title: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes (ALK)

status: Public on Dec 28 2018

city: Gent

first: Dries

last: Rombaut

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

summary: Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. Each of these driver genes controls the expression of a particular subset of lincRNAs, several of which are associated with poor survival and are differentially expressed in neuroblastoma tumors compared to neuroblasts. By integrating RNA sequencing data from both primary tumor tissue and cancer cell lines, we demonstrate that several of these lincRNAs are expressed in stromal cells. Deconvolution of primary tumor gene expression data revealed a strong association between stromal cell composition and driver gene status, resulting in differential expression of these lincRNAs. We also explored lincRNAs that putatively act upstream of neuroblastoma driver genes, either as presumed modulators of driver gene activity, or as modulators of effectors regulating driver gene expression. This analysis revealed strong associations between the neuroblastoma lincRNAs MIAT and MEG3 and MYCN and PHOX2B activity or expression. Together, our results provide a comprehensive catalogue of the neuroblastoma lincRNome, highlighting lincRNAs up- and downstream of key neuroblastoma driver genes. This catalogue forms a solid basis for further functional validation of candidate neuroblastoma lincRNAs.

overall_design: CLB-GA cells were treated with 500nM of crizotinib (3 samples) or with a control (3 samples) for 24 hours.

first: Pieter

last: Mestdagh

first: Katleen

last: De Preter

first: Frank

last: Speleman


title: Absence of the xenobiotic acetylating enzymes NAT1 and NAT2 in mice leads to deregulation of energy metabolism associated with decreased ability to oxidize fatty acids

status: Public on Dec 31 2018

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

summary: The NAT enzymes are polymorphic xenobiotic metabolizing enzymes that catalyze the transfer of an acetyl moiety from acetyl coenzyme A (acetyl-CoA) to the nitrogen or oxygen atom of primary arylamines, hydrazines, and their N-hydroxylated metabolites. NATs therefore play an important role in the detoxification and/or activation of arylamine drugs and carcinogens. The involvement of acetyl-CoA in energy metabolism suggests that there may be relationships between NAT activity and energy metabolism. Previous studies have suggested a role for NAT2 in insulin sensitivity that is exacerbated on high fat diet, using Nat1 knockout mice. To study mice with no NAT activity at all, we used a Nat1/Nat2 double-KO model, with animals fed either a regular chow or high fat/high sugar diet for 12 weeks. Analysis of basal parameters suggested a decrease in fatty-acid oxidation and hepatic gluconeogenesis. To further evaluate the cause of this, RNA was isolated and processed using Affymetrix Mouse Gene 2.0 microarrays.

overall_design: Adult male wildtype or Nat1/2 knockout mice were fed either a regular chow diet or high fat/high sucrose diet for 12 weeks (n = 16, divided into groups of 4 per condition). Similarly, adult female wildtype and Nat1/2 knockout mice (n = 3 each) were fed a high fat/high sucrose diet for 12 weeks.

first: Raphaël

middle: G

last: Denis

first: Florent

last: Busi

first: Julien

last: Castel

first: Wenchao

last: Zhang

first: Kim

middle: S

last: Sugamori

middle: D

first: Paul

middle: C

last: Boutros

first: Fernando

last: Rodrigues-Lima

first: Serge

last: Luquet

first: Jean-Marie

last: Dupret


title: Dental pulp cell-derived powerful inducer of TNF-alpha comprises PKR containing stress granule rich microvesicles (pDCvsGF)

status: Public on Dec 30 2018

city: Fukuoka

first: Takao

last: Fukuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Faculty of dental science

country: Japan

institute: Kyushu University

summary: It is well known that dental pulp tissue can evoke some of the most severe acute inflammation observed in the human body. We found that dental pulp cells secrete a factor that induces tumor necrosis factor-α production from macrophages, and designated this factor, dental pulp cell-derived tumor necrosis factor-α-inducing factor (DPTIF). DPTIF was induced in dental pulp cells and transported to recipient cells via microvesicles. Treatment of dental pulp cells with a PKR inhibitor markedly suppressed DPTIF activity, and weak interferon signals were constitutively activated inside the cells. In recipient macrophages, stimulation with DPTIF-containing supernatants from pulp cells resulted in activation of both nuclear factor-κB and MAP kinases like JNK and p38. Proteomics analyses revealed that many stress granule-related proteins were present in supernatants from dental pulp cells as well as microvesicle marker proteins like GAPDH, β-actin, HSPA8, HSPB1, HSPE1, and HSPD1. Furthermore, giant molecule AHNAK and PKR were detected in microvesicles derived from dental pulp cells, and gene silencing of AHNAK in pulp cells led to reduced DPTIF activity. Thus, it appeared that the core protein of DPTIF was PKR, and that PKR was maintained in an active state in stress granule aggregates with AHNAK and transported via microvesicles. The activity of DPTIF for TNF-α induction was far superior to that of gram-negative bacterial endotoxin. Therefore, we, report for the first time, that active PKR is transported via microvesicles as stress granule aggregates and induces powerful inflammatory signals in macrophages.

overall_design: To determine the differences in gene expression between cells with and without dental pulp cell-derived tumor necrosis factor-α-inducing factor (DPTIF) activity, we compared gene expression profiles between primary dental pulp cells (pDC) with DPTIF activity and gingival tissue-derived fibroblasts without DPTIF activity

first: Shigeki

last: Suzuki

first: Shintaro

last: Nagayasu

first: Jun

last: Nakanishi

first: Kazuma

last: Yoshida

first: Shizu

last: Hirata-Tsuchiya

first: Yuki

last: Nakao

first: Tomomi

last: Sano

first: Akiko

last: Yamashita

first: Satoru

last: Yamada

first: Hideki

last: Shiba

first: Kouji

last: Ohta

first: Fusanori

last: Nishimura


title: Gene expression profile upon TNF-a stimulation, forced expression of NICD, or TNF-a stimulation under forced expression of NICD, in human colon carcinoma-derived LS174T cells

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

institute: Tokyo Medical and Dental University

summary: A human colon carcinoma-derived cell line LS174T was modified to overexpress NICD, intracellular domain of  Notch1, upon doxycycline addition (designated as LS174T-tetON-NICD cells), using the T-rex system (Invitrogen). We have previously shown that these cells can overexpress NICD under the control of CMV promoter (Okamoto R et al, Am J Physiol, 296(1):G23-35, 2009), and the amont of the overexpressed NICD protein reaches to the maximal level in early as 3 hours from doxycycline addition (100ng/ml), which persists for up to 24 hours. In the present experiment, LS174T-tetON-NICD cells were treated with recombinant human TNF-a (50ng/ml) alone, doxycycline alone (100ng/ml), co-treated by both TNF-a and doxycycline, or left untreated (Control) for 24 hours, and subjected for analysis.  Experiment was done using a modified sub-line of LS174T cell (LS174T-tetON-NICD cells), in which overexpression of NICD can be induced by a Doxycycline dependent manner.

overall_design: Four-condition experiment, Control vs. TNF-a stimulation, Control vs Doxycycline addition (NICD overexpression) and Control vs TNF-a stimulation+Doxycycline addition (NICD overexpression). Biological replicates: One for each condition, independently grown and harvested. One replicate per array.

first: Ami

last: Kawamoto


title: Human Dental Pulp Cells FGF(+) vs FGF(-)

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

summary: We report the effects of donor-related differences in hDPCs treated with FGF2 on the recovery effect after SCI, as assessed by the locomotor functional scale (BBB score), electrophysiological tests, and morphological analyses, as well as gene expression analyses

overall_design: To indentify the genes regulated FGF2 treatment, we performed comprehensive gene expression analysis using DP1, DP31, and DP165

first: Ken

last: Sugiyama

first: Tomoko

last: Kawaguchi


title: Genome-wide analysis of histone H3 acetylation levels of wild type, hda6, hdc1, and hda19 in short day conditions [ChIP-seq]

city: Beijing

first: xinjian

last: He

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

country: China

institute: National Institute of Biological Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate whether the expression of upregulated genes in hdc1 and hda19 is assoiated with histone acetylation levels increased in the hdc1 and hda19 mutants, We carried out ChIP-seq to examine histone H3 acetylation at the whole-genome level.

overall_design: Examination of histone H3 acetylation levels in 4 samples.

first: Yongqiang

last: Ning

first: Rongnan

last: Lin

first: Xinjian


title: Site-specific microarray evaluation of spontaneous dermatitis in flaky tail mice II

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi,

department: Faculty of Medicine

institute: Oita University

summary: Flaky tail mice (FTM) with gene mutations to FLG and TMEM79 are known to spontaneously develop atopic dermatitis (AD)-like dermatitis with age. Interestingly, we have already reported that the spontaneous development of dermatitis exhibits site-specificity, i. e. , the face and neck develop spontaneous dermatitis, while the dorsal flank shows normal skin in old FTM. In fact, transepidermal water loss and stratum corneum (SC) pH increased, SC hydration decreased, and epidermis thickened in the neck, but not in the dorsal flank. The detailed pathogenic mechanisms of such site-specific emergence of dermatitis in FTM remain unclear. To clarify the pathogenesis of site-specificity, we analyzed skin of the neck and flank in old FTM using a microarray.

overall_design: The gene expressions of the skin on neck and flank in FTM were analyzed.

first: Chinatsu

last: Aoki

first: Yasuko

last: Mori

last: Yamate

first: Haruna

last: Matsuda-Hirose

first: Yutaka

last: Hatano


title: Gene expression profile of N2 and HPX-2 mutant C.elegans strains when exposed to E.coli and E.faecalis

status: Public on Dec 27 2018

city: Houston

first: Yi

last: Liu

address: 6431 Fannin Street

department: Microbiology and Molecular Genetics

country: USA

institute: University of Texas Health Science Center at Houston

type: Expression profiling by high throughput sequencing

summary: We use RNAseq analysis as an un-biased and highly sensitive measurement of global transcriptomic changes upon the loss of HPX-2. The RNAseq result provided insights into the potential physiological processes HPX-2 is involved in.

overall_design: L4 stage worms were exposed to E. faecalis or E. coli for 16 hours and total RNA was extracted for 5 biological replicates. Illumina Hiseq 4000 sequencer with 75 nt pair-ended read format was used to conduct the sequencing.

first: Danielle

last: Garsin

first: Ambro

last: van Hoof


title: miRNA Expression data from sulfisoxazole-treated breast cancer cell-derived exosome

status: Public on Dec 24 2018

city: Daegu

first: Moon-Chang

last: Baek

address: Gukchebosang-ro 680

country: South Korea

institute: Kyungpook National University

summary: Sulfisoxazole, a FDA-approved drug, is a promising repositioned drug candidate for the treatement of various cancers. Therefore we analyzed the gene expression by microarray to identified the up-regulated and down-regulated genes after SFX treatment in breast cancer cell-derived exosomes.

overall_design: Recently, breast cancer has a higher incidence in the world. In addition, breast cancer cell derived exosomes promote cancer progression. Therefore, we selected MDA-MB231 (breast cancer)  and analyzed the exosomal miRNA expression by microarray. Cells were treated with 100 μM of SFX for 24 hours under serum-free condition. Then, total RNA was collected using Total exosome RNA and protein isolation kit, and performed Affymetrix microarray.

first: Eun-Ju

last: Im


title: RNA-seq Analysis of Transcriptomes in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing αTC1-6 cells

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to determine the molecular mechanisms involved in the NIK regulation of α cell function.
Methods: mRNA profiles of β-Gal control, NIK, and NIK(KA) overexpressed αTC1-6 cells were generated by deep sequencing using an Illumina Hiseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.89) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of NIK-overexpressing aTC1-6 cell transcriptomes, generated by RNA-seq technology. Our results show that 328 genes were upregulated and 48 genes were downregulated following NIK overexpression. GO analysis indicated that the upregulated genes were primarily related to the immune response. KEGG pathway enrichment analysis showed that immune signaling pathways, including the TNF, NF-κB, and chemokine signaling pathways, were significantly activated by NIK overexpression in aTC1-6 cells, while genes related to metabolism-associated signal pathways were significantly decreased. NIK(KA), the dominant-negative mutant of NIK, does not affect gene expression in  aTC1-6 cells.

overall_design: mRNA profiles of β-Gal control, NIK, and NIK(KA) overexpression αTC1-6 cells were generated by deep sequencing, in a single test, using Illumina

first: Xinzhi

last: Li


title: Investigating the role of Osiris genes in Drosophila sechellia larval resistance to a host plant toxin

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue Biology Department

department: Biology

institute: Wesleyan University

summary: The underlying genetic basis of adaptive phenotypic changes are generally poorly understood, yet a growing number of case studies are beginning to shed light on important questions about the molecular nature and pleiotropy of such changes. We use Drosophila sechellia, a dietary specialist fruit fly that has evolved to specialize on a single toxic host plant: Morinda citrifolia, as a model for adaptive phenotypic change and seek to determine the genetic basis of traits associated with host specialization in this species. The fruit of M. citrifolia is toxic to other Drosophilids, primarily due to high levels of the defense chemical octanoic acid (OA) yet D. sechellia has evolved resistance to OA. Our prior work identified three Osiris family genes that reside in a fine-mapped QTL for OA resistance: Osiris 6 (Osi6), Osi7, and Osi8, that can alter OA resistance in adult D. melanogaster when knocked-down with RNA interference (RNAi) suggesting they may contribute to OA resistance in D. sechellia. Genetic mapping identified overlapping genomic regions involved in larval and adult OA resistance in D. sechellia, yet it remains unknown whether Osiris genes contribute to resistance in both life stages. Furthermore, because multiple genomic regions contribute to OA resistance, we aim to identify other gene(s) involved in this adaptation.  Here, we identify candidate larval OA resistance genes using RNA-sequencing to measure genome-wide differential gene expression in D. sechellia larvae after exposure to OA and functionally test identified genes for a role in OA resistance. We then test the Osiris genes previously shown to alter adult OA resistance for effects on OA resistance in larvae. While the genes identified by RNA-seq we tested in larvae thus far do not influence OA resistance, we found that Osi8 knockdown decreased OA resistance in D. melanogaster larvae.  These data suggest that evolved changes in Osi8 could impact OA resistance in multiple life stages while Osi6 and Osi7 may only impact adult resistance to OA.

overall_design: Differential gene expression analysis of D. sechellia larvae exposed to control food and food containing 0.2% octanoic acid using RNA-sequencing.

first: Stephen

middle: M

last: Lanno

first: Serena

middle: J

last: Shimshak

first: Rubye

last: Peyser

first: Samuel

last: Linde


title: BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (III)

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

country: Germany

institute: Medical School Hannover

summary:
Background: We got interested whether genes of airway basal cells  are enriched in sarcoidosis.

Methods: Bronchoscopy with bronchoalveolar lavage (BAL) was performed in 26 patients with sarcoidosis, chest-x-ray type III and IV, and 20 healthy donors and isolated BAL cells.Transcriptome of BAL cells were studied by using Affymetrix Human Affymetrix Whole-Transcript Human Gene 1.0 ST  array on an Affymetrix platform. Microarray data were imported, log2-transformed and quantile normalized using robust multi-array average (RMA). We tested enrichment for airway basal cells by global enrichment analysis.

Results: we did not find enrichment of airway basal cell genes in sarcoidosis compared to healthy volunteers.

overall_design:
Microarray data of BAL cells from 26 patients with sarcoidosis and 20 healthy volunteers were obtained. We tested for enrichment of genes highly expressed in airway basal cells and identified in GSE70864
Please note that sarcoidosis stage information for each individual patient was not provided since the information was not considered for the statistical data analysis.

first: Shelia

last: Violette


title: Genome-wide analysis of mechano-responsive gene expression of mesenchymal stem cells after laminar shear stress

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

summary: Analysis of mechano-regulation of mesenchymal stem cell gene expression level. The hypothesis tested in the present study was that laminar shear stress influences the cytoskeleton arrangement and amount and then triggers seriers of cell metabolism and cellular functions. Results provide important information of the response of mesenchymal stem cell to laminar shear stress, such as specific mechano-responsive genes, up- or down-regulated specific anabolic/catabolic cellular functions.

overall_design: Total RNA obtained from mesenchymal stem cells subjected to 15 min, 30 min, 45 min, 60 min, 4 hours in vitro larminar shear stress compared to control mesenchymal stem cells.

first: Wei-Ta

first: Jennifer

last: Hui-Chun Ho


title: BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (IV)

summary:
Background: We got interested whether genes of airway basal cells  are enriched in COPD.

Methods: Bronchoscopy with bronchial brushes and bronchoalveolar lavage was performed in 28 patients with COPD and 29 healthy donors and isolated BAL cells.Transcriptome of BAL cells were studied by using Affymetrix Human Genome U133 Plus 2.0 array on an Affymetrix platform. Microarray data were normalized data were imported, log2-transformed and quantile normalized using robust multi-array average (RMA). We tested enrichment for airway basal cells by ROMER enrichment analysis.

Results: we did not find enrichment of airway basal cell genes in COPD compared to healthy volunteers.

overall_design: Microarray data of BAL cells from 29 patients with COPD and 28 healthy volunteers were obtained. We tested for enrichment of genes highly expressed in airway basal cells and identified in GSE70864

first: Karsten

last: Quast

first: Jens

last: Hohlfeld


title: BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (II)

summary: Background: Idiopathic pulmonary fibrosis (IPF) is a fatal disease with variable outcome. Currently, there is little information whether changes in molecular pathways in the alveolar compartment of patients with IPF are indicative of disease progression.  To address this question we analyzed gene expression signatures in cells obtained from bronchoalveolar lavage (BAL) of patients with IPF.  Methods: BAL cells were harvested from 212 IPF patients and 20 healthy donors at the time of diagnosis. RNA was extracted, labeled and hybridized to Agilent gene expression arrays. Our study included a discovery cohort of 62 patients from Freiburg, Germany, and two independent validation cohorts, Siena, Italy (50 patients) and Leuven, Belgium (64 patients). Survival analysis was performed by applying Cox models and component-wise boosting. Results: We found 1582 genes predictive of mortality in the discovery cohort in univariate analyses adjusted for age and gender at FDR<0.05. A nine gene signature, developed by component-wise boosting in the Freiburg array dataset, performed well in both validation cohorts, Siena (p<0.0032) and Leuven (p=0.0033). The genes associated with mortality in BAL cells were significantly enriched for genes expressed in airway basal epithelial cells, airway progenitor cells recently implicated in fibrosis. Conclusions: Our results identify and validate a BAL cell gene expression signature that predicts mortality in IPF. This signature unmasks a potential novel role for airway basal epithelial cells in IPF.


title: Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: The biological role and therapeutic potential of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) are still to be investigated. Here, we studied the functional significance and the druggability of the oncogenic lncRNA MALAT1 in MM. Targeting MALAT1 by novel LNA-gapmeR anti-sense oligonucleotide antagonized MM cell proliferation and triggered apoptosis both in vitro and in vivo in a murine xenograft model of human MM. Of note, antagonism of MALAT1 dowmodulated the two major transcriptional activators of proteasome subunit genes, namely NRF1 and NRF2, and resulted in reduced trypsin, chymotrypsin and caspase-like proteasome activities and in accumulation of polyubiquitinated proteins. NRF1 and NRF2 decrease upon MALAT1-targeting was due to transcriptional activation of their negative regulator KEAP1, and resulted in reduced expression of anti-oxidant genes and increased ROS levels. In turn, NRF1 promoted MALAT1 expression thus establishing a positive feedback loop. Our findings demonstrate a crucial role of MALAT1 in the regulation of the proteasome machinery, and provide proof-of-concept that its targeting is a novel powerful option for the treatment of MM.

overall_design: A proprietary custom annotation pipeline of microarray data on lncRNA expression in different plasma cell (PC) dyscrasias, including 20 MGUS, 33 smoldering MM, 170 MM, 36 PC leukemia patients and 9 healthy donors, revealed high expression of MALAT1 in MM PCs [GSE66293]. On this finding, we investigated the functional significance of MALAT1 by using novel 16-mer LNA gapmeR synthetic ASOs, that trigger selective RNAse-H dependent degradation of MALAT1, in MM.1S and RPMI-8226 human myeloma cell lines.

first: Nicola

last: Amodio

first: Maria

middle: A

last: Stamato

first: Giada

last: Juli

first: Eugenio

last: Morelli

first: Mariateresa

last: Fulciniti

first: Martina

last: Manzoni

first: Elisa

last: Taiana

middle: E

last: Cantafi

first: Enrica

last: Romeo

first: Lavinia

last: Raimondi

first: Daniele

last: Caracciolo

first: Valeria

last: Zuccalà

first: Marco

last: Rossi

first: Antonino

last: Neri

first: Nikhil

last: Munshi

first: Pierosandro

last: Tagliaferri

first: Pierfrancesco

last: Tassone


title: Chemokine expression in murine RPE/choroid in response to systemic viral infection and elevated levels of circulating interferon-γ

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

summary:
Purpose
To examine how circulating immune mediators in vivo may affect gene and protein expression at the retinal pigment epithelium (RPE)/choroid interface.

Methods
Young mice were systemically infected with lymphocytic choriomeningitis virus (LCMV) or continuously infused with interferon (IFN)γ. RPE/choroid was isolated and analyzed with whole-transcriptome gene expression microarrays. Selected gene expression findings were validated at the protein level.

Results
Both the systemic immune activation from virus infection and the sterile systemically increased level of IFNγ resulted in increased expression of chemokine ligands, chemokine receptors and early complement components in isolates of RPE/choroid. These findings were largely absent from LCMV-infected mice deficient in either the interferon α/β receptor or IFNγ.

Conclusions
Together, these findings demonstrate that acute systemic immune activation results in a local response at the RPE/choroid interface that may include chemokine-dependent recruitment of inflammatory cells and engagement of the complement system. This may represent a link between the systemic low-grade inflammation and the retinal pathology observed in several multifactorial entities such as aging, age-related macular degeneration (AMD) and diabetes.

overall_design: Gene expression in murine WT, IFNAR-/- or IFNγ-/- RPE/choroid after systemic infection with LCMV or continuously infusion with IFNγ.

first: Helene

middle: B

last: Juel

first: Benjamin

last: Jensen

first: Jan

middle: P

last: Christensen

middle: U

last: Prause

first: Allan

middle: R

last: Thomsen

first: Mogens

middle: H

last: Nissen


title: Expression data from macrophages

status: Public on Dec 19 2018

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

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

overall_design: Refer to individual Series


title: A Lignin Molecular Brace Controls Precision Processing of Cell Wall Critical for Surface Integrity in Arabidopsis

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

institute: DGIST

summary: The cell wall is a defining feature of plant cells and glues cells to each other. To overcome this physical constraint, plants must process and disconnect cell wall linkages during growth and development. However, little is known about the mechanism guiding cell-cell detachment and cell wall remodeling.  Here, we identify two neighboring cell types in Arabidopsis that coordinate their activities to control cell wall processing, thereby ensuring precise abscission to discard organs.  One cell type produces a honeycomb structure of lignin, which acts as a mechanical ‘brace’ to localize cell wall breakdown and spatially limit abscising cells.  The second cell type undergoes transdifferentiation into epidermal cells, forming protective cuticle, demonstrating de novo specification of epidermal cells, previously thought to be restricted to embryogenesis. Loss of the lignin brace leads to inadequate cuticle formation, resulting in surface barrier defects and susceptible to infection.  Altogether, we show how plants precisely accomplish abscission.

overall_design: RECs (Residuum cells, abscission zone cells of the receptacle) and SECs (Secession cells, abscission zone cells of separated floral organs) were isolated using fluorescence-activated cell sorting of cells from transgenic plants harboring proQRT2::nlsGFP–GUS construct, and their transcriptomes were analyzed by RNA-sequencing.

first: Yuree

last: Lee

first: Taek-Han

last: Yoon

first: Jiyoun

first: So-Yeon

last: Jeon

first: Jae-Ho

first: Mi-Kyoung

first: Huize

last: Chen

first: Ju

last: Yun

first: Se-Yun

last: Oh

first: Xiaohong

last: Wen

first: Hui-Kyung

last: Cho

first: Hyunggon

last: Mang

first: June

last: Kwak


title: T-UCR and related gene expression quantification in the presence or not of CpG-ODN oligonucleotide 2006

city: Barcelona

first: Luis

last: Hernandez

address: Rossello 153, CEK building

department: Molecular Pathology

country: Spain

institute: IDIBAPS

summary:
Toll-like receptors (TLRs) are mediators in the innate immune response by recognizing nucleic acids derived from microbial components as for TLR9 binding ability for CpG rich bacterial DNA.
We studied the differential expression by microarrays of all known T-UCRs and near genes in a series of 6 primary B-CLL cases cells comparing cells treated in vitro with CpG ODN versus mock controls.

overall_design: CpG oligodeoxynucleotide (ODN) is a synthetic TLR9 agonist that has been considered for the treatment of several cancer types, including relapsed or refractory B-cell chronic lymphocytic leukemia (B-CLL) by their impact in proliferation and viability. Nevertheless, boosting of CpG ODN response for an effective therapeutic response depends on increasing the knowledge of the molecular pathways affected by this compound.

first: Riccardo

last: Bomben


title: Whole blood gene expression can distinguish benign from malignant lung nodules transitioning from microarrays to a nanostring platform

status: Public on Dec 20 2018

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Development of a non-invasive, whole blood microarray gene expression signature that accurately distinguishes malignant from benign lung nodules detected by LDCT and the successful transition of that signature to a custom NanoString panel with no loss of accuracy.

overall_design: Whole blood gene expression from patients with malignant (MN) and benign (BN) nodules

first: Louise

last: Showe

first: Andrew

last: Kossenkov


title: Dental pulp cell-derived powerful inducer of TNF-alpha comprises PKR containing stress granule rich microvesicles

city: Fukuoka

first: Takao

last: Fukuda

address: 3-1-1 Maidashi, Higashi-ku,


title: Expression data from Rapamycin treated Peripheral blood derived macrophages

first: Bernd

last: Denecke

summary:
Macrophages are at the front line of the innate immune system and differentiate from monocytes after infiltrating the infected tissue. Metabolic pathways are central to macrophage biology. We studied transcriptional differences between Rapamycin treated in vitro activated macrophages and untreated peripheral blood derived in vitro actiavted macrophages.
We used microarrays to detail the global programme of gene expression in Rapamycin treated adult blood derived  M(IL-10) and M(IFN-γ) macrophages and untreated adult blood derived  M(IL-10) and M(IFN-γ)macropahges

overall_design: Genome-wide transcriptome analyses of Rapamycin treated adult blood derived  M(IL-10) and M(IFN-γ) macrophages and untreated adult blood derived  M(IL-10) and M(IFN-γ)macropahges were performed in independent triplicates using HTA-2 arrays

first: Kim

last: Ohl

first: Klaus

last: Tenbrock


title: Diminished OPA1 expression and impaired mitochondrial morphology and homeostasis in Aprataxin-deficient cells

first: Jin

last: Zheng

address: 3b Blegdamsvej

summary:
Ataxia with oculomotor apraxia type 1 (AOA1) is an early onset progressive spinocerebellar ataxia caused by mutation in aprataxin (APTX). Here we use RNA-seq to identify genes that are affected by APTX-KO, APTX overexpression, and APTX mutant, thus contributes to understadning the mechanisms underlying AOA1 pathlogy.

Published: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz083/5319145

overall_design: Examination the chages of gene expressions in APTX proficient and APTX deficienc cells.

first: Deborah

middle: L

last: Croteau


title: Expression data from Cord blood and Peripheral blood derived macrophages

summary:
The risk of sepsis is particularly high in neonates compared to older children and adults; however the reasons behind are incompletely understood. Macrophages are at the front line of the innate immune system and differentiate from monocytes after infiltrating the infected tissue. We studied transcriptional differences between cord blood-derived in vitro activated macrophages and adult peripheral blood derived in vitro actiavted macrophages.
We used microarrays to detail the global programme of gene expression in cord blood derived M(IL-10) and M(IFN-γ) and in adult blood derived  M(IL-10) and M(IFN-γ)macropahges

overall_design: Genome-wide transcriptome analyses for cord blood derived M(IL-10) and M(IFN-γ) and for adult blood derived  M(IL-10) and M(IFN-γ)macropahges were performed in independent triplicates using  HTA-2 arrays

first: Stephan

last: Dreschers


title: Chromatin accesibility in mice T-ALL tumors

status: Public on Dec 21 2018

city: New York

first: Robert

last: Albero

state: New York

address: 1130 St Nicholas Ave

department: Institute of Cancer Genetics

institute: Columbia Unviersity

summary: Long-range enhancers play an important role in the temporal and spatial control of gene expression and are deregulated in many cancers. Yet, the mechanisms that govern enhancer activity during development and oncogenesis remain poorly understood. In this study we analyze the chromatin accesibility of mice T-ALL tumors.

overall_design: An ATAC-seq sample from T-ALL mice tumors

first: Adolfo

last: Ferrando

first: Laura

last: Belver

first: Aidan

last: Quinn

first: Agnieszka

last: Wendorff


title: The impact of Unc45A silencing on gene expression in the human breast cancer Hs578T (ATCC HTB-126) cell line

city: Augusta

first: Ahmed

last: Chadli

state: GA

address: 1410 Laney Walker BLVD

department: Cancer Center

institute: Augusta University

summary: The co-chaperone Unc45A is essential for cancer cell growth. We show that Unc45A, a cytoplasmic protein in normal cells, becomes nuclear in cancer cells. We used Microarray to determine the impact of UNC45A on gene expression.  We found that Unc45A unctions as a co-activator of the glucocorticoid receptor.  In this capacity, it differentially promotes expression of the mitotic kinase NEK7 and other genes possibly through regulation of nuclear receptors.

overall_design: Human breast triple negative Hs578T cancer cells were transfected with siRNA against Unc45A or non-targeting siRNA control.


title: Yarrow and marigold extracts and their effect in pancreatic cancer cells

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

institute: IMDEA ALIMENTACION


title: CDK2 depletion effect on human myeloid cell line undergoing differentiation

city: Hangzhou

first: Meidan

last: Ying

address: No.866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

summary:
Analysis of NB4 myeloid cells depleted for CDK2. Results provide insight into the role of CDK2 in myeloid cell differentiation.
We used microarrays to detail the global programme of gene expression underlying CDK2-depletion induced differentiation and identified distinct classes of up-regulated genes during this process.

overall_design: NB4 cells were transduced with the scrambled control or three different shRNAs targeting CDK2 (shCDK2 #1, #3 and #10) for 2 days (early differentiation stage) or 5 days (late differentiation stage). All cell samples were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Bo

last: Yang

first: Qiaojun

last: He


title: Genome-wide expression analysis of wild type, hda6, hdc1, and hda19 in long day conditions [RNA-seq]

city: Beijing

first: xinjian

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

institute: National Institute of Biological Sciences

summary: To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in long day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in long day conditions.

overall_design: Transcriptomes of wild type, hda6, hdc1, and hda19 grown in long day conditions for two weeks were generated by deep sequencing, using Illumina HiSeqXTen.

first: Yongqiang

last: Ning

first: Rongnan

last: Lin

first: Xinjian


title: Unbiased screen of RNA tailing enzymes reveals a poly(UG) polymerase required for genome integrity and RNA silencing

status: Public on Dec 08 2018

city: Madison

first: Melanie

last: Preston

state: WI

address: 433 Babcock Dr

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Ribonucleotidyl transferases (rNTases) add non-templated ribonucleotides to diverse RNAs. We developed a screening strategy in S. cerevisiae to identify sequences added by candidate enzymes from different organisms at single-nucleotide resolution. The rNTase activities of 19 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a C-adding enzyme that is likely part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, C. elegans MUT-2, which adds alternating U and G nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutations in the enzyme that are defective in silencing also fail to add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.

overall_design: We developed a screening approach to identify enzymes that add non-templated nucleotides to RNAs. Candidate rNTases were tethered in vivo to a reporter RNA in S. cerevisiae, and the number and identity of nucleotides they added were determined at single-nucleotide resolution using high-throughput sequencing.

first: Douglas

middle: F

last: Porter

first: Fan

last: Chen

first: Natascha

last: Buter

first: Christopher

last: Lapointe

first: Sunduz

last: Keles

first: Judith

last: Kimble

first: Marvin

last: Wickens


title: Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells

status: Public on Dec 18 2018

city: London

first: Miguel

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute


title: Cellular stress response of Sulfolobus acidocaldarius to nutrient limitation

city: Bielefeld

first: Andreas

last: Albersmeier

address: Universitätsstr. 27

institute: Bielefeld University

summary: This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. We further connect previously identified pH and salt stress responsive genes (1) with genes regulated in starvation and suggest that they constitute the core of stress responsive genes active under multiple stress sources.

overall_design: Differential gene expression analysis for transcriptomes of S.acidocaldarius MW001 before and 0.5, 1.5, 2 and 4 h after exposure to nutrient limitation; Three biological replicates per sample

first: Lisa

last: Bischof

first: M

last: Haurat

first: Lena

last: Hoffmann

first: Jacqueline

last: Wolf

first: Julia

last: Helmecke

first: Astrid

last: Neu

first: Trong

last: Pham

first: Stefan

last: Albaum

last: Schouten

first: Tobias

last: Jakobi

first: Meina

last: Neumann-Schaal

first: Phillip

last: Wright

first: Jörn

last: Kalinowski

first: Dietmar

last: Schomburg

first: Bettina

last: Siebers

first: Sonja-Verena

last: Albers


title: Chromatin accesibility in human DP3 thymocytes and T-ALL tumors

first: Robert

last: Albero

summary: Long-range enhancers play an important role in the temporal and spatial control of gene expression and are deregulated in many cancers. Yet, the mechanisms that govern enhancer activity during development and oncogenesis remain poorly understood. In this study we analyze the chromatin accesibility of DP3 minus cells and three human T-ALL leukemia.

overall_design: ATAC-seq sample from DP3 minus cells and three human T-ALL leukemia.

first: Adolfo

last: Ferrando

first: Laura

last: Belver

first: Francesca

last: Ginno


title: The Biological Embedding of Early Life Socioeconomic and Family Adversity in Children’s Genome-wide DNA Methylation

status: Public on Dec 07 2018

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by genome tiling array

summary: Early life social experiences are believed to confer persistent effects on individual’s biology and subsequent functioning and health. Using a diverse, longitudinal community sample of 178 children, we show that three different types of early life social experience: family income, parental education, and family psychosocial adversity, each predict DNA methylation within buccal epithelial cells. Each predictor was significantly associated with DNA methylation within a unique set of genomic CpG sites, with income showing the greatest number of associations. Findings were independently verified using pyrosequencing. Our results provide evidence for longitudinal associations between early life social environment and variation in DNA methylation during childhood, after adjusting for genetic ancestry and self-reported ethnic minority status. Gene ontology analyses of top, differentially methylated CpG sites point to genes serving immune and developmental regulation functions, suggesting potential pathways for the biological embedding of early life stress and its association with later development and health.

overall_design: This cohort consist of genomic DNA extracted from 178 buccal swabs, bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling.

first: Nicole

last: Bush

first: Rachel

last: Edgar

first: Mina

last: Park

last: MacIsaac

first: Lisa

last: McEwen

first: Nancy

last: Adler

first: Marilyn

last: Essex

first: W

middle: T

last: Boyce


title: Wnt1 silences CC/CXC motif chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma

city: Paris

first: Sebastian

last: Amigorena

state: --- Select a state ---

address: 26 rue Ulm

department: Center of Immunotherapy

country: France

institute: Curie Institute

summary: Lung adenocarcinoma (LUAD)-derived oncogenic Wnts increase cancer cell proliferative/stemness potential, but whether they also impact the immune microenvironment is unknown. Here we show that LUAD cells use paracrine Wnt1 signaling to induce immune resistance. Wnt1 correlated strongly with tolerogenic genes on the TCGA expression data. In another cohort, Wnt1 was inversely associated with T cell abundance. Altering Wnt1 expression profoundly affected growth of murine lung adenocarcinomas  and this was strongly dependent on conventional dendritic cells and T cells. Mechanistically, Wnt1 lead to transcriptional silencing of CC/CXC chemokines in dendritic cells and T cell cross-tolerance. Wnt-target genes were up-regulated in human intratumoral dendritic cells and decreased upon silencing Wnt1, accompanied by enhanced T cell cytotoxicity. siWnt1-loaded nanoparticles as single therapy or part of combinatorial immunotherapies acted at both arms of the cancer-immune ecosystem to halt tumor growth. Collectively, our studies show that Wnt1 enhances adaptive immune rejection of lung adenocarcinomas and highlight its potential targeting as a novel therapeutic strategy

overall_design: RNAseq data of two DC subsets of 4 patients with lung adenocarcinomas (LUADs).


title: Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells [RNA-seq]

first: Miguel

last: Branco

summary: Transposable elements (TEs) appear to have contributed to the evolution of tissue-specific gene regulatory networks in contexts such as early development, pregnancy and innate immunity, amongst others. In mouse embryonic stem cells (ESCs), TE families such as RLTR13D6 bind key pluripotency-associated transcription factors and are enriched for histone marks that are characteristic of distal enhancers. However, it remains unclear to what extent such lineage-specific TEs are important for maintaining gene expression programmes during preimplantation development. Here we have tested the gene regulatory function of RLTR13D6 elements in ESCs using epigenetic editing approaches. Whilst we identify some elements that are important to drive gene expression, these constitute a minority of all the putative TE-derived enhancers identified through epigenomic analyses, highlighting the importance of functional tests when assessing the contribution of TEs to gene regulatory networks.

overall_design: RLTR13D6 elements were silenced in mouse ESCs by CRISPRi with two sets of 4 sgRNAs each, using the empty sgRNA vector as a control. H3K27ac ChIP-seq and RNA-seq libraries were generated.

first: Christopher

last: Todd

first: Ozgen

last: Deniz


title: Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells [ChIP-seq]


title: single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy

status: Public on Dec 03 2018

city: Leiden

first: Anita

last: van den Heuvel

state: Zuid-Holland

address: Einthovenweg 20, Postbus 9600, 2300 RC Leiden

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing.

overall_design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals

first: Silvère

last: van der Maarel


title: ChIP-seq from GM23338 (ENCSR045YHA)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Non-lytic clearance of influenza B virus from infected cells

status: Public on Dec 05 2018

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

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

overall_design: Refer to individual Series


title: ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types Present Across Human Biofluids

status: Public on Dec 15 2018

city: San Diego

first: Louise

last: Laurent

address: 9500 Gilman Drive

institute: UC San Diego


title: Expression data from lung tissue of Zmpste24 defient or wildtype c57BL/6 mice

status: Public on Dec 04 2018

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

country: Mexico

institute: INER

summary:
Idiopathic pulmonary fibrosis is a devastating aging-associated disease of unknown etiology. Despite that aging is a major risk factor, the mechanisms linking aging with this disease are uncertain, and experimental models to explore them in lung fibrosis are scanty. We examined the fibrotic response to bleomycin-induced lung injury in Zmpste24-deficient mice, which exhibit nuclear lamina defects developing accelerated aging. We found that young WT and Zmpste24(-/-) mice developed a similar fibrotic response to bleomycin. Unexpectedly, while old WT mice developed severe lung fibrosis, accelerated aged Zmpste24-/- mice were protected showing scant lung damage. To investigate possible mechanisms associated with this resistance to fibrosis, we compared the transcriptome signature of the lungs and found that Zmpste24(-/-) mice showed downregulation of several core and associated matrisome genes compared with WT mice. Interestingly, some microRNAs that target extracellular matrix molecules such as miR23a, miR27a, miR29a, miR29b-1,miR145a, and miR491 were dysregulated resulting in downregulation of profibrotic pathways such as TGF-β/SMAD3/NF-κB and Wnt3a/β-catenin signaling axis. These results indicate that the absence of Zmpste24 in aging mice results in impaired lung fibrotic response after injury, which is likely associated to the dysregulation of fibrosis-related miRNAs.
Aging is a driving force of pulmonary fibrosis. Mice laking Zmpste24 have an accelerated aging phenotype. During the development of the disease there are several extracellular matrix genes, principally collagens upregulated. We use microarray to unveil changes associated with the pulmonary response in aged mice

overall_design: Lung samples 21 days after bleomycin injury were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain changes associated with the fibrotic response in young WT and Zmpste24 KO mice and old WT and Zmpste24 KO ones 21 days after administratiuon of bleomycin. We used three biological replicates for each condition.

first: Jazmin

last: Calyeca

middle: I

first: Raul

last: Olmos

first: Rogelio

last: Jasso

first: Vilma

last: Maldonado

first: Quetzali

last: Rivera

first: Moises

last: Selman

first: Annie

last: Pardo


title: MicroRNA expression data from gamma-oryzanol (GO) pre-incubated differentiating equine satellite cells exposed to hydrogen peroxide

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with GO) compared to control GO-untreated cells. Goal was to determine the effects of GO pre-incubation on miRNA expression in equine satellite cells exposed to hydrogen peroxide.

overall_design: Two-condition experiment, GO-treated (24h) differentiating equine satellite cells  and exposed to hydrogen peroxide (1h during 24h pre-incubation with GO) (3rd day of differentiation) vs. differentiating equine satellite cells without GO treatment (control). Biological replicates: 8 reps of examined condition , 8 control replicates

first: Anna

last: Ciecierska

first: Karolina

last: Chodkowska


title: Chlorogloeopsis sp. PCC 9212 wild type and mutants in response to erythromycin and light colors

city: University Park

first: Donald

middle: Ashley

last: Bryant

address: Althouse

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

summary: This transcription profiling analysis of Chlorogloeopsis sp. PCC 9212 is designed to study the role of RfpA, RfpB, and RfpC in response to light color change

overall_design: Chlorogloeopsis sp. PCC 9212 wild type and mutants cells were cultured in white light and far-red light with or without the supplement of erythromycin

first: Ming-Yang

last: Ho


title: Transcriptomic analysis of Arabidopsis anac044anac085 and sog1 mutnat under DNA damage condition.

city: Ikoma

first: Naoki

last: Takahashi

state: Nara

address: Takayama 8916-5

institute: Nara Institute of Science and Technology

summary: To identify genes whose expression is regulated by SOG1 and ANAC044/085 in response to double strand breaks, wild-type, anac044 anac085, and sog1-1 mutant plants were treated with or without bleomycin for 10 h and were subjected to microarray analysis using Agilent custom microarrays.

overall_design: Five-day-old WT, anac044-1 anac085-1, and sog1-101 plants were transferred to MS medium with or without 0.6 µg/ml bleomycin for 10 h. Total RNAs were extracted from roots, and subjected to microarray analysis. Two independent experiments were performed at each time points using different genotypes for each experiment.

first: Nobuo

last: Ogita

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Masaaki

last: Umeda


title: ChIP-seq from GM23338 (ENCSR987GXT)

first: ENCODE

last: DCC


title: RNF8 is responsible for ATRA resistance in variant acute promyelocytic leukemia with GTF2I/RARA fusion and the inhibition of the ubiquitin-proteasome pathway contributes to the reversion of ATRA resistance

status: Public on Nov 10 2018

city: changsha

first: wenzhe

last: yan

address: renmin middle road number 139

institute: the second xiangya hospital

summary: GTF2I-RARA is a newly identified RARA fusion gene in variant acute promyelocytic leukemia (APL) with t(7;17)(q11;q21). Clinical manifestation in the patient showed that it is a sort of ATRA-insensitive oncogene and is different from the classic PML-RARA in terms of therapeutic reaction. To reveal the functional characteristics and regulating mechanism of the GTF2I-RARA fusion gene, we established a GTF2I-RARA-transfected HL-60 cell model and confirmed its resistance to ATRA. Compared with PML-RARA, GTF2I-RARA has a higher affinity to HDAC3 under the treatment of ATRA. Using the ChIP-sequencing approach, we identified 221 GTF2I-RARA binding sites in model cells, and found that the RING finger protein 8(RNF8) is a target gene of GTF2I-RARA, which participated in the disease progression and therapy resistance in APL with GTF2I-RARA transcript. The elevated RNF8 expression promotes the interaction between RARA and RNF8 and induced RARA ubiquitylation and degradation, resulting in attenuated transcriptional activation of RARA. Our results suggested that RNF8 is a key GTF2I-RARA downstream event. Using the combination of MG132 and ATRA to treat the GTF2I-RARA-HL-60 cells, a synergistic effect leading to GTF2I-RARA-HL-60 cell differentiation was confirmed. Taken together, the targeting of RNF8 may be an alternative choice for treatment in variant APL with GTF2I-RARA fusion.

overall_design: exam the target gene of GTF2I-RARA in hl60 cell

first: Wenzhe

last: Yan


title: Comparative gene expression analysis of planktonic Porphyromonas gingivalis ATCC 33277 in the presence of a growing biofilm versus planktonic cells

status: Public on Nov 17 2018

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

summary: In this in vitro study, using DNA microarray we investigate the differential gene expression of Porphyromonas gingicalis ATCC 33277 when growing in the presence or in absence of its own monospecies biofilm.

overall_design: P. gingivalis ATCC 33277 cells were grown in modified Brain Heart Infusion medium until obtaining a final concentration of 10^8 colony-forming units per milliliter. This pure culture of P. gingivalis cells was incubated under two conditions within a multi-well culture plate: in the presence or absence of sterile ceramic calcium hydroxyapatite discs. Plates were incubated at 37ºC for 96 hours in anaerobic conditions. The progress was monitored by confocal laser scanning microscopy (CLSM). After incubation, free-floating P. gingivalis cells from both conditions were harvested and total RNA was extracted and purified. Three biological replicates for each condition were independently hybridized for transcriptomic comparisons. Linear model statistics were used to determine the differentially expressed genes in case of a 1.5-fold change (upregulated or downregulated) in gene expression with p-values<0.05. Results were confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR.

first: M

middle: C

last: Sánchez

first: P

last: Romero-Lastra

first: H

last: Vidal

first: A

last: Llama-Palacios

first: E

last: Figuero

first: D

last: Herrera

last: Sanz


title: Transcriptional profiling of dendritic cells in a mouse model of food-antigen induced anaphylaxis using RNA-Seq

status: Public on Nov 30 2018

city: Malaga

first: James

last: Perkins

state: Malaga

address: Bulevar Louis Pasteur

department: Molecular Biology and Biochemistry

institute: CIBERER / Universidad de Malaga

summary: We used RNA sequencing to study gene expression in lymph node derived DCs from anaphylactic mice sensitized intranasally with the major peach allergen Pru p 3, during the acute reaction phase, induced intraperitoneally. In total, 237 genes changed significantly, 181 showing at least two-fold changes. Almost three quarters of these increased during anaphylaxis

overall_design: 5 Female Balb/c mice aged 4-5 weeks, were sensitized to peach using intranasally administered Pru p 3 in combination with LPS and challenged intraperitoneally as described previously . 5 Littermates, treated with intranasally administered PBS (instead of Pru p 3 and LPS), and later given an intraperitoneal challenge as per the anaphylactic mice, were used for comparison.

first: Maria

middle: J

last: Rodriguez

first: Cristobalina

last: Mayorga


title: Transcriptome dynamics of protein-coding genes and microRNAs during flower development in Arabidopsis

status: Public on Nov 06 2018

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

type: Non-coding RNA profiling by high throughput sequencing


title: Transcriptome dynamics of protein-coding genes during flower development in Arabidopsis

summary: Flower development is a dynamics process in which floral organs are produced from pools of stem cells residing in meristems (Smyth et al., 1990). In order to obtain a high resolution map of the changes of gene expression during this process thus to provide insights into specific expression patterns and their underlying gene regulatory networks, an inducible system which allows us to obtain synchronized flowers (Wellmer et al., 2006) was used to collect stage-specific floral tissues at four stages (stages 0, 2, 4 and 8) for transcriptome profiling by RNA-seq . These stages represent the status of inflorescence meristem, floral meristem specification, floral organ specification and floral organ differentiation, respectively during Arabidopsis flower development.

overall_design: We used the AP1-GR system to conduct RNA-seq experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. Experiments were done in two or three biological replicates.

first: Kerstin

last: Kaufmann


title: Transcriptome profiling of Arabidopsis roots upon lateral root induction upon shy2-2 or slr-1 expression

status: Public on Nov 20 2018

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Center for Organismal Studies

institute: Heidelberg University

summary: To identify genes involved in the early phases of lateral root initiation, we profiled the transcriptomes of plants synchronously induced for lateral root initiation after 0, 1, 2, 4 and 6h of auxin treatment in conditions where IAA14 or IAA3-dependent auxin signaling is blocked. For this we used seedlings expressing non-degradable versions of the AUX/IAAs IAA14 (slr-1) or IAA3 (shy2-2) fused to the glucocorticoid receptor domain (slr-1:GR or shy2-2:GR) under the control of the pericycle and founder cell specific GATA23 promoter. Treatment with dexamethasone induces, specifically in pericycle cells, the nuclear translocation of the non-degradable AUX/IAA that acts as a dominant repressor of auxin signaling resulting in a complete block of lateral root formation

overall_design: Samples were prepared for harvesting following a modified version of the lateral root induction system protocol (Himanen, K. et al. The Plant Cell 14, 2339–2351 (2002)). Seeds of the pGATA23::shy2-2:GR and pGATA23::slr-1:GR lines were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 4d after germination under 16h light/8h dark conditions to 10µM NPA for 22h and shifted to plates containing 10µM NPA and 10µM DEX or DMSO control for 2h. Seedlings were then transferred to plates containing 10µM IAA, and 10µM DEX and DMSO control. Root tissue was harvested at 0, 2, 4 and 6 h after transfer onto auxin plates. All sampling points were performed in triplicate. For each sample, app. 200 segments of the lower two-thirds of the seedling roots were pooled.

first: Martin

last: Schubert


title: Non-lytic clearance of influenza B virus from infected cells [scRNA-seq]

first: Nicholas

last: Heaton

summary: Influenza B virus (IBV) is an acute respiratory pathogen that induces phenotypic alterations to the lung epithelium, such as the denudation of the respiratory cilium, during and after IBV infection.  It has been assumed that these epithelial changes are non-adaptive, and simply the result of cellular death following lytic virus infection. However, previous reports have shown that not all infected cells are killed after viral infection; some cells can completely clear viral RNA and protein and persist in the host long-term.  In this study, we utilized a novel recombinant virus in combination with a Cre recombinase-responsive transgenic mouse model to demonstrate that IBV infection leads to the formation of a population of survivor ciliated cells in the proximal airways of infected mice. To ensure that we were studying ciliated cells with markers that were maintained during viral infection in vivo, we performed single-cell transcriptional profiling on infected and surviving ciliated cell populations. We digested mouse lungs and sorted cells using tdTomato as a marker of infection. We sorted cell populations from the lungs of animals mock infected with PBS (Mock) and during active infection (2 DPI). The resulting data revealed that the marker CD24 is consistently expressed on ciliated cells before and during viral infection.

overall_design: Analysis of RNA from lung epithelial cells  from Mock and 2 days after influenza virus infection.

middle: S

first: Rebekah

last: Dumm


title: RNA co-immunoprecipitation coupled to RNA sequencing (RIP-seq) to identify somatic target mRNAs of the TRIM-NHL protein LIN41

status: Public on Nov 15 2018

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

summary: We perform RIP-seq experiments with two C. elegans worm lines: i) lin-41(n2914); him-5(e1490) with transgenic expression of a rescuing flag::gfp::lin-41 transgene (Aeschimann et al., Mol Cell, 2017) and ii) him-5(e1490) with transgenic expression of flag::gfp::sart-3 (Rüegger et al., NAR, 2015) as a control. The him-5(e1490) genetic background results in an increased frequency of males in the population. We used an anti-FLAG antibody for the IP and semi-synchronous populations of animals in the L3 and L4 larval stages as samples. The purpose of the experiment was to identify LIN41 mRNA targets in the soma. From the three independent replicates, we determined a set of LIN41-bound mRNAs using edgeR and FDR < 0.05 as a cutoff. This set contained only seven mRNAs, the previously known targets lin-29, mab-10, mab-3 and dmd-3 (Aeschimann et al., Mol Cell, 2017), as well as lin-41 and the unannotated genes F18C5.10 and C31H5.5. We conclude that LIN41 likely only binds to a few somatic mRNA targets. Intersecting this experiment with differential gene expression experiments upon dys-regulation of LIN41 (Aeschimann et al., Mol Cell, 2017) and phenotypic analysis of mutant strains, we further conclude that during larval development, LIN41 likely regulates only a four direct targets, namely lin-29, mab-10, mab-3 and dmd-3. Additionally, the lin-41 mRNA could be directly targeted by LIN41 as well, but the detection of lin-41 mRNA in the IPs may result from the immunoprecipitation of nascent FLAG::GFP::LIN41 protein, still bound to the translating ribosome on its own mRNA.

overall_design: We performed RNA co-immunoprecipitations using an anti-FLAG antibody coupled to RNA sequencing. We sampled semi-synchronous populations of animals in the L3 and L4 larval stages of two different genetic backgrounds: i) lin-41(n2914); him-5(e1490) with transgenic expression of a rescuing flag::gfp::lin-41 transgene (Aeschimann et al., Mol Cell, 2017) and ii) him-5(e1490) with transgenic expression of flag::gfp::sart-3 (Rüegger et al., NAR, 2015).

first: Florian

last: Aeschimann

first: Magdalene

last: Rausch

first: Helge

last: Großhans


title: Recombinant Surfactant Protein D reverses expression of specific genes induced by HIV-1 in EpiVaginal Tissues: Clues for a protective response

status: Public on Nov 29 2018

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: We report the HIV-1 induced gene signature of vaginal tissues (EpiVaginalTM, MatTek Corporation, Ashland, MA) using a customised  ex vivo model that mimics the vaginal transmission of HIV-1. Importantly, we demonstrate that recombinant fragment of human Surfactant Protein D (rhSP-D) (Mahajan et al., 2008) treated EpiVaginal tissues exhibited a remarkable but selective reversal of HIV-1 specific gene signature suggesting that epithelial behaviour significantly influences transmission events.

overall_design: Tissues were obtained in cell culture inserts and these inserts were transfered to a 12 well plate containing PBMCs.

first: Hrishikesh

last: Pandit

first: Kavita

last: Kale

first: Hidemi

last: Yamamoto

first: Gargi

last: Thakur

first: Sushama

last: Rokade

first: Payal

last: Chakraborty

first: Madavan

last: Vasudevan

first: Uday

last: Kishore

first: Taruna

last: Madan

first: Raina

last: Fichorova


title: Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Cardiology, University Health Network

country: Canada

institute: Toronto General Hospital Research Institute

summary: Mononuclear phagocytes promote injury and repair following myocardial infarction but discriminating functions within mixed populations remains challenging. We utilized fate mapping and single cell RNA-sequencing to delineate fate specification trajectories of heterogeneous cardiac macrophage subpopulations. In steady state, TIMD4 expression tracked with a dominant resident cardiac macrophage subset that persisted via in situ self-renewal with minimal monocyte input. Following ischemic injury, monocytes displayed significant plasticity, ultimately adopting transcriptional states similar to resident macrophages, but also multiple unique states. Ischemic injury reduced resident macrophage abundance within infarct tissue, and despite transcriptional similarity, TIMD4 expression distinguished resident from recruited macrophages. Specific lineage-based depletion of resident cardiac macrophages resulted in depressed cardiac function and adverse remodeling primarily within the peri-infarct zone, the only region of the myocardium where resident macrophages expanded numerically following injury. Together, these data highlight a non-redundant, cardioprotective role of resident cardiac macrophages, and the diverse transcriptional fates recruited monocytes can adopt.

overall_design: Single cell mRNA sequencing was used to investigate the transcriptomic differences between cardiac macrophages post myocardial infarction vs steady state.

first: S

last: Nejat


title: De Novo Genome Assembly of Guinea Grass Exposed to Elevated CO2 and Temperature

status: Public on Nov 07 2018

city: Urbana

first: Elizabeth (Lisa)

last: Ainsworth

state: IL

address: 1201 W Gregory Dr.

department: Plant Biology

institute: University of Illinois Urbana-Champaign

summary:
Introduction : By mid-century, global atmospheric carbon dioxide concentration ([CO2]) is predicted to reach 600 umol mol-1 with global temperatures rising by 2ºC. Rising [CO2] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions.
Objectives : This experiment aimed to understand the effects of elevated [CO2] (600 umol mol-1) and warming (+ 2°C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles.
Methods: We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO2] and temperature, and statistical analyses were used to integrate the data.
Results: The MiSeq library was quantified by qPCR and sequenced on one MiSeq flowcell for 301 cycles using paired-end sequencing. HiSeq paired-end sequencing was done with four quantified libraries per treatment which were pooled in equimolar concentration, and sequenced on two lanes for 161 cycles. The final read lengths for MiSeq and HiSeq were 300 nt and 160 nt in length. A total of 635,649,277 reads were assembled from the MiSeq/HiSeq pools. Quality control for reads generated from sequencing was performed using FastQC. Quality reads were used to perform de novo transcriptome assembly using Trinity. The initial assembly consisted of 187,216 genes. A filter was applied to keep only those genes that had at least 10 reads (across the 4 replicates) for an individual treatment. The resulting transcriptome contained 45,073 genes and reads. Functional annotation of the genes was done by using BLAST against Arabidopsis thaliana, Zea mays, and Setaria italica.

overall_design: 32 sample (n=4). Panicum maximum Jacq. (Guinea Grass) was planted in a complete replicated design at University of São Paul in Ribeirão Preto, São Paulo Brazil. 4 ambient temperature and [CO2] (C) plots, 4 elevated CO2 [600 ppm] and ambient temperature (eC) plots, 4 ambient [CO2] and elevated temperature (eT) [+ 2°C] plots, and 4 combined treatment (elevated [CO2] and elevated temperature (eCeT)) plots. Each plot was 2-m in diameter; [CO2] was controlled using Free Air CO2 Enrichment and canopy warming was provided by infrared ceramic heaters as described by Britto de Assis Prado et al. (2016). Treatment was started on April 22, 2014 in a 2500 m2 field. Samples for untargeted metabolomics (with GC-MS), de novo transcriptomics, and RNASeq, were taken 30 and 50 days post treatment exposure (May 22, 2014 and July 14, 2014). Lyophilized leaf material was sent to the University of Illinois Urbana-Champagin (Ainsworth lab) for the untargeted metabolomics, transcript assembly and RNASeq.

first: Jessica

middle: M

last: Wedow

first: Criag

last: Yendrek

first: Tathyana

last: Mello

first: Silvana

last: Creste

first: Carlos

middle: A

last: Martinez

first: Elizabeth


title: Bone marrow derived human B cells [normal proB]

status: Public on Oct 02 2018

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. hnRNPA1. hnRNPA1 3’UTR was most pervasively misspliced, yielding the transcript  subject to nonsense-mediated decay. Thus, we knocked it down in B-lymphoblastoid cells, identified 213 hnRNPA1-dependent splicing events, and defined the hnRNPA1 splicing signature in pediatric leukemias. One of its elements was DICER1, a known tumor suppressor gene; its LSVs involved the 5’ UTR, suggestive of splicing as a mechanism of translational deregulation. Additionally, we searched for LSVs in other leukemia and lymphoma drivers and discovered 81 LSVs in 41 genes. 77 LSVs were confirmed using two large independent B-ALL RNA-seq datasets. In fact, the twenty most common B-ALL drivers showed higher prevalence of aberrant splicing than of somatic mutations. Thus, post-transcriptional deregulation of SF can drive widespread changes in B-ALL splicing and likely contribute to disease pathogenesis.

overall_design: We profiled adult and pediatric early B pro B, pre B and immature B cells

first: Kathryn

last: Black

first: Ammar

last: Naqvi


title: Gender determines susceptibility to methamphetamine cardiomyopathy in mice

status: Public on Sep 01 2018

city: Honolulu

first: April

last: Darrow

state: HI

address: 651 Ilalo St.

institute: University of Hawaii

summary: In this study, we have created a mouse model of methamphetamine cardiomyopathy that reproduces the chronic, progressive dosing commonly encountered in addicted subjects.  We gradually increased the quantity of methamphetamine given to C57Bl/6 mice from 5 to 40 mg/kg over five months.  At the fifth month, heart weight was increased, echocardiograms showed a dilated cardiomyopathy and survival was lower in males, with less effect in females. Interestingly, these findings correspond to previous observations in human patients, suggesting greater male susceptibility to the effects of methamphetamine on the heart.Transcriptional analysis showed changes in genes dysregulated in previous methamphetamine neurological studies as well as many that likely play a role in cardiac response to this toxic stress. We expect that a deeper understanding of the molecular biology of methamphetamine exposure in the heart will provide insights into the mechanism of cardiomyopathy in addicts and potential routes to more effective treatment.

overall_design: Male and female C57BL/6 mice were given intraperitoneal injections of methamphetamine hydrochloride (Sigma Aldrich, St. Louis, MO) dissolved in sterile phosphate buffered saline (PBS) once per week for 5 months. The dose was gradually increased 2mg per week over the 20 week study period to achieve a final dose of 40mg/kg. Control mice were injected with sterile PBS on the same schedule. After 5 months, hearts were excised, and heart tissue RNA was extracted. Two independent experiments were preformed for the males, and one experiment was performed for the females. Whole genome microarrays were performed on the heart tissueRNA from 2-4 methamphetamine-treated mice and 2-3 PBS-treated controls from the male and female groups of Trial 1. Trial 2 included only male mice, and arrays were performed on 2 methamphetamine-treated males and 2 PBS-treated controls. Transcripts dysregulated in the hearts of male and female mice in response to methamphetamine exposure were identified as well as transcripts differentially dysregulated between the genders.

first: Ralph

middle: V

last: Shohet

first: Marie

last: Marcinko

first: Aaron

last: Tuia


title: Transcriptome Sequence of Antibiotic-Treated Pseudomonas aeruginosa

status: Public on Oct 31 2018

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

summary: Pseudomonas aeruginosa is known to tolerate antibiotic therapy during infection. This prevents clearance of infection and negatively impacts patient outcomes. Here, we report the transcriptome sequence of antibiotic-treated and untreated P. aeruginosa cultures and the differential gene expression observed when treated cells are compared to untreated cells.

overall_design: P. aeruginosa antibiotic tolerance, biofilm, planktonic, and stationary cultures

first: Esani

last: Saika

last: Tsute

first: Kai

middle: P

last: Leung

first: Tricia

last: Van Laar


title: T helper cells modulate intestinal stem cell renewal and differentiation

status: Public on Nov 01 2018

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Using single-cell RNA-seq of intestinal epithelial cells we identify surprising expression of MHC class II, which participates in a novel interaction between gut-resident CD4+ T cells and epithelial stem cells, governing the balance between stem cell differentiation and renewal.

overall_design: In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.

first: Moshe

last: Biton

first: Semir

last: Beyaz

first: Noga

last: Rogel

first: Christopher

last: Smillie

first: Karthik

last: Shekhar

first: Alexandra

last: Schnell

first: Zuojia

first: Chuan

last: Wu

first: Jose

last: Ordovas-Montanes

first: David

last: Alvarez

first: Rebecca

last: Herbst

first: Itay

last: Tirosh

first: Grace

last: Burgin

first: Danielle

last: Dionne

first: Michael

middle: E

last: Xifaras

first: Mei

last: Zhang

first: Alex

middle: K

last: Shalek

first: Ulrich

last: von Andrian

first: Daniel

middle: B

last: Graham

first: Orit

last: Rozenblatt-Rosen

first: Hai

middle: N

last: Shi

first: Vijay

last: Kuchroo

first: Omer

last: Yilmaz

first: Aviv

last: Regev

first: Ramnik

last: Xavier


title: Differential Expression of Immune Related Genes in Taste Buds of Fed and Fasted Mice

status: Public on Nov 16 2018

city: Gainesville

first: Sean

middle: Michael

last: Crosson

state: FL

department: Opthalmology

institute: University of Florida

summary:
Purpose: The goal of this study is to compare the taste bud transcriptome of fasted and fed mice. By doing this we hope to gain more information about the taste bud transcriptome as well as determine transcriptional changes that may be linked with pre or post-ingestive states.
Methods: Whole taste bud mRNA profiles of WT adult C57BL/6J mice were generated by Illumina HiSeq 2000 single end RNA sequencing. Prior to taste bud RNA isolation, mice were either food-deprived, fed, or given ad libitum access to standard rodent chow as a control. Sequence read quality was assesed using FastQC, and adapter sequences were trimmed using trimmomatic. Reads were then aligned to the GRCm38.p4 reference genome using Tophat2 followed by Cufflinks analysis, then gene level differential expression was conducted using Cuffdiff, and visualized via cummeRbund. Gene enrichment analysis of differentially expressed genes was performed using DAVID and Panther Gene Ontology.
Results: We mapped about 30 million sequence reads per sample to the mouse genome, build GRCm38.p4, and identified 144 differentially expressed genes (FDR of 5%) between the taste buds of food-restricted, fed, and ad libitum control mice. Gene enrichment analysis of differentially expressed genes showed enrichment of pathways associated with cytokines, immunity, cytoskeletal structure, chaperone proteins, and protease inhibitors.
Conclusions: Our study represents a detailed analysis of the murine taste bud transcriptome generated using RNA-seq technology. Our results highlight cellular pathways that may be differentially regulated in taste receptor cells during different pre/post-ingestive states.  Additionally, as limited transcriptome information is available for taste buds, this dataset  can serve as a resource for the discovery of genes novel to the taste bud.

overall_design: Whole taste bud mRNA profiles of 20-24 week old WT C57B/6J (fed, fasted, or ad libitum fed) were generated by RNA sequencing using Illumina HiSeq 2000.

first: Seth

last: Currlin

first: Oleksandr

last: Moskalenko

first: Svitlana

last: Yegorova

first: Cedric

middle: D

last: Dotson

first: Sergei

last: Zolotukhin


title: The pattern of Mesenchymal stem cell expression is an independent marker of outcome in multiple myeloma

status: Public on Aug 24 2018

city: Little Rock

first: Brian

last: Walker

state: AR

address: 4301 W Markham St.

institute: University of Arkansas for Medical Sciences

summary: Mesenchymal stem cells (MSCs) are an essential component of the bone marrow (BM) microenvironment and have shown to support cancer evolution in multiple myeloma (MM). Despite the increasing evidence that MM MSCs differ from their healthy counterparts, little knowledge exists as to whether MSCs independently influence disease outcome. The aim of the present study was to determine the importance of MSCs in disease progression and outcome in MM.

overall_design:
To determine the impact of MSCs on MM outcome in an in vivo system, we first identified genes from cultured MSCs that were specific to MSC expression and were not or minimally expressed in PCs or other cells present in BM aspirates. We then applied this MSC gene signature to whole BM biopsies of MM patients compared to healthy controls and determined MSC expression scores specific to MM and predictive of outcome.

Molecular subgroup definitions:
CD-1: CCND1/CCND3 (group 5)
CD-2: CCND1/CCND3 (group 6)
HY: Hyperdiploid
LB: Low bone disease
MF: MAF/MAFB
MS: MMSET
PR: Proliferation

Discussion of these molecular subgroups is available in: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1895543/

first: Carolina

last: Schinke


title: Differentially expressed gene and corresponding signaling pathway in an autochthonous mouse prostate cancer model

status: Public on Aug 30 2018

city: Cleveland

first: Shiv

middle: Shankar

last: Verma

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

summary: Our study evaluated the underlying pathways and its connection to human cancer, which may further help to assess the risk of prostate cancer progression and identify potential targets of adjuvant treatment.

overall_design: Normal prostate compared with TRAMP transgenic for early diagonosis of prostate cancer.

first: Sanjay

last: Gupta


title: RNA secondary structome of different cellular compartments in human and mouse

status: Public on Jul 31 2018

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

summary: We resolved the RNA secondary structure of three cellular compartments including chromatin (ch), nucleoplasm(np) and cytoplasm(cy) in HEK293 and mES cells based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyze the RNA structure dynamics among cellular compartments and different RNA processings. Also, we study which factors perturb the RNA structures.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Subcellular fractionation for HEK293 cells and mES cells was performed and tested by western and RT-qPCR. libraries of subcellular fractions were constructed as the icSHAPE protocol. The RNA structure in vivo and in vitro was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) and in vitro NAI-N3 treatment samples (T). irCLIP was constructed in Mettl3 WT and KO mES cells. Anti-Lin28A and anti-GFP (control) antibody was used in the two condition (Mettl3 WT and KO).

first: Furqan

last: Fazal

first: James

last: Broughton

first: Qiangfeng

last: Zhang

first: Howard

middle: Y

last: Chang


title: Expression data from sulfisoxazole-treated cancer cells

status: Public on Aug 02 2018

city: Daegu

first: Moon-Chang

last: Baek

address: Gukchebosang-ro 680

institute: Kyungpook National University

summary: Sulfisoxazole, a FDA-approved drug, is a promising repositioned drug candidate for the treatement of various cancers. Therefore we analyzed the gene expression by microarray to identified the up-regulated and down-regulated genes after SFX treatment in both, melanoma and breast cancer cells.

overall_design: Recently, breast cancer and melanoma have a higher incidence in the world. Therefore, we selected two cancer cell lines, SKMEL28 (melanoma) and MDA-MB231 (breast cancer) for analysis. Cells were treated with 100 μM of SFX for 24 hours under serum-free condition. Then, total RNA was collected using TRIZOL, and performed Affymetrix microarray.

first: Eun-Ju

last: Im


title: Expression data from knockdown of HSD3B1 in MDA-MD-231 breast cancer cell line

status: Public on Sep 08 2018

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

institute: MacKay Memorial Hospital

summary: HSD3B1 (3beta-hydroxysteroid dehydrogenase type 1) plays a vital role in steroidogenesis. Transcription profiling analysis was performed in MDA-MD-231 breast cancer cells transfected with negative control siRNA or siRNAs against HSD3B1.

overall_design: HSD3B1 expression was stably knocked-down in MDA-MB-231 cells. RNA was extracted from cells transfected with negative control siRNA or siRNAs against HSD3B1 and submitted to microarray analysis.

first: Yuan-Ching


title: Gene expression data from CD34+ BMMCs/PBMCs from JAK2V617F positive and CALR mutated MPN patients

status: Public on Oct 29 2018

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary:
Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) consist of primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocythemia (ET)
In this dataset, we compare the gene expression data of patients JAK2V617F vs. CALR-mutated MPN patients.

overall_design: 11 total samples were analyzed.

first: Julia

last: Czech

first: Julian

last: Baumeister

first: Tiago

last: Maié

first: Ivan

middle: G

last: Costa

first: Claudia

last: Schubert

first: Deniz

last: Gezer

first: Nicolas

last: Chatain

first: Steffen

last: Koschmieder


title: Effects of blackcurrant extract on gene expression on human follicle dermal papilla cells.

status: Public on Jul 20 2018

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

country: Japan

institute: Aomori University of Health and Welfare

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

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


title: Defining the RNA Interactome by Total RNA-Associated Protein Purification

status: Public on Sep 13 2018

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae ) and bacteria (E. coli). In all analyses, SILAC labeling was used to quantify protein recovery in the presence and absence of irradiation. For S.cerevisiae, we also compared crosslinking using 254nm (UVC) irradiation (TRAPP) with 4-thiouracil (4SU) labeling combined with 350nm  (UVA) irradiation (PAR-TRAPP). Recovery of proteins not anticipated to show RNA-binding activity was significantly higher in TRAPP compared to PAR-TRAPP. As an example of preferential TRAPP-crosslinking, we tested enolase (Eno1) and demonstrated its strong, but largely sequence independent, binding to RNA in vivo. We speculate that many protein-RNA interactions have biophysical effects on localization and/or accessibility, by opposing or promoting phase separation. Homologous metabolic enzymes showed RNA crosslinking in S. cerevisiae and E. coli, indicating conservation of this property. TRAPP allows alterations in RNA interactions to be followed and we initially analyzed the effects of weak acid stress. This revealed specific alterations in RNA-protein interactions; for example, during late 60S ribosome subunit maturation. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified following phospho-peptide enrichment combined with a bioinformatic pipeline (Xi). TRAPP is quick, simple and scalable, allowing rapid characterization of the RNA-bound proteome in many systems.

overall_design: CRAC datasets were collected for Eno1 and an untagged control (BY). Two replicates were collected for each.

first: Vadim

last: Shchepachev

first: Christos

last: Spanos

first: Elisabeth

last: Petfalski

first: Lutz

last: Fischer

first: Juri

last: Rappsilber

first: David

last: Tollervey


title: Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)

status: Public on Oct 04 2018

city: Madison

first: Hongli

last: Jiao

state: WI

address: 1111 Highland Ave WIMR 5039

department: Department of Orthopedics and Rehabilitation

institute: University of Wisconsin-Madison

summary: We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:SF-MSCs, iPSCs and iPSC-MSCs. Our results shown that iPSC-MSCs were more similar to SF-MSCs than iPSCs.

overall_design: Human SF-MSCs were reprogrammed through the non-viral, integration-free episomal approach into induced pluripotent stem cells (iPSCs), which were then subsequently differentiated into MSCs to establish iPSC-MSC lines.

first: Wan-Ju

last: Li

first: Madeleine

last: Lemieux


title: The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula

status: Public on Aug 23 2018

city: Auckland

first: Geoffrey

middle: Owen James

last: Thomson

address: Private Bag 92019

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

summary: Photoperiod regulated flowering is a well understood developmental pathway in the intensively studied Brassicaceae species Arabidopsis thaliana and in the monocot rice, but less so in other angiosperm groups. One such group, the temperate legumes in the Fabaceae family which are important both agriculturally and ecologically, accelerate their flowering in response to long-day photoperiods (LD), but lack functional homologues of key regulatory genes present in A. thaliana such as CO. Curiously previous work in the reference legume Medicago truncatula has shown that floral activator MtFTa1, which is upregulated by LD and vernalisation, does not exhibit a peak in expression at dusk like its homologue in A. thaliana FLOWERING LOCUS T, instead MtFTa1 maintains a near constant pattern of expression. In addition legumes possess for other FT-like genes such as the MtFTb genes expressed in LD which may also act in the regulation of flowering time. This study utilises RNA-Seq to identify genes which may regulate or be co-expressed with these FT-like genes in Medicago truncatula. Following a shift from short-day photoperiods to inductive long-days genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). Specifically this study focuses on the first few hours of the day in the young leaves which coincides with the first diurnal peak of the FTb genes. It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering. In the process this study identifies a number of potential candidate genes for future studies to consider.

overall_design: Combines two similar experiments where plants were grown in short-day photoperiods and shifted to long-day photoperiods after 10 days. Triplicate RNA-seq libraries from both short-day and long-day leaf tissue were generated in experiment 1 at ZT0 and ZT4 at 13 days. In experiment 2 at ZT4 at 15 days.

first: James

last: Taylor

first: Joanna

last: Putterill


title: Gene expression profiling predicts processing properties in short-term imbibition of wheat

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

institute: Tokyo University of Agriculture

summary:
Objective: Germination of wheat maximizes phytochemical content and antioxidant activity while altering chemical composition, gluten content, and pasting properties. We previously reported marked changes in gene expression in soybean prior to germination before the radicle had grown from a seed. The present study investigated whether imibibition induces similar changes in wheat.

Methods: Changes in gene expression profiles of wheat during short-term imbibition (0, 16, and 24 h) were evaluated by DNA microarray analysis. Gene Ontology (GO) analysis was carried out to categorize the function of genes with altered expression. The expression of genes encoding enzymes associated with starch breakdown was evaluated by quantitative real-time PCR, and changes in enzymatic activity were assessed with functional assays. Pasting properties of flour made from wheat seeds imbibed for different times were examined with a Rapid Visco Analyzer. The protein profile was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis, and gluten content was quantified.

Results: The GO analysis revealed that genes related to cellulose and cell wall synthesis were upregulated by imbibition for 16 h whereas those associated with polysaccharide catabolism and nucleosome assembly were upregulated in the subsequent 8 h. α-Amylase expression was highest after 24-h imbibition, with a corresponding increase in enzymatic activity. The pasting properties of wheat flour decreased when seeds were imbibed for over 16 h. Gluten was not degraded until 48 h imbibition.

Conclusion: Short-term imbibition of wheat can produce a new type of starch with improved physical and functional properties that may be more appealing to consumers.

overall_design: Seeds imbibed for 0-, 16-, and 24-h were collected for RNA extraction and hybridization on Agilent microarrays.

last: Tamura