title: Nutritional effects by beta-carotene in lung in males and females of control mice versus BCMO knockout mice

first: Evert

summary: Molecular mechanisms triggered by high dietary beta-carotene (BC) intake in lung are largely unknown. We performed microarray gene expression analysis on lung tissue of BC supplemented beta-carotene 15,150-monooxygenase 1 knockout (Bcmo1-/-) mice, which are—like humans—able to accumulate BC. Our main observation was that the genes were regulated in an opposite direction in male and female Bcmo1-/- mice by BC. The steroid biosynthetic pathway was overrepresented in BC-supplemented male Bcmo1-/- mice. Testosterone levels were higher after BC supplementation only in Bcmo1-/- mice, which had, unlike wild-type (Bcmo1+/+) mice, large variations. We hypothesize that BC possibly affects hormone synthesis or metabolism. Since sex hormones influence lung cancer risk, these data might contribute to an explanation for the previously found increased lung cancer risk after BC supplementation (ATBC and CARET studies). Moreover, effects of BC may depend on the presence of frequent human BCMO1 polymorphisms, since these effects were not found in wild-type mice.

overall_design: The experimental setup has been described previously for females and males (Van Helden et al., CMLS 2010 and Carcinogenesis, 2011, resp.). Twelve female (fe) and 12 male (ma) B6129SF1 (Bcmo1+/+) and 12 female and 12 male B6;129S-Bcmo1tm1dnp (Bcmo1-/-) mice were used for the dietary intervention, which was conducted in accordance with the German animal protection laws by the guidelines of the local veterinary authorities. During the breeding and weaning periods of the mice, mothers were maintained on KLIBA 3430 chow containing 14,000 IU vitamin A/kg diet (Provima Kliba AG, Kaiseraugst, Switzerland). Five-week-old female and male Bcmo1+/+ and Bcmo1-/- mice were caged in groups containing two to four siblings per group and were maintained under environmentally controlled conditions (temperature 24 C, 12 h/12 h light/dark cycle). Mice had ad libitum access to feed and water. Basic feed consisted of the pelletized diet D12450B (Research Diets Inc, USA) with a fat content of 10%. The diet was modified to contain 1,500 IU vitamin A/kg of diet, which is a vitamin A-sufficient diet, and the control diet (control) was supplemented with water-soluble vehicle beadlets (DSM Nutritional Products Ltd., Basel, Switzerland) containing DL-alpha-tocopherol and ascorbyl palmitate as stabilizers, as well as carriers such as gelatin, corn oil, sucrose and starch. The BC diet (BC) was supplemented with identical water-soluble beadlets containing BC (DSM Nutritional Products Ltd., Basel, Switzerland) to generate 150 mg BC/kg diet. Beadlets were added by the manufacturer before low temperature pelletting. Feed pellets were color marked and stored at 4 C in the dark. After 14 weeks of dietary intervention, mice were killed after isoflurane and ketamin anesthesia and blood and lung tissue isolated. Lungs were rinsed in phosphate-buffered saline (PBS) and snap frozen in liquid nitrogen, and subsequently stored at -80 C. Transcriptomic analyses were performed using Agilent whole genome 4x44K gene expression arrays according to the manufacturer's procedure.


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [GR ChIP-seq]

status: Public on Sep 24 2017

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Growth factors (GFs) suppression by steroid hormones  recurs in embryology and is co-opted in pathology. While studying mammary cell migration, which is stimulated by GFs and antagonized by glucocorticoids (GCs), we found that GCs inhibit positive feedback loops activated by GFs and stimulate the reciprocal negative loops. Although no alterations in DNA methylation accompany the transcriptional events instigated by either stimulus, forced demethylation of distal regions broadened the repertoire of inducible genes. Our data indicate that the crosstalk involve transcription factors like p53 and NF-kB, along with reduced pausing (and traveling) of RNA polymerase II (RNAPII) at the promoters (and bodies) of GF-inducible genes. In addition, while GFs hyper-acetylated chromatin at unmethylated promoters and enhancers of genes involved in motility, GCs hypo-acetylated the corresponding regions. In conclusion, stably unmethylated genomic regions that encode feedback regulatory modules and differentially recruit RNAPII and acetylases/deacetylases underlie suppression of growth factor signaling by glucocorticoids.

overall_design: Glucocorticoid Receptor (GR) ChIP-Seq – 2 biological replicates for each treatment


title: Histone H3K4 methylation-dependent and independent functions of Set1A/COMPASS in embryonic stem cell self-renewal and differentiation

status: Public on Sep 26 2017

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

type: Expression profiling by high throughput sequencing

summary: Of the six members of the COMPASS (complex of proteins associated with Set1) family of histone H3 Lys4 (H3K4) methyltransferases identified in mammals, Set1A has been shown to be essential for early embryonic development and the maintenance of embryonic stem cell (ESC) self-renewal. Like its familial relatives, Set1A possesses a catalytic SET domain responsible for histone H3K4 methylation. Whether H3K4 methylation by Set1A/COMPASS is required for ESC maintenance and during differentiation has not yet been addressed. Here, we generated ESCs harboring the deletion of the SET domain of Set1A (Set1AΔSET); surprisingly, the Set1A SET domain is dispensable for ESC proliferation and self-renewal. The removal of the Set1A SET domain does not diminish bulk H3K4 methylation in ESCs; instead, only a subset of genomic loci exhibited reduction in H3K4me3 in Set1AΔSET cells, suggesting a role for Set1A independent of its catalytic domain in ESC self-renewal. However, Set1AΔSET ESCs are unable to undergo normal differentiation, indicating the importance of Set1A-dependent H3K4 methylation during differentiation. Our data also indicate that during differentiation, Set1A but not Mll2 functions as the H3K4 methylase on bivalent genes and is required for their expression, supporting a model for transcriptional switch between Mll2 and Set1A during the self-renewing-to-differentiation transition. Together, our study implicates a critical role for Set1A catalytic methyltransferase activity in regulating ESC differentiation but not self-renewal and suggests the existence of context-specific H3K4 methylation that regulates transcriptional outputs during ESC pluripotency.

overall_design: Determining the role of Set1A methyltransferase activity in ESC self-renewal and differentiation by investigating histone methylation and gene expression.

first: Christie

middle: C

last: Sze

first: Clayton

middle: K

last: Collings

first: Patrick

middle: A

last: Ozark


title: SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters [ChIP-Seq]

status: Public on Sep 25 2017

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: BAF complex perturbations contribute to over 20% of human cancer, yet the mechanisms by which these alterations drive oncogenesis remain poorly understood. The driving role for BAF complex mutations in cancer was first documented in malignant rhabdoid tumor (MRT), an aggressive pediatric cancer in which loss of SMARCB1 (also known as BAF47, INI1, hSNF5), a core BAF complex subunit, is the hallmark genetic alteration. We find that loss of BAF47 destabilizes the biochemical affinity of BAF complexes on chromatin without significantly impairing complex integrity or subunit composition. Rescue of BAF47 in BAF47-deficient sarcoma cell lines results in global increases in BAF complex occupancy, which mediates a major gain in enhancer activation. In addition, we find BAF47 targets BAF complexes to bivalent promoters, resolving bivalency to activation through opposition of polycomb-mediated repression. These findings demonstrate collaborative gene activation by the BAF complex through distinct mechanisms, highlighting specific BAF complex functions that are coopted or abated to drive human cancers and developmental disorders.

overall_design: Malignant rhabdoid tumor (G401, TTC1240) or epithelioid sarcoma (HS-ES-2M, VA-ES-BJ) cell lines were lentivirally infected with either an empty vector control or a constitutive vector expressing BAF47, selected for 48 hours with blasticidin, then grown for 5 days, at which point cells were harvested for ChIP-seq preparation.

first: John

last: Pulice


title: Characterization of distinct states of human naive pluripotency

city: Crawley

first: Ethan

middle: Edward

last: Ford

state: WA

address: 35 Stirling Highway

department: Plant Energy Biology

country: Australia

institute: University of Western Australia

type: Methylation profiling by high throughput sequencing

summary: The extent of naive characteriztics of recently reported naive human pluripotent stem cells (hPSCs) obtained in different naive-permissive media, is unclear. Moreover, these naive hPSCs were mainly derived by conversion from primed hPSCs or by direct derivation from human embryos rather than by somatic cell reprogramming. Here, we derived genetically matched human naive hPSCs by direct reprogramming of fibroblasts as well as primed-to-naive conversion using different naive conditions (NHSM, RSeT, 5iLAF and t2iLGöY). Comprehensive characterization showed that naive hPSCs obtained in these different conditions represent a spectrum of naive characteriztics irrespective of whether they were derived by conversion or reprograming. Importantly, only t2iLGöY hPSCs displayed a similar transcriptome to human cells from the inner cell mass, karyotypic stability and require re-priming for trilineage differentiation. Furthermore, our analyses identified KLF4 as a key reprogramming factor which enables conversion of primed hPSCs into naive t2iLGöY hPSCs. These findings underscore the role that reprogramming factors can play for the derivation of bona fide naive hPSCs and provide a molecular and functional reference for all the analysed conditions, which will help accelerate the downstream applications of naive hiPSCs.

overall_design: Human pluripotent stem cells (hPSCs) have been traditionally maintained in a primed state. In the context of the current study we used a number of published or commercially available media to generated naive-like hiPS cells from fibroblasts by different reprogramming strategies as well as convert primed hPSCs into a naive-like state. Five hiPS cell lines were derived directly via somatic cell reprogramming using human fibroblasts in E8, NHSM, RSeT, 5iLAF and t2iLGöY conditions, P12 32F E8 primed line was used as the control. We also included a cell line obtained by converting naive rt2iLGöY iPSCs to primed iPSCs in E8 condition. Targeted methylation study was performed (n=1) to investigate and compare the DNA methylation profiles in these six samples.

first: Xiaodong

last: Liu

first: Christian

middle: M

last: Nefzger

first: Fernando

middle: J

last: Rossello

first: Jahnvi

last: Pflueger

first: Ryan

last: Lister

first: Jose

last: Polo


title: miRNA profiling in gallbladder carcinoma

status: Public on Sep 23 2017

city: Heidelberg

first: Justo

last: Lorenzo Bermejo

address: Im Neuenheimer Feld, 130.3

department: Statistical Genetics

country: Germany

institute: Institute of Medical Biometry and Informatics, University of Heidelberg

summary: Gallbladder carcinoma (GBC) is a rare cancer entity in Western Europe and the US with an incidence of less than 3/100.000 and a survival rate <10%. Radical surgery is the only potentially curative treatment option but most patients diagnosed with GBC are not resectable. Thus, there is a great need for the development of new treatment options, including targeted therapy for GBC.  To dissect the epigenetic regulation during GBC development, we performed global miRNA profiling of 40 GBC and 8 normal gallbladder tissues. MiRNAs that are associated with survival were functionally analysed by cell proliferation and colony formation assays. In addition, we performed whole genome gene expression analysis of cells expressing miRNA mimics or control and performed biochemical assays to dissect miR-145 signalling.  The GBC miRNA profiles exhibited large differences compared to normal gallbladder tissues with 49% of miRNAs being differentially expressed (FDR<0.001). In addition, 8 miRNAs were found to be down- and 16 to be up regulated in the GBCs with poor outcome (p<0.05). The most down regulated miRNA was miR-145-5p and the top up regulated miRNA was miR-575. Overexpression of miR-145 led to a significant reduction of cell proliferation and colony formation, whereas, opposite effects were observed for miR-575. Gene expression profiling of cells overexpressing miR-145 revealed activation of the STAT1 signalling pathway by inhibition of PTPRF in cholangiocellular but not hepatocellular carcinoma cells. Thereby, PTPRF directly bound to STAT1 and reduced STAT1 phosphorylation.  This study identified pro- and anti-tumorigenic miRNAs in GBC and provides new mechanistic insight in the tumour suppressive function of miR-145 loss leading to active STAT1 signalling.

overall_design: To study the expression profiles of miRNAs in gallbladder carcinoma

first: Stephanie

last: Roessler


title: Transcript profiling of Candida albicasn gtr1/gtr1 mutant

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary: The Target of Rapamycin complex (TORC1) is an essential regulator of metabolism in eukaryotic cells and in the fungal pathogen C. albicans regulates morphogenesis and nitrogen acquisition. Gtr1 encodes a highly conserved GTPase which in S. cerevisiae regulates nitrogen sensing and TORC1 activation. Here, were characterize the role of C. albicans GTR1 in TORC1 activation and compare with the previously characterized GTPase Rhb1. A homozygous gtr1/gtr1 mutant exhibited impaired TORC1-mediated phosphorylation of Ribosomal Protein S6 and increased susceptibility to rapamycin. Overexpression of GTR1 impaired nitrogen starvation induced filamentous growth, MEP expression and growth in BSA as the sole nitrogen source. Both GTR1 and RHB1 were shown to regulate genes involved in ribosome biogenesis, amino acid biosynthesis and expression of biofilm-growth induced genes. The rhb1/rhb1 mutant exhibited a different pattern of expression of Sko1 regulated genes and increased susceptibility to Congo Red and Calcofluor white. The homozygous gtr1/gtr1 mutant exhibited enhanced flocculation phenotypes and similar to the rhb1/rhb1 mutant exhibited enhanced biofilm formation on plastic surfaces. In summary, Gtr1 and Rhb1 link nutrient sensing and biofilm formation and this connectivity may have evolved to enhance competitiveness of C. albicans in niches where there is intense competition with other microbes for space and nutrients.

overall_design: gtr null/wildtype with four biological replicates.  Dye swap included.

middle: P


title: SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters

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

overall_design: Refer to individual Series


title: Genome-wide map of RNA polymerase occupancy of Salmonella enterica cells during cytosolic Mg2+ limitation.

city: Hershey

first: Mauricio

middle: Henriques

last: Pontes

state: PA

address: 500 University Drive

department: Pathology

institute: Penn State University

summary: We report the identification of genes displaying altered RNA polymerase occupancy in Salmonella enterica cells experiencing cytosolic magnesium starvation.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Comparison of RNA polymerase occupancies of cells experiencing cytosolic magnesium starvation with those that are experience physiological levels of cytosolic  magnesium.

middle: H

first: Eduardo

last: Groisman


title: Association of miR-197-5p, a circulating biomarker for heart failure, with myocardial fibrosis and adverse cardiovascular events among patients with stage C or D heart failure

city: Beijing

first: Tong

address: Anzhen road 2#, Chaoyang district

department: Department of Cardiology

country: China

institute: Bejing Anzhen Hospital,Capital Medical University

summary: The aim of this study was to identify end-stage heart failure (HF)-specific circulating micro-RNAs (miRNA), and examine whether the selected miRNAs are correlated with myocardial fibrosis (MF) and are reflective of the incidence of adverse cardiovascular events in patients with stage C or D HF.

overall_design: Circulating miRNAs which were differentially expressed in end-stage HF patients and matched healthy controls were detected by microarray analysis and validated by quantitative real-time polymerase chain reaction (qPCR). Multivariate Cox regression analysis was performed to determine whether the selected circulating miRNAs could be prognostic factors in patients with end-stage HF.

first: Wei

first: Shukuan

last: Ling


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone

first: Yehoshua

last: Enuka

type: Methylation profiling by genome tiling array


title: Thiol-linked alkylation for the metabolic sequencing of RNA [SLAM-seq in wildtype and Mettl3 knockout mES cells]

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s4U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and provides quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner.

overall_design: Wildtype (wt) mouse embryonic stem (mES) cells, clonal mES cells that had been transfected with non-targeting control guide RNAs (ctr), or Mettl3 depleted (Mettl3KO) mES cells were subjected to 3h and 12h s4U-pulse labeling followed by total RNA extraction, alkylation, mRNA 3´ end library preparation (QuantSeq, Lexogen) and high throughput sequencing.

first: Veronika

last: Herzog

first: Tobias

last: Neumann

first: Philipp

last: Rescheneder

first: Pooja

last: Bhat

first: Thomas

middle: R

last: Burkard

first: Wiebke

last: Wlotzka

first: Arndt

last: von Haeseler

first: Johannes

last: Zuber

first: Stefan

middle: L

last: Ameres


title: Thiol-linked alkylation for the metabolic sequencing of RNA [SLAM-seq of wildtype mES cell RNA +/- iodoacetamide treatment]

overall_design: Total RNA from wildtype mouse embryonic stem (mES cells) was extracted and subjected to alkylation or mock treatment prior to mRNA 3ʹ end library preparation (QuantSeq, Lexogen) and high throughput sequencing.


title: Thiol-linked alkylation for the metabolic sequencing of RNA [Transcriptional inhibition by Actinomycin D]

overall_design: 5 µg/ml Actinomycin D was added to wildtype mouse embryonic stem (mES) cells and total RNA was prepared at various time points after addition of Actinomycin D (0h, 0.25h, 0.5h, 1h, 3h and 10h). Total RNA was subjected to mRNA 3ʹ end library preparation (QuantSeq, Lexogen) and high througput sequencing.


title: Biocompatibility assessment of functionalized magnetic mesoporous silica nanoparticles in human HepaRG cells

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

country: France

institute: CEA

summary: We have employed whole genome microarray expression to distinguish the effect of diversely functionalized magnetic silica nanoparticles on human HepaRG cells. Cells were exposed in vitro, and datasets of differentially expressed genes were identified for NPs versus control samples.

overall_design: NPs induced expression profiles in HepaRG cells were measured at 24 hours and 48 hours after exposure. Minimum three independent experiments were performed for each experiment.

first: Cedric

last: Pisani


title: Thiol-linked alkylation for the metabolic sequencing of RNA [SLAM-seq pulse/chase labeling in wildtype mES cells]

overall_design: Wildtype mouse embryonic stem cells (mES cells) were subjected to s4U metabolic RNA labeling for 24 h (pulse, 100 µM s4U), followed by washout (chase) using non-thiol-containing uridine. Total RNA was prepared at various time points along the chase (0h, 0.5h, 1h, 3h, 6h, 12h, and 24h). Total RNA was then subjected to alkylation and mRNA 3ʹ end sequencing library preparation (QuantSeq, Lexogen).


title: Thiol-linked alkylation for the metabolic sequencing of RNA [SLAM-seq in wildtype and Xpo5 knockout mES cells]

overall_design: Wildtype (wt) mouse embryonic stem (mES) cells, clonal mES cells that had been transfected with non-targeting control guide RNAs (ctr), or Exportin-5 depleted (Xpo5KO) mES cells were subjected to 3h and 12h s4U-pulse labeling followed by total RNA extraction, alkylation, mRNA 3' end library preparation (QuantSeq, Lexogen) and high throughput sequencing.


title: Thiol-linked alkylation for the metabolic sequencing of RNA [Primer Extension Assays]

overall_design: Synthetic RNA oligo containing dme-let7 sequence without (no s4U) or with s4U at a single position (p9, +s4U) flanked by 3ʹ and 5ʹ adapter sequences were subjected to iodoacetamide (or mock) treatment, reverse transcription, gel-extraction of full-length product, PCR amplification and high-throughput sequencing.


title: Thiol-linked alkylation for the metabolic sequencing of RNA [Transcriptional output measurement by SLAM-seq in wildtype mES cells]

overall_design: Mouse embryonic stem (mES) cells were subjected to 45 min s4U-pulse labeling followed by total RNA extraction, alkylation, mRNA 3' end library preparation (Quant-seq, Lexogen) and high throughput sequencing.


title: Identification of Human Juvenile Chondrocyte-specific factors

status: Public on Sep 22 2017

city: Stanford

first: Nidhi

last: Bhutani

address: 300 Pasteur Drive

institute: Stanford University

summary:
Although regeneration of human cartilage is inherently inefficient, age is an important risk factor for Osteoarthritis (OA).
Recent reports have provided compelling evidence that juvenile chondrocytes (from donors below 13 years of age) are more efficient at generating articular cartilage as compared to adult chondrocytes.
However, the molecular basis for such a superior regenerative capability is not understood.
In order to identify the cell-intrinsic differences between juvenile and adult cartilage, we have systematically profiled global gene expression changes between a small cohort of human neonatal/juvenile and adult chondrocytes.
No such study is available for human chondrocytes although ‘young’ and ‘old’ bovine and equine cartilage have been recently profiled.

overall_design:
3 juvenile chondrocyte samples and 2 adult chondrocyte samples were profiled. Bone-marrow derived mesenchymal cells (MSC) from 2 donors were profiled.
We analyzed the changes in gene expression; genes with a fold-change ≥ or ≤1.5, with a difference in intensity of >100 and within the lower 90% confidence bound were selected.

first: Sarah

middle: E

last: Taylor

first: Piera

last: Smeriglio


title: RNA-seq profiling of thymic epithelial cells from Mcl1 knockout and wildtype mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: T cell differentiation is governed by interactions with thymic epithelial cells (TECs) and defects in this process undermine immune function and tolerance. To uncover new strategies to restore thymic function and adaptive immunity in immunodeficiency, we sought to determine the molecular mechanisms that control life and death decisions in TEC. We created a mouse model which specifically deleted the pro-survival gene Mcl1 in TEC. We found that while BCL-2 and BCL-XL were dispensable for TEC homeostasis, MCL-1 deficiency impacted on TEC as early as E15.5, resulting in early thymic atrophy and T cell lymphopenia, with near complete loss of thymic tissue by 2 months of age. MCL-1 was not necessary for TEC differentiation but was continually required for the survival of medullary TEC, including autoimmune regulator (AIRE) expressing TECs and the maintenance of overall thymic architecture. To understand the molecular mechanisms in more detail, RNA-seq profiling was undertaken of cortical and medullary thymic epithelial cells (cTECs and mTECs) from wildtype and knockout mice.

overall_design: The number of biological replicates was n=4 for WT cTECs, n=2 for WT mTECs, n=1 for KO cTECs and n=1 for KO mTECs.

first: Luke

last: Gandolfo

first: Reema

last: Jain

first: Daniel

last: Gray


title: Thiol-linked alkylation for the metabolic sequencing of RNA

first: Brian

last: Reichholf

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Effect of blood product - derived Cell Free Nucleic Acids (CFNA) on peripheral mononuclear cells gene regulation

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: PBMC were exposed to Cell Free Nucleic Acids (CFNA) extracted from blood products eligible for transfusion: Red Blood Cell units (RBC), Fresh Frozen Plasma units (FFP). PBMC alone exposed to the same extract from PBS were used as a control (PBMC+control). PBMC alone were also used as control. The used positive control was PBMC exposed to Lipopolysaccharide (LPS)

overall_design:
exposition of PBMC to CFNA, RNA extarction and gene expression array (24h)
PFC = FFP = Fresh Frozen Plasma units
CE = RBC = Red Blood Cell units
CP = PC = Platelet Concentrates

first: Pierre

last: Lau

first: Diderik

last: Tirefort

first: Olivier

last: Preynat-Seauve


title: Effect of Cell Free Nucleic Acids (CFNA) extracted from blood products (red blood cells, plasma, platelets) on macrophage/dendritic cells gene regulation

summary: Macrophages were exposed to CFNA from different blood products prior to gene expression array: Red Blood Cells units (RBC), Fresh Frozen Plasma Units (FFP) and Platelet Concentrates (PC). Extracts from PBS were used as controls. Biological triplicates were included with three different macrophage cell lines (M1, M2, M3).

overall_design:
CFNA extraction, exposition to human macrophages, RNA extraction after 24h, gene expression array
PFC = FFP = Fresh Frozen Plasma units
CE = RBC = Red Blood Cell units
CP = PC = Platelet Concentrates


title: Traumatic brain injury in Drosophila causes retention of long introns.

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

summary: Traumatic brain injury (TBI) can cause persistent pathological alteration of neurons. This may lead to cognitive dysfunctions, depression, and even increased susceptibility to life threatening diseases, such as epilepsy. To investigate the underlying genetic and molecular basis of TBI, Wasserman and colleagues developed an inexpensive and reproducible model for simulating TBI in Drosophila melanogaster (Fruit Fly). Using a modified version of this model, we subjected w1118 fruit flies to mild closed head trauma. To determine the transcriptomic changes which contribute to survival post TBI, we collected fly heads from the survivors at 2 time points; 4 hours and 24 hours post-trauma. We observed that the induction of transcriptomic changes occur 24 hours post-trauma in fly heads. Classification of these AS changes showed selective retention of long introns (>81bps), with a mean size of ~3000bps. Gene ontology analysis of the genes containing retained introns showed significant enrichment for critical regulators of glycolysis, citric acid cycle as well as vesicle mediated neurotransmitter release. Some of these genes also showed a significant reduction in transcript abundance. The retained introns were enriched for CA-rich motifs known to bind to Smooth (SM), an hnRNPL class of splicing factor.

overall_design: mRNA profile of w1118 wild-type  heads (±TBI) were generated by deep sequencing using 100bps paired-end reads.

first: Arko

last: Sen


title: Circular RNAs of the nucleophosmin (NPM1) gene in acute myeloid leukemia

city: Ulm

first: Lars

last: Bullinger

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University of Ulm

summary:
Gene expression in NPM1 wildtype and mutated AML patients with high or low hsa_circ_0075001 expression
In acute myeloid leukemia there is growing evidence for splicing pattern deregulation, including differential expression of linear splice isoforms of the commonly mutated gene nucleophosmin (NPM1). In this study, we detect circular RNAs of NPM1 and quantify circRNA hsa_circ_0075001 in a cohort of NPM1 wildtype and mutated acute myeloid leukemia (n=46). Hsa_circ_0075001 expression correlates positively with total NPM1 expression, but is independent of the NPM1 mutational status. High versus low hsa_circ_0075001 expression defines patient subgroups characterized by distinct gene expression patterns, such as lower expression of components of the Toll-like receptor signaling pathway in high hsa_circ_0075001 expression cases. Global evaluation of circRNA expression in sorted healthy hematopoietic controls (n=10) and acute myeloid leukemia (n=10) reveals circRNA transcripts for 47.9% of all highly expressed genes. While circRNA expression correlates globally with parental gene expression, we identify hematopoietic differentiation-associated as well as acute myeloid leukemia subgroup-specific circRNA signatures.

overall_design: AML Patient samples were collected at first diagnosis and chosen from the larger AMLSG_07-04 study cohort  (ClinicalTrials.gov identifier: NCT00151242). Mononuclear cells of AML samples were enriched via Ficoll-Hypaque density gradient, and the percentage of leukemic blasts was >85%. For the quantification of hsa_circ_0075001, 44 cytogenetically normal AML cases were selected of which 23 carried an NPM1 mutation.

first: Susanne

last: Hirsch


title: PML is a ROS sensor activating p53 upon oxidative stress

city: Paris

first: Michiko

last: Kawakita

address: 1 av. Claude-Vellefaux

institute: INSERM

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profiling of Pml wt and Pml KO mice liver after fasted 6h

summary: The Pml gene is essential to the formation of PML nuclear bodies, domains which have been associated with various functions such as apoptosis/senescence, DNA repair and cell proliferation( Lallemand-Breitenbach 2010). PML-NBs formation is regulated by cellular stress including oxidative stress(Jeanne 2010, de The 2012).  To investigate the role of PML in ROS response in vivo, we analyse the expression difference betweem Pml wt and Pml KO under fasted condition, which easily up-regulate ROS in BALB/cByJ background

overall_design: Liver samples were collected from Pml wt and Pml KO ad libitum(2 each) or fasted for 6 hours(3 each). Samples are stabilized in RNAlater and stored in -20°C.  Two ad libitum samples are used as a control. Fasted samples are 3 each genotype. Total RNA samples were extracted using QIagen kit.  Gene expression analysis was done in the plateform of Institute Curie using Affmetrix

last: Niwa-Kawakita

first: Omar

last: Ferhi

first: Hassane

last: Soilihi

first: Morgane

last: Le Bras

first: Valerie

last: Lallemand-Breitenbach

first: Hugues

last: de The


title: Epidermal growth factor receptor expression licenses T helper-2 cells to function in a T cell receptor-independent fashion

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Gastro-intestinal helminth infections trigger the release of interleukin-33 (IL-33), which induces type 2 helper T-cells (Th2 cells) at the site of infection to produce IL-13, thereby contributing to host resistance in a T cell receptor (TCR)-independent manner. Here we show that as a prerequisite for IL-33 induced IL-13 secretion, Th2 cells required the expression of the Epidermal Growth Factor Receptor (EGFR) and of its ligand, Amphiregulin, for the formation of a signaling complex between T1/ST2 (the IL-33R) and EGFR. This shared signaling complex allowed IL-33 to induce the EGFR-mediated activation of the MAP-kinase signaling pathway and consequently the expression of IL-13. Lack of EGFR expression on T cells abrogated IL-13 expression in infected tissues and impaired host resistance. EGFR expression on Th2 cells was TCR-signaling dependent, and therefore our data reveal a mechanism by which antigen-presentation controls the innate effector function of Th2 cells at the site of inflammation.

overall_design: RNA sequencing of CD4+ CD25− CD45Rbhi cells from spleens of wt and EGFRΔCD4 mice

first: M


summary: PML nuclear bodies (NBs) recruit partner proteins -including p53 and  its regulators- controlling their abundance or function. Investigating arsenic sensitivity  of acute promyelocytic leukemia, we proposed that PML oxidation  promotes NB-biogenesis. Yet, physiological links between PML and oxidative  stress response in vivo remain unexplored. Here we identify PML as a reactive  oxygen species (ROS) sensor. Pml-/- cells accumulate ROS, while PML  expression decreases ROS levels. Unexpectedly, Pml-/- embryos survive acute  glutathione depletion. Moreover, Pml-/- animals are resistant to acetaminophen  hepatotoxicity or fasting-induced steatosis. Molecularly, Pml-/- animals fail to  properly activate oxidative stress-responsive p53 targets, while NRF2 response  is accelerated. Finally, in an oxidative stress-prone background, Pml-/- animals  display a longevity phenotype, likely reflecting decreased basal p53 activation.  Thus, similar to p53, PML exerts basal anti-oxidant properties, but also drives  oxidative stress-induced changes in cell survival/proliferation or metabolism in  vivo. Through NB-biogenesis, PML therefore couples ROS-sensing to p53  responses, shedding a new light on PML role in senescence or stem cell  biology.

overall_design: Human primary fibroblasts transduced by empty or PML4-expressing viruses. Replicates of 2 independent experiments. Comparative gene expression analysis was done using Affymetrix U133plus v2.1 array (Curie Institute)

last: Fehri

first: Valérie

last: de Thé


title: Expression analysis of microRNA  by expression microarrays  of rectal cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

status: Public on Sep 21 2017

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

summary: We performed the expression microarray experiments for miRNA of rectal cancer tissue.

overall_design: microRNA were extracted from primary tumor of 137 rectal cancer patients, hybridized and scanned with Affymetrix miRNA 3.0 Arrays

first: Takashin

last: Akiyoshi


title: Genome-wide analysis of YAP and TFCP2 occupancy and regulated expression in liver cancer cells

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University


title: Determination of trastuzumab responsive microRNAs in SKBR3 and BT474 cells.

city: Ankara

first: Bala

last: Gur Dedeoglu

address: Dogol cad.

country: Turkey

institute: Ankara University Biotechnology Institute

summary:
To develop gene-miRNA and pathway-miRNA networks in trastuzumab treatment, we performed a recent  miRNA microarray profiling in trastuzumab treated/untreated SKBR3 and BT474 cell lines.
The cells were plated at a starting density of 2 millions in 100 mm cell culture dishes and then, they were treated with 6 ug/mL trastuzumab and PBS in two replicates. Total RNA was isolated with the TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

overall_design: RNA samples were isolated after 144h trastuzumab treatment.  A total of 4 samples from BT474 cells (2 from trastuzumab treated and 2 from PBS treated) and 4 samples from SKBR3 cells (2 from trastuzumab treated and 2 from PBS treated) were analyzed.

first: Emine

last: Cilek

middle: G

last: Dedeoglu


title: Chromatin State and Binding of Lhx2 and Ebf in Olfactory Sensory Neurons

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: The monoallelic expression of olfactory receptor (OR) genes is governed by the formation of large domain of heterochromatin over OR clusters and by enhancer elements embedded within these heterochromatic domains. Here we show that OR enhancers are bound by Ebf and Lhx2 in mature olfactory sensory neurons (OSNs), and that in the same cell population these sites are flanked by a histone modification characteristic of active enhancers (H3K7ac) as well as modifications characteristic of heterochromatin (H3K9me3 and H3K79me3). We use ATAC-Seq to show that the pattern of OR enhancer accessibility in subpopulations of mOSNs that express a specific OR gene is very similar to the pattern in mOSNs as a whole. Finally, we perturb Ebf and Lhx2 in mOSNs by conditionally deleting Lhx2 or by expressing an Ebf-Lhx2 fusion protein. We profile the effect of these perturbations on OR gene expression by RNA-seq and on chromatin state by ChIP-Seq and ATAC-Seq.

overall_design: Four types of data are included: ATAC-Seq to identify functional elements, Crosslinked ChIP-Seq to identify sites bound by Ebf and Lhx2, native MNase digested ChIP-Seq to identify regions enriched for specific histone modifications (H3K27ac, H3K9me3, H3K79me3), and RNA-Seq to profile changes in gene expression following perturbation of Lhx2 or expression of a dominant negative protein. ChIP-Seq data sets include an input control. The number of replicates varies between experiments.

first: Stavros

last: Lomvardas


title: Effect of cell free nucleic acids extracted from blood products on human leukocytes gene regulation: mononuclear cells and macrophages

first: Celine

last: Delucinge

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


title: Genome-wide analysis of YAP and TFCP2 down-regulated genes in liver cancer cells

summary: To identify YAP and TFCP2 co-regulated genes, RNA-seq was also performed in Bel-7402 cells before and after knocking down YAP or TFCP2. From the RNA-seq data, 2165 genes were found that were possibly co-regulated by YAP and TFCP2.

overall_design: Examination of YAP and TFCP2 down-regulated genes in Bel-7402 cells.

first: Xiao

last: Zhang


title: Function of human CD141+ DC and CD1c+ DC in a humanized mouse model in vivo

city: Woolloongabba

first: Kristen

last: Radford

address: Translational Research Institute, 37 Kent St

institute: Mater Research Institute – University of Queensland

summary: Human immune cell subsets develop in immunodeficient mice following reconstitution with human CD34+ haematopoietic stem cells. These “humanized” mice are useful models to study human immunology and human-tropic infections, autoimmunity and cancer. However, some human immune cell subsets are unable to fully develop or acquire full functional capacity due to a lack of cross-reactivity of many growth factors and cytokines between species. “Classical” (c) DC arise from a separate precursor to monocytes and initiate and direct T cell responses. In mice they can be further categorized into cDC1, which mediate Th1 and CD8+ T cell responses, and cDC2, which mediate Th2 and Th17 responses. The gene expression profiles and phenotype human CD141+ DC and CD1c+ DC subsets align with mouse cDC1 and cDC2 respectively but there are also key interspecies differences. Human CD141+ DC and CD1c+ DC develop in humanized mice but the extent to which they resemble their human blood counterparts is not yet known. We therefore analyzed the gene expression profiles of CD141+ DC and CD1c+ DC in humanized mice and demonstrated that they closely resemble those in human blood, making this an attractive model in which to study human DC in vitro or on vivo. We further used this model to explore changes in DC subsets after activation with TLR3 and TLR7/8 ligands, poly I:C and R848 in vivo. A core panel of genes consistent with DC maturation status were upregulated by both subsets. R848 specifically upregulated genes associated with Th17 responses by CD1c+ DC, whilst poly I:C upregulated IFN-λ genes specifically by CD141+ DC. Thus CD141+ DC and CD1c+ DC share a similar activation profiles in vivo but also have induce unique signatures that support specialized roles in CD8+ T cell priming and Th17 responses respectively.  '

overall_design: Gene expression analysis CD1c+ and CD141+ dendritic cells isolated by FACs from humanized mice bone marrow. Response to PolyI:C, R848, and a combination was studied by treatment of the donor mouse 2 hours prior to cell isolation.

first: Yoshihito

last: Minoda

first: Isaac

last: Virshup

first: Ingrid

last: Rojas

first: Oscar

last: Haigh

first: John

last: Miles

first: Christine

last: Wells


title: Evaluation of animal models of AD

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: This study was designed to measure expressional profile of genes from brain tissues of animal models of AD.

overall_design: Expressions of genes in the brain was measured from diverse models of AD. Total RNA was isolated and was subject to single channel microarray.


title: Expression data from PEG-GNRs treated cells

first: Hongyuan

last: Song

state: --- Select One ---

address: Department of Ophthalmoloty, Changhai Hospital, No. 168 Changhai Road, Yangpu District

department: Ophthalmology

institute: Changhai Hospital, Second Military Medical University

summary: We used microarrays to detail the global programme of gene expression treated with PEG-GNRs and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: HREC treated with PEG-GNRs were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression profiles for Human retinal micro endothelial cells (HREC) treated with PEG-GNRs.We divided two groups: (T1) control group were cultured HREC without treatment (T2) PEG-GNRs treated group were HREC treated with 100μg/mL PEG-GNRs


title: N-methyl-D-aspartate receptors mediate activity-dependent down-regulation of potassium channel genes during the expression of homeostatic intrinsic plasticity

city: Urbana

first: Hee Jung

last: Chung

address: 407 South Goodwin Avenue, 524 Burrill Hall

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary: Using whole-cell patch clamp recording and unbiased gene expression profiling in rat dissociated hippocampal neurons cultured at high density, we demonstrate here that chronic activity blockade induced by the sodium channel blocker tetrodotoxin leads to a homeostatic increase in action potential firing and down-regulation of potassium channel genes. In addition, chronic activity blockade reduces total potassium current, as well as protein expression and current of voltage-gated Kv1 and Kv7 potassium channels, which are critical regulators of action potential firing. Importantly, inhibition of N-Methyl-D-Aspartate receptors alone mimics the effects of tetrodotoxin, including the elevation in firing frequency and reduction of potassium channel gene expression and current driven by activity blockade, whereas inhibition of L-type voltage-gated calcium channels has no effect.

overall_design: High-density cultures of dissociated hippocampal neurons (330 neurons/cm2) were treated for 48 hours with vehicle contrl (DMSO), the sodium channel blocker tetrodotoxin (TTX) or the GABA-A receptor antagonist bicuculine, four replicates each

first: KwanYoung

last: Lee

first: Sara

last: Royston

first: Max

middle: O

last: Vest

first: Daniel

last: Ley

first: Seungbae

first: Eric

last: Bolton

first: HeeJung


title: Analysis of temporal lens gene expression microarrays to expand the eye gene discovery tool iSyTE

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary:
Purpose: While the bioinformatics gene-discovery tool iSyTE (integrated Systems Tool for Eye gene discovery) has proved effective in identifying new cataract-linked genes, it primarily depended on lens-enriched expression of just three wild-type mouse embryonic stages. To increase iSyTE’s efficacy, a broad range of embryonic (E) and postnatal (P) lens microarray datasets from wild-type and specific gene-perturbation mutant mice were analyzed and a new web-interface was developed for their effective access and downstream-analysis.
Methods: Five new mouse lens microarrays were generated and analyzed with all publicly available Affymetrix and Illumina lens datasets representing the stages E9.5, E10.25, E10.5, E11.5, E12.5, E15.5, E16.5, E17.5, E19.5, P0, P2, P4, P8, P12, P20, P28, P30, P42, P52, P56, P60 and mouse mutants for the genes: Brg1, CBP:p300, E2f1:E2f2:E2f3, Foxe3, Hsf4, Klf4, Mafg:Mafk, Notch2, Pax6, Sparc, Tdrd7.
Results: The integrated lens microarray analysis accurately reflects established gene expression patterns and defines a new lens-signature gene-set for embryonic and postnatal stages that includes several novel candidates namely, Grifin, Ogn, Fabp5, Mboat1, Tmem40, Dhx32, Aldoc, Pgam2, Hmgn3, Mocs2, Gprc5b, Gstm1, Npl, and Zbtb8b. Combined analyses of 32 developmental/genetic data-conditions identifies several new transcription and signaling factors that potentially function in lens development and/or homeostasis.
Conclusions: The updated iSyTE web-interface: (1) comprehensively informs on normal lens developmental and cataract-associated transcriptome dynamics and identifies new high-priority candidates for these processes, and (2) offers user-friendly visualization.

overall_design: Microarray comparison of lenses from multiple embryonic and postnatal stages vs. embryonic whole body control and mutant vs. control. This dataset includes lens samples from multiple postnatal stages, and embryonic whole body (minus eye) controls.

first: Salil

last: Lachke

first: Atul

last: Kakrana


title: Gene expression profiling of Pml wt and Pml KO mice liver with acetaminophen (apap) overdose (300mg/kg) i.p.

first: Michiko

last: Kawakita

summary: The Pml gene is essential to the formation of PML nuclear bodies, domains which have been associated with various functions such as apoptosis/senescence, DNA repair and cell proliferation( Lallemand-Breitenbach 2010). PML-NBs formation is regulated by cellular stress including oxidative stress(Jeanne 2010, de The 2012).  To investigate the role of PML in ROS response in vivo, we analyse the expression difference to the acetaminophen toxicity, which is initiated by ROS, in Pml wt and Pml KO mice.

overall_design: Liver samples were collected from Pml wt and Pml KO untreated or treated with acetaminophen at 2h or 6h time points. 2 samples each.  Samples are stabilized in RNAlater and stocked in -20°C. Untreated samples are used as a control. Total RNA samples were extracted using Qiagen kit. Gene expression analysis was done in the plateform of Institute Curie using Affmetrix

last: Niwa-Kawakita

first: Omar

last: Ferhi

first: Hassane

last: Soilihi

first: Morgane

last: Le Bras

first: Valerie

last: Lallemand-Breitenbach

first: Hugues

last: de The


title: Bach2 promotes B cell receptor-induced proliferation of B lymphocytes and represses cyclin-dependent kinase inhibitors

city: Sendai

first: Akihiko

last: Muto

state: Miyagi

address: Seiryou-machi 2-1

department: Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Bach2 (BTB and CNC homology-2) is a transcriptional repressor which is required for the formation of the germinal center (GC) and reactions including class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes in B cells within the GC. While BCR-induced proliferation is essential for GC reactions, the function of Bach2 in regulating B cell proliferation has not been elucidated. In this study, we demonstrate that Bach2 is required to sustain high levels of B cell proliferation in response to BCR signaling. Following BCR engagement in vitro, B cells from Bach2-deficient (Bach2-/-) mice showed lower incorporation of 5-bromo-2'-deoxyuridine (BrdU) and reduced cell cycle progression compared with wild-type (WT) cells. Bach2-/- B cells also underwent increased apoptosis as evidenced by an elevated frequency of sub-G1 cells and early apoptotic cells. Transcriptome analysis of BCR-engaged B cells from Bach2-/- mice revealed reduced expression of the anti-apoptotic gene Bcl2l1 encoding Bcl-XL, and an elevated expression of cyclin-dependent kinase inhibitor (CKI) family genes including Cdkn1a, Cdkn2a and Cdkn2b. Reconstitution of Bcl-XL expression partially rescued the proliferation defect of Bach2-/- B cells. Chromatin imunoprecipitation (ChIP) experiments showed that Bach2 bound to the CKI family genes, indicating that these genes are direct repression targets of Bach2. These findings identify Bach2 as a requisite factor for sustaining high levels of BCR-induced proliferation, survival and cell cycle progression, and promotes expression of Bcl-XL and repression of CKI genes, respectively. BCR-induced proliferation defects may contribute to impaired GC formation observed in Bach2-/- mice.

overall_design: In order to reveal the molecular mechanism of prolifrerative difects of Bach2-/- follicular zone B cells in response to B cell receptor signaling, gene expression profiles of Bach2-/- follicular zone B cells were compared to its of wild-type follicular zone B cells before and after B cell receptor stimulation.

first: Yuichi

last: Miura

first: Mitsuyo

last: Matsumoto

first: Kazuhiko

last: Igarashi


title: Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures

status: Public on Sep 20 2017

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Drive, Alway M-341

department: Genetics

institute: Stanford University

summary: We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) to quantify RNA editing levels at targeted sites in 32 isofemale lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate).  Editing levels were compared between different populations at 25˚C , and were also compared between 25˚C and 18˚C within populations.

overall_design: For each of the 32 isofemale fly lines from 'Evolution Canyon', quantification of RNA editing levels in the whole bodies of 3-5 day old male flies raised at 25˚C or 18˚C through RT-PCR amplification of 605 loci.  Two biological replicates are represented per fly line.

first: Arielle

last: Yablonovitch

first: Kexin

first: Eugenia

last: Rashkovetsky

first: Abraham

middle: B

last: Korol

first: Pawel

last: Michalak

first: Eviatar

last: Nevo


title: The Ets-family transcription factors PU.1 and SpiB are redundantly required by mature B cells to sense and respond to environmental cues

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: Humoral immunity requires B cells to respond to multiple stimuli, including antigen, membrane and soluble ligands and microbial products. Ets-family transcription factors regulate many aspects of hematopoiesis, although their roles in humoral immunity have proven difficult to decipher, potentially due to redundancy between the family members. Here we show that mice lacking both PU.1 and SpiB in mature B cells are unable to respond protein antigen, preventing germinal center formation and high-affinity antibody production. Mutant B cells also showed impaired survival following engagement of the CD40 and TLR pathways, but paradoxically enhanced plasma cell differentiation. PU.1 and SpiB control the expression of many components of the BCR signaling pathway and the receptors for CD40L, BAFF and toll ligands. Thus PU.1 and SpiB function enables B cells to appropriately respond to environmental cues.

overall_design: Transcriptional profiling of PU.1-/- and SpiB-/- activated B cells using RNA sequencing

first: Simon

middle: N

last: Willis

first: Yang

last: Liao

first: Stephen

last: Nutt


title: Expression data from MDS patients with der(1;7)(q10;p10)

city: Suzhou

first: Tongtong

last: Zhang

address: shizi street 188

institute: the First Affiliated Hospital of Soochow University

summary: Gene expression profiling was significantly different between der(1;7)(q10;p10) and -7/7q- patients by cluster analysis. There were total 1628 dysregulated genes in both der(1;7)(q10;p10) and -7/del(7q) cohorts.

overall_design: In order to identify the possible candidate genes implicated in the initiation or maintenance of MDS patients with der(1;7)(q10;p10), we  performed the gene expression array (Affymetrix Human Genome U133 Plus 2.0 Array, USA) in 7 der(1;7)(q10;p10)(A1,A2,A3,A5,A6,A11,A12) and 6 -7/7q- samples(B3,B4,B5,B6,B8,B9).

last: Xu

first: Jinlan

last: Pan

first: Hongzhi

first: Qinrong

last: Wang

first: Lijun

last: Wen

first: Depei

last: Wu

first: Aining

last: Sun

first: Suning

last: Chen


title: Genome-wide analysis of YAP and TFCP2 binding DNA in liver cancer cells

first: Weisheng

last: Zheng

summary: To seek additional evidence that YAP closely interacts with TFCP2, we performed ChIP-seq assays in Bel-7402 cells using anti-TFCP2 or anti-YAP antibodies. We found that a subset of YAP binding regions overlapped with the TFCP2-occupied sites, suggesting that YAP- and TFCP2-regulated transcriptional outputs are likely correlated.

overall_design: Examination of YAP and TFCP2 binding DNA in Bel-7402 cells.

first: Xiao


title: Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates

city: Stanford

first: Jin

last: Li

summary: We performed RNA-seq to profile gene expression in the heads and whole bodies of 32 isofemale fly lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate).  We also measured RNA editing levels in the head tissue of these flies.

overall_design: For each of the 32 isofemale fly lines from 'Evolution Canyon', gene expression profiles of whole bodies and heads, along with RNA editing profiles of heads of 3-5 day old male flies through RNA-seq.

first: Arielle

last: Yablonovitch

first: Jeremy

last: Fu

first: Kexin

first: Eugenia

last: Rashkovetsky

first: Abraham


title: The presence of satellite RNA exacerbates symptoms and transcriptomic response of Nicotiana benthamiana during peanut stunt virus infection

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: Peanut stunt virus (PSV) of Cucumovirus genus is serious vegetables and legume pathogen. Some PSV strains are associated with satellite RNA (satRNA). SatRNAs are dependent on their helper virus and their presence usually attenuates the severity of the disease symptoms induced by the virus. However, the final outcome of satRNA pathogenesis modification depends on the satRNA sequence, virus strain and external conditions. In this study we elucidated  the plant response to PSV-G strain which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA which causes exacerbation of pathogenesis in Nicotiana benthamiana. In order to study plant response to PSV infection and to explain mechanisms underlying symptoms exacerbation caused by satRNA we did transcriptome profiling of N. benthamiana challenged by PSV with/ without satRNA using species-specific microarrays.

overall_design: Agilent microarrays in 2x105k format (two microarrays per slide) were used  for hybridization of labeled RNA from upper parts of treated N. benthamiana plants (infected PSV-G, PSVG+satRNA or mock-inoculated) labeled with Cy5 versus a common reference (ref): pooled RNA extracted from a mix of tissues and treatments, labeled with Cy3. Three biological replicates were used for each treatment.

first: Michal

last: Goralski

first: Aleksandra

last: Obrepalska-Steplowska


title: Comprehensive understanding of identities and antigenicities of surface and secreted proteins in Toxoplasma gondii tachyzoites

city: Beijing

first: Feng

last: Xue

state: Beijing

address: No. 95, Yong'an Road

department: Department of Microbiology and Parasitology

institute: Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University

summary: Toxoplasma gondii is an obligate intracellular parasite which can cause toxoplasmosis. Surface and secreted proteins of T. gondii play important roles in infection and immunity, and also are antigen targets in immunological diagnosis and vaccine development. However, it is difficult to investigate identities and antigenicities of surface and secreted proteins due to limitation of surface protein extraction methods. In this study, a total of 785 potential surface and secreted proteins of T. gondii RH tachyzoites were identified using a method combination of biotin labeling, avidin chromatography isolation, and high flux proteomics (LC-MS/MS). Among the highly-expressed 65 proteins, 43 proteins (66%) were originally annotated as surface or secreted proteins in the released T. gondii genomes, which proved the method combination to be a credible strategy. Furthermore, the transcriptomic responses and cytokine secretions induced by the isolated proteins, the live T. gondii RH tachyzoites infection, and the live pathogenic E. coli infection, in the human peripheral blood monocyte THP-1 cell lines, were comparatively analyzed to reveal antigenicities and immunobiological properties of T. gondii surface and secreted proteins. The transciptomic profiles induced by the isolated proteins were similar to those induced by the live bacterium infection, but were different from those induced by the live parasite infection. Contrary to the low cytokine secretion induced by the live parasite infection, the isolated proteins induced significant cytokine and chemokines secretion. Especially, the secretions of several chemokines induced by the isolated proteins were even higher than those induced by the live bacterium infection. These data suggested that T. gondii surface and secreted proteins were effective antigens, while the live parasite could evade the host innate immunity. This study comprehensively revealed the identities and antigenicities of T. gondii surface and secreted proteins, which laid foundation for further screening new T. gondii antigens, developing immunological diagnosis methods, and studying host immune response to T. gondii infection.

overall_design: Human peripheral blood monocyte THP-1 cell lines were induced by the isolated T. gondii surface proteins, the live T. gondii RH tachyzoites infection, and the live pathogenic E. coli infection. Two biological replicates were designed for each sample type. There were totally 8 hybridizations included in this submission.


title: H. salinarum R1 wildtype vs cyc-

city: Bloemfontein

first: Walter

middle: Joseph

last: Muller

state: Free state

address: Decan Street

department: Biotechnology

country: South Africa

institute: University of the Free State

summary: Investigating the possible physiological role of CYP174A1 (cyc) in H. salinarum

overall_design: Wild type and Knock out strains were each cultured in triplicate to either logarithimic growth or stationary growth phase. Replicates were pooled before hybridization.

first: Melinda

middle: D

last: Capes

first: Shiladitya

last: DasSarma

first: Esta

last: van Heerden

first: Martha

middle: S

last: Smit


title: bli-1 12 DAG continuous light grown whole seedlings analyzed on a 44k single color Agilent microarray

city: Berlin

first: Daniel

last: Schubert

address: Königin-Luise-Str. 12-16 Raum 105

department: Institut für Biologie

institute: Freie Universität Berlin

summary:
Polycomb group (PcG) proteins are key epigenetic regulators of development. The highly conserved Polycomb repressive complex 2 (PRC2) represses thousands of target genes by trimethylating H3K27 (H3K27me3). Plant specific PcG components and functions are largely unknown, however, we previously identified the plant-specific protein BLISTER (BLI) as a PRC2 interactor. BLI regulates PcG target genes and promotes cold stress resistance. To further understand the function of BLI, we analyzed the transcriptional profile of bli‑1 mutants.
The goal of this experiment was to examine the transcriptional profile of bli-1 seedlings and compare it to the wild type Col-0.

overall_design: Each two biological replicates of Col-0 and bli-1 12 day old seedlings grown under continuous light conditions (grown on solid half-strength Murashige and Skoog medium supplemented with 0.5% sucrose and 0.05% MES) were compared here. Transcript levels of the two genotypes were evaluated using a 44k single colour Agilent microarray.

first: Julia

middle: A

last: Kleinmanns

first: Nicole

last: Schatlowski

first: David

last: Heckmann


title: Genome-wide analysis of changes in gene expression induced by Eph and ephrin stimulation of mouse neural progenitors

city: Toulouse

first: Alice

last: DAVY

address: 118 route de Narbonne

department: CBI

institute: CNRS

summary: The hypothesis tested in the present study was that activation of Eph or ephrin signaling in neural progenitors induces a transcriptional response which participate in the control of progenitor self-renewal. Results provide important information on transcriptional changes in response to activation of Eph receptors. They also show that activation of ephrin signaling does not induce a transcriptional response at genome-wide level.

overall_design: Total RNA obtained from dissociated mouse embryonic neural progenitors incubated for 2 or 6 hours with recombinant Eph or ephrin molecules compared to control treated neural progenitors.

last: Davy


title: Melanoma cell lines treated with dabrafenib ± trametinib

city: Macquarie University

first: Helen

last: Rizos

address: 2 Technology Place

institute: Macquarie University

summary: Rapid resistance to BRAF inhibitors in BRAFV600-mutant metastatic melanoma has produced an urgent need for new treatment options. BRAF inhibitor resistance commonly involves reactivation of mitogen-activated protein kinase (MAPK) signaling and yet inhibition of downstream kinases has not circumvented resistance, partly because MAPK is regulated via a complex network of feedback mechanisms that influence pathway rebound. To examine the transcriptome responses of melanoma cells to MAPK inhibition, a panel of 11 BRAFV600-mutant melanoma cell lines were treated with control (DMSO), 100nM dabrafenib alone (i.e BRAF inhibitor monotherapy) or 100nM dabrafenib + 10nM trametinib (i.e combination BRAF + MEK inhibition) for 24h.

overall_design: Eleven melanoma cell lines were grown in DMEM/10%FBS and treated with either 100nM dabrafenib and/or 10nM trametinib or DMSO for 24h.

first: Gulietta

last: Pupo


title: Gene expression profiling in LoVo-P compared with LoVo-C cells

city: Guangzhou

first: Zhonghua

last: Chu

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital,Sun Yat-sen University

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

summary: The differential expression of mRNA in LoVo-P cells compared with LoVo-C cells was successfully detected using the Arraystar Human LncRNA/mRNAArray V4.0, that used for the global profiling of 20730 human mRNA and 40173 long non-coding RNA (LncRNA) transcripts.

overall_design: In the study presented here, colorectal cancer cell line LoVo expressed low levels of PRL-3, and we selected LoVo cells for constructing PRL-3 overexpression lines. The stable transfection of pAcGFP-PRL-3 (LoVo-P) and pAcGFP (LoVo-C) vectors was achieved, resulting in the over expression of PRL-3 and control vector. LoVo-P and LoVo-C cells was used to acquire expression profiles of a total of 20730 human mRNA and 40173 long non-coding RNA (LncRNA) transcripts

first: Qiusheng

last: Lan


title: Mitotic Transcription and Waves of Gene Reactivation During Mitotic Exit

city: Philadelphia

first: Katherine

middle: Claire

last: Palozola

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: The genome is thought to be transcriptionally silent during mitosis. Technical limitations have prevented the sensitive mapping of mitotic transcription and transcription reactivation during mitotic exit, and thus the networks by which transcriptome dynamics govern the generation of daughter cells have been unclear. We used 5-ethynyluridine to pulse-label intact transcripts during mitosis and mitotic exit and find that the first round of transcription activates genes that are involved in macromolecular synthesis, rather than cell identity. Many interphase genes exhibit residual transcription in mitosis, as confirmed by different methods of  assessment, and a subset of genes are more highly transcribed in mitosis than in interphase. We suggest that mitotic transcription may serve an epigenetic function in restoring proper transcription patterns during mitotic exit.

overall_design: All samples in triplicates A, B, and C; experimental time points = 0, 40, 80, 105, 165, 300, EU; No label control = NoEU. Samples in triplicates D, E, F: mitotic, async; samples in duplicate: NoEU D, E.

middle: C

first: Greg

last: Donahue

first: Gregory

last: Grant

first: Justin

last: Becker

first: Allison

last: Cote

first: Hong

last: Liu

first: Hongtao

last: Yu

first: Arjun

last: Raj

first: Kenneth

last: Zaret


title: Protein Arginine Methyltransferase 5 (PRMT5) has prognostic relevance and is a druggable target in Multiple Myeloma

status: Public on Sep 19 2017

city: Boston

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Arginine methyltransferases critically regulate cellular homeostasis by modulating the functional outcome of their substrates. The protein arginine methyltransferase 5 (PRMT5) is an enzyme involved in growth and survival pathways promoting tumorigenesis. However, little is known about the biologic function of PRMT5 and its therapeutic potential in multiple myeloma (MM). In the present study, we identified and validated PRMT5 as a new therapeutic target in MM. PRMT5 is overexpressed in patient MM cells and associated with decreased progression free survival and overall survival. Either genetic knockdown or pharmacological inhibition of PRMT5 with the inhibitor EPZ015666 significantly inhibited growth of both cell lines and patient MM cells. Furthermore, PRMT5 inhibition abrogated NF-kB signaling. Interestingly, mass spectrometry identified a tripartite motif-containing protein 21 TRIM-21 as a new PRMT5-partner, and we delineated a TRIM21-dependent mechanism of NF-kB inhibition. Importantly, oral administration of EPZ015666 significantly decreased MM growth in a humanized murine model of MM. These data both demonstrate the oncogenic role and prognostic relevance of PRMT5 in MM pathogenesis, and provide the rationale for novel therapies targeting PRMT5 to improve patient outcome.

overall_design: We compared KMS11 cell lines with and without EPZ025666 treatment

first: Annamaria

last: Gulla

middle: K

last: Anderson


title: JNK activation of BIM promotes hepatic  oxidative stress, steatosis and insulin resistance in obesity

city: Fitzroy

first: Esteban

last: Gurzov

state: Victoria

address: 9 Princes Street

institute: St Vincent’s Institute of Medical Research

summary: The BCL-2 family are crucial regulators of the mitochondrial pathway of apoptosis in normal physiology and disease. Besides their role in cell death, BCL-2 proteins have been implicated in the regulation of mitochondrial oxidative phosphorylation and cellular metabolism. However, it remains unclear whether these proteins have a physiological role in glucose homeostasis and metabolism in vivo. Here we report that fat accumulation in the liver increases JNK-dependent BIM expression in hepatocytes. We generated liver-specific BIM knockout (BLKO) mice to determine the consequences of hepatic BIM deficiency in diet-induced obesity. BLKO mice had lower hepatic lipid content, increased insulin signalling and improved global glucose metabolism. Consistent with this, lipogenic and lipid uptake genes were downregulated and lipid oxidation enhanced in obese BLKO mice. Moreover, oxidative stress, oxidation of protein tyrosine phosphatases and activation of PPAR-g/STAT1/CD36 were decreased in livers/hepatocytes from BLKO mice, suggesting a mechanism for their metabolic phenotype. Importantly, adenovirus-mediated knockdown of BIM reduced fat accumulation and improved insulin sensitivity in high fat fed mice. Our data postulate BIM as a novel therapeutic target regulating mitochondrial bioenergetics and liver function in obesity.

overall_design: 6 batch of C57BL/6 mouse hepatocytes were RNA sequenced: 3 with tissue-specif BIM knock-out and 3 wild-type

first: Jean-Valery

last: Turatsinze


title: Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

first: Jin

last: Li

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Oocyte Specific Homeobox 1 (Obox1) Facilitates Somatic Cell Reprogramming by Promoting Mesenchymal-to-Epithelial Transition and Mitigating Cell Hyper-proliferation

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

institute: tongji university

summary: Mammalian oocytes possess fascinating unknown factors, which can reprogram terminally differentiated germ cells (sperm) or somatic cells into totipotent embryos. Here, we demonstrate that oocyte specific homeobox 1 (Obox1), an oocyte-specific factor, can markedly enhance the generation of induced pluripotent stem cells (iPSCs) from mouse fibroblasts in a proliferation-independent manner and can replace Sox2 to achieve pluripotency. Overexpression of Obox1 can greatly promote mesenchymal-to-epithelial transition (MET) at early stage of OSKM-induced somatic cell reprogramming and meanwhile, the cell hyper-proliferation can be significantly slowed down. Subsequently, the proportion of Thy1 negative cells and Oct4-GFP positive cells increased dramatically. Further analysis of gene expression and targets of Obox1 during reprogramming indicates that the expression of Obox1 can promote epithelial genes expression and repress cell cycle-related genes expression. Taken together, we conclude that the oocyte-specific factor Obox1 serves as a strong activator for somatic cell reprogramming through promoting the MET and mitigating cells hyper-proliferation.

overall_design: The reprogrammable MEFs derived from the transgenic mice carrying the tetO-OSKM transgene and Oct4-GFP/Rosa26-M2rtTA were used in the experiments. The reprogrammable MEFs that were not induced with doxycycline were designated as “MEF” (control). The reprogrammable cells with or without Obox1’s overexpression were induced with doxycycline (1ug/ml) for 3 days. The cells were harvested and performed RNA sequencing (RNA-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq).

first: Li

first: Shiyang

last: Zeng


title: Expression data from mice liver drinking Hydrogen water

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

institute: Nagoya University Graduate School of Medicine

summary:
Liver RNA samples from C57BL6 mice drinking Hydrogen water for 4 weeks
We used microarrays to detail the gene expression after drinking hydrogen water.

overall_design: We analyzed mRNA expression in liver from 4 control and 4 Hydrogen drinking mice using the Affymetrix  GeneChip Mouse Gene 1.0 ST Array. Array data was proceeded by Affymetrix Expression console sftoware.

first: Kinji

last: Ohno


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases II

first: Oleg

last: Butovsky

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

summary:
Microglia play a pivotal role in the maintenance of brain homeostasis, but lose their homeostatic function during the course of neurodegenerative disorders. We identified a specific APOE-dependent molecular signature in microglia isolated from mouse models of amyotrophic lateral sclerosis, multiple sclerosis and Alzheimer’s disease (SOD1, EAE and APP-PS1) and in microglia surrounding neuritic A-plaques in human Alzheimer’s disease brain. This is mediated by a switch from a (M0)-homeostatic to (MGnD)-neurodegenerative phenotype following phagocytosis of apoptotic neurons via the TREM2-APOE pathway. TREM2 induces APOE signaling which is a negative regulator of the transcription program in M0-homeostatic microglia. Targeting the TREM2-APOE pathway restores the M0-homeostatic signature of microglia in APP-PS1 and SOD1 mice and prevents from neuronal loss in an acute model of neurodegeneration. In SOD1 mice, TREM2 regulates MGnD in a gender-dependent manner. APOE-mediated MGnD microglia lose their tolerogenic function. Taken together, our work identifies the TREM2-APOE pathway as a major regulator of microglial functional phenotype in neurodegenerative diseases and serves as a novel target to restore homeostatic microglia.
MG534 custom-design Nanosting chips were used to identify disease-associated vs. homeostatic molecular microglia signature in microglia in different disease models and transgenic models.

overall_design: Nanostring MG534 chip profile of FCRLS+ sorted microglia.  Note: data show mRNA transcriptoms/100ng RNA

first: O


title: Ronin governs early heart development by controlling core gene programs

city: New York

first: Marion

middle: Dejosez

last: Zwaka

state: NY

address: 1425 Madison Ave

department: Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

summary: Ronin (THAP11), an idiosyncratic DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence through which it controls a variety of developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions elsewhere in development. Here, we present evidence indicating that Ronin performs a novel function within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation through its control of a core set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me3 levels at specific target genes, suggesting the involvement of an epigenetic mechanism.  On the strength of these findings, we propose that Ronin activity during cardiogenesis may offer a template that could be used to understand how important gene programs are sustained across different cell types within a developing organ, such as the heart.

overall_design: Analysis of total RNA isolated from control and Nkx2.5- or MHC-driven Ronin knockout mouse heart tissue at different developmental stages

first: Thomas

middle: P


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases III

state: MA

summary:
Microglia play a pivotal role in the maintenance of brain homeostasis, but lose their homeostatic function during the course of neurodegenerative disorders. We identified a specific APOE-dependent molecular signature in microglia isolated from mouse models of amyotrophic lateral sclerosis, multiple sclerosis and Alzheimer’s disease (SOD1, EAE and APP-PS1) and in microglia surrounding neuritic A-plaques in human Alzheimer’s disease brain. This is mediated by a switch from a (M0)-homeostatic to (MGnD)-neurodegenerative phenotype following phagocytosis of apoptotic neurons via the TREM2-APOE pathway. TREM2 induces APOE signaling which is a negative regulator of the transcription program in M0-homeostatic microglia. Targeting the TREM2-APOE pathway restores the M0-homeostatic signature of microglia in APP-PS1 and SOD1 mice and prevents from neuronal loss in an acute model of neurodegeneration. In SOD1 mice, TREM2 regulates MGnD in a gender-dependent manner. APOE-mediated MGnD microglia lose their tolerogenic function. Taken together, our work identifies the TREM2-APOE pathway as a major regulator of microglial functional phenotype in neurodegenerative diseases and serves as a novel target to restore homeostatic microglia.
MG550 custom-design Nanosting chips were used to identify disease-associated vs. homeostatic molecular microglia signature in microglia in different disease models and transgenic models.

overall_design: Nanostring MG550 chip profile of FCRLS+ sorted microglia.  Note: data show mRNA transcriptoms/100ng RNA


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases


title: Critical functions for STAT5 tetramers in the maturation and survival  of natural killer cells

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interleukin-15 (IL-15) is essential for the development and maintenance of natural killer (NK) cells. IL-15 activates STAT5 proteins, which can form dimers or tetramers. We previously found that NK cell numbers are decreased in Stat5a-Stat5b tetramer-deficient double knockin (DKI) mice, but the mechanism was not investigated. Here we show that STAT5 dimers are sufficient for NK cell development, whereas STAT5 tetramers mediate NK cell maturation and the expression of maturation-associated genes. Unlike the defective proliferation of Stat5 DKI CD8+ T cells, Stat5 DKI NK cells have normal proliferation to IL-15 but are susceptible to death upon cytokine withdrawal, with lower Bcl2 and increased active caspases. These findings underscore the importance of STAT5 tetramers in maintaining NK cell homeostasis. Moreover, defective STAT5 tetramer formation could represent a cause of NK cell immunodeficiency, and interrupting STAT5 tetramer formation might serve to control NK leukaemia.

overall_design: ChIP-Seq analyses using purified splenic NK cells from both WT and Stat5 DKI, with rabbit IgG or anti-STAT5B. RNA-Seq analyses using total RNA from bone marrow NK cells and splenic NK subpopulations from both WT and Stat5 DKI mice.

first: Jian-Xin

last: Lin

first: Ning

last: Du

first: Majid

last: Kazemian

first: Tesfay

last: Gebriorgis

first: Rosanne

last: Spolski

first: Warren

middle: J

last: Leonard


title: Gene expression assessed by genome wide hybridization bead array in T84 polarized tight monolayers after challenge with celiac disease-associated bacteria [CTR 32 33 34]

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

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

overall_design: Stimulation with CD-associated bacteria was done from the apical side of polarized tight monolayers of T84 cells by replacing the medium in the upper chamber with 0.5 mL challenge medium containing 5x10^7 bacteria. For each stimulant three parallel wells were used to carry out the experiment and wells treated with challenge medium only served as experimental controls. The challenge was done under anaerobic condition and at 37°C for four hours. T84 tight monolayers were challenged with two isolates Prevotella jejuni (isolate CD3:33) P. histicola (isolate CD3:32) and P. melaninogenica (isolate CD3:34).

first: Grzegorz

last: Pietz


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases I

summary:
Microglia play a pivotal role in the maintenance of brain homeostasis, but lose their homeostatic function during the course of neurodegenerative disorders. We identified a specific APOE-dependent molecular signature in microglia isolated from mouse models of amyotrophic lateral sclerosis, multiple sclerosis and Alzheimer’s disease (SOD1, EAE and APP-PS1) and in microglia surrounding neuritic A-plaques in human Alzheimer’s disease brain. This is mediated by a switch from a (M0)-homeostatic to (MGnD)-neurodegenerative phenotype following phagocytosis of apoptotic neurons via the TREM2-APOE pathway. TREM2 induces APOE signaling which is a negative regulator of the transcription program in M0-homeostatic microglia. Targeting the TREM2-APOE pathway restores the M0-homeostatic signature of microglia in APP-PS1 and SOD1 mice and prevents from neuronal loss in an acute model of neurodegeneration. In SOD1 mice, TREM2 regulates MGnD in a gender-dependent manner. APOE-mediated MGnD microglia lose their tolerogenic function. Taken together, our work identifies the TREM2-APOE pathway as a major regulator of microglial functional phenotype in neurodegenerative diseases and serves as a novel target to restore homeostatic microglia.
MG468 custom-design Nanosting chips were used to identify disease-associated vs. homeostatic molecular microglia signature in microglia in different disease models and transgenic models.

overall_design: Nanostring MG468 chip profile of FCRLS+ microglia sorted from spinal cords of WT and SOD1 mice.  Note: data show mRNA transcriptoms/100ng RNA


title: Pitx1 directly controls the core limb development program to implement hindlimb identity [ChIP-Seq]

city: Montreal

first: Stephen

last: Nemec

state: Quebec

address: 110 Av. des Pins Ouest

country: Canada

institute: IRCM

summary: Pitx1, critical regulator of a limited hindlimb-specific gene network, targets the limb development program common to both fore- and hindlimbs in order to implement hindlimb-specific limb morphology.

overall_design: The gene regulatory networks governing forelimb vs. hindlimb development in mouse were investigated using expressing profiling of morphologically stage-matched e10.5 forelimbs and e11.0 hindlimbs, ChIPseq of chromatin marks, and ChIPseq of limb-specific transcription factors Pitx1 and Tbx5. The makeup of the Pitx1-directed components of the hindlimb gene network were investigated using expression profiling of Pitx1 null hindlimbs at two stages (e11.0 and e11.5).

first: Maëva

last: Luxey

first: Aurélie

last: Sung

first: Deepak

last: Jain

first: Tomi

last: Pastinen

first: Jacques

last: Drouin


title: P68 protein inhibited the growth and invasion of glioma cells by adjusting the DUSP5

city: Harbin

first: Rui

last: Wang

address: 157 BaoJian Road Nangang District, Harbin, Heilongjiang, China

institute: Harbin medical university

summary: Preliminary research shows that,The P68 protein was highly expressed in the glioma tissue specimen and was associated with the patient's survival.Inhibition of P68 protein expression in glioma cell lines inhibits the growth, invasion and appreciation of tumor cells.In this study, gene chip was used to search for new downstream genes DUSP5 that affect the growth of glioma.The expression of inhibition or overexpression of P68 protein in glioma cell lines was consistent with the expression of expression  DUSP5 and the effect of reduction DUSP5 on the growth of the tumor.The ability of the tumor to recover after the expression of DUSP5 expression in glioma cells was reduced,This indicates that P68 regulates the growth, increment and invasion of glioma cells.Through affymetrix  gene chip, we use 3 biological specimens.That is three SIP68 , control of the glioma cells that infect NC.Try to get P68 protein regulated downstream gene by knocking down P68 protein.

overall_design: Two samples, 3 replicates/sample were analyzed using Gene Chip.


title: Pitx1 directly controls the core limb development program to implement hindlimb identity


title: Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation [MeDIP-seq]

city: Research Triangle Park

first: Pishun

last: Li

state: NC

address: 111 T.W. Alexander Drive

department: ESCBL

institute: National Institute of Environmental Health Sciences

summary: Transposable elements, including endogenous retroviruses (ERVs), constitute a large fraction of the mammalian genome. They are transcriptionally silenced during early development to protect genome integrity and aberrant transcription. However, the mechanisms that control their repression are not fully understood. To systematically study ERV repression, we carried out an RNAi screen in mouse embryonic stem cells (ESCs) and identified a list of novel regulators. Among them, Rif1 displays the strongest effect. Rif1 depletion by RNAi or gene deletion led to increased transcription and increased chromatin accessibility at ERV regions and their neighboring genes. This transcriptional de-repression becomes more severe when DNA methylation is lost. On the mechanistic level, Rif1 directly occupies ERVs and is required for repressive histone mark H3K9me3 and H3K27me3 assembly and DNA methylation. It interacts with histone methyltransferases and facilitates their recruitment to ERV regions. Importantly, Rif1 represses ERVs in human ESCs as well, and the evolutionally-conserved HEAT-like domain is essential for its function. Finally, Rif1 acts as a barrier during somatic cell reprogramming, and its depletion significantly enhances reprogramming efficiency. Together, our study uncovered many previously uncharacterized repressors of ERVs, and defined an essential role of Rif1 in the epigenetic defense against ERV activation.

overall_design: ChIP-Seq profiling, RNA-Seq profiling, ATAC-seq profiling, MeDIP-seq profiling on mouse ES cells

first: Brian

last: Bennett

first: Guang

last: Hu


title: Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation [RNA-seq]


title: Gene expression profiling of thymus samples from myasthenia gravis patients.

city: Washington DC

first: Manjistha

last: Sengupta

state: District of Columbia

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

department: Neurology

institute: George Washington University

summary:
Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease.
A large proportion of MG patient show the presence of ectopic germinal centers (GC) in thymus that are absent in normal individuals. However, the exact mechanism how this change in thymus morphology is triggered and if this is related to pathophysiology of the disease remains unknown.
In this study we have compared the mRNA profile of thymus samples obtained during a clinical trial (Thymectomy Trial in Non-Thymomatous Myasthenia Gravis Patients Receiving Prednisone Therapy. ClinicalTrials.gov Identifier: NCT00294658).
We have compared the mRNA profile of thymus samples that have distinct germinal centers with those that lack them using Affymetrix human transcriptome array 2.0 to identify the differentially expressed genes with in the two groups.

overall_design:
Thirteen frozen tissue samples collected during MGTX trial were cryo-sectioned and were stained with haematoxylin and eosin to examine morphological features and presence of germinal centers.
The H and E sections were evaluated by two blinded observers and graded depending on presence (Grades 1-4) or absence of germinal centers (Grade 0). Total RNA was isolated from the remaining tissue using Trizol.
The RNA samples were processed and applied to Affymetrix human transcriptome array 2.0. Array data was normalized, batch corrected and analyzed (1-way ANOVA) using Partek Genomics Suite program.

first: Bi-Dar

first: Norman

middle: H

last: Lee

first: Linda

middle: L

last: Kusner

first: Henry

last: Kaminski


title: Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation [ATAC-seq]


title: Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation [ChIP-seq]


title: Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae

status: Public on Sep 18 2017

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Cdc7 kinase is known to initiate DNA replication, but it is unknown where Cdc7 is found within the genome.  We modified the Calling Cards method that uses the Ty5 retrotransposon to investigate Cdc7 binding in the genome.  The Ty5 retrotransposon is inserted into the genome by DNA transcription factors or replication factors binding within the genome.  We find that Cdc7 inserts Ty5 transposons throughout chromosomes and furthermore creates more Ty5 insertions into regions of DNA that are known to replicate early.  Cdc7 does not solely integrate Ty5 at origins or replication, but rather throughout the genome.

overall_design: 4 single read sequencing runs. All using Calling Cards to identify binding sites of cdc7kd, cdc7kdΔcterm and Gal4 transcription factor within the yeast genome.

first: Daniel

last: Rossbach

first: Robert

last: Sclafani

first: D

last: Bryan


title: Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: We show that heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. Our approach utilizes tethering of components of the piRNA pathway to the transcript of a reporter and then small RNA cloning from total RNA from Drosophila ovaries. Our approach allows discrimination of proteins involved in transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. piRNA processing correlates with localization of the substrate RNA to nuage, a distinct membraneless cytoplasmic compartment, which surrounds the nucleus of germ cells, suggesting that sequestration of RNA to this subcellular compartment is both necessary and sufficient for selecting piRNA biogenesis substrates.

overall_design: Examination of small RNAs mapping to the mKate2 reporter in D. melanogaster ovaries upon tethering and concomitant knockdown of piRNA pathway factors

first: Katalin

last: Fejes Toth


title: RNA-seq in spermatogonia from PRC1ctrl and dKO mice

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

summary: RNA-seq was performed using Thy1- and c-Kit+ spermatogonia from 7-days-old PRC1ctrl or dKO mice.

overall_design: Duplicate RNA-seq analyses using spermatogonia from 7-days-old PRC1ctrl or dKO mice

first: Artem

last: Barski

first: Satoshi

last: Namekawa


title: FACS sorting of human adipose tissue stromal vascular fraction

city: Stockholm

first: Jurga

last: Laurencikiene

address: Hälsovägen 7

institute: Karolinska Institutet

summary: Adipose tissue from 6 non-obese patients was collagenase treated and adipocytes separated from the stromal vascular fraction(SVF). SVF was then FACS sorted for the following fractions CD45-/CD34+/CD31+ (endothelial), CD45-/CD34+/CD31- (progenitor), CD45+/CD14+ (monocyte/macrophage), CD45+/CD14-(Leukocyte). RNA was isolated from adipocyte, SVF, progenitor, macrophage/monocyte and leukocyte fractions and analyzed on the Affymetrix Human Transcriptome 2.0 array. We also sorted SVF from an additional 13 (10 non-obese, 9 obese) patients and sent progenitor RNA for Affymetrix Human Transcriptome 2.0 array analysis.

first: Anna

last: Ehrlund


title: Real-time quantitative PCR analysis of 232 microRNAs in human oral tissues

city: Taoyuan

first: Yi-Hsuan

last: Lai

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: Oral squamous cell carcinoma (OSCC) is the sixth most common cause of cancer mortality worldwide, and the five-year survival rate remains low in patients with advanced OSCC. Many studies indicate that microRNAs (miRNAs) may paly critical roles in OSCC carcinogenesis, but the dynamic composition and functions of miRNAs-mRNAs regulatory networks in OSCC pathogenesis remain largely unknown. Thus, detailed investigations of OSCC-associated miRNAs and their regulated networks may provide insights into mechanistic understanding of OSCC progression and development of new strategies of OSCC management. To this end, we first sought to compile from a systems perspective the miRNA-mRNA networks underlying OSCC pathogenesis. Our targeted, qRT-PCR-based expression profiling of 232 miRNAs in 49 human oral tissue samples (including 19 normal and 30 OSCC specimens) identified 49 differentially expressed miRNAs (p-value < 0.01 and fold change > 2) in OSCC tissues.

overall_design: Total 19 normal and 30 OSCC specimens were collected, and the miRNA-specific RT-qPCR was performed

first: Bertrand

last: Tan


title: Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch [6 NaV1.8+ Il4raF/F mice treated with MC903 compared to skin from 4 littermates]

city: St. Louis

first: Landon

middle: Kyle

last: Oetjen

state: MO

address: 660 S Euclid Avd

country: USA

institute: Washington University

summary: Mammals have evolved neurophysiologic reflexes such as coughing and scratching to expel invading pathogens and noxious environmental factors. It is well established that these responses are also associated with chronic inflammatory diseases such as asthma and atopic dermatitis. However, the mechanisms by which inflammatory pathways promote sensations such as itch remain poorly understood. Here, we show that type 2 cytokines directly stimulate sensory neurons in both mice and humans. Further, we demonstrate that chronic itch is dependent on neuronal IL-4Rα and JAK1 signaling. Based on these observations, we show that patients with recalcitrant chronic itch markedly improve when treated with JAK inhibitors in proof-of-concept clinical studies. Thus, signaling mechanisms previously ascribed to the immune system may represent novel therapeutic targets within the nervous system. Collectively, these studies reveal an evolutionarily conserved paradigm in which the sensory nervous system employs classical immune signaling pathways to influence mammalian behavior.

overall_design: Ear skin from 6 NaV1.8+ Il4raF/F mice treated with MC903 compared to skin from 4 littermates treated with 1 nM topical calipotriol (MC903) daily for 12 days.

first: Brian

last: Kim


title: Expression of Piwi protein MIWI2 defines a distinct population of multiciliated cells

city: Boston

first: Matthew

middle: Robert

last: Jones

address: 72 East Concord Street

department: Medicine

institute: Boston University School of Medicine

summary: We find that MIWI2 protein is expressed in a discrete population of multiciliated airway epithelial cells of the lung. The isolation and the next generation sequencing of the MIWI2-positive multiciliated cells revealed that they are phenotypically distinct from neighboring MIWI2-negative multiciliated cells.

overall_design: RNA-seq analysis of sorted tdTomato-positive multiciliated cells versus tdTomato-negative multiciliated cells

middle: R

first: Gregory

last: Wasserman