)
Tg2 = FLAG-floxP-neo-pH11 with mutant PKD2  (c.T1967G/p.L656W-3)
Tg3 = FLAG-floxP-neo-pH11 with mutant PKD2 (c.C2224T/p.R742X-3)

first: Jin

last: He


title: Binary Fate Choice Between Closely Related Interneuronal Types is Determined by a Fezf1-Dependent Postmitotic Transcriptional Switch

status: Public on Dec 04 2019

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

country: USA

institute: University of California, Los Angeles

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Loss of tyrosine kinase receptor Ephb2 impairs proliferation and stem cell activity of spermatogonia in culture

city: New York

first: Marco

last: Seandel

state: NY

department: Surgery

institute: Weill Cornell Medical College

summary: In long-term in vitro culture, we report on gene expression in wild-type adult mouse SSCs compared to Ephb2-KO SSCs

overall_design: 6 samples, 3 wild-type replicates and 3 KO replicates

first: Thierry

last: N'Tumba-Byn


title: High RNA polymerase II occupancy on herpes simplex virus 1 late genes early in infection suggests progression to elongation is a critical switch to trigger late viral gene expression

city: Ithaca

first: Joel

middle: D

last: Baines

address: 235 Hungerfordhill Rd

institute: Cornell University

summary: We report the PRO-seq data generated from our analysis of RNA Polymerase II location along the HSV-1 genome at 3 and 6 hpi.  This data set includes analysis of the 3hr time point in cells infected in the presence of cycloheximide and the 6hr time point in cells infected in the presence of  phosphonoacetic acid, flavopiridol and acyclovir.  We have compared the data set to a cytoplasmic mRNA seq data set which is also included.  This consisted of polyadenylated, cytoplasmic RNA analyzed at 3 and 6 hpi post infection. Here we are depositing the results from this analysis providing the raw data sequence files along with our bigwig files produced when aligning it to a concatenated genome file containing the drosophila dm3 genome build, the human hg38 genome build, and the included HSV-1 (F-strain) genome with the external repeat sequences deleted.  This data provides a nucletide-resolution map of RNA Pol II location in all of the described conditions.  By comparing differences between cytoplasmic mRNA production and between Pol II occupancy patterns between samples, we have been able to discern that HSV-1 transcription is a highly regulated process, that involves mechanisms downstream of RNA Pol II recruitment to a HSV-1 promoter region.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: PRO-seq analysis in HSV-1 infected HeP2 cells at 3 hpi with and without cycloheximide, and at 3hpi with and without flavopiridol, phophonoacetic acid, and acyclovir. Cytoplasmic, mRNA transcript levels of HSV-1 gens was gathered by an mRNAseq analysis of HSV-1 polyadenylated, cytoplasmic transcript levels at 3 and 6 hpi.  These levels were then correlated back to Pol II occupancy from the PRO-seq analysis.

first: Claire

last: Birkenheuer


title: The SINEB1 Element in the Long Non-coding RNA Malat1 is Necessary for TDP-43 Proteostasis

status: Public on Dec 03 2019

city: Houston

first: Jiaofang

last: Shao

state: Texas

address: 6431 Fannin St

department: Department of Biochemistry and Molecular Biology

institute: McGovern Medical School, University of Texas Health Science Center

summary: Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely ”hijacked” by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA-protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.

overall_design: To investigate whether SINE deletion causes alterations in TDP-43 binding to Malat1 and other transcripts, we performed eCLIP-seq to capture and identify genome-wide TDP-43 binding sites on RNAs of WT, ΔSINE and ΔCER cells.

first: Tuan

middle: M

last: Nguyen

first: Wenbo

last: Li


title: Ex vivo expanded human 3D Nephrospheres engraft long term and repair chronic renal injury in mice

city: Ramat Gan

first: Tomer

last: Kalisky

address: Max and Anna Webb

department: Electrical Engineering

country: Israel

institute: Bar Ilan University

summary: End-stage renal disease is a worldwide epidemic requiring renal replacement therapy. Harvesting tissue from failing kidneys and autotransplantation of expanded committed progenitors giving rise to renal parenchyma could theoretically allow for the restoration of kidney function delaying or preventing the need for dialysis or a renal allograft. Here we utilized healthy and end-stage human adult kidneys to robustly expand proliferative kidney epithelial cells and establish 3D-kidney epithelial cultures termed nephrospheres (nSPH). Formation of nephrospheres recapitulates renal developmental programs to reestablish renal identity and revitalize renal epithelia in primary cultures. Transplantation into NOD/SCID mice show that 3D-nSPH restore self-organogenetic properties lost in adherent cultures, allowing in turn efficient engraftment and long-term survival as tubular structures and demonstrating self-organization as critical to prolonged in vivo cell survival. Moreover, long-term tubular engraftment of human nSPH proved to be functionally beneficial in murine models of chronic kidney disease. Remarkably, in vitro, nSPH inhibited pro-fibrotic collagen production in cultured fibroblasts via paracrine modulation of STAT6/IL13 while in vivo, transplanted nSPH induced transcriptional signatures of proliferation and a release from the quiescent state in host tubules potentially re-activating endogenous regeneration. These data support the use of human nSPH for autologous renal cell therapy.

overall_design: Primary human kidney epithelial cells were compared to nephrospheres derived thereof from both healthy and sick individuals, with respect to global gene expression.

first: Nissim

last: Ben-Haim


title: CERES is an eIF4E-interacting protein that forms non-canonical translation initiation complexes and modulates translation during the diel cycle in plants

city: MADRID

first: M.

middle: MAR

last: CASTELLANO

address: Crta. de la Coruña, km 7,5

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA (CBGP)

summary: Translation is a fundamental step in gene expression that regulates multiple developmental and stress responses. One key step of translation is the association between eIF4E and eIF4G. This process is regulated in different eukaryotes by proteins which bind to eIF4E and block the formation of the eIF4E/eIF4G complex. Here, we report the discovery of CERES, the first functional eIF4E regulator described in plants. CERES is a modular protein that contains a LRR domain and a canonical eIF4E binding site (4E-BS), critical for CERES interaction with eIF4E in planta. CERES/eIF4E interaction excludes eIF4G from the complex. Despite this observation, CERES promotes translation in vivo interacts with eIF4A and with eIF3 in vivo and cosediments with translation initiation complexes in sucrose gradients. Moreover, ceres mutants display a sharp increase of the 80S peak and a reduction of polysome content at specific periods of the diel cycle. Super-resolution ribosome profiling demonstrates that these mutants show a change of translation efficiency of mRNAs related to light response and glucose management. Consistently, these mutants show a hypersensitive response to glucose. These data show that CERES is a “non canonical” translation initiation factor that, through the formation of alternative translation initiation complexes, modulates translation during the light cycle in plants.

overall_design: Ribo-seq and RNA-seq of Arabidopsis Col-0 and ceres mutants. 3 replicates each.

first: R

last: Toribio

first: A

last: Muñoz

middle: B

last: Castro-Sanz

first: C

last: Merchante

first: M

last: Castellano


title: Signaling response to personalized exercise therapy in skeletal muscle from heart failure patients with reduced ejection fraction.

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

summary: In chronic heart failure (CHF), functional and metabolic alterations are detected not only in cardiac muscle but also in skeletal muscle tissue. The molecular mechanisms responsible for muscle dysfunction in patients with CHF remain unknown as well as the biological processes responsible for the positive effect of physical exercise training. In this work, using the results of transcriptome sequencing (3' mRNA-Seq), authors identify the molecular mechanisms responsible for reducing muscle dysfunctions in patients with CHF undergoing a personalized program of physical rehabilitation. 3 patients with CHF were enrolled in the study, biopsies of gastrocnemius muscle were taken before and after 12 weeks of individual training program (intensity was determined at 90% of lactate inflection point). Analysis of RNA-Seq data shows the strong upregulation of pathways that control skeletal muscle cell differentiation, muscle contraction, recovery of membrane potential.

overall_design: To understand the effect of exercise therapy on gene expression in skeletal muscle tissue of heart failure patients, we profiled the transcriptomes (using 3' mRNA-seq), of gastrocnemius muscle tissue biopsies taken from patients before and after 12 weeks of physical rehabilitation program. The individual training intensity was determined at 90% of lactate inflection point.

first: O

last: A Ivanova

last: A Sergushichev

first: T

last: A Lelyavina

first: V

last: L Galenko

first: E

last: V Ignatieva

last: Y Komarova

last: I Dmitriva


title: DNA methylation analysis validates organoids as a viable model for studying human intestinal aging (methylation)

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

summary: The epithelia of the intestine and colon turn over rapidly and are maintained by adult stem cells at the base of crypts. While the small intestine and colon have distinct, well-characterized physiological functions, it remains unclear if there are fundamental regional differences in stem cell behavior or region-dependent degenerative changes during aging. Mesenchyme-free organoids provide useful tools for investigating intestinal stem cell biology in vitro and have started to be utilized for investigating age-related changes in stem cell function. However, it is unknown whether organoids maintain hallmarks of age in the absence of an aging niche. Here we test whether stem cell enriched organoids preserve the DNA methylation-based aging profiles associated with the tissues and crypts from which they were derived. To address this, we use standard human methylation arrays and the human 'epigenetic clock' as a biomarker of age to analyze in vitro derived three-dimensional stem cell-enriched intestinal organoids.  We find that human stem cell-enriched spheroids maintain segmental differences in methylation patterns and that age, as measured by the epigenetic clock, is largely maintained in spheroids. Surprisingly, we find that small intestine spheroids exhibit striking epigenetic age reduction relative to colon spheroids.

overall_design: Bisulphite converted DNA from the 84 samples were hybridised to the Illumina Infinium Human Methylation 450K or MetylationEPIC Beadchip

first: Sophie

last: Lewis

first: Leanne

last: Jones


title: Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances

city: Konstanz

first: Marcel

last: Leist

address: Universitätsstraße 10

country: Germany

institute: University of Konstanz

summary: The first in vitro tests for developmental toxicity made use of rodent cells. Newer teratology tests, e.g. developed during the ESNATS project, use human cells and measure mechanistic endpoints (such as transcriptome changes). However, the toxicological implications of mechanistic parameters are hard to judge, without functional/morphological endpoints. To address this issue, we developed a new version of the human stem cell-based test STOP-tox(UKN). For this purpose, the capacity of the cells to self-organize to neural rosettes was assessed as functional endpoint: pluripotent stem cells were allowed to differentiate to neuroepithelial cells for six days in the presence or absence of toxicants. Then, both transcriptome changes were measured (standard STOP-tox(UKN)), and cells were allowed to form rosettes. After optimization of staining methods, an imaging algorithm for rosette quantification was implemented and used for an automated rosette formation assay (RoFA). Neural tube toxicants (like valproic acid), which are known to disturb human development at stages when rosette-forming cells are present, were used as positive controls. Established toxicants led to distinctly different tissue organization and differentiation stages. RoFA outcome and transcript changes largely correlated concerning (i) the concentration-dependence, (ii) the time-dependence, and (iii) the set of positive hits identified amongst 24 potential toxicants. Using such comparative data, a prediction model for the RoFA was developed. The comparative analysis was also used to identify gene dysregulations that are particularly predictive for disturbed rosette formation. This ‘RoFA predictor gene set’ may be used for a simplified and less costly setup of the STOP-tox(UKN) assay.

overall_design: We applied a test system (referred as the STOP-tox(UKN) or UKN1 test system) of developmental toxicity, related to the generation of neuroectoderm from human embryonic stem cells (hESCs), and exposed cells for six days to 24 different compounds (dimethyl sulfoxide, BIO, CHIR99021, lithium chloride, retinoic acid, geldanamycin, galnon, gleevec, estradiol, bisphenol A, interferon beta, cycloporin A/FK506, valproic acid, trichostatin-A, vorinostat, belinostat, panobinostat and entinostat, methylmercury, thimerosal, mercury(II)chloride, mercury(II)bromide, 4-chloromercuribenzoic acid and phenylmercuric acid). After 6 days, total RNA was isolated and gene expression studies were performed applying the human Genome U133 plus 2.0 arrays. Expression changes are always shown relative to an untreated control. At least three independent experiments have been performed.

first: Agapios

last: Sachinidis


title: The fate switch between ON and OFF SACs is determined by Fezf1

first: Yi-Rong

last: Peng

summary: The goal of this experiment was to define genes differentially expressed between E17.5 Fezf1Hete and Fezf1KO SAC cells, which were isolated by FACS from mice retinae.

overall_design: E17.5 Fezf1Hete and Fezf1KO SACs were isolated by FACS in pools of 100 cells. 13 Fezf1Hete and Fezf1KO replicates were collected from Fezf1GFP/+ and Fezf1GFP/GFP retinas, repectively. cDNA libraries were prepared with Smart-seq2 and Nextera XT (Picelli et al., 2014). Libraries were sequenced on the Illumina NextSeq with paired-end 75bp reads.

first: Joshua

middle: R

last: Sanes


title: DNA methylation analysis validates organoids as a viable model for studying human intestinal aging

type:
Expression profiling by array
Methylation profiling by array


title: ON and OFF SACs identified by scRNA-seq

summary: The goal of this experiment was to investigate the heterogeneity of SACs via scRNA-seq

overall_design: P0 ChATCre:Thy1-STP-YFP (line#15) retinas were digested with papain (Worthington, LS003126) at 37°C for 10 mins. Retinas were then dissociated and triturated into single cell suspensions. YFP labeled SACs were further isolated by FACS. Single SAC suspensions were loaded into 10X Chromium Single Cell A Chips at a concentration of ~1,000 cells/µL. Single cell libraries were prepared using the Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) as previously described (Peng et al., 2019). Libraries were sequenced on the Illumina HiSeq 2500 (Paired-end reads: Read 1, 26bp, Read 2, 98bp).


title: Altered expression and Downstream targets of uc.323

city: Guangzhou

first: Yu

last: Sun

address: 58 Zhongshan Road 2

country: China

institute: the First Affiliated Hospital of Sun Yat-Sen University

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: mRNA seq for determining differential expression of  mRNAs in the heart in cancer cachexia

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

summary: Seven week C57BL6 male mice were injected with LLC1 lung adenocarcinoma cells or vehicle.  Fourteen days later cardiac tissue was harvested for RNA isolation.

overall_design: Control or experimental male mice received vehicle or tumor cells.  Fourteen days following implantation of cells or administration of vehicle, cardiac function was assessed by echocardiography and following euthanasia ventricular tissue was  dissected for isolation of RNA.


title: The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation [RNA-seq]

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

summary: Interphase chromatin is hierarchically organized into higher-order architectures that are essential for gene functions, yet the biomolecules that regulate these 3D architectures remain poorly understood. Here, we show that scaffold attachment factor B (SAFB), a nuclear matrix (NM)-associated protein with RNA- binding functions, modulates chromatin condensa- tion and stabilizes heterochromatin foci in mouse cells. SAFB interacts via its R/G-rich region with heterochromatin-associated repeat transcripts such as major satellite RNAs, which promote the phase separation driven by SAFB. Depletion of SAFB leads to changes in 3D genome organization, including an increase in interchromosomal interactions adjacent to pericentromeric heterochromatin and a decrease in genomic compartmentalization, which could result from the decondensation of pericentromeric heterochromatin. Collectively, we reveal the integrated roles of NM-associated proteins and repeat RNAs in the 3D organization of heterochromatin, which may shed light on the molecular mechanisms of nuclear architecture organization.

overall_design: RNAseq data in Ctrl and Safb KD AML12 cells.


title: Transcriptomic analysis of Glioblastoma Multiform (GBM) neurospheres treated with BMI1 inhibitors.

status: Public on Dec 02 2019

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Boul. l’Assomption

country: Canada

institute: Hopital Maisonneuve-Rosemont

summary: This study is designed to decipher the early transcriptomic events upon BMI1 inhibition in the GBM.

overall_design: GBM cell lines derived from patients were treated 24h with two BMI1 inhibitors called PTC596 and A1016. DMSO was ued as control. Alternatively BMI1 was knocked out by CRISPR/Cas9 in the same GBM cell line.

first: Anthony

last: Flamier


title: Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

city: Bethesda

first: Assaf

last: Magen

state: MD

address: 37 Convent Dr

institute: NIH

summary: We used single-cell mRNA sequencing to analyze the response of tumor-specific CD4+ tumor infiltrating lymphocytes (TILs) and draining lymph node (dLN) T cells. Computational approaches to characterize subpopulations identified TIL transcriptomic patterns strikingly distinct from acute and chronic anti-viral responses and dominated by diversity among T-bet-expressing T helper type 1 (Th1)-like cells. In contrast, the dLN response includes T follicular helper (Tfh) cells but lacks Th1 cells. We identify a type I interferon-driven signature in Th1-like TILs and show that it is found in human cancers, in which it is negatively associated with response to checkpoint therapy.

overall_design: Single-cell RNA sequencing of CD4+ T cells specific for a defined recombinant tumor antigen, sorted from the tumor microenvironment and draining lymph nodes.

first: Jia

last: Nie

first: Rémy

last: Bosselut


title: Transcriptome splicing analysis in K562 cells expressing rare and private spliceosomal mutations

city: Seattle

first: Robert

last: Bradley

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch

summary: Genes encoding RNA splicing factors are frequently mutated in clonal hematopoesis and diverse cancers. Most spliceosomal mutations affect specific hotspot residues, causing changes in exon and splice site recognition that promote disease. However, a subset of patients carry splicesomal mutations in non-hotspot residues, and their contribution to disease are unknown. Here we systematically characterized the function of several rare and private spliceosomal mutations in order to determine their potential disease relevance. We discovered that several rare and private spliceosomal mutations phenocopy the mechanistic splicing alterations induced by their "hotspot" counterparts. Our data suggest that many rare and private spliceosomal mutations contribute to disease pathogenesis.

overall_design: RNA-seq of K562 cells that were stably transduced with a lentiviral vector expressing several mutants of SRSF2 and U2AF1

first: Joseph

last: Pangallo

first: Jean-Jacques

last: Kiladjian

first: Bruno

last: Cassinat

first: Aline

last: Renneville

first: Justin

last: Taylor

first: Jacob

middle: T

last: Polaski

first: Khrystyna

last: North

first: Omar

last: Abdel-Wahab

middle: K


title: New insights into the molecular basis of induced resistance triggered by potassium phosphite in potato

city: Mar del Plata

first: Mariana

middle: Laura

last: Feldman

state: Buenos Aires

address: Funes 3250 4to nivel

country: Argentina

institute: IIB-CONICET- Univ. Nac. de Mar del Plata

summary: The aim of the present work was to gain insight into the mechanisms of action of potassium phosphite. To achive this, we performed microarray analysis to determine changes in gene expression of potato leaves treated with potassium phosphite for  72 hs and the abundance of KPhi primed genes after Phythophtora infestans infection. We have also analyzed in silico their promoters for common cis elements involved in their regulation.

overall_design: Total RNA was extracted from potato leaves treated for 72 hs with Kphi, pre-treated with Kphi and challenged to Pinfestans, directly infected with P. infestans or treated with water.

middle: L

first: María

middle: C

last: Guzzo

first: Milagros

middle: F

last: Machinandiarena

last: Rey-Burusco

middle: V

last: Beligni

first: Julio

last: Di Rienzo

first: Martín

middle: A

last: Castellote

first: Gustavo

last: Daleo

first: Adriana

last: Andreu


title: Global transcriptomic investigation of the human macrophage response towards pathogenic/non-pathogenic mycobacteria

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

summary: We present an infection study with pathogenic and non-pathogenic mycobacterial strains that have vastly different characteristics. The early/late host response to infection with these detergent-free cultured strains will be analysed through Ampliseq and further validated through qPCR in an attempt to provide information on the subtleties which may ultimately contribute to the virulent phenotype. Proceeding to the next objective of the study is to knock-down (siRNA)/knock-up (saRNA) selected differentially expressed mRNA to study their role in the intracellular survival of M. tuberculosis

overall_design: PBMC isolated from human blood, infected with either pathogenic (R179) or non-pathogenic (M. bovis BCG or M. Smegmatis). Total RNA extracted and subjected to Ion AmpliSeq to detect differentially expressed genes. DE genes detected was validated using qPCR

first: Bienyameen

last: Baker


title: The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [HiChIP]

status: Public on Dec 01 2019

first: Luzhang

last: Ji

summary: Eukaryotic chromosomes fold into topologically associating domains (TADs), which further gather in active (A) or inactive (B) genomic compartments. Here we show that Scaffold Attachment Factor B (SAFB), a nuclear matrix-associated protein with RNA binding functions, modulates global chromatin condensation in a dosage-dependent manner. Upon the depletion of SAFB, the genome coverage of Lamina-associated-domains (LADs) decreases from 53.33% to 45.93%, and both inter- and intra-TAD chromatin-chromatin interactions in compartment B decrease significantly. In the nucleus, SAFB favorably co-localizes with H3K9me3, a marker of heterochromatin, and the disruption of SAFB leads to a collapse of H3K9me3 foci. Furthermore, we show that SAFB proteins can form liquid-liquid phase separation in the cell and in vitro. Intriguingly, SAFB interacts with RNAs from repetitive elements enriched in heterochromatin (e.g., Major Satellites and LINE1), which can promote SAFB-mediated phase separation, depending on the density of SAFB recognizing motifs in the RNAs.

overall_design: H3K9me3 HiChIP data in Ctrl and Safb KD AML12 cells.


title: Genome-wide maps of nuclear lamina interactions in AML12 cells upon Safb KD [DamID]

type: Genome variation profiling by genome tiling array

overall_design: LAMINB1 DamID data in Ctrl and Safb KD AML12 cells.


title: The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [RIP-seq]

overall_design: Identification and characterization of RNAs associated with SAFB in AML12 cells


title: The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [Hi-C]

overall_design: Hi-C data in Ctrl and Safb KD AML12 cells.


title: The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [H3K9me3 ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K9me3 ChIP-seq data in Ctrl and Safb KD AML12 cells.


title: P120-catenin dependent glioma-cell networks drive growth and diffuse brain infiltration

city: Nijmegen

first: Nader

last: Atlasy

state: Gerderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: The poor prognosis of diffuse gliomas is the consequence of adaptive growth and survival programs coupled to their unsurmountable capacity to infiltrate the brain. Diffuse brain infiltration is a particularly detrimental hallmark of gliomas, however the underlying cellular and signaling mechanisms remain elusive. Histological analysis of glioma samples suggests brain invasion by individual glioma cells extending along blood vessels and nerve tracts, consistent with individual-cell growth and invasion programs. However, using thick 3D tissue sections, we here show that human diffuse gliomas consist of multicellular networks in both tumor center and invasion region. This was confirmed in three orthotopic human glioma xenograft models in mouse brain reflecting neuronal, proneural and mesenchymal subtypes. The connections between glioma cells are provided by either branched filamentous protrusions connecting cells across distance or epithelial-like linear adherens junctions between directly adjacent cells. These intercellular contacts showed dynamic turn-over kinetics, which enabled intercellularly synchronized calcium signaling waves, directionally persistent migration as network and network plasticity. Interference with the stability of adherens junction by downregulating p120-catenin causes irreversibly compromised cell-cell interaction, near-complete inhibition of diffuse brain infiltration and a severe growth defect and marginalized microlesions as outcome. Mining of human glioma cohorts revealed an inverse association of p120 with patient survival and, using next-generation RNA sequencing, profound cell reprogramming with perturbed cell adhesion and axonal guidance pathways was uncovered after p120 downregulation. In conclusion, reminiscent of neuronal and glial progenitor programs during morphogenesis and repair, diffuse gliomas progress as neuronal-like, collective network the subunits of which cooperate by complex cell-cell signaling to promote cell growth and detrimental brain infiltration. Targeting adherens junctions and cell-cell cooperation thus represent unanticipated therapeutic principles to prevent glioma progression.

overall_design: Transcriptome RNAseq profile of 6 samples of glioma cell lines of p120-kd and NT-shRNA samples, two replicates for each

first: Pavlo

last: Gritsenko

first: Cindy

last: Dieteren

first: Anna

last: Navis

first: Jan-Hendrik

last: Venhuizen

first: Cornelia

last: Veelken

first: Dirk

last: Schubert

first: Amparo

last: Acker-Palmer

first: Bart

last: Westerman

first: Thomas

last: Wurdinger

first: William

last: Leenders

first: Pieter

last: Wesseling

first: Hendrik

last: Stunnenberg

first: Peter

last: Friedl


title: Estrous cycle impacts microRNA content in extracellular vesicles that modulate bovine cumulus cell transcripts during in vitro maturation

city: Pirassununga

first: Juliano

middle: Coelho

last: da Silveira

state: São Paulo

address: Duque de Caxias Norte 235

department: Veterinary Medicine

country: Brazil

institute: University of São Paulo

summary:
Purpose: Extracellular vesicles (EVs) are nanoparticles that can be secreted by different cells, including cells found within the ovarian follicle. Currently, EVs are considered an important form of intercellular communication, since they carry biological contents. The goal of this study was to survey the effects of small EVs from follicles at different estrous cycle stage in bovine cumulus cells.

Methods: We used an established model to obtain follicular fluid (FF) at early and late estrous cycle stage according to corpus luteum appearance, corresponding to low and high progesterone (P4) levels, respectively. We collected FF from 3-6 mm follicles and isolated small EVs, which were used as a supplement during in vitro maturation (IVM). Cumulus cells were collected from cumulus-oocyte complexes (COCs) pools and the RNAs were obtained and subjected to RNA sequencing.

Results: The results showed that small EVs from different estrous cycle stage are capable to affect transcripts in cumulus cells and modulate different pathways and biological processes related to oocyte maturation, ovulation and immune response.

Conclusion: This study demonstrated that small EVs from low and high P4 group impact the RNA profile in cumulus cells after 9 hours of in vitro maturation.

overall_design: Cumulus-oocyte complexes (COCs; n=20) were maintained in maturation media without small EVs (EVs free FCS) or with small EVs from low or high P4 follicles for 9 hours. Six replicates of IVM were performed. Cumulus cells from 2 replicates were pooled to form 3 pools of which supplementation group, which were used for RNA sequencing.

first: Ana

last: de Ávila

first: Ricardo

middle: P

last: Nociti


title: Growth rate of mammary cancers arising in irradiated mice is associated with pattern of immune infiltrate

city: San Francisco

first: Jade

last: Moore

state: California

address: 2340 Sutter St, S371

institute: University of California San Francisco

summary: To determine how host irradiation affects tumor profiles in 10 month aged mice treated with HZE or gamma irradiation.

overall_design: Total RNA was extracted from mammary tumors derived from transplantations of non-irradiated p53 null mammary fragments into irradiated hosts. We analyzed 43 tumors from 10-month aged whole body  irradiated hosts with (1) sham n = 10, 50, 100 cGy γ-ray sparsely ionizing radiation (SIR) n = 15, or at equivalent fluences of 350 Mev/amu Ar, 350 Mev/amu Si or 600 Mev Fe densely ionzing radiation (DIR) n = 19

first: Lin

last: Ma

first: Coral

last: Omene

last: Mims

first: Haoxu

last: Ouyang

first: Irineu

last: Illa-Bochaca

last: Chou

first: Manan

last: Patel

first: Christopher

last: Sebastiano

first: Sandra

last: Demaria

first: Jian-Hua

last: Mao

first: Kubra

last: Karagoz

first: Michael

last: Gatza

first: Mary

middle: H

last: Barcellos


title: RNA seq of tumors derived from irradiated versus sham hosts transplanted with Trp53 null mammary tissue and fed either Control diet versus Caffeic Acid Phenethyl Ester (CAPE) diet.

summary: Irradiated hosts gave rise to significantly more Trp53 null mammary cancers that grew more rapidly than those in sham-irradiated mice and exhibited an immunosuppressive tumor microenvironment . CAPE prevented the effect of host irradiation on tumor growth rate, immune signature and immunosuppression.

overall_design:
10 week-old BALB/c mice were transplanted with Trp53 null mammary tissue 3 days after exposure to low doses of ionizing g-radiation radiation.  Over the next 600 days, tumors were collected. In order to test the hypothesis that host irradiation promotes chronic inflammation, radiation-genetic chimera mice were fed chow containing a honeybee-derived compound with anti-inflammatory and immunomodulatory properties, caffeic acid phenethyl ester (CAPE).
RNA sequencing was done on ER negative tumors usingTruSeq RNA Sample Preparation Guide Protocol by Illumina® (#15008136 A). Raw sequencing data were received in FASTQ format.  Read mapping was performed using Tophat 2.0.9 against the mm10 human reference genome.  The resulting BAM alignment files were processed using the HTSeq 0.6.1 python framework and respective mm10 GTF gene annotation, obtained from the University of California, Santa Cruz (UCSC) database.  Subsequently, the Bioconductor package DESeq2(3.2) was used to identify differentially expressed genes (DEG).

first: William

last: Barcellos-Hoff


title: Cistrome-partitioning reveals convergence of somatic mutations and risk-variants on  master transcription regulators in primary prostate tumors

city: AMSTERDAM

first: Yanyun

last: Zhu

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

summary: Thousands of noncoding somatic Single Nucleotide Variants (SNVs) of unknown  function are reported in tumors. Partitioning the genome according to cistromes,  reveals the enrichment of somatic SNVs in prostate tumors as opposed to adjacent  normal tissue cistromes of master transcription regulators, including AR, FOXA1 and  HOXB13. This parallels enrichment of prostate cancer genetic predispositions over  these transcription regulators’ tumor cistromes, exemplified at the 8q24 locus harboring  both risk-variants and somatic SNVs in cis-regulatory elements, upregulating MYC  expression and altering the binding of transcription regulators to DNA. However, Massively-Parallel Reporter Assays reveal that few SNVs can alter the transactivation  potential of individual CREs. Instead, SNVs accumulate, similarly to inherited riskvariants,  in cistromes of master transcription regulators required for prostate cancer  development.  Significance  Difficulties in inferring the biological significance of noncoding mutations have limited  their inclusion in precision genomics medicine pipelines. Most attempts to delineate a  role for noncoding mutations relied on detecting evidence for positive selection within  individual CREs, such as reported for the TERT gene promoter. By considering the  enrichment of noncoding mutations in cistromes as opposed to individual CREs, we  reveal their specificity towards master transcription regulators that promote prostate  cancer development, a feature shared with inherited risk-variants. Overall, our work  provides a blueprint for the functional interpretation of noncoding mutations in genomic  tests relying on defining cis-regulatory units according to cistrome-partitioning to  identify cancer driver transcription regulators.

overall_design:
AR, HOXB13 and FOXA1 ChIP-seq data for prostatectomy specimens

The raw data cannot be stored with GEO due to patient privacy and will be uploaded to the European Genome/Phenome Archive

first: Wilbert

last: Zwart

first: Tesa

last: Severson


title: Gut microbiota from old mice confers neurogenic and pro-longevity signatures in young germ-free mice

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

country: Singapore

institute: DUKE-NUS Graduate Medical School

summary:
Transplantation of differential microbiota in young germ-free donors show distinct metabolic signatures.
We used microarrays to understand pathway level changes in the livers and small intestines of differential-microbiota conventionalized young recipeint mice.

overall_design: Microbiota from ~24-month-old or 5- to 6-week-old mice were transplanted into 5- to 6-week-old germ-free recipient mice, which were then housed in a controlled environment for 8 weeks. The livers and small intestines of the recipient mice were used for microarray analysis.

first: Parag

last: Kundu

first: Sven

last: Pattersson

first: Sujoy

last: Ghosh


title: The MAPK14/MAPK7/BCL6B pathway creates a positive feedback loop to drive spermatogonial stem cell (SSC) self-renewal via ROS amplification.

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

summary: Reactive oxygen species (ROS) play critical roles in self-renewal division for various stem cell types. However, it remains unclear how ROS signals are integrated with self-renewal machinery. Here we report that the MAPK14/MAPK7/BCL6B pathway creates a positive feedback loop to drive spermatogonial stem cell (SSC) self-renewal via ROS amplification. The activation of MAPK14 induced MAPK7 phosphorylation in cultured SSCs, and targeted deletion of Mapk14 or Mapk7 resulted in significant SSC deficiency after spermatogonial transplantation. The activation of this signaling pathway not only induced Nox1 but also increased ROS levels. Chemical screening of MAPK7 targets revealed many ROS-dependent spermatogonial transcription factors, of which BCL6B was found to initiate ROS production by increasing Nox1 expression via ETV5-induced nuclear translocation. Because hydrogen peroxide or Nox1 transfection also induced BCL6B nuclear translocation, our results suggest that BCL6B initiates and amplifies ROS signals to activate ROS-dependent spermatogonial transcription factors by forming a positive feedback loop.

overall_design: mRNA profiles of wild type, Nox1-/-, Mapk7f/f, Mapk7-/-, Bcl6b-/-, Mapk14f/f and Mapk14-/- were generated by deep sequencing, in duplicate, using Illumina NextSeq 500.

first: Hiroko

last: Morimoto

first: Takuya

last: Yamamoto


title: Characterization of the European sea bass (Dicentrarchus labrax) gonadal transcriptome during different stages of development

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

institute: Institut de Ciencies del Mar

summary: We have further tested and validated a reproduction-enriched microarray designed specifically for European sea bass providing a reliable tool to study gene expression patterns in this fish species. Results obtained by using this platform helped to increase our knowledge in the gene cascade of sex differentiation and give evidence of the complexity of the molecular processes. We described the gene expression profile of genes and pathways required to differentiate bipotential tissue to either an ovary or testis providing a deep transcriptomic analysis in the developing gonads. Resulting data may help to improve sex control in fish culture particularly in the European sea bass

overall_design: A total of 41 samples were analysed. The set of samples consisted of eleven undifferentiatied gonadal tissues at 110 dpf, six testes and six ovaries at 250 dpf and nine testes and nine ovaries at 350 dpf. Gonads were fully isolated in fish at 250 and 350 dpf. Samples were  hybridized on a custom European sea bass microarray platform and data were analysis by several bioinformatic softwares.

first: L

first: B

last: Crespo

first: N

last: Sánchez-Baizán

first: D

last: Xavier

first: H

last: Kuhl

first: J

last: Rodríguez

last: Díaz

first: S

last: Boltañá

last: MacKenzie

first: R

last: Reinhardt

first: F

last: Moran

last: Zanuy

first: A

last: Gómez

last: Piferrer


title: Downstream targets of uc.323-mediated cardiomyocyte hypertrophy

status: Public on Nov 30 2019

first: Yu

last: Sun

summary: To further characterize the downstream targets of uc.323, we performed global microarray analysis after knockdown of uc.323 in cardiomyocytes to gain broad insight into uc.323-mediated transcriptome changes.

overall_design: Scrambled siRNA (si-scramble) (50 nmol/L) or si-uc.323 (50 nmol/L) in serum-free medium was added to each well, and the cells were incubated for 3 hours. After another 21 hours of serum starvation.Samples of cardiomyocytes was measured.Three independent experiments were performed for each experiment.

first: Chen

last: Liu


title: Long-range single-molecule mapping of chromatin accessibility in eukaryotes

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

type: Methylation profiling by high throughput sequencing

summary: Active regulatory elements in eukaryotes are typically characterized by an open, nucleosome-depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used tool in the arsenal of modern functional genomics. However, existing approaches for profiling chromatin accessibility are limited by their reliance on DNA fragmentation and short read sequencing, which leaves them unable to provide information about the state of chromatin on larger scales or reveal coordination between the chromatin state of individual distal regulatory elements. To address these limitations, we have developed a method for profiling accessibility of individual chromatin fibers at multi-kilobase length scale (SMAC-seq, or Single-Molecule long-read Acessible Chromatin mapping sequencing assay), enabling the simultaneous, high-resolution, single-molecule assessment of the chromatin state of distal genomic elements. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases (CpG and GpC 5-methylcytosine (5mC) and N6-methyladenosine (m6A) enzymes) and the ability of long-read single-molecule nanopore sequencing to directly read out the methylation state of individual DNA bases. Applying SMAC-seq to the budding yeast Saccharomyces cerevisiae, we demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule protection footprints of nucleosomes and transcription factors, and quantify the correlation between the chromatin states of distal genomic elements

overall_design: ATAC-seq, RNA-seq, ChIP-seq and dSMF/PBAT control libraries associated with the project

first: Zohar

last: Shipony

first: Matthew

last: Swaffer

first: William

middle: J

last: Greenleaf


title: Transcriptomic analysis of DOXO-Resistant cells compared to parental DOXO-Sensitive mda-mb-436 cell line

city: Montréal

first: isabelle

last: sirois

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

institute: McGill University

summary: The major obstacle in successfully treating triple negative breast cancer (TNBC) is resistance to cytotoxic chemotherapy, the mainstay of treatment in this disease. Previous pre-clinical models of chemoresistance in TNBC have suffered from a lack of clinical relevance. Using a single high dose chemotherapy treatment, we developed a novel MDA-MB-436 cell-based model of chemoresistance characterized by a unique and complex morphological phenotype, which consists of polyploid giant cancer cells (PGCCs) giving rise to neuron-like mononuclear daughter cells filled with smaller but functional mitochondria and numerous lipid droplets. This resistant phenotype is associated with metabolic reprogramming with a shift to a greater dependence on fatty acids and oxidative phosphorylation. We validated both the molecular and histologic features of this model in a clinical cohort of primary chemoresistant TNBCs and identified several metabolic vulnerabilities including a dependence on PLIN4, a perilipin coating the observed lipid droplets, expressed both in the TNBC resistant cells and clinical chemoresistant tumors treated with neoadjuvant doxorubicin-based chemotherapy. These findings thus reveal a novel mechanism of chemotherapy resistance that has therapeutic implications in the treatment of drug resistant cancer.

overall_design: The MDA-MB-436 cell line (referred to as parental cells), representative of a mesenchymal TNBC subtype (16), was exposed to a single high dose (IC75) of DOXO or PTX followed by drug removal after 48h. Parental cells treated with either DOXO or PTX exhibited the same phenotypic response to these treatments. First, after massive cell death, a few small, round mononucleated cells appeared one-week post-treatment. At 3-weeks post-treatment, polyploid giant cancer cells (PGCCs) exhibiting a massive cytoplasm and growing extrusions appeared (Fig. 1B) and, after 5 weeks, colonies of smaller mononuclear cells with thin cellular projections had appeared around these PGCCs. Biological replicates of colonies selected with DOXO (named C1 and C8) and PTX (CA, CD and CF) were isolated and grown individually without drug and then re-tested for chemosensitivity at different passages. Colonies C1 and C8 were resistant to DOXO (henceforth called DOXO-R). Colonies selected with PTX (CA, CD, CF) were also resistant to DOXO on re- testing even though they shared the cellular phenotypic response.

first: Isabelle

last: Sirois

first: Adriana

last: Aguilar-Mahecha

first: Josiane

last: Lafleur

first: Emma

last: Fowler

first: Viet

last: Vu

first: Michelle

last: Scriver

first: Marguerite

last: Buchanan

first: Catherine

last: Chabot

first: Aparna

last: Ramanathan

first: Banujan

last: Balachandran

first: Stephanie

last: Legare

first: Ewa

last: Przybytkowski

first: Cathy

last: Lan

first: Urszula

last: Krzemien

first: Luca

last: Cavallone

first: Olga

last: Aleynikova

first: Cristiano

last: Ferrario

first: Marie-Christine

last: Guilbert

first: Naciba

last: Benlimame

first: Amine

last: Saad

first: Moulay

last: Alaoui-Jamali

first: Horace

last: Uri Saragovi

first: Sylvia

last: Josephy

first: Ciara

last: O'Flanagan

first: Stephen

middle: D

last: Hursting

first: Vincent

last: Richard

first: Rene

last: Zahedi

first: Christoph

last: Borchers

first: Eric

last: Bareke

first: Sheida

last: Nabavi

first: Peter

last: Tonellato

first: Josee-Anne

last: Roy

first: Andre

last: Robidoux

first: Elizabeth

last: Marcus

first: Catalin

last: Mihalcioiu

first: Jacek

last: Majewski

first: Mark

last: Basik


title: Gene expression profiling of SKOV-3 cells with or without PDK1 knocked down (Control versus siPDK1)

city: Hong Kong

first: Michelle

middle: KY

last: Siu

address: Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: O&G

country: Hong Kong

institute: University of Hong Kong

summary: To examine the downstream targets of PDK1 in ovarian cancer.

overall_design: siRNA specifically targeting PDK1 (sc-36203) and control siRNA (Santa Cruz Biotechnology) were introduced into SKOV-3 cells using SilentFect for 48 hr.


title: Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

summary: We report the application of RNA sequencing technology for high-throughput profiling of RNA expression in monkey tissues. By obtaining over four billion bases of sequence of brain, liver and muscle from MCPH1 trasngenic monkey and two control monkeys. We find that brain tissue showed more differentially expressed genes compared with those in liver and muscle. Finally, we show that This result implies that the overexpressed huMCPH1 may have a global impact on multiple organs of the transgenic monkey, and it has the largest impact on the brain in terms of gene numbers.

overall_design: Tissue transcriptomes from 4 cortex layers, 8 individual monkeys, were sequenced and compared(three transgenic monkeys,five wild type monkeys)

first: Lei

last: Shi

first: Bing

last: Su


title: Inhibition of TNBC metastasis by Gpx1

city: Seoul

first: AHYOUNG

last: CHOI

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

summary: Gpx1 plays a vital role in the metastasis of TNBC cells by regulating cell adhesion. Depletion of Gpx1 reduces the survival, migration, and invasion of TNBC cells in vitro. Transcriptomic and signaling pathway analyses demonstrate that depletion of Gpx1 essentially impairs cell adhesion/spreading by down-regulating FAK/c-Src activation.

overall_design: Examination of transcriptome on control and Gpx1-depleted TNBC breast cancer cell lines by deep sequencing, in replicate.

first: Sangwon

last: Kang

first: Sanghyuk

last: Lee

first: Eunkyung

first: Ahyoung

last: Choi


title: Aging triggers H3K27 trimethylation hoarding in the chromatin of Nothobranchius furzeri skeletal muscle

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Aging associates with progressive loss of skeletal muscle function leading up to sarcopenia, a process characterized by impaired mobility and weakening of muscle strength. Molecular mechanisms underpinning sarcopenia are still poorly characterized. Since aging associates with profound epigenetic changes, epigenetic landscape alteration analysis in the skeletal muscle promises to highlight molecular mechanisms of age-associated sarcopenia. The study was conducted exploiting the short-lived Nothobranchius furzeri (Nfu), a relatively new model for aging studies. The epigenetic analysis suggested for a less accessible and more condensed chromatin structure in old Nfu skeletal muscle. Specifically, an accumulation of heterochromatin regions was observed as consequence of increased levels of H3K27me3, HP1a, polycomb complex subunits and senescence associated heterochromatic foci (SAHFs). Consistently, euchromatin histone marks, including H3K9ac, decreased. The integrative bioinformatics analysis of RNASeq and ChIPSeq, related to skeletal muscle of Nfu at different ages, revealed a down-modulation of transcripts involved in cell cycle, differentiation and DNA repair and an up-regulation of inflammation and senescence genes. Undoubtedly, more studies are needed to disclose the detailed mechanisms, but this approach shed light on unprecedented specific features of Nfu skeletal muscle aging, potentially associated with sarcopenia onset and consequent impairment of swimming and mobility typical of old Nfu.

overall_design: ChIPSeq for H3K27me3 and H3K9ac in Nothobranchius furzeri during aging.

first: Chiara

last: Cencioni

first: Johanna

last: Heid

first: Anna

last: Kreplova

first: Seyed

middle: M

first: Carsten

last: Kuenne

first: Stefan

last: Guenther

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

first: Francesco

last: Neri

last: Spallotta

first: Carlo

last: Gaetano


title: Distinct Metabolic Adaptation of Liver Circadian Pathways to Acute and Chronic Patterns of Alcohol Intake

city: New York

first: Sanam

last: Shahid

state: New York

address: 1275 York Avenue

department: Department of Pediatrics

institute: Memorial Sloan Kettering Cancer Center

summary: We reveal differential reprogramming of the circadian transcriptome in the liver using acute versus chronic ethanol feeding. Specifically, rewiring of diurnal SREBP transcriptional pathway leads to distinct hepatic signatures in acetyl-CoA metabolism that are translated into the subcellular patterns of protein acetylation distinct to chronic exposure to ethanol.  Therefore, distinct drinking patterns of alcohol result in differential circadian reprogramming that may contribute to ALD pathogenesis.

overall_design: Examination of circadian transcriptome in mouse liver under acute and chronic ethanol feeding conditions.

first: Jonathan

last: Gaucher

first: Kenichiro

last: Kinouchi

first: Nicholas

last: Ceglia

first: Emilie

last: Montellier

first: Carolina

last: Greco

first: Shahaf

last: Peleg

first: Andreas

last: Schmidt

first: Ignasi

last: Forne

first: Pierre

last: Baldi

first: Selma

last: Masri

first: Axel

last: Imhof

first: Paolo

last: Sassone-Corsi


title: Cdk5-mediated phosphorylation ensures robust neuronal differentiation

status: Public on Nov 29 2019

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 1 Research Link,  National University of Singapore

institute: Temasek Life Sciences Laboratory

summary: Tet3 converts 5-methylcyotsine to 5-hydroxymethylcytosine (5hmC), although it remains unclear how its functions can be regulated. We showed that Tet3 is phosphorylated by cyclin-dependent kinase 5 at a highly conserved serine residue within its catalytic domain, which leads to an increase in its dioxygenase activity in vitro. Interestingly, when stably expressed in Tet triple-knockout mouse embryonic stem cells (mESCs), wild-type Tet3 elicited higher 5hmC enrichment and expression of genes involved in neurogenesis whereas phosphor-mutant Tet3 caused elevated 5hmC and expression of metabolic pathways genes. Expression of wild-type, but not phosphor-mutant Tet3 in Tet3-knockout mESCs, causes optimal expression of BRN2, Hes1 and Hey2 transcription factors which lead to robust terminal differentiation measured by MAP2 expression. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 ensures robust activation of neuronal transcriptional programs during differentiation.

overall_design: RNA-seq, ChIP-seq (H3K27ac) and 5hmC-DNA-IP in Tet1,2,3 triple knockout mouse embryonic stem cells rescued with wild-type or phosphor-mutant Tet3

first: C

last: Ong

first: A

last: Swarnaseetha

first: G

last: Tham

first: V

last: Rao

first: W

middle: Q

last: Lin


title: Altered expression of uc.323 during aortic banding-induced cardiac hypertrophy in mice

city: Guangzhou

first: Yu

last: Sun

address: 58 Zhongshan Road 2

institute: the First Affiliated Hospital of Sun Yat-Sen University

summary: To investigate the changes in T-UCR (transcribed ultraconserved regions) transcription during aortic banding-induced cardiac hypertrophy, we performed lncRNA microarray analysis on the hearts of mice subjected to sham or aortic banding surgery.

overall_design: Samples of murine hearts 4 weeks after sham or aortic banding surgery was measured.  Four independent experiments were performed for each experiment.

first: Chen

last: Liu


title: Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-?

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

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

overall_design: Refer to individual Series


title: An immune-centric exploration of BRCA1 and BRCA2 germline mutation related breast and ovarian cancers

status: Public on Nov 28 2019

city: Storrs

first: Sheida

last: Nabavi

address: 371 Fairfield Way

institute: University of Connecticut

summary:
Background:This study was a hypothesis generating exploration of genomic data collected at diagnosis for 19 patients, who later participated in a clinical trial. BRCA1/2 germline mutation related hereditary cancers are candidates for new immune therapeutic interventions. However, contrary to what is expected of tumors with compromised DNA repair, a prominent tumor mutation burden (TMB) in hereditary breast and ovarian cancers in this cohort, was not correlated with high global immune activity in their microenvironments. More information is needed about the relationship between genomic instability, phenotypes and immune microenvironments of BRCA1/2 related hereditary tumors in order to find appropriate markers of immune activity and the most effective anticancer immune strategies.
Methods:Mining and statistical analyses of the original DNA and RNA sequencing data and data available from The Cancer Genome Atlas (TCGA) were performed using the R computing environment. To interpret the data, we have used published literature and web available resources such as Gene Ontology Tools, The Cancer immunome Atlas (TCIA) and the Cancer Research Institute iAtlas.
Results: We found that BRCA1/2 germline related breast and ovarian cancers do not represent a unique phenotypic identity, but that they express a range of phenotypes similar to sporadic cancers. Importantly, BRCA2 germline mutation related breast tumors have a different profile of genomic instability compared to those related to BRCA1. However, all breast and ovarian BRCA1/2 related tumors are characterized by high homologous recombination deficiency (HRD) and low aneuploidy. Interestingly, all sporadic high grade serous ovarian cancers (HGSOC) and most of the subtypes of triple negative breast cancers (TNBC), but not other types of breast cancer, also express a high degree of HRD.
Conclusion: : Tumor mutation burdon (TMB) is not associated with the magnitude of the immune response in hereditary BRCA1/2 related breast and ovarian cancers or in sporadic TNBC and sporadic HGSOC. Hereditary tumors express phenotypes as heterogenous as sporadic tumors with various degree of “BRCAness” and various characteristics of the immune microenvironments. The subtyping criteria developed for sporadic tumors can be applied for the classification of hereditary tumors and possibly also characterization of their immune microenvironment. A high HRD score may be a good candidate biomarker for response to platinum, and potentially PARP-inhibition.

overall_design: RNA sequencing data from FFPE samples of 19  patients with recurrent Triple Negative Breast Cancer (TNBC) or High Grade Serous Ovarian Cancer (HGSOC) from a Phase I clinical trial study  (9 TNBC and 10 HGSOC) and 5 normal tissues are generated.

first: Gerburg

last: Wulf


title: ChIP-Seq of Arabidopsis Transcription Factors MYC2 and MYC3

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

summary: The genome-wide target genes of transcription factors MYC2 and MYC3 were determined in etiolated (dark-grown) seedlings of Arabidopsis thaliana. Chromatin immunoprecipition of MYC2 and MYC3 was performed as described in O’Malley et al (2016;  doi: 10.1016/j.cell.2016.04.038), using transgenic A. thaliana expressing MYC2::YpET and MYC3::YpET fusion proteins from their native promoters, generated by recombineering (Gimenez-Ibanez et al. 2017; doi: 10.1111/nph.14354 ). Three-day old etiolated seedlings were treated with methyl JA for 2 h (as described in Schweizer et al., 2013), then harvested for ChIP-Seq.

overall_design: Two biological replicates were conducted for MYC2 and one for MYC3. IgG controls (in place of anti-GFP) from a number of ChIP-seq reactions performed on non-transgenic Arabidopsis material were used to normalize for non-specific recovery of DNA from the Arabidopsis genome.

first: Joseph

middle: R

last: Ecker


title: Hepatic gene expression data from Gpr146 WT and KO male mice

status: Public on Nov 27 2019

city: Boston

first: Haojie

last: Yu

state: MA

address: 3 Blackfan Cir

department: Cardiology

country: USA

institute: BIDMC

summary:
GPR146 is a susceptible gene associated with plasma cholesterol levels in humans, its physiological and molecular functions have not been fully characherized. In this study, we generated Gpr146 whole-body knockout mice and found that depletion of GPR146 led to substantilly reduced plasma total cholesterol levels.
We used microarrays to detail the global programme of gene expression in liver of Gpr146 WT and KO male mice upon 6-hour refeeding after a 16-hour fast.

overall_design: There are 6 liver samples, each from an individual mouse. Liver tissue samples were collected from Gpr146 whole-body knockout (KO) mice and wild-type (WT) littermates of 24 week-old from the C57BL/6J background upon 6-hour refeeding after a 16-hour fast. n=3 for each genotype.

first: Chad

last: Cowan


title: Comparison between THP-1 cells obtained from either ATCC or DSMZ biorepository

city: Liege

first: Gregory

last: Ehx

state: Liege

address: Avenue de l'Hopital, 1

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: THP-1 cells obtained from ATCC or DSMZ were compared for their expression of MHC-I, their HLA type and their gene expression. Our results show that the two cell lines differ on many points.

overall_design: THP-1 cells were expanded in identical conditions and compared thoroughly.

first: N

last: Noronha

last: Perreault


title: Transcriptome of diurnal human blood neutrophils

city: Baltimore

first: Jose

last: Adrover

state: Maryland

address: 855 N Wolfe St

department: Cell Biology

institute: Johns Hopkins University

summary: Our study aims to analyze time-dependent changes in neutrophil phenotype

overall_design: Blood neutrophils isolated from healthy volunteers at 8am and 14pm. Low Input RNA-Seq.

last: Hidalgo

first: J

last: Aroca-Crevillen


title: Zileuton Liver Toxicity Study in DO Mice

city: Durham

first: Alison

last: Harrill

state: NC

address: P.O. Box 12233, Mail Drop K2-17

institute: National Institute of Environmental Health Sciencees

summary: In this study, female DO mice were administered zileuton or vehicle i.g. daily for seven days, and assessed for the toxic outcomes in the livers. In addition to the clinical and histopathological assessment, RNA-seq analysis was performed to identify the differentially expressed genes in animals susceptible to the zileuton toxicity. Pathway analysis on the differentially expressed genes was performed to investigate the molecular mechanisms underlying the sensitivity to the liver toxicity.

overall_design:
Transcriptome profile of 41 vehicle-treated and 49-zileuton treated DO mice liver samples, sequenced by the Illumina HiSeq 2000, and aligned/analyzed by Partek flow
A full clinical dataset of our samples can be found at: https://doi.org/10.22427/NTP-DATA-002-00076-0001-0000-6

first: Dahea

last: You

first: Lascelles

middle: E

last: Lyn-Cook Jr.

first: Daniel

last: Gatti

first: Natalie

last: Bell

first: Philip

last: Mayeux

first: Laura

last: James

first: William

middle: B

last: Mattes


title: Small RNA seq from Ago1-IP of fly heads at different temperatures and circadian timepoints

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this set of experiments is to determine the differences in circadian rhythms in fly at different temperatures

overall_design: Flies were grown at 3 temperatures, heads from them were collected at 4 circadian timepoints


title: MicroRNA expression profiles in sporadic malignant peripheral nerve sheath tumors

status: Public on Nov 26 2019

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary: Malignant peripheral nerve sheath tumors (MPNST) are aggressive cancers that occur spontaneously (sporadic MPNST) or from pre-existing, benign plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs metastasize easily, are resistant to therapeutic intervention and are frequently fatal. The molecular changes underlying the transition to malignancy in the NF1 setting are incompletely understood. Here we investigate the involvement of microRNAs in this process. Using an RT-PCR platform microRNA expression profiles were determined from a unique series of archival paired samples of plexiform neurofibroma and MPNST. At least 90 differentially expressed microRNAs (p<0.025; FDR<10%) were identified between the paired samples. Most microRNAs (91%) were found downregulated and 9% of the microRNAs were upregulated in MPNST. Based on the fold changes and statistical significance three downregulated microRNAs (let-7b-5p, miR-143-3p, miR-145-5p) and two upregulated microRNAs (miR135b-5p and miR-889-3p) were selected for further functional characterization. Their expression levels were validated in a relevant cell line panel and a series of unpaired fresh frozen tumor samples containing plexiform neurofibromas, atypical neurofibromas and MPNSTs. As part of the validation process we also determined and analyzed microRNA expression profiles of sporadic MPNSTs observing that microRNA expression discriminates NF1-associated and sporadic MPNSTs emphasizing their different etiologies. The involvement of microRNAs in tumorigenesis and cancer progression was examined in NF1-derived MPNST cell lines through modulating microRNA levels by transient transfection of microRNA mimics or inhibitors. The effects of microRNAs on cellular proliferation, migration, invasion and Wnt/ẞ-catenin signaling were determined. Our findings indicate that, some of the selected microRNAs affect migratory and invasive capabilities and Wnt signaling activity. It was observed that the functional effects upon microRNA modulation are distinct in different cell lines. From our study we conclude that miRNAs play essential regulatory roles in MPNST facilitating tumor progression.

overall_design: MicroRNA expression profiles were determined from 10 Formalin-fixed paraffin-embedded (FFPE) sporadic MPNST. TaqMan® Low Density Array (TLDA) Human MicroRNA Cards (A card v2.0, B card v3.0; Applied Biosystems/Thermo Fisher Scientific) were used. The microRNA expression profiling data was used for a comparison between sporadic and NF1-associated MPNST in order to determine differentially expressed microRNAs.

first: Azadeh

last: Amirnasr

first: Robert

last: Verdijk

first: Patricia

last: van Kuijk

first: Pinar

last: Kartal

first: Anne

middle: L

last: Vriends

first: Pim

last: French

first: Martin

last: van Royen

first: Walter

last: Taal

first: Stefan

last: Sleijfer


title: The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA

status: Public on Nov 25 2019

city: Bern

first: Yeji

last: Kim

address: Freiestrasse 3

department: Department of Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

summary: RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remained elusive. 28S rRNA carries a single m6A modification, found at position A4220 (alternatively referred to as A4190) within a stem-loop structure, and here we show that the MTase ZCCHC4 is the enzyme responsible for introducing this modification. Accordingly, we found that ZCCHC4 localises to nucleoli, the site of ribosome assembly, and that proteins involved in RNA metabolism are overrepresented in the ZCCHC4 interactome. Interestingly, the absence of m6A4220 perturbs codon-specific translation dynamics and shifts gene expression at the translational level. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.

overall_design: Identifying RNA methyltransferase ZCCHC4 in human haploid cells

first: Rita

last: Pinto

first: Cathrine

last: Vågbø

first: Magnus

last: Jakobsson

first: Marijke

last: Baltissen

first: Marie-Francoise

last: O'Donohue

first: Ulises

last: Guzmán

first: Jędrzej

last: Małecki

first: Jie

last: Wu

first: Finn

last: Kirpekar

first: Jesper

last: Olsen

first: Pierre-Emmanuel

last: Gleizes

first: Michiel

last: Vermeulen

last: Leidel

first: Geir

last: Slupphaug

first: Pål

middle: Ø

last: Falnes


title: MicroRNA expression profiles in malignant peripheral nerve sheath tumors

first: Erik

last: Wiemer


title: Placenta-specific genes and their regulation during villous trophoblast differentiation.

city: Budapest

first: Gábor

middle: Nándor

last: Than

address: Magyar tudósok krt. 2

department: Institute of Enzymology

country: Hungary

institute: Research Centre for Natural Sciences

summary: Analysis of genome-wide gene expression during the differentiation of villous trophoblasts isolated from healthy term placentas.

overall_design: Total RNA (n=24) was isolated from primary villous trophoblasts harvested on Days 0-7 of differentiation, 3-3 samples on each of the 8 days.

first: Nándor

first: Zsolt

last: Gelencsér

first: András

last: Szilágyi

first: Roberto

last: Romero

first: Yi

last: Xu

first: Adi

last: Tarca


title: miRCURY LNA™ Universal RT microRNA PCR, Urine Exosome Focus Panel

status: Public on Nov 20 2019

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

summary: qPCR-RT pre-designed plate to study miRNAs expression in urinary exosome from LN patients before and after treatment. We have included 14 LN patients. Of them, there is 7 LN patients with clinical response and 7 with no clinical response.

overall_design: qPCR gene expression profiling. We will compared LN patients with clinical response vs no clinical response before and after treatment. Four compartion will be designed: 1) Patients with clinical remission vs Patients with no clinical remission (before treatment); 2) Patients with clinical remission vs Patients with no clinical remission (after treatment); 3) Patients before vs after treatment (patients with clinical response); 4) Patients before vs after treatment (patients with no clinical response)

first: Josefina

last: Cortés-Hernández

last: Sole


title: A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6

status: Public on Nov 21 2019

city: Valencia

first: Susana

last: Rodríguez Navarro

state: Valencia

address: Jaume Roig, 11

department: Patología y Terapia Molecular y Celular

institute: Instituto de Biomedicina de Valencia

summary: We studied the heat-shock response in wild-type (wt) and in absence of Mip6, an RNA binding protein with roles at multiple levels of the gene expression pathway. This study include; their transcriptome (RNA-seq), metabolome (targeted NMR) and H4K12ac epigenome (ChIP-seq) using an experimental desing that ensures that the same samples are used across all omics determinations. This facilitates data analysis approaches that can leverage fully matched, longitudinal, replicated data. These data will faciliate studies of covariation patterns across multiple molecular layers controlling and responding to RNA biogenesis.

overall_design: RNA-seq, histone H4 ChIP-seq and H4K12Ac ChIP seq of four biological replicates of wt and mip6D yeast cells growth at: (i) normal conditions; (ii) 20 minutes of heat shock at 39ºC and (iii) 120 minutes of heat shock at 39ºC.

first: Carme

last: Nuño-Cabanes

first: Manuel

last: Ugidos

first: Sonia

last: Tarazona

first: Alberto

middle: F

last: Riquelme

last: Rodríguez-Navarro

first: Ana

last: Conesa


title: Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing

status: Public on Nov 19 2019

city: København N

first: Bertil

last: Gummesson

address: OLE MAALØES VEJ 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Here we report on an RNAseq method in combination with spike-in cells to measure global changes in the transcription pattern after valine-induced isoleucine starvation of a standard E. coli K12 strain. Due to the spike-in method we were able to show that ribosomal RNA is degraded during isoleucine starvation and we showed how this change in cellular RNA content affect the estimated regulation of mRNA levels compared to if spike-in were not utilized. Our analysis also showed that induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS and Lrp regulons

sample_organism:
Escherichia coli B
Escherichia coli K-12

overall_design: Three samples were collected during steady-state growth immediately before starvation and five samples in total were collected in a time series; 5, 10, 20, 40 and 80 minutes after L-valine addition. In Addition, 4 rifampicin treated samples in total was collected after 80 minutes of Isoleucine starvation in a time series; 10, 15, 25 and 45 minutes after addition of rifampicin. All samples were spiked-in with a culture grown in a parallel,  expressing Vibrio cholerae sRNA (qrr2) in high amounts.  1% spike-in culture were added to each sample based on sample OD

first: Shiraz

middle: A

last: Shah

first: Alexander

middle: S

last: Borum

first: Mathias

last: Fessler

first: Namiko

last: Mitarai

first: Michael

last: Sørensen

first: Sine

last: Svenningsen


title: Transcriptomics Library Data of Chitosan-coated Cavendish Banana

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

summary: We report the first RNA sequencing data of 1.25% chitosan-coated and uncoated (control) fruit of Musa acuminata (AAA Group, Subgroup Cavendish) at unripe (day 1) and ripe (day 7) stage

overall_design: Fruit pulp mRNA of uncoated (control) and chitosan (1.25%)-coated fruit of Cavendish banana (Musa acuminata, AAA Group, Subgroup Cavendish)

first: Husna

last: Nugrahapraja

first: Eiichiro

last: Fukusaki

first: Sastia

last: Putri

first: Cindy

last: Novianti

first: Septhy

middle: K

last: Radjasa

first: Tessa

last: Fauziah

first: Lutfi

last: Sari


title: Identification of specific ceRNA signatures in prostate cancer (PCa)

city: Shanghai

first: jin

last: wang

address: 2901 Caolang Road, Jinshan District,

country: China

institute: Shanghai Public Health Clinical Center, Fudan University,

summary: In order to develop novel biomarkers in prostate cancer, we applied a competing endogenous RNA (ceRNA) microarray to identify differentially expressed mRNAs, circRNAs and lncRNAs in PCa tissue.

overall_design: Four pairs of prostate cancer and paracancerous tissues were used for the microarray assay to investigate the differentially expressed mRNAs, circRNAs and lncRNAs  between the tumor tissues and paracancerous tissues

first: Jin

last: Wang

first: Jianghua

last: Zheng


title: Study of visceral leishmaniasis establishment - Gene expression from (un)infected (non-)vaccinated mouse spleen samples

city: Philadelphia

first: Theresa

last: Busch

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary: Visceral leishmaniasis (VL) caused by Leishmania donovani and L. infantum is a potentially fatal disease. To date there are no registered vaccines for disease prevention despite the fact that several vaccines are in preclinical development. Thus, new strategies are needed to improve vaccine efficacy based on a better understanding of the mechanisms mediating protective immunity and mechanisms of host immune responses subversion by immunopathogenic components of Leishmania. In the present study, determination of the immune mechanisms related to infection or protective immune responses against VL using an experimental nanovaccine as a vaccine model was conducted through microarray analysis.

overall_design: For the 5 different conditions (4/16-weeks post challenge vaccinated/non-vaccinated mice and naïve, uninfected control mice), 10 samples were analyzed. Experiments were conducted in biological duplicate.

first: Maria

last: Agallou

first: Evita

last: Athanasiou

first: Olga

last: Kammona

first: Spyros

last: Tastsoglou

first: Artemis

last: Hatzigeorgiou

first: Costas

last: Kiparissides

first: Evdokia

last: Karagouni


title: RAG1+ multipotent progenitors emerge directly from hemogenic endothelium of human PSC derived haemopoietic organoids [bulk RNA-seq]

city: Parkville

first: Ali

last: Motazedian

state: Victoria

address: Royal Children's Hospital

department: Stem Cell Technology

institute: Murdoch Children's Research Institute

summary: The Recombination Activation Gene, RAG1, expression of which presages T-cell receptor gene rearrangement, is a key marker of T-cell commitment. Using RAG1:GFP human pluripotent stem cell reporter lines, we examined human T-cells genesis in the context of haemtopoietic organoids. We show that T-cell commitment occurs concomitantly with the emergence of blood cells from AGM-like haemogenic endothelium, predating the surface expression of CD5 and CD7. In this system, RAG1 marks an early haematopoietic progenitor emerging from SOX17+ endothelium, prior to down regulation of CD90 and VCAM and upregulation of the blood cell marker, CD45. Sort and re-culture experiments show that early RAG1+ cells possess T-cell, B-cell, myeloid and erythroid potential. However, under conditions that favor T-cell development, early RAG1+ cells progress to the CD4+CD8+CD3+ stage, vindicating their classification as bone fide T-cell progenitors. These observations suggest that like the zebrafish and mouse, humans can execute a non-HSC derived wave of T-cell development that includes a multipotent RAG1+ progenitor.

overall_design: Examination of gene expression (RNAseq) during various stages of T-lymphocyte differentiation using 2 pluripotent stem cell lines.

first: Ed

last: Stanley


title: RAG1+ multipotent progenitors emerge directly from hemogenic endothelium of human PSC derived haemopoietic organoids [single cell RNA-Seq]

overall_design: sinlge cell transcriptional profiling of RAG1+ cells generated early on (day 20 and 16) during air-liquid interface culture of haemopoietic organoids


title: ChIP-seq for CTCF, H3K4me3 and H3K27ac following CTCF RNAi in LNCaP cells and IMR90 cells

status: Public on Nov 18 2019

city: Darlinghurst

first: Amanda

last: Khoury

state: NSW

address: 384 Victoria St.

institute: Garvan Institute

summary:
This study aimed to ascertain the effect of CTCF RNAi on gene expression, chromatin conformation and the chromatin environment in prostate cancer cell line, LNCaP
This study aimed to confirm loss of CTCF sites following CTCF RNAi in IMR90 cells

overall_design: We performed ChIP-seq for CTCF, H3K4me3 and H3K27ac following 144hrs of Non-Target or CTCF RNAi in LNCaP cells. We performed ChIP-seq for CTCF following 144hrs of Non-Target or CTCF RNAi in IMR90 cells. Each ChIP-seq was performed in duplicate.

first: Susan

last: Clark


title: BCL9 provides multi-cellular communication properties in colorectal cancer by interacting with paraspeckle proteins

status: Public on Nov 16 2019

city: brookline

first: Ruben

last: Carrasco

state: MASSACHUSETTS

address: 450 brookline ave

department: Pathology Oncology

institute: dana farber cancer institute

summary: Colorectal cancer (CRC) is the third most commonly diagnosed cancer, which despite recent advances in treatment, remains incurable due to molecular heterogeneity of tumor cells. The B-cell lymphoma 9 (BCL9) oncogene functions as a transcriptional co-activator of the Wnt/β-catenin pathway, which plays critical roles in CRC pathogenesis.  Here we have identified a β-catenin-independent function of BCL9 in a poor-prognosis subtype of CRC tumors characterized by expression of stromal and neural associated genes. In response to spontaneous calcium transients or cellular stress, BCL9 is recruited adjacent to the interchromosomal regions, where it stabilizes the mRNA of calcium signaling and neural associated genes by interacting with paraspeckle proteins. BCL9 subsequently promotes tumor progression and remodeling of the tumor microenvironment (TME) by sustaining the calcium transients and neurotransmitter-dependent communication among CRC cells. These data provide additional insights into the role of BCL9 in tumor pathogenesis and point towards additional avenues for therapeutic intervention.

overall_design: Examination of different gene expression in RKO wild type or BCL9 deficiency cell line with or without poly I:C treatment

first: Meng

last: Jiang


title: Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

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

overall_design: Refer to individual Series


title: Muscle H3K27ac landscape remodeling with glucocorticoid steroid regimens

city: Chicago

first: Mattia

last: Quattrocelli

state: IL

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

summary: Duchenne muscular dystrophy is caused by genetic defects in the gene encoding dystrophin and leads to progressive muscle degeneration. Glucocorticoid steroids are current mainstay pharmacological regimen to decrease muscle inflammation and prolong the ambulatory period in these patients, but daily intake of glucocorticoids like prednisone and deflazacort causes adverse side effects like osteoporosis, adrenal suppression, insulin resistance and obesity. Intermittent steroid dosing has been proposed as alternative to maintain benefits and limit side effects, but a detailed understanding of the mechanisms underpinning the regimen-specific effects in muscle is still missing. Here we explore how once-daily versus once-weekly prednisone (4 week-long treatment) affect the epigenomic landscape in mdx mouse muscle (genetic model of Duchenne muscular dystrophy; DBA/2J background) through H3K27 acetylation profiles.

overall_design: 3 vehicle control samples; 3 once-daily prednisone (1mg/kg i.p.) samples; 3 once-weekly prednisone (1mg/kg i.p.) samples. Each sample is ~10ng immunoprecipitated from the myofiber fraction of quadriceps muscles (2 pooled per mouse) using a rabbit anti-H3K27ac polyclonal antibody (ActiveMotif #39133)

first: Elizabeth

last: McNally


title: Epigenetic characterization of glioblastoma stem cells

status: Public on Nov 14 2019

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids


title: Expression profile of circRNAs in a mouse model of laser-induced choroidal neovascularization

status: Public on Nov 10 2019

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

summary: To identify the circRNA expression profile in laser-induced choroidal neovascularization (CNV) and controls in mice, we used circRNA microarray analysis to examine the expression of circRNAs in RPE-choroid-sclera complexes of CNV and control mice.

overall_design: Arraystar Mouse circRNA Array V2 was used to identify differentially expressed circRNAs in 3 RPE-choroid-sclera complexes samples of CNV (day 7) mice and 3 RPE-choroid-sclera complexes samples of control mice.

first: Xiao

last: Liu


title: Detection of tetraploidization in chromophobe renal cell carcinoma: insights and pitfalls [Affymetrix OncoScan_CNV]

status: Public on Nov 15 2019

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary:
Chromophobic renal cell carcinomas (chRCC) typically have a hypodiploid genome, including a loss of chromosomes 1, 2, 6, 10, 13, 17 and 21, but few cases in the literature showed a gain of many chromosomes, suggesting a tetraploidy. The detection of this characteristic performed  by  comparative genomic hybridization (CGH-array), is very helpful for the diagnosis. To better characterize the phenomenon of tetraploidization and to explore the consequence and the difficulties of its detection, we studied a subset of 26 chRCC, including five cases of tetraploid chRCC, for which complementary analyses were performed.
Our main objective was to determine whether these four cases displayed chromosomal losses typical of chRCC whitin a near-polyploid genome instead within a near-diploid one. We discuss the hazards and limitations of different molecular methods in the detection of polyploidization and its potential clinical consequences. In our study we show that this  phenomenon of tetraploidization affects about 19% of chRCC and  that is probably overlooked using standard molecular methods. The potential clinical consequences of this phenomenon are not identified yet.

overall_design: Retrospective and prospective molecular study of 26 cases of chRCC retrieved among 643 renal tumors (2012-2019).  All 26 tumor samples were histologically examined and further analyzed using array-CGH (Agilent aCGH for one cases, Affymetrix aCGH for 3 cases and both technologies for 22 cases). We performed in silico manual centralization of the fluorescence ratio and array-CGH coupled to single nucleotide polymorphism (array-SNP) in the four index cases.

first: Ilaria

last: MAURO

first: Damien

last: AMBROSETTI

first: Louis

last: VIGNOT

first: Jean-François

last: ROUSSEL

first: Bérengère

last: DADONE-MONTAUDIE

first: Annie-Claude

last: PEYRON

first: Hervé

last: QUINTENS

first: Matthieu

last: DURAND

first: Jean

last: AMIEL

first: Florence

last: PEDEUTOUR


title: Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes [monolayer]

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary: HPV alters the host transcriptional program to establish infection and complete its lifecycle. Infection of keratinocytes has been difficult until our development of extracellular matrix (ECM)  to cell transfer system that allows efficient infection of primary keratinocytes.  Using this model, the transcriptional program of HPV infected keratinocytes at different times post infection was analyzed by mRNA-seq.

overall_design: mRNA profiles of control, HPV16-infected or HPV16- immortalized  human foreskin primary keratinocytes were generated by deep sequencing, in triplicate, using Illumina.

first: Martin

last: Sapp


title: Transcriptome anaylisis of WT and GFAT-1 G451E engineered N2a cells by RNA-Seq

city: Cologne

last: Denzel

address: Joseph-Stelzmann-Str. 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: Transcriptome of N2a cells carrying a GFAT-1 gain-of-function point mutation that results in a G451E amino acid substitution were compared to WT N2a transcriptome profiles. Three replicates of both cell lines were analyzed. Additionally WT N2a cells were treated with 10 mM GlcNAc for 24h prior to transcriptome analysis resulting in a third dataset with 3 replicates.

overall_design: Cell lines of neuroblastoma cells.

first: Moritz

last: Horn

first: Franziska

last: Metge


title: Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

status: Public on Nov 09 2019

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences


title: Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (smallRNA-seq)

summary: Intronic RNAs are spliced from precursor-messenger RNAs and are usually subjected to degradation in eukaryotes. COLDAIR, a previously reported intronic long noncoding RNA (lncRNA), is produced from the first intron of a MADS-box gene, Flowering Locus C (FLC), which encodes a repressor of flowering time. Here we show that overexpression of a foreign COLDAIR sequence causes enhanced expression of FLC in trans, resulting in a late-flowering phenotype. In COLDAIR-overexpression lines, enhanced expression of FLC is correlated with up-regulation of the active histone mark H3K4me3 and down-regulation of the repressive histone mark H3K27me3. We demonstrate that overexpression of COLDAIR makes the corresponding FLC intronic region accessible to the histone H3K4 methyltransferase ATX1 but exclusive to the histone H3K27 methyltransferase CLF. Furthermore, we demonstrate that overexpression of intronic lncRNAs from many other MADS-box genes also activate the expression of their host genes in trans, suggesting that intronic lncRNAs act as enhancer RNAs in many MADS-box genes. Considering that MADS-box genes are highly conserved in multicellular eukaryotes, we suggest that involvement of intronic lncRNAs from MADS-box genes in gene activation may represent an evolutionarily conserved mechanism.

overall_design: Examination of the smallRNA expression in Arabidopsis

first: Zhang-wei

last: Liu

first: Yin-na

last: Su

first: Xin-jian


title: Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (ChIP-seq)

overall_design: Examination of histone modification in Arabidopsis.


title: Phenotypic and Transcriptomic Analysis of Two Pinellia ternata Varieties T2 line and T2Plus line

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

summary: Pinellia (Pinellia ternata (Thunb.) Breit.), as important medicinal plant, has been used to treat various ailments for a long time. The sixteen ploid plant (2n=16*13=208) Pinellia T2Plus line was obtained from an octoploid (2n=8*13=104) T2 line by chromosome-doubling technique. Compared with T2 line, the content of various medicinal components (polysaccharide, guanosine, adenosine and ephedrine) was increased in T2Plus line. In this study, the transcriptome of T2 line and T2Plus line were characterized by RNA sequencing (RNA-seq) technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis on differential expressed unigenes (DEGs) revealed that multiple metabolic pathway were enriched significantly, such as ‘Starch and sucrose metabolism’, ‘Purine metabolism’, ‘Photosynthesis’ and six transcription factors (MYB, WRKY, bHLH, LBD lateral organ boundaries domain (LBD), HD-ZIP homeodomain-zipper (HD-ZIP) and ERF Ethylene-responsive factor (ERF) ) play a key role in difference of transcriptome between T2 line and T2Plus line. These metabolic pathways and transcription factors may play an important role in the difference of medicinal components and epigenetic features between these two Pinellia  cultivars. This conclusion provides a robust theoretical basis for the mechanism of the formation of medicinal ingredients in Pinellia cultivars.

overall_design: The transcriptome of Pinellia ternata (Thunb.) Breit. T2P line(2n=16*13=208) and T2 line(2n=8*13=104)

first: Jishuang

last: Chen

first: Jun

last: Lu


title: RNA-seq on Enasidenib or DMSO Treated CD71+ Cells from Umbilical Cord Blood (UCB)

status: Public on Nov 08 2019

city: Palo Alto

first: Ritika

last: Dutta

state: CA

address: 265 Campus Drive

institute: Stanford School of Medicine

summary: We aim to identify differentially expressed genes between enasidenib and DMSO treated CD71+ erythroid progenitors.

overall_design: We first enriched CD34+ cells from UCB and cultured them for 6 days in StemSpan II with Erythroid Differentiation Supplement (StemCell Technologies). The cells were then sorted on the CD71+ population and treated with either DMSO or Enasidenib 10uM for 24 hours before isolating RNA for RNA seq. RNA-seq was performed with Girihlet.


title: RNA-seq data corresponding to: AZD4573 is a highly selective CDK9 inhibitor that suppresses Mcl-1 and induces apoptosis in hematological cancer cells

city: Waltham

first: Steven

middle: W

last: Criscione

address: 35 Gatehouse Drive

department: Oncology Bioinformatics

institute: AstraZeneca

summary: A time-course RNA-seq experiment testing the effect of drug treatment using selective CDK9 inhibitor AZD4573. The experiment was done using a resistant cell-line to AZD4573: the MCF7 breast cancer cell-line.

overall_design: The experiment tests the effect of CDK9 inhibitor AZD4573 at 4 hrs. and 8 hrs. time-points vs. a DMSO untreated control in MCF7 cell lines.

first: Justin

last: Cidado

first: Scott

last: Boiko

first: Theresa

last: Proia

first: Douglas

last: Ferguson

first: Maryann

last: San Martin

first: Petar

last: Pop-Damkov

first: Nancy

first: Wenlin

last: Shao

first: Raphael

last: Koch

first: David

last: Weinstock

first: Michael

last: Zinda

first: Stephen

last: Fawell

first: Lisa

last: Drew


title: Molecular analyses of antifibrotic effect of BK channel activatior on rat livers in fibrosis

status: Public on Nov 07 2019

first: Linli

last: Yang

address: Shanghai ,Xianxia Road 720#

institute: Shanghai Jiaotong University

summary: Liver fibrosis is a high-morbidity and high-mortality chronic disease throughout the world without any satisfying treatment Large-conductance Ca2+- and voltage-activated K+ (Slo1, BK) channels are widely expressed in human body and important for numerous physiological processes. Previous studies have shown that BK channels are expressed in HSCs of patients with liver fibrosis and they are involved in contraction/relaxation of the HSCs To investigate the molecular mechanism of antifibrotic effect of BK channel opener rottlerin using in vivo fibrosis models. transcriptomic analyses of differential expression genes in livers from rats of vehicle, CCl4 and CCl4 combined with rottlerin treatment were for discrimination. The RNA samples were extracted from three samples of each group for microarray profiling and performed in Affymetrix Rats Genome 230 2.0 arrays for gene expression profiling analysis, which contained 31 042 probe sets. The biotinylated cRNA targets were hybridized with the microarray. After hybridization, arrays were stained in the Fluidics Station 450 and scanned on the Affymetrix Scanner 3000. The microarray experiments were performed by following the protocol of Affymetrix Inc at Shanghai Biotechnology Corporation. Under the criteria fold change > 1.5 or < 0.67, we obtained 10672 differential expressed genes (DEGs) between CCl4 and CCl4 combined with rottlerin treatment group, and the data was applied to further analysis.

overall_design: Examination of rat livers  from vehicle, CCl4 and CCl4 combined with BK channel activator rottlerin treatment group

first: Shangwei

last: Hou