title: RNA-seq profiling in Botryosphaeria dothidea reveals differentially expressed genes response to heat stress

status: Public on Apr 30 2019

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

type: Expression profiling by high throughput sequencing

summary: RNA-seq sequencing was applied to detected differentially expressed genes response to heat stress in Botryosphaeria dothidea

overall_design: For each sample type, sequencing was performed on an Illumina Hiseq 4000 platform

first: Bo

last: Wang

first: Guangyu

last: Sun


title: Pulmonary effects of ozone and allergen exposure in the absence of surfactant protein-D in mice.

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

country: USA

institute: University of Colorado

summary:
Ozone and allergen inhalation causes pulmonary inflammation and impairs lung function in mice. These effects are heightened in the absence of the immunosuppressive surfactant protein-D. Increased expression of inflammatory mediators is critical for the initiation of inflammation and impairment of lung function following ozone and allergen inhalation.
An Affymetrix microarray was used to understand global changes in gene expression that occurred after ozone inhalation and/or allergen sensitization and challenge in the abscence of surfactant protein-D. Identification of the set of genes up and down regulated in response to ozone and/or allergen led us to study specific cellular inflammatory pathways. This study has important implications for the study of lung diseases like asthma.

overall_design: C57BL/6, Balb/c and SP-D-/- mice were sensitized and challenged with the allergen Aspergillus fumigatus (Af), then exposed to air or ozone for 2 hours. Mice were also exposed to air or ozone alone. Mice were euthanized and a single-cell suspension of whole lung homogenate was generated at 12 hours post air or ozone exposure, 24 hours post Af/12 hours post air or ozone, 96 hours post Af/12 hours post air or ozone, or 168 hours post Af/12 hours post air or ozone. Whole lung homogenate gene expression was studied via Affymetrix microarray.

first: Angela

last: Haczku

first: Cameron

middle: H

last: Flayer

first: Shu-Yi

last: Liao


title: Microarray analysis of lung SPC/GFP+ EpCAM+ cells

status: Public on Apr 26 2019

city: Tokyo shinjukuku

first: Akihiro

last: Tsutsumi

country: Japan

institute: Keio University

summary:
We extracted RNA of sorted lung SPC/GFP+ EpCAM+ cells and performed microarray analyses. Total RNA was extracted from sorted Ep-CAMhigh/GFPhigh cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The RNA integrity was examined on an Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA). Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix/Thermo Fisher Scientific). Fragmented and labeled ss-cDNA were hybridized on a GeneChip Clariom S Array (Affymetrix/Thermo Fisher Scientific) (n =3/group).
We used microarrays to detail the global gene expression of SPC/GFP+ EpCAM+ cells from the control mice(G29-5_(Clariom_S_Mouse)) and the 3 months smoke mice(G29-6_(Clariom_S_Mouse)), and identified distinct classes of up-regulated genes during this process.

overall_design: Lung SPC/GFP+ EpCAM+ cells from the control mice and the 3 months smoke mice were sortd, RNA extraction from these cells was hybridized on Affymetrix microarrays.

last: Tstsumi


title: Murine model of oxygen-induced retinopathy - 3 time points [blood]

city: Krakow

first: Anna

last: Madetko-Talowska

state: Krakow

address: Wielicka 265

department: Medical Genetics Chair of Pediatriics

country: Poland

institute: jagiellonian university medical College

summary: To study early and late transcriptional changes introduced to blood and retinal tissue in murine oxygen-induced retinopathy (OIR). From blood MNCs total RNA was extracted at three time points: immediately after end of hyperoxia (P12), at P17 and P28.

overall_design: Transcriptional profiling of mouse retinal cells with the use of SurePrint G3 Mouse Gene Expression microarrays (Agilent). Comparison between hyperoxia and normoxia conditions, 3 different time pionts (P12, P17 and P28).

first: Magdalena

last: Zasada

first: Cecilie

last: Revhaug

first: Anne

middle: G

last: Rognlien

first: Lars

middle: O

last: Baumbusch

first: Ola

middle: D

last: Saugstad

first: Teofila

last: Ksiazek

first: Katarzyna

last: Szewczyk

first: Agnieszka

last: Grabowska

first: Mirosaw

last: Bik-Multanowski

first: Jacek

middle: J

last: Pietrzyk

first: Przemko

last: Kwinta


title: Gene Expression Changes due to Rat Lung Ischemia-Reperfusion Injury

city: Chapel Hill

first: Thomas

middle: Michael

last: Egan

state: NC

address: Med Schol Wing C Room 354

department: Surgery

institute: University of North Carolina

summary:
Ischemia-reperfusion injury (IRI) is a major cause of morbidity and mortality following conventional lung transplantation and warm ischemia may limit success of transplanting lungs from non-heart-beating donors. We sought to determine alterations in gene expression in rat lung tissue subjected to warm ischemia in vivo followed by reperfusion.
Keywords: time course

overall_design:
We compared gene expression from 6 normal lungs to left lungs subjected to 2 hours of in situ warm ischemia by hilar clamping, reperfused for 30 minutes (n=3) or 3 hours (n=3).  We also analyzed gene expression in the contralateral right lungs retrieved at the same time points.
Anesthetized ventilated male Sprague-Dawley rats underwent left lung hilar clamping for two hours, then the left lungs were reperfused and ventilated for 30 minutes (n=3) or 3 hours (n=3).  Both the right and left lungs were retrieved for RNA extraction.  RNA retrieved from lungs of six rats retrieved immediately after sacrifice served as controls.  RNA was reverse transcribed into cDNA and hybridized to Affymetrix® REA 230A gene arrays.  Expression data was analyzed by GeneSpring software 7.2.

middle: M

first: Masharn

last: Doanes

first: J

middle: P

last: Jin

first: Scott

last: Randell


title: Murine model of oxygen-induced retinopathy - 3 time points [retina]

status: Public on Apr 27 2019

summary: To study early and late transcriptional changes introduced to blood and retinal tissue in murine oxygen-induced retinopathy (OIR). From retinal cells RNA was extracted at three time points: immediately after end of hyperoxia (P12), at P17 and P28.


title: Investigating Proteome and Transcriptome Defense Response of Grapes Induced by Yarrowia lipolytica

city: zhenjiang

first: meiyan

last: wang

address: xiangshanjiedao

institute: jiangsu university

summary: We report the application of next generation sequencing technology for analyzing the differentially expressed genes of grapes after treated with or without Y. lipolytica. After analyzing the differentially expressed gene, we selected some important genes related to the resistance of grapes to do RT-qPCR.

overall_design: Examination of differentiallly expressed genes related to the resistance of  2 types of grape tissues which treated with or without Y. lipolytica. RT-qPCR was performed using SYBR Green assays.

first: Hongyin

last: Zhang

first: Meiyan

last: Wang


title: Functional Landscape of PCGF Proteins Reveals Both RING1A/B Dependent and Independent Specific Activities

status: Public on Apr 29 2019

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb repressive complexes 1 and 2 (PRC1 and PCR2) control cell identity by establishing facultative heterochromatin repressive domains at common sets of target genes. PRC1, which deposits H2Aub1 through the E3 ligases RING1A/B, forms six biochemically distinct subcomplexes containing one type of PCGF protein (PCGF1–6); it is unclear whether these subcomplexes also have specific activities. Here we show that PCGF1 and PCGF2 largely compensate for each other, but that the other PCGF proteins have high levels of specificity for distinct target genes, with little functional crosstalk. PCGF2 associates with transcription repression, while PCGF3 and PCGF6 associate with actively transcribed genes. Notably, PCGF3 and PCGF6 complexes can assembly and be recruited to several active sites independently of RING1A/B activity (therefore, of PRC1). For chromatin recruitment, the PCGF6 complex requires the combinatorial activities of its MGA-MAX and E2F6-DP1 subunits, while PCGF3 requires an interaction with the USF1 DNA binding transcription factor.

overall_design: RNA-seq and ChIP-seq with different genotypes of E14 cells

first: Andrea

last: Scelfo

first: Daniel

last: Fernandez-Perez

first: Marika

last: Zanotti

first: Simone

last: Tamburri

first: Monica

last: Soldi

first: Tiziana

last: Bonaldi

first: Karin

last: Ferrari


title: Contrasting roles of transcription factors spineless and EcR in the highly dynamic chromatin landscape of butterfly wing metamorphosis

city: Ithaca

middle: Revka Loek

last: van der Burg

state: NY

address: 215 Tower Road, Corson Hall

department: EEB

institute: Cornell University

summary:
Background: We studied the chromatin accessibility landscsape in wings during butterfly metamorphosis, and investigate which transcription factors might be driving changes in accessibility
Methods: We sequencing the Junonia coenia genome, and we studied chromatin accessibility using ATAC seq in multiple stages of wing development in both forewings and hindwings. For sites showing a large change in accessibility, we investigate which motifs are enriched, and correlate this with changes in gene expression of associated transcription factors. We confirm promising candidates with ChIP-seq
Results: We find a highly dynamic landscape, with multiple peaks showing a double increase in accessibility throughout development. We show that transcription factor spineless, but not ecdysone receptor, is highly predictive of opening sites
Conclusions: This work provides a characterization of the chromatin dynamics of insect wing metamorphosis, identifies novel candidate chromatin remodeling factors in insects, and provides the first genome assembly of the model butterfly Junonia coenia, with gene and cis-regulatory element annotations

overall_design: RNA-seq from various tissues at various developmental stages.

middle: R

first: James

last: Lewis

first: Arnaud

last: Martin

first: H

middle: F

last: Nijhout

first: Charles

last: Danko

first: Robert

last: Reed


title: Monocyte phenotype indicates a poor prognosis in paracetamol (acetaminophen) induced acute liver failure but not in non-ae hepatitis: a prospective observational cohort study

city: EDINBURGH

first: Kenneth

last: Simpson

address: SCRM building, 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

summary:
Acute liver failure (ALF) is a rare but serious medical syndrome associated with significant morbidity and mortality. Paracetamol (acetaminophen) hepatotoxicity is the most common cause in many parts of the world. Recent studies have implicated the patient’s immune response to the tissue injury is important in dictating clinical outcome, especially monocyte/macrophage cells of the innate immune system.
Patients with the worst clinical outcomes after a paracetamol overdose (POD) (death/emergency liver transplant) had a significant and prolonged monocytopenia characterised by reduced classical and expanded intermediate monocyte subset population. This same change was seen in the mouse monocytes but did not occur in patients with non-AE hepatitis. In POD patients, this was associated with reduced circulating lymphocytes and NK cells, peripheral cytokine patterns suggestive of a “cytokine storm” and increased circulating concentrations of cytokines associated with monocyte egress from the bone marrow. Monocyte gene expression did not differentiate patient outcome.    Severe paracetamol induced hepatotoxicity is associated with profound changes in the cells of the peripheral blood compartment that are related to patient outcome especially the circulating monocytes. This is not seen in patients with non-AE hepatitis. Such changes may allow earlier definition of prognosis or highlight potential for therapeutic intervention utilising monocytes to improve outcomes.

overall_design: Study contains data from 24 humann peripheral monocyte samples, comprising 5 from controls, 7 from patients with acute liver injury (ALI), and 12 from patients with liver failure (ALF). Of the liver failure group, 6 subsequently died or received a liver transplant. Please note that two ALI samples were removed due to quality issues, resulting in total 22 samples.

first: Joanna

middle: K

last: Moore

first: Alison

middle: C

last: MacKinnon

first: Tak

middle: Y

last: Man

first: Jonathan

last: Manning

first: Stuart

last: Forbes


title: Next Generation Sequencing Facilitates Quantitative Analysis of Developed Seed Transcriptomes in Linseed Flax

city: Beijing

first: Yan

last: Long

state: China

address: Zhongguancun South street No.12

institute: Chinese Academy of Agricultural Sciences

summary: The goal of the study is to identify gene expression during seed development process in linseed flax.

overall_design: One flax cultivar, Heiya No.14 was used for sequencing. Four samples with two replicates representing 4 developing stages were used.


title: Human pluripotent stem cell-derived mesenchymal stem cells regenerate injured GUNN rat liver

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

summary: Gunn rats bear a mutation within the uridine diphosphate glucuronosyltransferase-1A1 (Ugt1A1) gene resulting in high serum bilirubin levels as seen in Crigler-Najjar syndrome. In the present study, the Gunn rat was used as an animal model for heritable liver dysfunction. Human pluripotent stem cell-derived mesenchymal stem cells (iMSCs) were transplanted into Gunn rats after partial hepatectomy. The iMSCs engrafted and survived in the liver for up to 2 months without the need for immunosuppression. The transplanted iMSCs differentiated into functional hepatocytes and partially suppressed hyperbilirubinemia. Furthermore, human Albumin as well as the human immunomodulatory factors, RANTES and SERPINE1, were detected in the rat serum upon iMSC transplantation. The differentiation of iMSCs into hepatocytes was confirmed by qPCR and/or immunohistochemistry, detecting expression of human hepatocyte nuclear factor 4α, UGT1A1, cytokeratin 18, α-fetoprotein and Albumin. These findings indicate transplanted iMSCs differentiated into hepatocytes and thus contributed to tissue repair in an injury model of hepatocyte-based liver regeneration.

overall_design: The transcriptomes of iMSCs from human fetal MSC-dervied iPSCs and human ESC line H1 were compared to native human fetal MSCs as well as to the pluripotent prcursor ESCs and fetal MSC-derived iPSC by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Lucas

last: Spitzhorn


title: Cortical astroglia transcriptomic dysregulation in the G93A SOD1 ALS mouse model

city: Baltimore

first: Sean

middle: James

last: Miller

state: MD

address: 855 North Wolfe St.

department: Neurology-Neuromuscular Medicine

institute: Johns Hopkins School of Medicine

summary: Astroglia are the most abundant cell type in the central nervous system. They play essential roles in the homeostasis of the CNS. Astroglia are extremely diverse. In Amyotrophic Lateral Sclerosis (ALS) astroglia in spinal cord undergo dramatic transcriptomic dysregulation. However there is little to no data on the effects that cortical astroglia undergo during ALS pathogenesis. In this study we isolated pure cortical astroglia in end stage ALS mice. We performed microarray analysis and discovered dysregulated pathways and genetic markers. This may serve as a database for scientists to understand the effects that abnormal cortical astroglia have on cortical motor neurons and overall ALS pathology.

overall_design: 4 ALS mice vs 3 Controls were used.

first: Jeffrey

last: Rothstein


title: Expression data from murine lung derived alveolar macrophages

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University, College of Medicine

summary:
Lung alveolar macrophages are self-renewing tissue resident macrophages primarily relying upon GM-CSF signal as a main source.
We used microarrays to detail the global programme of gene expression underlying homeostasis and functions of alveolar macrophages in absence of phosphatase Ssu72

overall_design: Alveolar macrophages were sorted from Lysm-Cre mice and Lysm-CreSsu72fl/fl mice

first: Doo

last: Chung

first: Yeon


title: Global transcriptional analysis of human functional hepatocytes Long-term maintained by small-molecule cocktails by RNA-seq

first: Yifang

last: Liu

address: Haidian District

institute: Peking University

summary: Functional maintenance of terminally differentiated cells outside the in vivo microenvironment has proved challenging. Current strategies that manipulate cell-cell or cell-matrix connections are difficult to constitute complex regulatory networks for cell function maintenance. Small molecules are easily combined for flexible spatiotemporal modulations, theoretically favorable for synergetic regulation of cell-innate signaling pathways to maintain cell function in vitro. Here, we developed small-molecule cocktails enabling robust maintenance of primary human hepatocytes (PHHs) longer than four weeks, with gene expression profiles, resembling those of freshly isolated PHHs; and prolong-cultured PHHs, for the first time, could maintain drug-metabolizing activities of enzymes accounting for over 80% of drug-oxidation and support hepatitis B virus infection in vitro for over one month. Importantly, this cocktail also promotes functional maturation of human pluripotent stem cell-derived hepatocytes. Our study demonstrates that this chemical approach effectively maintains terminally differentiated hepatocytes in vitro, which could be extended to various cell types.

overall_design: Total of 26 samples were analyzed, which included primary human hepatocytes (PHHs) cultured in different condition in vitro. To figure out how terminally differentiated cells rapidly lose their function in vitro, two PHHs samples were compared, which included 24h-Cultured hepatocytes and fresh primary human hepatocytes (F-PHHs). For comparison of global gene expression of primary human hepatocytes (PHHs) maintained with small molecules for different time periods, sample3-41 were analyzed. For underling mechanism of small molecules, twelve samples were analyzed, which included sample 42 to sample 53.

first: Chengang

last: Xiang

first: Yuanyuan

last: Du

first: Hongkui

last: Deng


title: Long-term Functional Maintenance of Primary Human Hepatocytes In Vitro

city: beijing

first: meng

middle: gao

last: fan

state: Haidian District/Beijing

address: yiheyuan road no.5

institute: peking university

summary: Functional maintenance of terminally differentiated cells outside the in vivo microenvironment has proved challenging. Current strategies that manipulate cell-cell or cell-matrix connections are difficult to constitute complex regulatory networks for cell function maintenance. Small molecules are easily combined for flexible spatiotemporal modulations, theoretically favorable for synergetic regulation of cell-innate signaling pathways to maintain cell function in vitro. Here, we developed small-molecule cocktails enabling robust maintenance of primary human hepatocytes (PHHs) longer than four weeks, with gene expression profiles, resembling those of freshly isolated PHHs; and prolong-cultured PHHs, for the first time, could maintain drug-metabolizing activities of enzymes accounting for over 80% of drug-oxidation and support hepatitis B virus infection in vitro for over one month. Our study demonstrates that this chemical approach effectively maintains terminally differentiated hepatocytes in vitro, which could be extended to various cell types.

overall_design: Total of 29 samples were analyzed, which included primary human hepatocytes (PHHs) cultured in different condition in vitro. To figure out how terminally differentiated cells rapidly lose their function in vitro, two PHHs samples were compared, which included 24h-Cultured hepatocytes and fresh primary human hepatocytes (F-PHHs) [GSM2893923 and GSM2893924]. For comparison of global gene expression of primary human hepatocytes (PHHs) maintained with small molecules or sandwich culture for different time periods, sample3-29 were analyzed [GSM2893935 - GSM2893963][GSM3629857-GSM3629862].

first: Gaofan

last: Meng


title: Effects of avobenzone on whole-genome scale transcription of normal human epidermal keratinocytes

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

institute: Seoul National University

summary: Avobenzone, also known as butyl methoxydibenzoylmethane, is extensively used in sunscreen formulations as a long-wave UV A filter to protect human skin from UV A irradiation-induced skin damage. This study was aimed to elucidate the genome-scale transcriptional profile of normal human epidermal keratinocytes (NHEKs) in response to  avobenzone.

overall_design: Normal human epidermal keratinocytes (NHEKs) were treated with 10 microM of avobenzone for 24 hours and harvested for total RNA extraction and hybridization on Affymetrix Human GeneChip 133 2.0 microarrays.


title: Sequencing of Raw 264.7 cells with a CRISPR mediated genetic deleltion of NRE1

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

institute: University of Utah

summary: RNA collected from media treated and M1 stimulated (IFNγ/LPS) cells

overall_design: Examination of genes regulated by the deletion of NRE1 in Raw 264.7 cells

first: Thomas

last: Huffaker


title: An ARF6-Exportin-5 Axis Delivers pre-miRNA Cargo to Tumor Microvesicles.

city: Notre Dame

first: Ye

last: Zhang

state: IN

address: Galvin Life Sciences Center

department: Biological sciences

institute: University of Notre Dame

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA sequencing reads in TMVs showed a significant increase with ARF6 activation

overall_design: Examine the miRNA populations in TMVs shed by LOX parental cells and ARF6-active cells

first: Crislyn

last: D'Souza-Schorey


title: Genomewide Association Study of Tacrolimus Pharmacokinetics Identifies Novel Single Nucleotide Polymorphisms in Convalescence Phase and Stabilizing Phase of Liver function Respectively

city: Shanghai

first: Yuan

state: Shanghai

address: No.277 Chongqingnan Road, Huangpu Distict,Shanghai

institute: Shanghai Jiaotong University school of medicine

type: Genome variation profiling by genome tiling array

summary: Following liver transplantation, the liver function of a patient is gradually restored over a period of time, which is divided into a convalescence period (CP) and a stabilizing period (SP). Tacrolimus (TAC), a commonly-used immunosuppressant for the prevention of organ rejection, shows variability in plasma concentration in these patients as a result of variation in its metabolism. The effects of genetic and clinical factors on its plasma levels seem to differ in the CP and SP. To establish a model explaining TAC trough concentration variation between individuals in both the CP and SP, we conducted a retrospective, single-center, discovery study, involving 115 pairs of patients (115 donors and 115 matched recipients) who had undergone liver transplantation. Donors and recipients were genotyped by genomewide association study (GWAS) using an exome chip.

overall_design: Paired 115 liver transplant patients (115 donor + 115 recipient livers)

first: Zhihai

last: Peng


title: Chromatin conformation links enhancers in intracranial aneurysm associated regions to potential candidate genes

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary: Background and Purpose: We previously showed that intracranial aneurysm (IA)-associated single nucleotide polymorphisms (SNPs) are enriched in promoters and putative enhancers of the human circle of Willis (CoW), on which IAs develop, suggesting a role for such regulatory regions in IA. In this study we further investigated the role of these putative enhancers in the pathogenesis of IA by identifying the target genes of these enhancers and validating their regulatory activity.   Methods: We selected putative enhancers in IA-associated regions from genome wide association studies, using our previously published CoW chromatin immunoprecipitation and sequencing data. Next, we used a chromatin conformation capture technique (4C) to identify physical interactions between these putative enhancers and the promoters of their target genes. Subsequently, we assessed the activity of the identified enhancers in vivo in zebrafish embryos and we analyzed gene expression of the target genes identified with 4C in CoW RNA-sequencing data and by in situ hybridization on CoW paraffin sections.  Results: We identified fifteen enhancers that interact with the promoters of six target genes: SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6. For eight out of eleven enhancers that could be tested, we confirmed in vivo activity in the zebrafish embryos. These eight enhancers reside in four out of six IA-associated GWAS regions. All six target genes are expressed in the CoW and in situ hybrdization showed that these genes are expressed in multiple cell types in the CoW.   Conclusions: In four out of six IA-associated GWAS regions we identified eight enhancers that are active in vivo and interact with six nearby genes, suggesting that these genes are regulated by the identified enhancers. These genes, SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6, are potential candidate genes involved in IA pathogenesis and should be studied using animal models in the future.

overall_design: Two circles of Willis samples were used to investigate enhancer-promoter interactions through 40 different 4C experiments, 7 of these experiments were performend in both circles of Willis samples

first: Melanie

last: Laarman

first: Geert

last: Geeven

first: Phil

last: Barnett

first: Gabriël

middle: E

last: Rinkel

first: Wouter

last: de Laat

first: Jeroen

last: Bakkers


title: Exosomes from microglia attenuate photoreceptor injury and neovascularisation in an animal model of retinopathy of prematurity

status: Public on Apr 25 2019

city: Xi'an

first: WENQIN

last: XU

address: 15 Changle West Road

department: Ophthalmology

institute: The Fourth Military Medical University

summary: Total RNAs from exosomes was used for miRNA library preparation and sequencing.The preparation and sequencing of exosome miRNA were performed by Ribobio (Guangzhou, China). First, total RNA samples were fractionated by using 15% Tris-borate-EDTA (TBE) polyacrylamide gel (Invitrogen), then small RNAs ranging from 18 to 30 nucleotides were used for library preparation. Amplification of these small RNAs was then accomplished by PCR. Next, the Illumina HiSeq 2500 platform was used to sequence these RNAs.

overall_design: We investigated the miRNA expression profiles of microglia-Exos using Illumina HiSeq 2500 high-throughput sequencing (miRNA-seq)

first: Wenqin

last: Xu

first: Yusheng

last: Wang


title: Genome-wide transcriptional analysis of human iPSC-derived healthy control vs. schizophrenia cortical interneurons.

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: We report specific changes in schizophrenia developmental interneurons by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons vs. schizophrenia interneurons. Fourteen independent iPSC lines per group with two independent differentiations

first: Sangmi

last: Chung


title: Effector TH17 cells give rise to long-lived TRM cells that are essential for an immediate response against bacterial infection

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

summary: Mucosal barrier surfaces serve as the critical first line of defense separating our bodies from the plethora of pathogenic microorganisms that inhabit our environment. Adaptive immunity provides life-long protection through the generation of a central and effector memory T-cell pool, memory B cells and the recently described population of tissue resident memory cells (TRM). The cellular origin of TRM CD4 cells is unknown and the contribution of this CD4 memory population to host defense still remains elusive.  By using IL-17A tracking-fate-mouse models we found that a significant fraction of the  CD4 TRM cells derive from IL-17A producing effector (TH17) cells following primary immunization. Maintenance of these resting exTH17 TRM cells is mediated by IL-7, produced by lymphatic endothelial cells. During a memory response, we show that neither antibodies, nor gd T cells, nor circulatory memory T cells are sufficient for the rapid host defense required to eliminate the pathogen. Using parabiosis and depletion studies, we demonstrated that CD4 exTH17 TRM cells play an important role in respiratory defense and bacterial clearance. Upon infection, exTH17 TRM cells rapidly produce IL-17A and IFN-γ to promote neutrophil infiltration and bacterial clearance. These studies delineate the origin, function and importance of airway CD4 TRM cells during bacterial infection, offering novel strategies for targeted vaccine design, which is especially imperative for those pathogens that are resistant to antibiotic treatment.

overall_design: We profiled the transcriptome of draining lymph node (LN)  naïve CD4 T cells (2 replicates), memory CD4 T cells (2 replicates) and the 3 populations of TRM cells present in the lung 35 days after immunization with heat-killed Klebsiella pneumoniae (TH17, exTH17 (3 replicates) and YFPneg (2 replicates)).

first: Maria

last: Amezcua Vesely

first: Paris

last: Pallis

first: Piotr

last: Bielecki

first: Jun

last: Siong Low

last: Zhao

first: Lina

last: Kroehling

first: Ruaidhri

last: Jackson

first: Will

last: Bailis

first: Pauls

last: Licona-Limon

first: Hao

first: Norifumi

last: Iijima

first: Padmini

middle: S

last: Pillai

first: Daniel

last: Kaplan

first: Casey

last: Weaver

first: Yuval

last: Kluger

first: Monika

last: Kowalczyk

first: Akiko

last: Iwasaki

first: Joao

last: Pereira

first: Enric

last: Esplugues

first: Nicola

last: Gagliani

first: Richard

middle: A

last: Flavell


title: Neratinib, a Pan ERBB/HER Inhibitor, Restores Sensitivity of PTEN-null, BRAFV600E Melanoma to BRAF/MEK Inhibition

city: Chapel Hill

first: Evan

last: DuBose

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC Chapel Hill

summary: The  A375, human BRAFV600E mutant melanoma, cell line (wildtype), two PTEN-null, BRAFV600E cell lines (KO5 and KO11), and PI3K overexpression cells (WT and PI3K H1047R mutant) were treated with small molecule inhibitors (dabrafenib, BRAF inhibitor; trametinib, MEK inhibitor alone and in combination for 0, 1 and 7 days

overall_design: 30 experimental samples from 2 experiments (9 samples-2 reps; 12 samples)

first: Steven

last: Angus


title: The spinal transcriptome after cortical stroke – In search of molecular factors regulating spontaneous recovery in the spinal cord

city: Zürich

first: Julia

last: Kaiser

address: Winterthurerstrasse 190

country: Switzerland

institute: Brain Research Institute

summary: In response to cortical stroke and unilateral corticospinal tract degeneration, compensatory sprouting of spared corticospinal fibers is associated with recovery of skilled movement in rodents.  To date, little is known about the molecular mechanisms orchestrating this spontaneous rewiring. In this study, we provide insights into the molecular changes in the spinal cord tissue after large ischemic cortical injury in adult female mice, with a focus on factors that might influence the re-innervation process by contralesional corticospinal neurons. We mapped the area of cervical grey matter re-innervation by sprouting contralesional corticospinal axons after unilateral photothrombotic stroke of the motor cortex in mice using anterograde tracing. The mRNA profile of this re-innervation area was analyzed using whole-genome sequencing to identify differentially expressed genes at selected time points during the recovery process. Bioinformatic analysis revealed two phases of processes: Early after stroke (4-7 days post injury), the spinal transcriptome is characterized by inflammatory processes, including phagocytic processes as well as complement cascade activation. Microglia are specifically activated in the denervated corticospinal projection fields in this early phase. In a later phase (28-42 days post injury), biological processes include tissue repair pathways with up-regulated genes related to neurite outgrowth. Thus, the stroke-denervated spinal grey matter, in particular its intermediate laminae, represents a growth-promoting environment for sprouting corticospinal fibers originating from the contralesional motor cortex. This data set provides a solid starting point for future studies addressing key elements of the post-stroke recovery process, with the goal to improve neuroregenerative treatment options for stroke patients.

overall_design: RNA-Sequencing of spinal tissue was compared between different time points after cortical stroke (4, 7, 14, 28, 42dpi).

first: Martina

last: Maibach

first: Iris

last: Salpeter

first: Niels

last: Hagenbuch

first: Vladimir

last: Souza

first: Mark

last: Robinson

first: Martin

last: Schwab


title: Questioning the purity of the media - Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

summary: In the research field of extracellular vesicles (EVs), the use of EV-depleted fetal bovine serum (FBS) for in vitro studies is highly recommended to eliminate the confounding effects of media derived EVs. EV-depleted FBS may either be prepared by ultracentrifugation or bought commercially, nevertheless these depletion methods do not guarantee an RNA-free preparation. In this study we have addressed the RNA contamination issue in FBS, ultracentrifuged EV-depleted FBS, commercially available EV-depleted FBS, and also from our recently developed filtration based EV depleted FBS. Commercially available serum-free, xeno-free defined media were also screened for RNA contamination.

sample_organism:
Bos taurus
other sequences

platform_organism:
Bos taurus
other sequences

overall_design: Small non-coding RNA profiles of extracellular vesicles derived from different types of cell media were generated by next-generation sequencing. Samples included FBS (n=2), commercial exosome-depleted FBS (n=2), ultracentrifuged EV-depleted FBS (n=2), ultrafiltrated EV-depleted FBS (n=2) and defined serum-free medium (n=1)

first: Bettina

last: Mannerström

first: Riku

middle: O

last: Paananen

first: Ahmed

last: Abu-Shahba

first: Jukka

last: Moilanen

first: Riitta

last: Seppänen-Kaijansinkko


title: LNCaP prostate cancer cells stably transfected with shRNAs targeting ADRB2

city: Oslo

first: Peder

middle: Rustøen

last: Braadland

state: Oslo

address: Ullernchausseen 70

department: Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: Gene expression profiling of prostate adenocarcinoma LNCaP cells stably transfected with shRNAs targeting ADRB2 (shADRB2-2 and shADRB2-3) or control shRNA (shCtrl) incubated in 10% FCS.

overall_design: The results provide insight into changes in gene expression levels upon stable knockdown of ADRB2 in LNCaP cells.

first: Helene

middle: H

last: Grytli

first: Håkon

last: Ramberg

first: Kristin

last: Taskén


title: High throughput small RNA and transcriptome sequencing reveal reproduction-related microRNAs and mRNA in ovary of Geese in Counter-Season Production

city: Chengdu

first: jinshan

last: ran

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agriculture University

summary:
Purpose: To understand the function differences of goose at broody and breeding stage
Methods: RNA-seq analysis of oviduct tissues in reproductive and broody goose
Results: Our study screened differential expressed mRNA and pathways involved in broodiness
Conclusions:The differential expressed mRNA and pathways identified in this study may contribute to understand the broodiness occurs in goose

first: Jinshan

last: Ran


title: Astrocyte-to-astrocyte contact and a positive feedback loop of growth factor signaling regulate astrocyte maturation

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

institute: UCLA

summary: Astrocytes were purified from postnatal day 2 mouse cortices by immunopanning with HepaCAM. Inhibitors and DMSO were added on in-vitro day 2. HBEGF was depleted on the cell prep day and till in-vitro day 7. In-vitro day 2, 7 and 14 samples were collected on designed timepointed.

overall_design: Three EGFR inhibitor samples and three relative DMSO control samples, three P53 inhibitor samples and three relative DMSO control samples, two HBEGF samples and two HBEGF withdrawal samples, three samples for each in-vitro day 2, 7 and 14.

first: J

first: Y

last: Zhang


title: Hypoxia-regulated miRNAs in Human Mesenchymal Stem Cells

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

summary: miRNA microarray expression analysis of Human Bone Marrow Stem Cells from healthy (BM) and end-stage  critical limb ischemia (CLI) patients (PZ) in normal and hypoxic conditions

overall_design: 4 samples were analyzed in duplicates

first: Carmela

last: Dell'Aversana


title: Contrasting roles of transcription factors spineless and EcR in the highly dynamic chromatin landscape of butterfly wing metamorphosis

city: Ithaca

first: Karin

last: van der Burg

address: 215 Tower Road, Corson Hall

institute: Cornell University

summary:
Background: We studied the chromatin accessibility landscsape in wings during butterfly metamorphosis, and investigate which transcription factors might be driving changes in accessibility
Methods: We sequencing the Junonia coenia genome, and we studied chromatin accessibility using ATAC seq in multiple stages of wing development in both forewings and hindwings. For sites showing a large change in accessibility, we investigate which motifs are enriched, and correlate this with changes in gene expression of associated transcription factors. We confirm promising candidates with ChIP-seq
Results: We find a highly dynamic landscape, with multiple peaks showing a double increase in accessibility throughout development. We show that transcription factor spineless, but not ecdysone receptor, is highly predictive of opening sites
Conclusions: This work provides a characterization of the chromatin dynamics of insect wing metamorphosis, identifies novel candidate chromatin remodeling factors in insects, and provides the first genome assembly of the model butterfly Junonia coenia, with gene and cis-regulatory element annotations

overall_design: ATAC-seq from left and right forewings and hindwings at four developmental stages.

first: James

middle: J

last: Lewis

first: Arnaud

last: Martin

first: H

last: Nijhout

first: Charles

middle: G

last: Danko

first: Robert

middle: D

last: Reed


title: Targeting tumor mitochondrial metabolism overcomes resistance to antiangiogenics

city: Madrid

first: Silvana

last: Mouron

state: Madrid

address: Calle Melchor Fdez Almagro

department: Clinical Research

country: Spain

institute: CNIO

summary: Epithelial malignancies are effectively treated by antiangiogenics; however, acquired resistance is a major problem in cancer therapeutics. Epithelial tumors commonly have mutations in the MAPK/Pi3K-AKT pathways, which leads to high-rate aerobic glycolysis. Here, we show how novel multikinase inhibitor antiangiogenics (TKIs) induce hypoxia correction in spontaneous breast and lung tumor models. When this happens, the tumors down-regulate glycolysis and switch to long-term reliance on mitochondrial respiration. A transcriptomic, metabolomic and phosphoproteomic study revealed that this metabolic switch is mediated by down-regulation of HIF1α and AKT and up-regulation of AMPK, allowing uptake and degradation of fatty acids and ketone bodies. The switch renders mitochondrial respiration necessary for tumor survival. Agents like phenformin or ME344 induce synergistic tumor control when combined with TKIs, especially in a sequential schedule, leading to metabolic synthetic lethality. Our study uncovers new mechanistic insights in the process of tumor resistance to TKIs, and may have clinical applicability.

overall_design: Treatment induced gene expression in mouse mammary tumors was measured after treatment to B20, nintedanib or vehicle compounds.

first: Paloma

last: Navarro

first: Maria

last: Bueno

first: Ivana

last: Zagorac

first: Tamara

last: Mondejar

first: Jesus

last: Sanchez

first: Javier

last: Muñoz

first: Gonzalo

last: Gomez-Lopez

first: Veronica

last: Jimenez-Renard

first: Francisca

last: Mulero

first: Navdeep

last: Chandel

first: Miguel

last: Quintela-Fandino


first: Karin

middle: Revka Loek

last: van der Burg

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

overall_design: Refer to individual Series


title: Generation, transcriptome profiling, and functional validation of cone-enriched human retinal organoids

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Macula degenerations affect vision the most and are incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-enriched human retinal organoids differentiated from hESCs. Transcriptome profiling using bulk RNA-seq demonstrated that retinal differentiation in vitro recapitulated retinogenesis in vivo in the temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. Single-cell RNA-seq of 8-month retinal organoids identified clusters of cone and rod photoreceptors and confirmed the cone enrichment initially revealed by immunostaining. Notably, comparisons of single-cell transcriptomes demonstrated the similarity between retinal organoids and human macula in cones and rods. Cones in retinal organoids exhibited electrophysiological functions. Collectively, we have established cone-enriched retinal organoids and a reference of transcriptomes that are rich resources for retinal studies.

overall_design: To globally characterize the transcriptomes during human retinal cell differentiation, we performed bulk RNA-seq of retinal organoids at multiple time points (15 days, 1, 3, 6.5, and 9 months, three replicates per time point, Supplemental Table S1), starting from the stage preceding retinal ganglion cell differentiation to the stage when photoreceptors display outer segments.

first: Albert

last: Lowe

first: Rachayata

last: Dharmat

first: Yumei

last: Li

first: Rui

last: Chen

first: Wei

last: Liu


title: Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Our goal was to find correlations between gene expression patterns and impaired vascular pathophysiolgy in rheumatoid arthritis
Patients with rheumatoid arthritis were recruited and venous blood samples were collected, then peripheral blood mononuclear cells were separated. After RNA isoltaion, we used Affymetrix PrimeView arrays to obtain whole gene expression data.

overall_design: Samples of 19 patients with rheumatoid arthritis were examined. Sub-groups based the following clinical parameters flow-mediated vasodilation (FMD), pulse-wave velocity (PWV) and common carotid intima-media thickness (IMT) status were created and differentially expressed genes were determined in each sub-groups.

first: Tímea

last: Bessenyei

first: Edit

last: Végh

first: Attila

last: Hamar

first: Anita

last: Pusztai

first: Andrea

last: Váncsa

first: Nóra

last: Bodnár

first: Szilvia

last: Szamosi

first: Mária

last: Csumita

first: György

last: Kerekes

first: Zoltán

last: Szabó

last: Nagy

first: Gabriella

last: Szücs

first: Sándor

last: Szántó

first: Gábor

last: Zahuczky

first: László

last: Szekanecz


title: Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

summary: Virtually every mammalian tissue exhibits rhythmic expression in thousands of genes, which activate tissue-specific processes at appropriate times of the day. Much of this rhythmic expression is thought to be driven cell-autonomously by molecular circadian clocks present throughout the body. However, increasing evidence suggests that systemic signals, and more specifically rhythmic food intake (RFI), can regulate rhythmic gene expression independently of the circadian clock. To determine the relative contribution of cell autonomous clocks versus RFI in the regulation of rhythmic gene expression, we developed a system that allows long-term manipulation of the daily rhythm of food intake in the mouse, and analyzed liver gene expression by RNA-Seq in mice fed ad libitum, only at night, or arrhythmically (mouse eating 1/8th of their daily food intake every 3 hours). We show that 70% of the cycling mouse liver transcriptome loses rhythmicity under arrhythmic feeding. Remarkably, this loss of rhythmic gene expression under arrhythmic feeding is independent of the liver circadian clock, which continues to exhibit normal oscillations in core clock gene expression. Many genes that lose rhythmicity participate in the regulation of metabolic processes such as lipogenesis and glycogenesis, likely contributing to an increased sensitivity to insulin that was observed in arrhythmically-fed mice. We also show that night-restricted feeding significantly increases the number of rhythmically expressed genes as well as the amplitude of the rhythms. Together, these results indicate that metabolic transcription factors control a large fraction of the rhythmic mouse liver transcriptome, and demonstrate that systemic signals driven by rhythmic food intake play a more important role than the cell-autonomous circadian clock in driving rhythms in liver gene expression and metabolic functions.

overall_design: 3' mRNA sequencing on mice livers under 4 different feeding paradigms at 6 timepoints in triplicate

first: Ben

last: Greenwell


title: Root transcriptional profile of 1103P and SO4 grapevine rootstock plants grown in presence and absence of magnesium

city: Verona

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: Differences in root transcriptional profile between two grapevine rootstocks (1103P and SO4) showing different tolerance to Mg deficiency were analyzed after 4 and 14 days of growth with (+Mg) or without (-Mg).

sample_organism: Vitis cinerea var. helleri x Vitis rupestris

sample_organism: Vitis cinerea var. helleri x Vitis riparia

overall_design: Half part of microcuttings of 1103P and SO4, after a 2-week hydroponic grown using a dilute nutrient solution, were treated for 4 and 14 days with a new solution containing Mg (250 µM)  and the other half with a solution without Mg (equivalent mole of CaSO4). Three biological replicates were obtained by three independent experiments and collecting roots after 4 and 14 days.

first: Zamboni

last: Anita

first: Livigni

last: Sonia

first: Varanini

last: Zeno


title: Transcriptome analysis of wildtype and sox3-/- zebrafish adult ovary

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

summary: The goals of this study are to compare the differentially expressed genes between wildtype and sox3-/- zebrafish ovaries based on RNA-seq data and some of these genes were validated by qRT–PCR. Further, the differentially expressed genes were devided into up-regulated and down-regulated genes for GO and KEGG analysis.

overall_design: Ovary mRNA profiles of adult wildtype and sox3-/- zebrafish were generated by deep sequencing.

first: Cong

last: Li


title: Genome-wide profiling of cervical RNA-binding proteins identified HPV regulation of RNASEH2A expression by viral E7 and E2F1

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: RNA-binding proteins (RBPs) have been shown to control mRNA processing, stability, transport, editing and translation. Application of large-scale quantitative technologies has facilitated genome-wide identification of RBPs and linked their defects to human diseases and carcinogenesis. We have recently conducted transcriptome analysis comparing normal cervical tissues with HPV-positive cervical cancer tissues by using two different RNA-seq platforms. As the results, 614 differentially expressed protein-coding transcripts were identified, which are enriched in cancer related pathways and consist of 95 known RBPs. TaqMan RT-qPCR was used to verify altered expression of 26 genes with a cohort of 72 cervical samples, including 24 normal cervical, 25 CIN 2-3, and 23 cervical cancer tissues. LY6K, FAM83A, CELSR3, ASF1B, IQGAP3, SEMA3F, CLDN10, MSX1, CXCL5, ASRGL1, ELAVL2, GRB7, KHSRP, NOVA1, PTBP1 and RNASEH2A were identified being novel candidates in association with cervical lesion progression and carcinogenesis. We further demonstrated that HPV16 or HPV18 infection leads to altered expression of 8 RBP genes (CDKN2A, ELAVL2, GRB7, HSPB1, KHSRP, NOVA1, PTBP1, and RNASEH2A) in human vaginal and foreskin keratinocytes.  While both viral E6 and E7 decrease NOVA1 expression, viral E7 was found to increase the expression of both RNASEH2A and PCNA in an E2F1 dependent manner, two key factors closely associated with the progression of cervical neoplasia. By illustration of the first comprehensive cervical genome expression atlas, we have identified the altered expression of many novel genes due to HPV infection, which could be biomarkers for better diagnosis and treatment of cervical cancer.

overall_design: Gene expression patterns of seven normal cervical tissues were compared with that of seven cervical cancer tissues by two different RNA-seq platforms. Additional 72 clinical samples and HPV-infected keratinocytes were analyzed by RT-qPCR to verify the HPV-infection altered gene expression.

first: Junfen

last: Xu

first: Xiaohong

last: Wang

first: Jun

last: Zhu

first: Zhi-Ming

last: Zheng


title: Microarray of IRF2 overexpress in iKAP primary cultured cells (#3346)

first: Guocan

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: We used microarrays to study the global gene expression and identified differentially expressed genes in IRF2-overexpressing 3346 iKAP cells, aiming to identify genes and pathways that are regulated by IRF2.

overall_design: IRF2 ORF and GFP control in pLenti6.3 constructs were stabley overexpressed in iKAP primary cultured cells (#3346) cells. The samples used in the microarray analysis were in triplicate.

first: W

middle: T

last: Liao

first: G

first: R

last: DePinho

first: Y


title: Targeting FGFR overcomes EMT-mediated resistance in EGFR mutant non-small cell lung cancer

city: Boston

first: Sana

last: Raoof

address: 175 Cambridge St

institute: Massachusetts General Hospital

summary: Acquired drug resistance to tyrosine kinase inhibitor (TKI) targeted therapies remains a major clinical challenge. In EGFR mutant non-small cell lung cancer (NSCLC), therapeutic failure of EGFR TKIs can result from both genetic and epigenetic mechanisms of acquired drug resistance. Histologic and gene expression changes consistent with an epithelial-to-mesenchymal transition (EMT) have been associated with resistance to EGFR TKIs in both experimental models and in patients, and may coincide with genetic mechanisms of resistance such as the EGFRT790M gatekeeper mutation. While therapeutic approaches targeting EGFRT790M have been developed, a strategy for overcoming EMT-related resistance remains unclear. We performed whole-genome CRISPR screening on patient-derived, mesenchymal EGFRT790M-positive cell lines and identified FGFR1 as a critical gene promoting resistance to third generation EGFR TKIs. The FGFR1-3 inhibitor, BGJ398 (infigratinib), resensitized resistant mesenchymal-like cell lines to EGFR inhibition in a synergistic manner. Combining EGFR + FGFR inhibitors also inhibited the in vitro survival and expansion of EGFR mutant drug tolerant cells with mesenchymal-like features prior to the development of drug resistance, and delayed the development of in vivo resistance in EGFR mutant NSCLC xenograft tumors. These results suggest that dual EGFR + FGFR blockade may be a promising clinical strategy for preventing and overcoming EMT-associated acquired drug resistance in EGFR mutant NSCLC.

overall_design: PC9, HCC4006, HC1975, HCC827, MGH119 treated for two weeks with vehicle or with 300nM Gefitinib (300nM WZ4002 for H1975). Triplicates (duplicate for PC9 and MGH119)

first: Aaron

middle: N

last: Hata

first: Heidie

last: Frisco-Cabanos

first: Fei

last: Ji

first: Yotam

last: Drier


title: Sex-dependent effects of Siah2 on brown adipose tissue whitening and inflammation with a high fat diet

city: Baton Rouge

first: Thanh

last: Dang

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: The goal of this experiment was to examine the sex-dependent effect of Siah2 in brown adipose tissue

overall_design: Total RNA obtained from brown adipose tissues of male or female mice with global knockout of Siah2 subjected to 20 weeks of 45% high fat or 10% low fat diet compared to brown adipose tissue of male or female wild-type mice on the same diet.

first: Elizabeth

last: Floyd

first: Gail

last: Kilroy

first: Lauren

last: Carter

first: Susan

last: Newman

first: Sujoy

last: Ghosh


title: Comparative Transcriptomic Analysis of Dermal Wound Healing Reveals De Novo Skeletal Muscle Regeneration in Acomys cahirinus

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

summary: This project is a comprehensive analysis of gene expression following full-thickness excisional dermal wounds in the African spiny mouse and the laboratory mouse.

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design:
8mm excisional wounds were made on the dorsal skin. Wounds were harvested on day 7 and 14 after wounding. Normal, unwounded (day 0) skin was used as a control. N=4 for each time point for each species. 2x150 bp paired-end reads. DSN library was equal amounts of all Acomys samples, pooled, and normalized using duplex-specific nuclease.
The 'Mus_Day-0_rep3' sample was removed from downstream analysis due to poor QC results, and is not included here.

first: J

middle: L

last: Boatwright


title: Generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids

first: Sangbae

last: Kim

summary: The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Here we report the generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids differentiated from hESCs.  Single-cell RNA-seq of 8-month retinal organoids identified clusters of cone and rod photoreceptors and confirmed the cone enrichment initially revealed by immunostaining. Collectively, we have established cone-enriched retinal organoids and a reference of transcriptomes that are rich resources for retinal studies.

overall_design: To globally characterize the transcriptomes during human retinal cell differentiation, we performed single cell RNA sequencing  of 8M retinal organoids.

first: Albert

last: Lowe

first: Rachayata

last: Dharmat

first: Yumei

last: Li

first: Rui

last: Chen

first: Wei

last: Liu


title: The effects of different chemical forms of iron fertilizer on cadium accumulation in dwarf Polish wheat are reflected in the differentially expressed genes

status: Public on Apr 24 2019

first: Qin

last: Yao

address: Huimin Road

institute: Sichuan Agricultural University

summary:
Purpose: To understand the effects of two different chemical forms of iron fertilizer on cadmium accumulation
Methods:Cultivation and treatment for three weeks of dwarf Polish wheat seedlings by hydroponics, in triplicate, qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Iron fertilizer can effectively reduce cadmium concentration in plants
Conclusions: Our study represents the different chemical forms of iron fertilizer have different mitigation effects on cadmium. The transcriptome gata showed that iron fertilizer have changed the cadimium metabolism

overall_design: The groups treated with two fertilizers and CdCl2 solution before collected.The samples were collected after one week treatment. The roots samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis.

first: Yao

last: Qin


title: Pilot transcriptome analysis of human iPSC-derived healthy control vs. schizophrenia cortical interneurons

city: Greenville

first: Weihua

last: Huang

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: We report specific changes in schizophrenia developmental interneurons by genome-wide transcriptome analysis.

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons vs. schizophrenia interneurons. Nine independent iPSC lines per group.

first: Sangmi

last: Chung


title: Gene expression profiling of metastasising and non-metastasising canine primary oral melanomas

city: Newmarket

first: Mike

last: Starkey

address: Lanwades Park

institute: Animal Health Trust

summary: In this study the global expression profiles of primary oral melanomas that metastasised were compared with those of primary tumours that did not metastasise. The objective was to identify genes involved in oral melanoma metastatic progression that may represent targets for therapeutic intervention and biomarkers for prediction of tumour metastasis.

overall_design: Canine Gene 1.1 ST Arrays were employed for gene expression analysis of formalin-fixed, paraffin-embedded biopsies of oral melanomas borne by 18 dogs that died due to confirmed oral melanoma metastasis and 10 dogs that were still alive more than 540 days post-surgery.

middle: P


title: Polysome profiling of a human glioblastoma reveals intratumoral heterogeneity

city: São Paulo

first: Glaucia

last: Hajj

state: SP

address: Rua Taguá 440

country: Brazil

institute: AC Camargo Cancer Center

summary: Glioblastoma (GBM) is one of the most aggressive cancers, with median survival of less than 2 years. Despite of considerable advance in molecular classification of GBMs, no improvements in therapy have been described. The scenario is further complicated by tumor heterogeneity and the relationship among genetic, transcriptional and functional findings. Classically, gene expression has been evaluated by steady-state mRNA, however, this does not take translational control into consideration, which contributes considerably to the composition of the proteome. In this study, we evaluated the transcriptomic and translatomic signature of a GBM obtained from a single patient focusing in tumor heterogeneity. In a sampling of eight fragments, we investigated the translation rates, mTORC1 and ERK1/2 pathways and identified both total and polysome associated mRNAs. An increased translation rate was observed in fragments with high-grade histological features. High-grade histology was also associated with the expression of genes related to extracellular matrix (ECM) and angiogenesis, in both transcriptomes and translatomes. However, genes associated with epithelial to mesenchymal transition and stress response, were observed only in translatomes from high-grade fragments. Overall, our results demonstrate that isolation of translated mRNA can be used to identify biomarkers and reveal previously unrecognized determinants of heterogeneity in GBMs.

overall_design: Six histologically distinct fragments from a secondary glioblastoma, which were classified as high- or low-grade, by an experienced pathologist according to the 2016 World Health Organization Classification of Tumors of the Central Nervous System. Total mRNA and polysome-associated (poly) mRNA were purified using Trizol (Life Technologies). RNA integrity was verified by Agilent 2100 Bioanalyzer with an RNA Pico 6000 microfluidics kit (Agilent Technologies). Gene expression in total and poly mRNA was determined using a two-color microarray-based gene expression (Whole Human Genome 4x44K microarray platform) and the Quick Amp Labeling Kit (Agilent Technologies, CA, USA) according to the manufacturer’s recommendations. Microarrays for total and poly mRNA from each of the six fragments were run in duplicates. RNA from the GBM cell line LN-229 (ATCC® CRL-2611™) was used as reference in all reactions (Cy5 channel).

first: Fernanda

last: Lupinacci


title: Next Generation Sequencing Quantitative Analysis of HepG2, hyper-glycolytic model cell, oxamate treated cells

city: Daejeon

first: Yi-deun

last: Jung

address: 125 Gahac-ro, Yusung-Gu

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To determine the genes potentially responsible for the lactate-mediated gene expression regulation in hepatocellular carcinoma, we performed RNA-seq analyses on parental HepG2, HepG2/metR and oxamate-treated HepG2/metR cells. To gain mechanistic insights into the lactate-induced pro-migratory phenotypes, we established a cell model that acquired a resistance to metformin while producing lactate at a high level by selecting HepG2 cells that survived a chronic exposure to metformin for more than 5 months (HepG2/metR). In HepG2/metR cells, glycolysis rates were increased by more than 3 folds compared with parental cells, and consequently, lactate production was also highly enhanced. To clarify the gene expression regulation between the lactate level in the HepG2/metR model, we treated the cells with oxamate, an inhibitor of lactate dehydrogenase, and found that it significantly. Using a 2-fold change cut-off value in transcriptome, we selected 1,757 genes significantly up-regulated in HepG2/metR vs parental HepG2 cells. 690 genes were down-regulated by oxamate treatment in HepG2/metR cells. Eventually, we selected 136 genes that are common in the two gene sets, which may directly respond to lactate signaling

overall_design: mRNA profiles of HepG2 cells, HepG2/metR (hyper-glycolytic cell model), oxamate treated HepG2/metR (decreased lactate concentration cell) were generated by deep sequencing using Illumina Nextseq 500

first: Young-Il

last: Yeom

first: Dong-Chul

last: Lee


title: Identification of Pregnancy-specific Transcriptional Mediators of Pancreatic Islet Adaptation Regulated by Prolactin Receptor Signaling in Mice

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary:
To identify nodal transcriptional regulators and effector of PRLR signaling gene targets and networks within beta-cells during pregnancy, we compared the transcriptional signatures of islets from βPRLRKO mice relative to those of littermate controls.
Gene expression was assessed using Affymetrix GeneChip® Mouse Gene 2.0 ST Array. Target genes were technically validated using real-time quantitative PCR.

overall_design: 6 pancreatic beta islet samples were analyzed by Affymetrix array: 3 wild-type samples; 3 bPRLR-KO samples.

first: Ronadip

middle: R

last: Banerjee


title: Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: One of the most widely used agricultural compounds worldwide is the herbicide glyphosate (N-(phosphonomethyl)glycine), commonly known as Roundup. The current study using a transient exposure of gestating F0 generation female rats found negligible impacts of glyphosate on the directly exposed F0 generation or F1 generation offspring, but dramatic increases in pathologies in the F2 generation grand-offspring and F3 transgenerational great-grand-offspring. The transgenerational pathologies observed include prostate disease, obesity, kidney disease, ovarian disease, and parturition (birth) abnormalities. Epigenetic analysis of the F1, F2 and F3 generation sperm identified altered DNA methylation.

overall_design: Analysis of the transgenerational actions of glyphosate used outbred Sprague Dawley female rats (F0 generation) transiently exposed (25 mg/kg body weight glyphosate daily) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure). A control lineage used F0 generation gestating females administered vehicle control dimethyl sulfoxide (DMSO) or phosphate buffered saline (PBS). The control and glyphosate lineages were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts in either the control or glyphosate lineages. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation for analysis, as previously described.

first: Deepika

last: Kubsad

first: Eric

last: Nilsson

first: Stephanie

middle: E

last: King

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: Remodeling Group 3 medulloblastoma: MYC overexpression alone transforms progenitors of astrocytes and granule neurons in the postnatal cerebellum

city: Washington

first: Yanxin

last: Pei

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology

institute: Children's National Medical Center

summary: Group 3 medulloblastoma is often associated with MYC amplification or overexpression, while whether MYC overexpression alone is sufficient to induce tumorigenesis is unknown and the cell type(s) which can be transformed by MYC is unclear. Here, by generating a new mouse model, we demonstrated that overexpression of Myc alone is sufficient to transform astrocyte progenitors and granule neuron progenitors (GNP) in the early postnatal cerebellum following orthotopic transplantation. The resulting tumors resemble human Group 3 medulloblastoma in terms of both histology and gene expression profiles. Using these models we found that inhibition of lactate dehydrogenase A (LDHA) significantly reduced both murine and human MYC-driven tumor growth, but did not affect SHH medulloblastoma, indicating that LDHA is potential and specific therapeutic target for MYC-driven medulloblastoma.

overall_design: We generated tumors from Sox2+  or Math1+  cells in the postnatal cerebellum. Sox2+ or Math1+ cells were purified by FACS sorting from cerebella of P5-P6 Sox2-GFP or Math1-GFP mice. The cells were then infected with Myc lentivirus, cultured for 16 hr and injected into the cerebella of immunodeficient mice. Animals were sacrificed when they developed symptoms of brain tumors. The resulting tumors generated from Sox2+ or Math1+ cells were named SOX2 tumors or MATH1 tumors. Tumor cells, Sox2+ and Math1+ normal cerebellar cells were used for RNA isolation, subsequent cDNA libraries construction and RNA-sequencing using Illumina HiSeq 4000.

first: Ran

last: Tao

first: Najiba

last: Murad

first: Zhenhua

last: Xu

first: Peng

last: Zhang

first: Konstantin

last: Okonechnikov

first: Marcel

last: Kool

first: Samuel

last: Rivero-Hinojosa

first: Brian

last: Rood

first: Christopher

last: Lazarski

first: Charles

last: Eberhart

first: Roger

last: Packer


title: High-throughput exploration of the network dependent on AKT1 in mouse ovarian granulosa cells.

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

summary: We depleted Akt1 in murine primary granulosa cells and assessed the molecular consequences at the transcript level. We were able to corroborate the involvement of AKT1 in the regulation of metabolism, apoptosis, cell cycle or cytoskeleton dynamics in this ovarian cell type.

overall_design: Single Read 75 pb runs, on an Illumina NextSeq500 instrument, using NextSeq 500 High Output 75 cycles kits.

first: Maëva

last: Elzaiat

first: Anne-Laure

first: Reiner

last: Veitia


title: Genome-wide analysis of senecent MCF7 cells induced by irridiation and ectopic overexpression of p21

city: Chicago

first: Stephen

last: Kron

state: IL

department: MGCB

institute: University of Chicago

summary: Analysis of genes in senescent MCF7 cells induced by irridiation and ectopic expression of p21

overall_design: MCF7 cells were induced to senescence and total RNA were obtained after 5 days and compared to control untreated samples.

first: Ding

last: Wu


title: Effect of EGFR activation on mouse chondrocytes

city: Hangzhou

first: Heng

last: Sun

state: Zhejiang

address: 866# Yuhangtang Road

department: Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

summary: We examined the change of chondrocyte transcriptome after EGFR activation by TGF-α and inhibition by gefitinib. Data analysis showed that EGFR activation down-regulates cartilage ECM biosynthesis and promotes ECM degradation. Gefitinib can reverse the effects of EGFR on chondrocytes.

overall_design: Cells: P2 mouse epiphyseal chondrocytes; Groups: Control (PBS), TGF-α (10 ng/ml, 48 h), TGF-α + Gefitinib (10 μM, 48 h)


title: Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

summary: The samples were respectively from three replicates of the Cd-stress treatment and the control, then we obtained six cDNA libraries. In total, 237，866 transcripts and 191，370 unigenes were constructed. We got a total of 23，424 differentially expressed genes (DEGs), of which 12，558 were up-regulated and the other 10，866 were down regulated under the Cd treatment.

overall_design: We select the robust plants with consistent growth for soil Cd stress treatment. Each plastic flowerpot was planted with one seedling, 15 pots per treatment. The experiment was repeated three times with a total of 90 pots. The control group （T01）did not add Cd solution, the concentration of Cd in the experimental group was 100mg/kg(T02). 20 days after Cd stress, all the plants were harvested. In this experiment, the seedings were grown in ambient conditions with a photoperiod of 14 h at 24±3℃ and a relative humidity of 75%.  roots mRNA profiles of the development were generated by deep sequencing, in  triplicate, using Illumina HiSeq.

first: Zhen-yu


title: Genome-wide maps of IRF2 targets

city: houston

first: Wenting

last: Liao

address: 1881 east road

institute: md anderson

summary: Using ChIP-seq technology, we tried to find out the whole genome targets for IRF2 in mouse colorectal cancer (CRC) cells. More than 7000 genes were defined as the target of IRF2.

overall_design: Examine IRF2 binding peaks in primarily cultured iKAP CRC cells as compared with input.

first: Wen-Ting

first: Zheng

last: Lan

first: Ming

last: Tang


title: High-throughput sequencing technology identify the CGMMV responsive genes, lncRNAs and cirRNAs in watermelon

first: li

last: lei

address: xiashas street num 6

summary: The DEGs, lncRNAs and cirRNAs in responsive to the CGMMV infection in watermelon leaves were obtained through deep sequencing.

overall_design: watermelon leaves at true-leaf stages were inoculated with CGMMV, samples were collected at 0h (ck), 48h and 25d post CGMMV infection and used for high-throughput sequencing

first: Yuyan

first: Min

last: Fan


title: Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

summary: Ecdysone signaling has long been studied as a paradigm for how hormones can synchronize development events in tissues throughout the animal. At the genetic level, ecdysone acts through its receptor, EcR, which has been classically thought to act at a relatively small number of canonical, ecdysone-responsive genes which then go on to activate the effectors of cellular processes. However, in spite of the decades of work studying EcR, the understanding of how EcR promotes changes in gene expression genome-wide in vivo remains incomplete. To examine EcR’s role in promoting changes in gene expression, we use a tissue-specific GAL4 driver to knockdown EcR throughout wing development and perform RNAseq on both WT wings and EcR-RNAi wings at -6h after puparium formation (APF) and +6hAPF. We find that EcR is required to promote thousands of gene expression changes genome-wide. To determine whether EcR is directly effecting these changes, we perform CUT&RUN in wings to identify EcR binding sites genome-wide. We find that EcR directly binds thousands of sites genome-wide, including many genes important for wing development. Collectively, these data suggest that EcR does not only act the top of a signaling cascade, but, instead, directly effects the response to ecdysone at multiple levels.

overall_design: Total-RNAseq from wing tissue at -6hAPF (3rd larval wandering, 3LW) and +6hAPF in WT and EcR-RNAi genotypes; CUT&RUN from WT wing tissue at -6hAPF and +6hAPF

middle: M

first: Daniel

last: McKay


title: Microarray of TBK1 WT and Mutant pancreatic tumors in the KIC model

city: Dallas

first: Emily

middle: Nicole

last: Arner

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

summary: Analysis of gene expression changes that occur in pancreatic tumors when global TBK1 is lost.

overall_design: Total RNA obtained from isolated fresh pancreatic tumor tissue in KIC GEMM at 8wks of age.

first: Victoria

last: Cruz


title: Bisulfite sequencing of medaka sperm methylomes

status: Public on Apr 23 2019

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

institute: University of North Carolina Greensboro

summary: Medaka sperm methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

overall_design: Three replicates


title: Cellular response of mesenchymal stem cells transplanted into spinal cord injury

city: Stockholm

first: Mikael

last: Svensson

state: Stockholm

address: Solnavägen 30

department: Clinical neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Mesenchymal stem cells (MSCs) and their cellular response to various stimuli have been characterized in great detail in culture conditions. In contrast, the cellular response of MSCs in an in vivo setting is still uncharted territory. In this study, we investigated the cellular response of MSCs following transplantation into spinal cord injury (SCI).Mouse bone marrow-derived MSCs were transplanted 24h following severe contusion SCI in mice. As controls, MSCs transplanted to uninjured spinal cord and non-transplanted MSCs were used. At seven days post transplantation, the MSCs were isolated from the SCI, and their global transcriptional changes investigated using RNA-sequencing. We found that MSCs transplanted into SCI down-regulate their response to cytokines, tendency to adhere and to undergo phagocytosis but up-regulate their ability to repair DNA and proliferate.

overall_design: Evaluation of transcriptional changes in transplanted mesenchymal stem cells.

first: Ramil

last: Hakim

first: Ruxandra

last: Covacu

first: Vasilios

last: Zachariadis

first: Arvid

last: Frostell

first: Sreenivasa

last: Sankavaram

first: Lou

last: Brundin


title: ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells [ATAC-seq]

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Estrogen signaling through estrogen receptor alpha (ER) plays a major role in endometrial cancer risk and progression; however, the molecular mechanisms underlying ER’s regulatory role in endometrial cancer are poorly understood. In breast cancer cells, ER genomic binding is enabled by FOXA1 and GATA3, but the transcription factors that control ER genomic binding in endometrial cancer cells remain unknown. We previously identified ETV4 as a candidate factor controlling ER genomic binding in endometrial cancer cells and here we explore the functional importance of ETV4. Homozygous deletion of ETV4, using CRISPR/Cas9, led to greatly reduced ER binding at the majority of loci normally bound by ER. Consistent with the dramatic loss of ER binding, the gene expression response to estradiol was dampened for most genes. ETV4 contributes to estrogen signaling in two distinct ways; ETV4 loss impacts chromatin accessibility at some ER bound loci and impairs ER nuclear translocation. The diminished estrogen signaling upon ETV4 deletion led to decreased growth, particularly in 3D culture where hollow organoids were formed. Our results show that ETV4 plays a necessary role in estrogen signaling in endometrial cancer cells.

overall_design: ATAC-seq was used to analyze chromatin accessibility changes due to ETV4 knockout

first: Adriana

middle: C

last: Rodriguez


title: Gene expression analysis of WT and ZIP13-depleted human mesenchymal stem cells

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to identify the genes whose expression was perturbed by ZIP13, we performed a gene expression microarray analysis for the RNAs isolated from WT and ZIP13-depleted human mesenchymal stem cell.

overall_design: Duplicate experiments were performed for WT and ZIP13 knock-down human mesenchymal stem cells. Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturer's protocols.

first: Bum-Ho

last: Bin


title: TET3 prevents terminal differentiation of adult NSCs by a non-catalytic action at Snrpn

city: Burjassot

first: Sacri

middle: R.

last: Ferron

state: Valencia

address: Calle Doctor Moliner, 50

department: Cell Biology

institute: University of Valencia

summary: Ten-eleven-translocation (TET) proteins catalyze DNA hydroxylation, playing an important role in demethylation of DNA in mammals. Remarkably, although hydroxymethylation levels are high in the mouse brain, the potential role of TET proteins in adult neurogenesis is unknown. We show here that a non-catalytic action of TET3 is essentially required for the maintenance of the neural stem cell (NSC) pool in the adult subventricular zone (SVZ) niche by preventing premature differentiation of NSCs into non-neurogenic astrocytes. This occurs through direct binding of TET3 to the paternal transcribed allele of the imprinted gene Small nuclear ribonucleoprotein-associated polypeptide N (Snrpn), contributing to transcriptional repression of the gene. The study also identifies BMP2 as an effector of the astrocytic terminal differentiation mediated by SNRPN. Our work describes a novel mechanism of control of an imprinted gene in the regulation of adult neurogenesis through an unconventional role of TET3.

overall_design: 6 samples: 3 controls and 3 condition samples

first: Raquel

last: Montalbán-Loro

first: Anna

last: Lozano-Ureña

last: Ferrón


title: Altered Glutamate Receptor Ionotropic Delta Subunit 2 expression in Stau2 deficient cerebellar Purkinje cells in the adult brain

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Staufen2 (Stau2) is an RNA-binding protein that is involved in dendritic spine morphogenesis and function. Several studies have recently investigated the role of Stau2 in the regulation of its neuronal target mRNAs, with particular focus on the hippocampus. Here, we provide evidence for Stau2 expression and function in cerebellar Purkinje cells. We show that Stau2 downregulation (Stau2GT) lead to an increase of the glutamate receptor ionotropic delta subunit 2 (GluD2) in Purkinje cells when animals performed physical activity by voluntary wheel running. Furthermore, Stau2GT mice showed lower performance in motor coordination assays but enhanced motor learning abilities, concomitantly with an increase in dendritic GluD2 expression. Together, our results suggest a novel role of Stau2 in Purkinje cell synaptogenesis in the mouse cerebellum

overall_design: Total RNA isolated from wildtype and Stau2 knockout mice brain before and after behavioural training.

first: Helena

middle: F

last: Pernice

first: Rico

last: Schieweck

first: Mehrnoosh

last: Jafari

first: Martin

last: Bilban

first: Michael

middle: A

last: Kiebler

first: Bastian

last: Popper


title: RNA-seq of developing Cyprinodon variegatus exposed to oil, hypoxia, or both

city: Florence

first: Elizabeth

last: Jones

state: SC

address: 4822 E. Palmetto St.

institute: Francis Marion University

summary: The objective of this project was to investigate the impacts of oil exposure in combination with environmental stressors on gene expression in developing C. variegatus.

overall_design: C. variegatus from three different life stages (embryonic,  ≤ 15 h post-fertilization; post-hatch, ≤ 24 h post-hatch, post-larval ≤ 4 d post-hatch) were exposed to oil, hypoxia, or both for 48 hours.  Oil solutions used in exposures were derived from high energy water accommodated fractions (HEWAF) prepared using Macondo well oil following explosion of the Deepwater Horizon oil rig in 2010.  Exposure hypoxia was defined as ≤ 2 mg/L of oxygen.  All treatments were performed in triplicate.  Following exposure, 10 larvae from each replicate were processed for RNA extraction and RNA sequencing.

first: Danielle

middle: J

last: Simining

first: Maria

middle: S

last: Sepulveda

first: Thijs

last: Bosker

first: Sylvain

last: DeGuise

first: Robert

last: Griffitt


title: Transcriptome analysis of Riociguat and Vehicle control treatment in human hematopoietic stem and progenitor cells

city: Indianapolis

first: Xinxin

last: Huang

state: IN

address: 950 W. Walnut St R2 304

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: The goal of this study is to compare differetial gene expressions between Riociguat and Vehicle control treatment in human hematopoietic stem and progenitor cells

overall_design: Human cordd blood CD34+ cell mRNA profiles after 16 hours treatment of Riociguat or Vehicle control

first: Sheng

last: Liu

first: Jun

last: Wan

first: Hal

last: Broxmeyer


title: Theiler’s Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses [array]

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

summary: Theiler’s murine encephalomyelitis virus (TMEV) induces different diseases in the central nervous system (CNS) and heart, depending on the mouse strains and time course, where cytokines play a key role for viral clearance and immune-mediated pathology (immunopathology).  In SJL/J mice, TMEV infection causes chronic TMEV-induced demyelinating disease (TMEV-IDD) in the spinal cord around 1 month post infection (p.i.).  Unlike other immunopathology models, both pro-inflammatory and anti-inflammatory cytokines can play dual roles in TMEV-IDD.  Pro-inflammatory cytokines play a beneficial role in viral clearance while they also play a detrimental role in immune-mediated demyelination.  Anti-inflammatory cytokines suppress not only protective anti-viral immune responses but also detrimental autoreactive immune responses.  On the other hand, in C3H mice, TMEV infection induces a non-CNS disease, myocarditis, with three phases: phase I, viral pathology with interferon and chemokine responses; phase II, immunopathology mediated by acquired immune responses; and phase III, cardiac fibrosis.  Although the precise mechanism how a single virus, TMEV, induces the distinct diseases in different organs is unclear, principal component analysis (PCA) of transcriptome data allows us to identify the key factors contributing to distinct immunopathology.  The PCA demonstrated that in vitro infection of a cardiomyocyte cell line could reproduce the transcriptome profile of phase I in TMEV-induced myocarditis; distinct interferon/chemokine-related responses were induced in vitro in infected cardiomyocytes, but not in infected neuronal cells.  In addition, the PCA of in vivo CNS transcriptome data showed that decreased lymphatic marker expression was associated with inflammation in TMEV infection.  Here, dysfunction of lymphatic vessels may contribute to immunopathology by delaying clearance of cytokines and immune cells from the inflammatory site, although this might confine the virus at the site, preventing virus spread via lymphatic vessels.   On the other hand, in the heart, dysfunction of lymphatics was associated with reduced lymphatic muscle contractility by pro-inflammatory cytokines.  Therefore, TMEV infection could induce different cytokine expressions as well as lymphatic vessel dysfunction by the distinct mechanism between the CNS and heart, which might contribute to organ-specific immunopathology.

overall_design:
Transcriptome analysis of RNA samples from a mouse myocardial cell line, HL-1, infected with Theiler's murine encephalomyelitis virus (TMEV)
We analyzed gene expression profiles in TMEV-infected HL-1 cells, using Affymetrix GeneChip Mouse Gene 1.0ST Array. Array data was processed using R.

first: Eiichiro

last: Kawai

first: Ikuo

last: Tsunoda


title: Targeting the perivascular niche sensitizes disseminated tumour cells to chemotherapy

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The presence of disseminated tumour cells (DTCs) in bone marrow predicts poorer metastasis-free survival of breast cancer patients with localized disease, and their eradication improves long-term prognosis. DTCs persist in distant tissues despite administration of adjuvant chemotherapy, ostensibly because the majority of DTCs are quiescent. Here, we provide evidence that the microenvironment of DTCs protects them from chemotherapy independent of cell cycle status. We show that chemoresistant DTCs associate with the perivascular niche (PVN) of distant tissues, and that they are protected from therapies by vascular endothelium. Inhibiting key integrin-mediated interactions between DTCs and the PVN, driven partly by endothelial-derived von Willebrand Factor, sensitizes DTCs to chemotherapy and prevents bone metastasis. Importantly, chemosensitization is achieved without inducing DTC proliferation, or exacerbating chemotherapy-induced toxicities. These results suggest that prefacing adjuvant therapy with integrin inhibitors is a viable clinical strategy to eradicate DTCs and prevent metastasis.

overall_design: RNA sequencing of bone marrow mesenchymal stem cells (MSCs) and bone marrow microvascular niches (MVNs) by RNAseq using Illumina HiSeq 2500.

first: Patrick

last: Carlson

first: Arko

last: Dasgupta

first: Candice

last: Grzelak

first: Jeanna

last: Kim

first: Alexander

last: Barrett

first: Ryann

last: Shor

first: Erica

middle: T

last: Goddard

first: Jinxiang

last: Dai

first: Emma

last: Schweitzer

first: Andrea

last: Lim

first: David

last: Cheresh

first: Peter

last: Nelson

first: Kirk

last: Hansen

first: Cyrus

last: Ghajar


title: Functional relationship of GUN1 and FUG1 in plastid proteostasis

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: GUN1 integrates retrograde signals in the chloroplast but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcript level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and systems-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transient additive phenotypes with respect to photosynthesis, leaf coloration, growth and cold acclimation. Variegation of the var2 mutant is enhanced by gun1-103 in terms of increasing the fraction of white sectors, in contrast to fug1-3 that acts as suppressor. The transcriptomes of fug1-3 and gun1-103 are very similar, but absence of GUN1 alone has almost no effects on protein levels, whereas chloroplast protein accumulation is markedly decreased in fug1-3. In gun1 fug1 double mutants, effects on transcriptomes and particularly proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased translation (fug1) or degradation (var2) of chloroplast proteins. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 operates in chloroplast proteostasis.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana gun1, fug1 and gun1 fug1 mutants compared to wild type in three replicates


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

first: Tobias

last: Straub

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

overall_design: Refer to individual Series


title: Genome-wide mapping of H3K27ac marked regions during flower development

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

summary: Flower developmental stage specific genome-wide H3K27ac loci were mapped in this study. By quantifying the enrichment of H3K27ac modification at each stage, we revealed the dynamic landscape of H3K27ac during flower development. The dynamic of H3K27ac was found to contribute to stage specific gene expression. We found that H3K27ac always locate in proximal region of transcription starting sites but hardly appear in distal intergenic region.

overall_design: In this study, we take advantage of an inducible flower development system,pAP1::AP1-GRap1cal,which allows to manipulate the developmental process of flower formation. Synchronized flower tissue of specific stage could be harvested, which provide the possibility to map stage-specific H3K27ac targets and study the dynamic of this modification across flower development.

first: Wenhao

last: Yan

first: Kerstin

last: Kaufmann


title: Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how post-translational modification of histones such as activating trimethylated histone 3 lysine 4 (H3K4me3), or histone demethylases including the H3K4 demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.

overall_design: MNase-Seq of  murine shLuc and Kdm5b ES cells


title: Effects of rosiglitazone on human omental adipose tissue gene expression

city: Boston

first: Mi-Jeong

last: Lee

state: MA

address: 650 Albany St 810

department: Medicine

institute: Boston University

summary:
The cellular mechanisms by which PPARγ improves metabolism in mature human adipocytes and potential depot differences in its actions are poorly understood.
To assess the global effects of PPARγ activation on human omental gene expression, we conducted microarray analysis of control vs. rosiglitazone-treated omental tissues from human subjects.

overall_design: Adipose tissues fragemnts from 2 independent donors were treated with rosigltiazone (μM) for 7 days. Total RNA was extracted and used for micorray analysis using Affymatrix.  Technical duplicates of the first subject were averaged with the values from the second subject prior to statistical analysis.


title: The Aged Microenvironment Enhances the Tumorigenic Potential of Malignant Prostate Epithelial Cells

first: Ilsa

last: Coleman

summary: The incidence of prostate cancer is directly linked to age, but we still lack an adequate understanding of the prostatic aging-associated changes that facilitate carcinogenesis. In this study, we investigated possible associated factors in the aged prostate microenvironment, using an orthotopic mouse model of prostate cancer. We found that aged mice showed accelerated growth of TRAMP-C2 cells, compared with young mice. Metastatic lesions following intravenous injection were also more numerous in aged mice. TRAMP-C2 tumors from young and aged mice showed no significant differences concerning their proliferation index, apoptosis or angiogenesis. However, analysis of tumor-infiltrating immune cells by immunohistochemistry and RNA-seq gene expression revealed that aged mice present higher numbers of macrophages in normal prostatic tissue and that these are quickly polarized towards an M2 phenotype upon TRAMP-C2 cells engraftment.

overall_design: RNA sequencing of TRAMP-C2 tumors from young and aged mice using the Illumina TruSeq Stranded mRNA LT library kit and sequenced on Illumina HiSeq 2500.

first: Daniella

last: Bianchi-Frias

first: Mamatha

last: Damodarasamy

first: Susana

last: Hernandez

first: Rui

last: Gil da Costa

first: May

last: Reed


title: Genomic aberrations in metaplastic breast carcinomas and adenomyoepitheliomas

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

institute: Medizinische Hochschule Hannover

summary: Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

overall_design: Copy number analysis using Affymetrix Oncoscan arrays was performed for 43 primary breast cancers

first: Jana

last: van Luttikhuizen

first: Stephan

last: Bartels

first: Hans

last: Kreipe


title: Genome-wide maps of chromatin state in in vivo- and in vitro-derived chondrocytes

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Here we assess chormtin modifications in chondrocytes across different stages of human ontogeny and in chondroyctes derived during from human pluripotent stem cells. These data demonstrate that at early stages of development or differentiation, genes associated with non-chondrogenic fates have more activating histone marks which are lost with increased developmental age or differentiation time.

overall_design: Examination of 4 different histone modifications in 4 cell types.

first: Gabriel

last: Ferguson

first: Ben

last: Van Handel