title: Klotho suppresses colorectal cancer through modulation of the unfolded protein response

status: Public on Aug 09 2018

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
Study the role of klotho as a tumor suppressor in colorectal cancer.
[abstract] Klotho is an anti-aging transmembrane protein, which can be shed and function as a hormone. Accumulating data indicate klotho as a tumor suppressor in a wide array of malignancies and indicate the subdomain KL1 as the active region of the protein. We aimed to study the role of klotho as a tumor suppressor in colorectal cancer. Bioinformatics analyses of TCGA datasets indicated reduced klotho mRNA levels in human colorectal cancer, along with negative regulation of klotho expression by hypermethylation of the promoter and 1st exon, and hypomethylation of an area within the gene. Overexpression or treatment with klotho or KL1 inhibited proliferation of colorectal cancer cells in vitro. The in vivo activity of klotho and KL1 was examined using two models recapitulating development of tumors in the normal colonic environment of immune-competent mice. Treatment with klotho inhibited formation of colon polyps induced by the carcinogen azoxymethane, and KL1 treatment slowed growth of orthotopically-implanted colorectal tumors. Gene expression array revealed that klotho and KL1 expression enhanced the unfolded protein response (UPR) and this was further established by increased levels of spliced XBP1, GRP78 and phosphorylated eIF2α. Furthermore, attenuation of the UPR partially abrogated klotho tumor suppressor activity. In conclusion, this study indicates klotho as a tumor suppressor in colorectal cancer and identifies, for the first time, the UPR as a pathway mediating klotho activities in cancer. These data suggest that administration of exogenous klotho or KL1 may serve as a novel strategy for prevention and treatment of colorectal cancer.

overall_design: Gene expression profiling performed for 9 Samples (arrays) representing HCT 116 cells transfected with KL-FL, KL1, or control vector (pcDNA3).

first: Tammi

last: Rubinstein

first: Shiri

last: Shahmoon

first: Ehud

last: Zigmond

first: Tal

last: Etan

first: Keren

last: Merenbakh-Lamin

first: Gil

middle: H

last: Zahav

first: Iris

last: Barshack

first: Gilad

last: Vainer

first: Nir

last: Skalka

first: Rina

last: Rosin-Arbesfeld

first: Chen

last: Varol

first: Tami

last: Rubinek

first: Ido

last: Wolf


title: Medium chain unsaturated fatty acid ethyl esters inhibit persister formation of Escherichia coli via antitoxin HipB

status: Public on Aug 08 2018

city: Chicago

first: Seok Hoon

last: Hong

state: IL

address: 10 West 33rd Street, Perlstein Hall 127

department: Chemical and Biological Engineering

country: USA

institute: Illinois Institute of Technology

type: Expression profiling by high throughput sequencing

summary: Persisters represent a small bacterial population that is dormant and that survives under antibiotic treatment without experiencing genetic adaptation. Persisters are also considered one of the major reasons for recalcitrant chronic bacterial infections. Although several mechanisms of persister formation have been proposed, it is not clear how cells enter the dormant state in the presence of antibiotics or how persister cell formation can be effectively controlled. A fatty acid compound, cis-2-decenoic acid, was reported to decrease persister formation as well as revert the dormant cells to a metabolically active state. We reasoned that some fatty acid compounds may be effective in controlling bacterial persistence because they are known to benefit host immune systems. This study investigated persister cell formation by pathogens that were exposed to nine fatty acid compounds during antibiotic treatment. We found that three medium chain unsaturated fatty acid ethyl esters (ethyl trans-2-decenoate, ethyl trans-2-octenoate, and ethyl cis-4-decenoate) decreased the level of Escherichia coli persister formation up to 110-fold when cells were exposed to ciprofloxacin or ampicillin antibiotics. RNA sequencing analysis and gene deletion persister studies elucidated that these fatty acids inhibit bacterial persistence by regulating antitoxin HipB. A similar persister cell reduction was observed for pathogenic E. coli EDL933, Pseudomonas aeruginosa PAO1, and Serratia marcescens ICU2-4 strains. This study demonstrates that fatty acid ethyl esters can be used to disrupt bacterial dormancy to combat persistent infectious diseases.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Exponential phase E. coli BW25113 was exposed to 1 µg/mL of ciprofloxacin with and without 500 µM of ethyl trans-2-decenoate (ET2DA) for 1 h. Total RNA was isolated and rRNA was depleted. After generating RNA library, RNA was sequenced using Illumina NextSeq 500.

first: Mengya

last: Wang

first: Kuili

last: Fang

first: Sung Min

middle: C

first: Inwha

last: Kim

first: Ik-Soon

last: Jang


title: Genome wide transcriptome analysis provides bases on colonic mucosal immune system development in neonatal calves affected by colostrum feeding strategies in neonatal calves

city: Edmonton

first: Michael

last: Steele

state: AB

address: 116 St. and 85 Ave.

country: Canada

institute: University of Alberta

summary: Delivery of colostrum within the first several hours after birth is vital for establishing successful passive immunity in neonatal dairy calves. However, it is unclear whether the difference in colostrum feeding strategy can affect the development of the calf gastrointestinal tract. The aim of this study was to evaluate the effect of colostrum feeding time within the first 12 h after birth on the colonic mucosal immune system in neonatal calves using a genome wide transcriptome analysis.RNA sequencing based transcriptome analysis of colon tissues collected from twenty-seven male Holstein calves which were randomly assigned to one of three colostrum feeding strategies (immediately after birth (TRT0); 6 h after birth (TRT6); 12 h after birth (TRT12)) and were euthanized at 51 h of age detected 15935 ± 210, 15332 ± 415, and 15539 ± 440 expressed genes in groups, respectively. The core transcriptome of the colon in dairy calves included 12,678 genes, with enriched “cellular process” and “metabolic process” as the top three biological functions. Expression of 802 immune related genes were detected in the colon tissue. Principal component analysis of the transcriptomes did not display a clear separation by colostrum feeding strategy, and differential abundance analyses showed no significant difference in the expression of immune related genes among the treatments.Transcriptome analysis indicates that the development of the colonic mucosal immune system in neonatal calves may be independent of the timing of initial colostrum meal within 12 h after birth.

overall_design: RNA sequencing based transcriptome analysis was conducted for colon tissues collected from twenty-seven male Holstein calves which were randomly assigned to one of three colostrum feeding strategies (immediately after birth (TRT0); 6 h after birth (TRT6); 12 h after birth (TRT12))

first: Le

middle: L

last: Guan

first: Zhixiong

last: He

first: Yang

last: Song


title: miRNA expression profiling in mouse embryonic stem cell conditioned media

city: Daegue

first: Jae-Ryong

address: Hyunchung-Ro

country: South Korea

institute: Yeungnam University

summary: To identify novel putative factors that the anti-senescence effects of mouse embryonic stem cell conditioned media (E-CM) against celllular senescence, we conduvted a miRNA array analysis on E-CM and the mouse embryonic fibroblast (MEF)-CM The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States).

overall_design: CM was collected from ESCs in OPTI-MEM on gelatin without feeder, FBS or other supplements. We have used CM to define ESC-specific secretory factors excluding potential factors from FBS and MEFs Gelatin coating was used to feeder free conditions, but some feeder cells may remain in culture. M-CM was used as a control to exclude remaining feeder cell effects. We collected conditioned media from MEF (mouse embryonic fibroblast) cells cultured in OPTI-MEM. We isolated the total RNA from these 3 samples and performed the miRNA array (Affymetrix platform) to identify the differentially expressed miRNAs in E-CM and MEF-CM

first: Yun-Ui

last: Bae

first: Youlim

last: Son

first: Chang-Hyun

first: Kwang

middle: S

first: Se

last: Hyun

first: Hyun

middle: G

last: Woo

first: Byul

middle: A

last: Jee

first: Jun-Hyuk

last: Choi

first: Hoon-Ki

last: Sung

first: Hyung-Chul

first: So

middle: Y

last: Park

first: Ju-Hyun

first: Kyung-Oh

last: Doh


title: Maps of histone variant H4.V deposition in Trypanosoma brucei brucei

status: Public on Aug 24 2018

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where histone variant H4.V is deposited. A previously generated cell line (Siegel et al., 2009) in which both endogenous H4.V alleles are knockout out and ectopic overexpression of a Ty1-tagged version of H4.V can be induced was used. During the ChIP experiment, the DNA was digested with MNase to obtain mononucleosomes. Nucleosomes containing H4.V were pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and mononucleosomal DNA is purified and prepared for Illumina sequencing.

overall_design: Mnase ChIPs were done in duplicates, input control samples were included for each ChIP sample.

first: Laura

last: Müller

first: T

middle: N

last: Siegel


title: Maps of histone variant H3.V deposition in Trypanosoma brucei brucei

summary: Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where histone variant H3.V is deposited. This was achieved by deletion of one H3.V allele and N-terminal tagging of the second H3.V allele with a Ty1 tag. During the ChIP experiment, the DNA was digested with MNase to obtain mononucleosomes. Nucleosomes containing H3.V were pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and mononucleosomal DNA is purified and prepared for Illumina sequencing.


title: Expression data from  cerebral CD163+ perivascular and meningeal macrophages (PV) obtained from controls (C) and ischemic (I) rats

city: Barcelona

first: Anna

last: PLANAS

state: - If in U.S, Select a State -

address: Rossello 161 planta 6

country: Spain

institute: Spanish Research Council (CSIC)

summary:
We used adult male Sprague-Dawley rats (280-329 g body weight). Controls were naïve rats. Ischemic rats were subjected to 1-hour occlusion of the right middle cerebral artery and 16h reperfusion.
The goal was to identify the changes in the gene expression profile of PV after brain ischemia.

overall_design: We used 3 control brain samples and 3 samples of ischemic brain tissue.

first: Roger

last: Cugota

first: Mattia

last: Gallizioli

first: Ferran

last: Brianso

first: Jordi

last: Pedragosa

first: Angelica

last: Salas-Perdomo

middle: M

last: Planas


title: Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae

status: Public on Aug 04 2018

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: Single-stranded DNA breaks (nicks) were tagged by biotin-dCTP in wild-type budding yeast cells and mapped by nick-ChIP coupled to whole-genomic microarrays.

overall_design: Live budding yeast cells were fixed by 1% formaldehyde and encapsulated into low-melting point agarose plugs. After cell lysis, free 3'-OH DNA termini were tagged by limited in situ nick translation using E Coli DNA pol I holoenzyme, incorporating bioin-dCTP.  As a positive control of nick labeling, part of the samples were treated by nickase enzyme introducing site-specific exogenous ss breaks (nickase-treated samples). Nucleic acid was from control and nickase-treated samples and purified and fragmented by sonication (to an average size of 300-500 bp) and immunoprecipitated by anti-biotin monoclonal antibodies (Sigma). After WGA (whole genome amplification) input samples were lablelled by Cy3, IP sample were labelled by Cy5 and were co-hybridized to 4x44k Agilent microarrays.

first: Lóránt

last: Székvölgyi

first: Halász

last: László


title: 3D interaction maps in wild-type and histone variant deletion mutants generated by chromosome conformation capture [Hi-C I]

summary: Interaction matrices were generated by applying in situ Hi-C to wild-type and deletion mutant trypanosomes.

overall_design: DNA-DNA interactions were captured in situ in Trypansoma brucei nuclei, digested with MboI and re-ligated to obtain chimeric DNA molecules of previously interacting chromatin. The ligation products were purified and prepared for paired-end Illumina sequencing. Experiments were performed in duplicates for both the wild-type and the deletion mutant.

first: Raúl

middle: O

last: Cosentino

middle: U


title: Comparision of gene expression in adipose progenitors(AP) relative to adipose tissue(AT)

status: Public on Aug 22 2018

city: Pittsburgh

first: Yang

last: Zhang

state: PA

address: 100 Technology Dr.

department: Medicine

institute: University of Pittsburgh

summary: To identify of candidate transcriptional regulators of AP function, microarray was utilized to analyze gene expression in freshly isolated AP from stromal-vascular fractions relative to whole adipose tissue (AT) from the same mouse.

overall_design: We utilized negative selection strategy, utilizing antibody coated magnetic beads to deplete hematopoietic cells (lineage+) and CD31+ endothelial cells from the stromal-vascular fraction after enzymatic dissociation of AT depots, which yielded putative APs from the inguinal (SAT) and perigonadal (VAT) depots of several mice in approximately 30 minutes.

first: Soomin

last: Kim

first: Matthew

last: Steinhauser


title: Expression profile of whole murine lung adenocarcinomas with or without overexpression of Snail

status: Public on Aug 03 2018

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: We used microarrays to study the changes in the transcriptional profile upon Snail overexpression in murine lung adenocarcinomas

overall_design: Lung tumors were isolated from KPR mice infected with Pgk-Cre_TRE-Snail lentiviral constructs and fed with doxycycline diet from the day of infection, RNA was extracted, amplified and hybridized with Affymetrix mouse gene 2.0ST arrays.

first: Svenja

last: Groeneveld

last: Zangger

first: Julien

last: Faget

first: Etienne

last: Meylan


title: Single-cell RT-PCR analysis of Tgd17 progenitors

status: Public on Aug 21 2018

city: Worcester

first: Nicholas

last: Spidale

state: MA

address: 368 Plantation St.

department: Pathology

institute: University of Massachusetts Medical School

summary:
The indicated thymic progenitor population was sorted via FACS and then loaded into a Fluidigm C1 small cell capture chip for single-cell capture, lysis, reverse transcription, and preamplification.  Preamplified products were analyzed on a BioMark HD with EvaGreen chemistry.  The genes analyzed were selected based on bulk RNA sequencing data and/or prior publications, including genes relevant for gamma/delta T cells and T cell progenitors.  B6=C57BL/6J, Rag=B6.Rag1-/-, Tcrd=B6.Tcrd-/-, DN1d=Live/TCRd-/Lin-/CD44+/CD25-/CD24+/cKit-, DN2=Live/TCRd-/Lin-/CD44+/CD25+/cKit+, cKit-=Live/TCRd-/Lin-/CD44+/CD25-/cKit-.  Lin=CD3/CD8/CD11b/CD11c/CD19/Gr-1/NK1.1/TCRb/Ter-119
Sample naming nomenclature is as follows:  MouseLine_CellPopoulation_DateCaptured_CaptureChamber_CellNumberInChamber

overall_design: Single-cell qPCR analysis using the Fluidigm C1 platform.  Cell capture, lysis, RT, and preamp is all automated to avoid the potential for operator-introduced inconsistencies.  All preamplified products (~3.5 microliters) were diluted with an additional 5 microliters of C1 DNA Dilution Reagent prior to qPCR analysis.

first: Joonsoo

last: Kang


title: Expression profile of whole murine lung adenocarcinomas with or without Snail

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

overall_design: Refer to individual Series


title: Lithocholic acid significantly extends the lifespan in Drosophila melanogaster by targeting multiple lifespan-extending pathways

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary:
Primary bile acids are produced in the liver whereas secondary bile acids such as lithocholic acid (LCA) are generated by gut bacteria from primary bile acids that escape the ileal absorption. Besides their well-known function as detergents in lipid digestion, bile acids are important signaling molecules mediating effects on the host’s metabolism. As energy metabolism is closely linked to aging and longevity we supplemented fruit flies (Drosophila melanogaster) with 50 µmol/l LCA either for 30 days or throughout their lifetime. LCA supplementation resulted in a significant induction of the mean (+12 days), median (+10 days) and maximum lifespan (+ 11 days) in comparison to untreated control flies. This lifespan extension was accompanied by an induction of spargel (srl), the fly homolog of mammalian PPARG co-activator 1a(PGC1A. In srl mutant flies, LCA failed to induce longevity emphasizing the essential role of srl in the observed lifespan extension. In addition, the administration of antibiotics to wild type flies abrogated LCA-mediated effects on both lifespan and srl expression, suggesting a substantial contribution of the intestinal microbiota to the LCA-induced longevity.
In the present study, we show that the secondary bile acid LCA significantly induced the mean, the median and the maximum survival in Drosophila melanogaster. Our data suggest that besides an up-regulation of the PGC1a-homolog srl unidentified alterations in the structure or metabolism of gut microbiota contribute to the longevity effect of LCA.

overall_design: Flies were grown for 30 days with either control or  lithocholic acid (LCA) supplemented (50 µmol/l) diet and RNA  extracted from pools 10 flies per sample.

first: Anika

last: Wagner

first: Christian

last: Sina

first: Axel

last: Künstner


title: Neonatal lactocrine deficiency affects the adult porcine endometrial transcriptome at pregnancy day 13

status: Public on Aug 20 2018

city: Auburn

first: Frank

middle: F

last: Bartol

state: Alabama

address: 1130 Wire Road

department: College of Veterinary Medicine

institute: Auburn University

type: Non-coding RNA profiling by high throughput sequencing

summary: Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13. On the first day of postnatal life, gilts were assigned to high or low iCrit groups. Adult high (n = 8) and low (n = 7) iCrit gilts were bred (PxD 0), humanely slaughtered on PxD 13 when tissues and fluids were collected. The endometrial transcriptome was defined for each group using mRNAseq and microRNAseq. Reads were mapped to the Sus scrofa 11.1 genome build. Mature microRNAs were annotated using miRBase 21. Differential expression was defined based on fold change (≥ ± 1.5). Lactocrine deficiency did not affect corpora lutea number, uterine horn length, uterine wet weight, conceptus recovery, or uterine luminal fluid estrogen content on PxD 13. However, mRNAseq revealed 1157 differentially expressed endometrial mRNAs in high versus low iCrit gilts. Differentially expressed genes had functions related to solute transport, endometrial receptivity, and immune response. Six differentially expressed endometrial microRNAs included five predicted to target 62 differentially expressed mRNAs, affecting similar biological processes. Thus, lactocrine deficiency on the first day of postnatal life can alter uterine developmental trajectory with lasting effects on endometrial responses to pregnancy as reflected at the level of the transcriptome on PxD 13.

overall_design: On the first day of postnatal life, gilts were assigned to high (n = 8) or low (n = 7) iCrit groups. Adult high and low iCrit gilts were bred (PxD 0), humanely slaughtered on PxD 13 when reproductive tissues and fluids were collected.

first: Carol

last: Bagnell

first: Ashley

last: George


title: Lysogenization of Staphylococcus aureus RN450 by phages phi11 and phi80alpha leads to the activation of the SigB regulon

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

summary: Staphylococcus aureus is a major opportunistic pathogen and notable efforts are currently under way to develop new methods to combat staphylococcal infections. It is becoming increasingly clear that understanding the ecology of pathogenic bacteria is important to design improved disinfection and therapeutic strategies. Like many microbes, S. aureus commonly forms biofilms on various biotic and abiotic surfaces. Also, most isolates are known to carry prophages in their genomes. With this in mind, it seems that acquiring a better knowledge of the impact of prophages on the physiology of S. aureus biofilm cells would be useful for the development of strategies to eliminate this pathogen from industrial and hospital surfaces or human tissues. Here, we examined the impact of lysogeny on the transcriptome of S. aureus cells during biofilm development. The observed changes in gene expression indicated activation of the regulon controlled by the alternative sigma factor SigB. This response, typically triggered by stress conditions, leads to a greater production of the carotenoid pigment staphyloxanthin and a reduced production of extracellular proteins involved in biofilm dispersion. Overall, this study lays the foundations for characterizing the complex molecular interactions between temperate staphylophages and their host, and understanding their impact on microbial community dynamics.

overall_design: 6 samples were analyzed, correponding to 2 biological replicates of three different strains (prophage-free RN450 strain and its derived lysogens carrying phages phi11 and phi80alpha)

first: Silvia

last: Gonzalez

first: Nuria

last: Quiles-Puchalt

first: José

middle: R

last: Penadés

first: Ana

last: Rodriguez

first: Pilar

last: Garcia

first: Diana

last: Gutiérrez


title: A rationally designed JAZ subtype-selective agonist of jasmonate perception

status: Public on Aug 05 2018

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary:
Gene expression profiles of  WT, jaz9 and jaz10 mutant treated with mock or with 3, 6, or 8 was performed using the custom microarray Agilent-034592
The experiments were designed to explore the effect of antagonist of jasmonate perception in WT and two mutants

overall_design: Gene expression by the treatment of ligands (3, ent6 or 8, 1 µM) for 8 h in A. thaliana WT seedlings. Gene expression by the treatment of ligands (3 or 8, 1 µM) for 8 h in A. thaliana jaz9/10 mutant seedlings

first: Yousuke

last: Takaoka

first: Mana

last: Iwahashi

first: Andrea

last: Chini

first: Hiroaki

last: Saito

first: Yasuhiro

last: Ishimaru

first: Syusuke

last: Egoshi

first: Nobuki

last: Kato

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Roberto

last: Solano

first: Minoru

last: Ueda


title: Gene expression in Trp53 and Rb1 double knockout mouse prostate epithelial cancer cells expressing PIM1

city: Tucson

first: JIN

last: SONG

state: AZ

address: 1515 N Campbell Ave

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: To identify the downstream molecules that mediate PIM1 induced aggressive prostate cancer cells, p53 and Rb-deficient mouse prostate epithelial cells were transduced with PIM1 lentivirus and performed a gene expression profile microarray.

overall_design: Differential gene expression between PIM1 and Control (EV; empty vector) cells was performed with a gene expression profile microarray.

first: Jin

last: Song

first: Andrew

last: Kraft


title: Longitudinal expression analysis during acquisition of Mycobacterium tuberculosis infection in adolescents from South Africa

status: Public on Aug 18 2018

city: Cleveland

first: Rafick-Pierre

last: Sekaly

state: OH

address: 2103 Cornell Rd. 5129 WRB

institute: Case Western Reserve University

summary: Time-course expression analysis profiling whole blood samples collected from healthy South African adolescents while monitoring their potential acquisition of a Mycobacterium tuberculosis infection.

overall_design: Whole blood samples were collected in PAXgene tubes at multiple time points (6 months apart). Individuals were monitored for acquisition of Mycobacterium tuberculosis by QFT positivity.

first: Ali

last: Filali-Mouhim

first: Khader

last: Ghneim

first: Yueh-hsiu

last: Chien

first: Roshni

last: Chowdhury

first: Francesco

last: Vallania

first: Qiantian

last: Yang

first: Cesar

middle: J

last: Lopez Angel

first: Fatoumatta

last: Darboe

first: Adam

last: Penn-Nicholson

first: Virginie

last: Rozot

first: Elisa

last: Nemes

first: Stephanus

last: Malherbe

first: Katharina

last: Ronacher

first: Gerhard

last: Walzl

first: Willem

last: Hanekom

first: Mark

last: Davis

first: Jill

last: Winter

first: Xinchun

last: Chen

first: Thomas

last: Scriba


title: Hepatic Sel1L-Hrd1 ER-Associated Degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH

status: Public on Aug 17 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Fibroblast growth factor 21 (Fgf21) is a liver-derived, fasting-induced hormone with broad effects on growth, nutrient metabolism and insulin sensitivity. Here, we report the discovery of a novel mechanism regulating Fgf21 expression under growth and fasting-feeding. The Sel1LHrd1 complex is the most conserved branch of mammalian endoplasmic reticulum (ER)- associated degradation (ERAD) machinery. Mice with liver-specific deletion of Sel1L exhibit growth retardation with markedly elevated circulating Fgf21, reaching levels close to those in Fgf21 transgenic mice or pharmacological models. Mechanistically, we show that the Sel1LHrd1 ERAD complex controls Fgf21 transcription by regulating the ubiquitination and turnover (and thus nuclear abundance) of ER-resident transcription factor Crebh, while having no effect on the other well-known Fgf21 transcription factor Pparα. Our data reveal a physiologically regulated, inverse correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 levels under fasting-feeding and growth. This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic “ERADCrebh- Fgf21” axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation.

overall_design: Gene expression was profiled in livers of 3-week-old and 9-week-old WT and hepatocyte-specific Sel1L-deficient mice.

first: Asmita

last: Bhattacharya

first: Shengyi

last: Sun

first: Heting

last: Wang

first: Ling

last: Liu

first: Qiaoming

last: Long

first: Lei

last: Yin

first: Sander

last: Kersten

first: Kezhong

last: Zhang

last: Qi


title: Newly identified AP2-ERF transcription factors produce thickened primary cell wall in fiber cells of nst1 nst3 double mutant  in Arabidopsis

status: Public on Aug 13 2018

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Primary cell wall is an essential cell structure for plant playing major roles in plant growth, differentiation, and stress responses. Here we demonstrate that a group of AP2-ERF transcription factor regulates primary cell wall formation and can induce massive accumulation of it in empty fiber cell of the nst1-1 nst3-1 mutant lacking secondary cell wall in Arabidopsis. The transgenic plants expressing one of the AP2-ERF transcription factors fused with VP16 transcriptional activation domain under the control of NST3 promoter in the nst1-1 nst3-1 mutant showed similar level of cell wall contents with wild type by the massive accumulation of cell wall which lacks lignin and xylan. The transgenic plants showed 70% higher saccharification efficiency than wild type. Gene expression analysis using microarray revealed that genes related to primary cell wall were highly upregulated in the transgenic plant. Moreover, chimeric-activator of the AP2-ERF transcription factor accelerated cell wall regeneration of mesophyll protoplast of Arabidopsis while the chimeric-repressor retarded it. These data suggest that the group of AP2-ERF transcription factor is key regulator of the primary cell wall formation in plant and could be employed to produce massive cell wall with readily extractable feature.

overall_design: Transcriptomes of stem of NST3pro:ERF035-VP16 nst1-1 nst3-1 plant and that of nst1-1 nst3-1 plant were measured to see their difference.

first: Shingo

last: Sakamoto


title: Co-evolution of Met amplification and Hgf overexpression mediate resistance to BRAF inactivation in mouse anaplastic thyroid cancers.

status: Public on Aug 02 2018

city: New York

first: Jeffrey

last: Knauf

state: NY

address: 1275 York Ave

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary:
Affymetric arrays were performed on thyroid samples collected from GEMMs: normal thyroid, TPO-Cre/LSL-Braf (PTC), TPO-Cre/tetO-BRAF/LSL-rtTAiresGFP/p53-flox (ATC) and TPO-Cre/tetO-BRAF/LSL-rtTAiresGFP/p53-flox (recurrent tumors)
As above

overall_design: Thyroids and tumor-bearing thyroid glands were isolated from various mouse models at baseline

first: James

last: Fagin


title: Analysis of transcriptome changes in Neisseria gonorrhoeae exposed to sublethal levels of hydrogen-peroxide

city: Chicago

first: H

middle: Steven

last: Seifert

address: 303 East Chicago Ave.

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

summary: We report 293 Neisseria gonorrhoeae genes that show differential transcript abundance in response to 15 mM hydrogen peroxide treatment by RNA-Seq. We analyze the major physiological functional groups of genes affected by hydrogen peroxide exposure. In addition, we analyze which genes in our hydrogen peroxide-responsive set of genes belong to major known transcriptional regulatory circuits like iron homeostasis, anaerobiosis and others. We annotate which of the 293 hydrogen peroxide-responsive genes belong to operons. We annotate global transcriptional start sites and identify transcriptional start sites that are only present in hydrogen peroxide-treated bacteria. We validate the RNA-Seq data for a subset of representative genes by RT-qPCR and whether transcript abundance in this same subset of genes differs upon treatement with other reactive oxygen species encountered during infection, like organic peroxide, super oxide anion, and bleach.

overall_design:
Examination of transcriptional changes in sublethal 15 mM hydrogen peroxide-treated Neisseria gonorrhoeae in liquid culture compared to untreated controls

Please note that the +TEX data was only used for visualization of peaks to determine transcription start sites (see the .wig files) and was not used in any way to quantify overall transcript abundances. Thus, the differential expression component of our analysis relied only on noTex samples and these are the only samples that were quantified (TPM) for.

first: S

last: Quillin

first: AJ

last: Hockenberry

first: M

last: Jewett


title: Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to Day 14 in cattle?

status: Public on Aug 15 2018

city: Dublin 4

first: PATRICK

last: LONERGAN

address: Belfield

country: Ireland

institute: University College Dublin

summary: This study relates to embryo-maternal interaction. The aim was to compare the transcriptome and ability of the ipsilateral and contralateral uterine horns to support preimplantation conceptus survival and growth to Day 14. Although differences in gene expression exist between the endometrium of uterine horns ipsilateral and contralateral to the CL in cattle, they do not impact conceptus survival or length between Days 7 and 14.

overall_design: The endometrial samples from both uterine horns were collected from synchronized heifers slaughtered on Day 5, 7, 13 or 16 post-estrus (n = 5 per time) and subjected to RNA sequencing.

first: José

last: Sánchez

first: Claudia

last: Passaro

first: Niamh

last: Forde

first: John

last: Browne

first: Susanta

middle: K

last: Behura

first: Beatriz

last: Fernández-Fuertes

first: Daniel

last: Mathew

first: Alan

last: Kelly

first: Stephen

middle: T

last: Butler

first: Thomas

middle: E

last: Spencer

first: Patrick

last: Lonergan


title: Next Generation Sequencing Facilitates Quantitative Analysis of seed development of Tartary buckwheat  Transcriptomes

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiao Tong University

summary: We generated 76.61 Gb of high-quality sequencing data (~8.51 Gb per sample) and catalogued the expression profiles of 9,765 annotated Tartary buckwheat genes in each sample. The analysis showed differences of transcriptomes during the development of buckwheat seed. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in development of buckwheat seed. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to development.

overall_design: buckwheat seeds mRNA profiles of the development were generated by deep sequencing, in  triplicate, using Illumina HiSeq4000.


title: Expression data from HEK293T cells

city: Hangzhou

first: Hanchu

last: Xiong

address: Jiefang Road NO.88

institute: Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University

summary: cGAS-STING expression in HEK293T cells could up regulate a series of genes. Above them, Vpx significantly suppressed the NF-κB activated genes but had only a slight influence on the IRF3-activated genes. Diverse HIV-2 and SIV Vpx proteins showed an ability to inhibit DNA sensing-activated innate immune responses, suggesting an evolutionarily conserved function for Vpx.

overall_design: The cGAS, STING, and HIV-2/SIV Vpx or its control vector were transfected in HEK293T cells. Twenty hours later, mRNA samples were prepared and analyzed using Affymetrix microarrays. We sought to obtain up-regulated genes by cGAS-STING and to which of them were suppressed by Vpx specifically.

first: Yajuan

last: Rui


title: Expression profile of whole murine lung adenocarcinomas with or without knockdown of Snail

first: Nadine

last: Fournier

summary: We used microarrays to study the changes in the transcriptional profile upon Snail knockdown in murine lung adenocarcinomas

overall_design: Lung tumors were isolated from KPR mice infected with Pgk-Cre_U6-shSnail or Pgk-Cre_U6-shp53 (control) lentiviral constructs, RNA was extracted, amplified and hybridized with Affymetrix mouse gene 2.0ST arrays.

first: Svenja

last: Groeneveld

last: Zangger

first: Julien

last: Faget

first: Etienne

last: Meylan


title: RNA-seq profiling of patient-derived xenograft models in Urothelial Cancer

status: Public on Aug 01 2018

first: Li

last: Wang

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

summary: To probe the tissue source (cancer cell VS stromal cell) of gene expression in the mixed tumor samples, we took advantage of a set of Urothelial Cancer patient-derived xenograft (PDX) models given that the transcriptome in these models is a mixture of human RNA (derived from cancer cells) and mouse RNA (derived from stromal cells).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The cohort includes 5 different patient-derived PDX models, 3 replicates for each model, and thus a total of 15 samples

first: Josep

last: Domingo-Domenech


title: ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

status: Public on Aug 14 2018

city: Eugene

first: Vincent

last: Bicocca

state: OR

address: 1229 University of Oregon

institute: University of Oregon

summary: ASH-1 orthologs are H3K36-specific methyltransferases that are conserved from fungi to humans but are poorly understood, in part because they are typically essential for viability. Here we examine the H3K36 methylation pathway of Neurospora crassa, which we find has just two H3K36 methyltransferases, ASH-1 and RNA polymerase II-associated SET-2. Our investigation of the interplay between SET-2 and ASH-1 uncovered a regulatory mechanism connecting ASH-1-catalyzed H3K36 methylation to repression of poorly transcribed genes. Our findings provide new insight into ASH-1 function, H3K27me2/3 establishment, and repression at facultative heterochromatin.

overall_design:
RNA-seq: We analyzed gene expression changes in Neurospora crassa by poly-A+ mRNA-sequencing performed in duplicate. A wild type strain (N3752) serves as the reference strain (deposited in GSE82222).
ChIP-seq: We analyzed the distribution of histone H3 lysine 27 methylation (H3K27me2/3), H3K36me2/3, and H3K27ac in Neurospora crassa by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.

first: Tereza

last: Ormsby

first: Keyur

last: Adhvaryu

first: Shinji

last: Honda

first: Eric

last: Selker


title: RNA-sequencing of WT and ΔMSN1 strains of N. crassa over a circadian time course

city: Heidelberg

first: Michael

last: Brunner

state: Baden-Württemberg

address: Im Neuenheimer Feld 328

department: Biochemistry Center

institute: Heidelberg University

summary: We performed high throughput sequencing of the transcriptome of N. crassa to quantify ultradian (<24h period) rhythms in the wild-type (FGSC#2489) and  NCU02671 (msn-1) knockout (FGSC#11345) strains.

overall_design: Sampling of liquid culture grown N. crassa every 2h over 22h in the dark from light to dark transition

first: Bharath

last: Ananthasubramaniam


title: Ret and substrate-derived TGFb maverick regulate space-filling dendrite growth in Drosophila sensory neurons

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

institute: University of California, San Francisco

summary: Microarray profiling of amplified total RNA isolated from FACS-sorted class IV da neurons

overall_design: Independent replicates collected from each sample group, RNA isolated and amplified. Hybridized as a one color experiment.

first: Charles

middle: C

first: Jay

middle: Z

last: Parrish


title: Comparison of FTDP-17 IVS10+16 patient derived hiPSC and ZFN engineered hiPSC

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary:
The development of an effective therapy against tauopathies like Alzheimer’s disease (AD) and frontotemporal dementia (FTD) remains challenging, partly due to limited access to fresh brain tissue, the lack of translational in vitro disease models and the fact that underlying molecular pathways remain to be deciphered. Several genes play an important role in the pathogenesis of AD and FTD, one of them being the MAPT gene encoding the microtubule-associated protein tau. Over the past few years, it has been shown that induced pluripotent stem cells (iPSC) can be used to model various human disorders and can serve as translational in vitro tools. Therefore, we generated iPSC harboring the pathogenic FTDP-17 (frontotemporal dementia and parkinsonism linked to chromosome 17) associated mutations IVS10+16 with and without P301S in MAPT using Zinc Finger Nuclease technology. Whole transcriptome analysis of MAPT IVS10+16 neurons reveals neuronal subtype differences, reduced neural progenitor proliferation potential and aberrant WNT signaling. Notably, all phenotypes were recapitulated using patient-derived neurons. Finally, an additional P301S mutation causes an increased calcium bursting frequency, reduced lysosomal acidity and tau oligomerization.
Altogether, these tau mutant iPSC lines allow us to study IVS10+16 and P301S mutations in an isogenic background and to unravel a potential link between pathogenic 4R tau expression and FTDP-17.

overall_design:
This study includes 24 samples. There are 8 conditions considered, each with three biological replicates.
Patient V97 (patient 1) and TSM (patient 2) have been described in more detail in PMID:26136155 and Verheyen et al., submitted
Cells were lysed either at neural progenitor stage (NPC), which corresponds to DIV31 of hiPSC differentiation, or 5 weeks (W5) after plating of NPCs (DIV65 from hIPSC differentiation) and subjected to microarray
Sigma CTR  = control iPSC line provided by Sigma (iPSC0028)
Sigma IVS10 = gene edited Sigma line with a MAPT mutation (IVS10+16) using Zinc Finger Nucleases (ZFN)
Patient IVS10 V97 = patient 1 (PMID:26136155; Verheyen et al., submitted)
Patient IVS10 TSM = patient 2 (PMID:26136155; Verheyen et al., submitted)

last: Verheyen

first: Joke

last: Reumers

first: Kirsten

last: Van Hoorde

first: Annick

last: Diels

first: Ilse

last: Van Den Wyngaert

first: Ronald

last: De Hoogt

first: Jacobine

last: Kuijlaars

first: Louis

last: De Muynck

first: Alexis

last: Brettevill

first: Steffen

last: Jaensch

first: Alfredo

last: Cabrera-Socorro

first: Mark

last: Gerber

first: Jason

last: Gustin

first: Selena

last: Wray

first: Andreas

last: Ebneth

first: Peter

last: Roevens

first: Ines

last: Royaux

first: Pieter

last: Peeters


title: Metabolic pathway activation distinguish transcriptional signatures of CD8+ T cells from HIV-1 elite controllers

city: Cambridge

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

summary: Elite controllers (EC), defined as persons maintaining undetectable levels of HIV-1 replication in the absence of antiretroviral therapy, represent living evidence that sustained, natural control of HIV-1 is possible, at least in relatively rare instances. Understanding the complex immunologic and virologic characteristics of these specific patients holds promise for inducing drug-free control of HIV-1 in broader populations of HIV-1 infected patients.

overall_design: We used an unbiased transcriptional profiling approach to characterize CD8 T cells, the strongest correlate of HIV-1 immune control identified thus far, in a large cohort of EC (n = 51); HAART-treated patients (n = 32) and HIV-1 negative (n = 10) served as reference cohorts.

first: Fatema

last: Chowdhury

first: Zhengyu

last: Ouyang

first: Maria

last: Buzon

first: Bruce

middle: D

last: Walker

first: Mathias

last: Lichterfeld


title: Integrative analysis of differentially expressed genes and miRNAs predicts complex T3-mediated protective circuits in a rat model of cardiac ischemia reperfusion

status: Public on Jul 31 2018

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

summary: mRNA and miRNA expression profiling shows that the T3 supplementation reverted the expression of 87 genes and 11 miRNAs that were dysregulated in the untreated group

overall_design: A rat model of myocardial IR, with or without an early short-term T3-replacement, was used to predict putative T3-dependent miRNA-gene interactions targeted to mitochondria quality control and wound healing repair. One Sham, two IR, and two IRT3 rats were collected for mirna profiling.

first: Francesca

last: Forini

first: Giuseppina

last: Nicolini

first: Claudia

last: Kusmic

first: Milena

last: Rizzo

first: Mario

last: Baumgart

first: Marco

last: Groth

first: Stefano

last: Doccini

first: Giorgio

last: Iervasi

first: Letizia

last: Pitto


title: Real-time quantitative PCR analysis of human cardiovascular progenitor cells flown aboard the International Space Station

status: Public on Jul 26 2018

city: Loma Linda

first: Jonathan

last: Baio

address: 24941 Stewart St, Room 326

department: Pathology and Human Anatomy

institute: Loma Linda University School of Medicine

type:
Expression profiling by RT-PCR
Other

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of human cardiovascular progenitor cells flown aboard the International Space Station [Custom mRNA array]

summary: Adult and neonatal human cardiovacular progenitor cell clonal populations were flown aboard the ISS for 12 days prior to fixation in RNAprotect. Gene expression analysis was performed against clone-, patient-, and passage-matched ground control samples.

overall_design: qPCR gene expression profiling.  Human CPCs from three neonates and three adults were individually cultured on the ground or aboard the ISS.

first: Mary

last: Kearns-Jonker

first: Aida

last: Martinez

first: Ivan

middle: S

last: Silva

first: Carla

middle: V

last: Hoehn

first: Stephanie

last: Countryman

first: Leonard

last: Bailey

first: Nahidh

last: Hasaniya

first: Michael

last: Pecaut


title: CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer

status: Public on Jul 14 2018

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: The centrosomal protein, CEP55 is a key regulator of cytokinesis and its overexpression is linked to genomic instability, a hallmark of cancer. However, the mechanism by which it mediates genomic instability remains elusive. Here, we showed that CEP55 overexpression/knockdown impacts survival of aneuploid cells. Loss of CEP55 sensitizes breast cancer cells to anti-mitotic agents through premature CDK1/Cyclin B activation and CDK1-Caspase-dependent mitotic cell death. Further, we showed that CEP55 is a downstream effector of the MEK1/2-MYC axis. Blocking MEK1/2-PLK1 signaling therefore reduced outgrowth of basal-like syngeneic and human breast tumors in in-vivo models. In conclusion, high CEP55 levels dictate cell fate during perturbed mitosis. Forced mitotic cell death by blocking MEK1/2-PLK1 represents a potential therapeutic strategy for MYC-CEP55-dependent basal-like, triple-negative breast cancers.

overall_design: CEP55-overexpression and CEP55-knockdown cancer cell lines

first: Murugan

last: Kalimutho

first: Debottam

last: Sinha

first: Jessie

last: Jeffery

first: Sriganesh

last: Srihari

first: Winnie

last: Fernando

first: Pascal

middle: H

last: Duijf

first: Claire

last: Vennin

first: Prahlad

last: Raninga

first: Devathri

last: Nanayakkara

first: Deepak

last: Mittal

first: Jodi

last: Saunus

first: Sunil

last: Lakhani

first: J

middle: A

last: López

first: Kevin

last: Spring

first: Paul

last: Timpson

first: Brian

last: Gabrielli

first: Nicola

last: Waddell

first: Kum


title: Expression data from mid-third intsar Drosophila melanogaster larvae

status: Public on Jul 20 2018

city: Dallas

first: Rupali

last: Ugrankar

state: TX

address: 6000 Harry Hines Blvd

department: Cell Biology

institute: University of Texas Southwestern Medical Center

summary:
Loss of Ck1alpha produces 'flyabetic' larvae that are feeding defective. In addition we found other larvae with glucose elevations show feeding aversion.
We performed microarray to identify potential candidates that are involved in glucose-regulated feeding behaviors

overall_design: We extracted RNA from larvae with fat body-targeted Ck1alpha loss of function by RNAi (Dcg-Gal4 X UAS-Ck1alphaRNAi) and from controls (Dcg-Gal4 X w1118) for hybridization on Affymetrix microarrays. We used 20 larvae per sample.

first: Jonathan

middle: M

last: Graff


title: Real-time quantitative PCR analysis of human cardiovascular progenitor cells flown aboard the International Space Station [miRNA]

last: Baio

summary: Adult and neonatal human cardiovacular progenitor cell clonal populations were flown aboard the ISS for 12 days prior to fixation in RNAProtect, total RNA purification, and microRNA expression analysis against clone-, patient-, and passage-matched ground control samples.

overall_design: qPCR microRNA expression profiling.  Human CPCs from three neonates and three adults were individually cultured on the ground or aboard the ISS.

first: Mary

last: Kearns-Jonker

first: Aida

last: Martinez

first: Ivan

last: Silva

first: Carla

last: Hoehn

first: Stephanie

last: Countryman

first: Leonard

last: Bailey

first: Nahidh

last: Hasaniya

first: Michael

last: Pecaut


title: Plasma exosomal miRNAs microarray in polymicrobial sepsis

status: Public on Jul 10 2018

city: Baltimore

first: Lin

last: Zou

state: MD

address: 20 Penn Street, HSF II-GS003C

department: Anesthesiology

institute: University of Maryland School Of Medicine

summary: Exosomal RNA isolated from plasma was successfully profiled  with a total of 65 immunology-related miNRAs in 13 mouse samples

overall_design: In the study presented here, exosomal RNA isolated from 5 sham and 8 CLP mice at 24 hours after surgery was profiled

first: Wei

last: Chao

first: Jinjin

last: Xu


title: Inhibition of Neogenin Fosters Resolution of Inflammation and Tissue Regeneration

status: Public on Jul 18 2018

city: Tuebingen

first: Andreas

last: Körner

address: Hoppe-Seyler-Straße 3

department: Clinic of Anesthesiology and Intensive Care Medicine

institute: University of Tuebingen

summary: Protein and phosphorylation (TGF-β Phospho Antibody Array, FullMoonBioscience, #PTG176) profiling of peritoneal monocytes (pooled lavages from 4 mice / condition) was carried out according to the manufacturer’s instructions.

overall_design: Peritoneal monocytes/macrophages from WT and Neo-/- mice were used following 12 h of ZyA-induced peritonitis.

first: Valbona

last: Mirakaj


title: Copy number profiling of prostate cancers from 40 African American patients

status: Public on Jun 06 2018

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: African  American (AA) men have a significantly higher mortality rate from prostate cancer (PCa) compared to European American (EA) men. AA men are twice as likely to die from PCa compared to EA men and 8 times as likely as Asian American men to die from PCa. The biological basis for these differences in PCa mortality are unclear. We carried out Copy Number Alteration (CNA) studies on a new set of 40 highly tumor-enriched primary PCas and matched benign prostate tissues from AA men using high resolution Affymetrix 6.0 SNP arrays and expression array analysis using RNAs (GSE71016) from the same tissues using high purity tumors from AA men and matched benign tissue. We have confirmed the specific loss of 4p16.3 described previously and identified a novel tumor suppressor gene, RGS12 at this locus that shows significantly decreased expression in AA PCa but not EA EA PCa.

overall_design: Profiles were generated on Affymetrix SNP 6.0 chips. In all, 40 tumors and 40 paired normal samples were profiled, 40 profiles in all. Each tumor was centered on its corresponding normal pair to define copy number alterations (CNA) in that tumor.

last: Ittamann

first: Yiqun

last: Zhang


title: Real-time quantitative PCR analysis of human cardiovascular progenitor cells flown aboard the International Space Station [conventional RT-PCR]

last: Baio

summary: Adult and neonatal human cardiovacular progenitor cell clonal populations were flown aboard the ISS for 12 days prior to fixation in RNAprotect. Gene expression analysis was performed against clone- and passage-matched ground control samples.

overall_design: qPCR gene expression profiling.  Human CPCs from three neonates and three adults were individually cultured on the ground or aboard the ISS. Three measurements were taken per sample. All measurements are included in the supplementary files.


title: Medullary breast carcinoma, a triple-negative breast cancer subtype associated with BRCAness.

status: Public on Jun 20 2018

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Genome profiling was compared between medullary breast carcinoma (MBC) and non medullary basal-like breast carcinoma (non-MBC BLC).

overall_design: Copy number of 19 MBC and 35 non-MBC BLC were analyzed using Affymetrix SNP6.0 Arrays.

first: Pierre

last: Romero

first: Vanessa

last: Benhamo

first: Gabrielle

last: Deniziaut

first: Laetitia

last: Fuhrmann

first: Frédérique

last: Berger

first: Elodie

last: Manié

first: Jaydutt

last: Bhalshankar

first: Cécile

first: Sophie

last: Vacher

first: Elisabetta

last: Marangoni

first: Nadège

last: Gruel

first: Gaetan

last: MacGrogan

first: Fabien

last: Reyal

first: Roman

last: Rouzier

first: Olivier

last: Delattre

first: Tatiana

last: Popova

first: Marc-Henri

last: Stern

first: Dominique

last: Stoppa-Lyonnet

last: Bièche

first: Anne

last: Vincent-Salomon


title: Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model (MBD-seq)

status: Public on Jun 14 2018

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

type: Methylation profiling by high throughput sequencing

summary: We found that LP daughters have lower birthweight, alterations in mammary gland morphology and higher rates of mammary cancer. Further, we found that mammary glands and tumors of LP daughters are metabolic rewired, with alterations in the AMPK and amino-acid metabolism pathways. These changes were associated with differential expression of miRNAs 451a, miR-200c and miR-92a.  Importantly, some of the same miRNAs and target genes alterations were detected in breast tumors of women from populations with high rates of low birthweight.

overall_design: Male mice were fed AIN93G-based diets containing either 17.7% (control) or 8.9% (LP) energy from protein from 3 to 10 weeks of age.  Males on either group were mated to females raised on a control diet. Female offspring control and LP fathers were treated with 7,12-dimethylbenz[a]anthracene (DMBA) to initiate mammary carcinogenesis. Mature sperm from fathers and mammary tissue from female offspring were used for DNA methylation analyses.

first: Raquel

last: Santana

first: Elissa

last: Carney

first: Johan

last: Clarke

first: Hong

last: Cao

first: M

middle: I

last: Cruz

first: Carlos

last: Benitez

first: Yi

last: Fu

first: Zuolin

last: Cheng

first: Yue

last: Wang

first: Sonia

last: de Assis


title: Structural biochemistry of the 180 kDa Arp8-module of INO80 defines its function during chromatin remodelling

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180 kDa Arp8-module of S. cerevisiae INO80 and establish its role as an extranucleosomal DNA binding element. The actin-fold of Arp8 engages N-actin in a novel “side-to-front” interaction and specifies thereby recruitment of the Arp4-N-actin heterodimer to the segmented, “two plug” scaffold of the helical HSA domain of Ino80. The HSA domain spans a distance over 120 Å and provides a binding platform for extranucleosomal DNA, which is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryoEM structure of INO80Core-nucleosome complex, our results provide insights into the mechanism by which INO80 senses 40 bp extranucleosomal entry DNA to conduct highly processive chromatin remodelling.

overall_design: There are 10 samples analyzed in total. Within those 10 samples we used Drosophila histones. Samples consist of the INO80 WT protein and three mutants. Those 10 samples also contain replicates. The salt gradient dialysis samples are used as control samples.

first: Kilian

last: Knoll

first: Sebastian

last: Eustermann

first: Vanessa

last: Niebauer

first: Elisa

last: Oberbeckmann

first: Philipp

last: Korber


title: Genome-wide analysis of CD14+ monocytes from healthy and paired pre-therapy/post-cycle NHL21 patients

status: Public on Jun 30 2018

city: Woolloongabba

first: Gayathri

last: Thillaiyampalam

address: 37 Kent Street

department: UQDI

institute: University of Queensland

summary: Gene expression level analysis of healthy, pre-therapy and post-cycle 4 NHL21 patients treated with R-CHOP to show the distinct clustering of healthy/post-cycle 4 monocytes versus pre-therapy and to identify the differentially expressed genes under three different conditions.

overall_design: Total RNA obtained from FACS sorted CD14+ monocytes isolated from 6 healthy participants and paired pre-therapy/post-cycle 4 monocytes from 6 NHL21 patients and analysed using Illumina Human HT12v4 Bead Array for whole genome expression.

first: Clare

last: Gould

first: Colm

last: Keane

first: Maher

last: Gandhi

first: Alex

last: Cristino

first: Qingyan

last: Cui


title: Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

status: Public on Jun 21 2018

city: New York

first: Stephane

middle: Emile

last: Castel

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Edited mendelian disease SNP rs199643834 responsible for Birt-Hogg-Dubé Syndrome into 293T cells using CRISPR/Cas9

overall_design: Human 293T cells were edited using CRISPR/Cas9 and a homologus template containing the desired SNP. Monoclonal lines were generated and genotyped.

first: Tuuli

last: Lappalainen


title: Chromatin accessibility dynamics across C. elegans development and ageing [scap]

status: Public on Jun 01 2018

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,918 protein-coding promoters and 17,918 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

overall_design: Short capped chromatin associated RNA-seq was performed to monitor transcription initiation in wild-type C. elegans at six developmental stages

first: Jürgen

last: Jänes


title: Molecular classification of primary cultures of glioblastoma multiforme

city: Nantes

first: Raluca

last: TEUSAN

address: IRS-UN - 8 quai Moncousu - BP 70721

institute: Inserm

summary:
Primary cultures of glioblastoma multiforme (GBM) were isolated from samples provided as section of areas immediately adjacent to the region used for the histopathological diagnosis and cultured in defined media.
Transcriptomic analysis was performed with high-quality RNA extracted from cells after early passages in cultures (<2 passages).

overall_design: Molecular classification of 12 primary cultures of GBM using Agilent-028004 SurePrint G3 Human GE 8x60K Microarrays.

first: François

last: Vallette

first: Claire

last: Pecqueur


title: Genetic defects affecting the development of severe Buruli Ulcer

status: Public on Apr 23 2018

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

summary: Buruli ulcer (BU) is a tropical infectious disease caused by Mycobacterium ulcerans. BU causes profound skin ulcerations and eventually bone infections. Life-long functional sequelae are observed in more than 20% of patients, most of whom are children. Several observations, in particular the large variability in the clinical severity of the disease after infection, suggested the role of human genetic factors in the development of BU. Here, we report two children with severe BU, born of consanguineous parents. The deep genetic exploration of this family led to the identification of a small deletion on chromosome 8 in both patients. The corresponding article is in press in PloS Neglected Tropical Diseases

overall_design: DNA was extracted from whole blood according to the Nucleon BACC2 Genomic DNA extraction protocol (GE Healthcare), assayed with the QuantIt Picogreen dsDNA kit (Life Technologies) and processed for the genotyping of >900,000 single nucleotide polymorphisms (SNPs) used for both linkage and copy number variant (CNV) analysis and >900,000 monomorphic nucleotides used for CNV analysis by the Affymetrix Genome-Wide 6.0 array

first: Laurent

last: Abel

first: Alexandre

last: Alcais


title: Chromatin accessibility dynamics across C. elegans development and ageing [ATAC-seq]

overall_design: ATAC-seq was used to profile chromatin accessibility across development and aging


title: Gene expression in healthy and lesional psoriatic dermis from human skin biopsies (laser capture microdissection): set 1

status: Public on May 01 2018

city: Lille

first: Denis

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

institute: INSERM

summary: We performed microarray analysis on laser-microdissected dermis from healthy volunteers and psoriatic patients to identify genes dysregulated in lesional psoriatic dermis

overall_design: Epidermis and dermis were obtained from human skin biopsies by laser capture microdissection using Arcturus XT (MDS Analytical Technologies) system, followed by RNA isolation with Arcturus Picopure RNA isolation Kit. 10 ng RNA were amplified with ExpressArt Kit and labeled with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) and hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies). Two sets of samples (3 lesional psoriatic and 2 healthy epidermis samples in set 1 and 3 lesional psoriatic and 3 healthy epidermis samples in set 2, or 3 lesional psoriatic and 2 healthy dermis samples in set 1 and 3 lesional psoriatic and 2 healthy dermis samples in set 2) were processed and normalized separately.

first: David

last: Dombrowicz


title: Dysregulated genes in connexin 30 deficient mice microglia

status: Public on Apr 04 2018

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

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

department: Neurology

institute: Kyushu University

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

overall_design: Refer to individual Series


title: Gene epression in healthy and lesional psoriatic dermis from human skin biopsies (laser capture microdissection): set 2

summary: We performed microarray analysis on laser-microdissected dermis from healthy volunteers and psoriatic patients, and identified genes dysregulated in lesional psoriatic dermis


title: Chromatin accessibility dynamics across C. elegans development and ageing [lcap]

overall_design: Capped nuclear RNA-seq of wild-type and glp-1 was performed to monitor transcription elongation across C. elegans development and ageing. Two biological replicates were done for each time point (six developmental stages and five ageing timepoints).


title: Human OCI-AML3 cells: Control vs. Atg5-shRNA  or NPM1-shRNA inducibly expressed

status: Public on Mar 31 2018

city: Stanford

first: Min

last: Huang

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

summary:
Transcriptional profiling of human OCI-AML3 cells stably expressing inducibly Atg5 shRNA or NPM1-shRNA
Goal was to determine the effects of knockdown of Atg5 or NPM1 on global ES gene expression of human Leukemia OCI-AML3 cells.

overall_design: Control (Dox-) vs. inducible knock down of Atg5  (Dox+) or NPM1 (Dox+) by doxycycline. Biological replicates: 3 control replicates, Atg5-shRNA 2 replicates, NPM1-shRNA 3 replicates

first: Xuhuai

last: Ji

last: huang


title: Chromatin accessibility dynamics across C. elegans development and ageing [DNase, MNase]

city: Cambridge

overall_design: DNase, MNase-seq was used to profile chromatin accessibility across development


title: Expression data from murine sarcoma cells treated with either DMSO or a combination of SAHA and JQ1 for 48 hours

status: Public on Mar 01 2018

city: Philadelphia

first: T.S. Karin

last: Eisinger

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary:
SAHA/JQ1 reduces in vivo tumorigenesis and proliferation of KP sarcoma cells. This model recapitulates human undifferentiated pleomporphic sarcoma (UPS).
We used microarrays to investigate changes in global gene expression in response to these drugs.

overall_design: Cells were treated for 48 hours with control or drug in triplicate for  RNA extraction and hybridization on Affymetrix microarrays.

first: T

first: Adrian

last: Rivera-Reyes


title: Gene expression in Fuchs endothelial corneal dystrophy and healthy cultured cells

status: Public on Mar 20 2018

city: Québec

first: Stéphanie

last: Proulx

state: Qc

address: 1050 Chemin Ste-Foy

institute: Université Laval

summary: Fuchs endothelial corneal dystrophy (FECD) is a vision impairing pathology affecting the endothelial cells of the cornea. To better understand the disease, we developed a method to cultivate FECD cells isolated from surgical specimens. Using gene profiling, we compared the mRNA profiles of passage 2 FECD cells with passage 2 non-pathological corneal endothelial cells isolated from eye bank donor corneas.

overall_design: Six Fuchs endothelial corneal dystrophy and six healthy eye bank corneal endothelial cells at passage 2 are analyzed by gene profiling

first: Isabelle

last: Brunette

first: Patrick

last: Rochette

first: Mathieu

last: Thériault

first: Sébastien

middle: P

last: Gendron

first: Olivier

last: Roy


title: Spatiotemporal transcriptome of the mouse dentate gyrus

status: Public on Mar 22 2018

city: Kyoto

first: Tetsuya

last: Imura

address: kamigyo-ku, kajiicho 465

department: Pathology

institute: Kyoto Prefectural University of Medicine

summary: Analysis of LCM samples isolated from the inner (subgranular zone-side, neurogenic site) and outer (molecular zone-side) granule cell layer of either young adult or senile dentate gyrus. Results provide insight into the molecular signatures of young and old granule cells.

overall_design: Gene expression was analyzed in the laser captute miccrodissected (LCM) samples isolated from the inner (subgranular zone-side) and outer (molecular zone-side) granule cell layer of the dorsal dentate gyrus at the age of either 3-month-old (young adult) or 20-24-month-old (senile).  Each sample was pooled from 8 independent female mice .


title: Expression data from KP and KPY murine sarcoma tumors

summary:
YAP depletion in the KP tumor system results in smaller tumors and delayed tumor latency.
We used microarrays to investigate changes in global gene expression due to YAP1 loss in KP tumors

overall_design: Tumors were generated in KP and KPY animals by injection of Adeno virus expressing Cre recombinase into the leg muscle.

first: Shuai

last: Ye


title: Transcriptional responses of continuously cultured Nitrosomonas europae to chonic TiO2 nanoparticle stress

status: Public on Feb 27 2018

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

institute: Southeast University

summary: To further explore the biotoxicity mechanisms of TiO2 nanoparticles (NPs) and the recovery potentials of the impaired Nitrosomonas europaea (N. europaea, ATCC 19718) cells, a genome-sequenced model ammonia oxidizing bacterium (AOB) commonly detected in the activated sludge of biological wastewater treatment plants, the whole-genome microarray analysis was applied to retrieve the induced transcriptional responses during the long-term exposure, after the toxicity effects and the recovery potentials were assessed at both physiological and metabolic levels.

overall_design: The whole-genome expressions were measured after 12-d and 40-d exposure to 50 ppm TiO2 NPs in the chemostat bioreactor, respectively.Three independent experiments were performed for each experiment.

first: Ran

last: Yu


title: Molecular Profiling of Spitz Nevi (SN) in Relation to Nevocellular Nevi (NCN)

status: Public on Feb 15 2018

city: Maastricht

first: Lisa

middle: Maria

last: Hillen

state: Limburg

address: P. Debyelaan 25

department: Department of Pathology

institute: Maastricht University Medical Center

summary:
The molecular properties of benign melanocytic lesions are poorly understood. Only few studies have been performed on specific nevi subtypes, including common nevocellular nevi (NCN) or Spitz nevi (SN). Genomic alterations in melanoma-associated oncogenes are typically absent in SN. In the present study, mRNA expression of 25 SN and 15 NCN were analyzed. Molecular profiling was done using the RNA NanoString nCounter Gene Expression Platform (No. of genes = 770). Marker discovery was performed with a training set consisting of 7 SN and 7 NCN samples from the same patients, and validation was performed using a second set consisting of 18 SN and 8 NCN samples. Using the training set, 197 differentially expressed genes were identified in SN versus NCN. Of these, 74 genes validated in the validation set (FDR Q value ≤ 0.13). In addition, using Random Forest and LASSO feature selection a molecular signature of SN versus NCN was identified including 15 top-ranked genes. Gene set analysis showed upregulation of gene pathways with increased expression of transcripts related to immunomodulatory, inflammatory and extracellular matrix interactions as well as angiogenesis associated processes in SN.
Although the molecular characteristics of malignant melanoma have been studied in detail, the molecular properties of benign melanocytic lesions such as common nevocellular nevi (NCN) and Spitz nevi (SN) remain poorly understood. This limited knowledge hinders a better understanding of atypical and malignant transformation of melanocytes. The present study identified a distinct molecular expression profile in SN compared to NCN, even when lesions were obtained from the same patients. These findings strongly indicate that SN represent a distinct group of melanocytic neoplasms and evolve differentially and not sequentially from NCN.

overall_design: mRNA expression of 25 Spitz nevi (SN) and 15 Nevocellular nevi (NCN) were analyzed. Molecular profiling was done using the RNA NanoString nCounter Gene Expression Platform (No. of genes = 770). Marker discovery was performed with a training set consisting of 7 SN and 7 NCN samples from the same patients, and validation was performed using a second set consisting of 18 SN and 8 NCN samples. All analyses were performed with R-/Bioconductor.  Each assay included 6 positive and 8 negative controls. A positive control normalization factor was calculated (with the geometric mean method). The negative controls were used to estimate background (mean + 2 × standard deviation). Testing for differential expression of the nCounter data in SN versus NCN was done using the limma and voom method in R.

first: Milan

last: Geybels

first: Dorit

last: Rennspiess

first: Ivelina

last: Spassova

first: Catrhrin

last: Ritter

first: Jürgen

last: Becker

first: Marjan

last: Garmyn

first: Axel

last: zur Hausen

first: Joost

last: van den Oord

first: Véronique

last: Winnepenninckx


title: Molecular basis of flowering under natural long-day conditions in Arabidopsis

status: Public on Apr 01 2018

city: Seattle

first: Takato

last: Imaizumi

state: WA

address: 24 Kincaid Hall, Box 351800

department: Department of Biology

institute: University of Washington

summary:
Plants sense light and temperature changes to regulate flowering time. The expression of the florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the lab. Providing our lab growth conditions with a red/far-red light ratio similar to open field conditions and average natural temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Here, we use RNA-seq to identify and understand the molecular differences between natural growth conditions, conventional lab growth conditions, and supplemented lab growth conditions that mimic natural conditions.

Non-NIH grant(s):
Grant ID: NSF 1656076
Grant title: Exploring Seasonal Flowering Mechanisms
Affiliation: University of Washington
Name: Takato Imaizumi

overall_design: Examination of 3 different long-day growth conditions samples at two different times of day.

first: Michael

middle: F

last: Covington

first: Akane

last: Kubota


title: 3D interaction maps in wild-type and histone variant deletion mutants generated by chromosome conformation capture [Hi-C II]

status: Public on Aug 24 2018

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Interaction matrices were generated by applying in situ Hi-C to wild-type and deletion mutant trypanosomes.

overall_design: DNA-DNA interactions were captured in situ in Trypansoma brucei nuclei, digested with MboI and re-ligated to obtain chimeric DNA molecules of previously interacting chromatin. The ligation products were purified and prepared for paired-end Illumina sequencing. Experiments were performed in duplicates for both the wild-type and the deletion mutant.

first: Laura

last: Müller

first: T

middle: N

last: Siegel

first: Raúl

middle: O

last: Cosentino

middle: U


title: Whole blood gene expression from lung transplanted patients with chronic lung allograft dysfunction

status: Public on Feb 23 2018

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

institute: CHU Nantes - INSERM- Nantes Universite

summary: Chronic lung allograft dysfunction (CLAD) limits the long term survival after lung transplantation. CLAD is diagnosed late on the decline in lung function, when any immuno-intervention is ineffective. Identification of early forerunners of CLAD is therefore essential to prevent the progression of the disease before irreversible damages to the allograft. We used large-scale gene expression profiling of whole blood cells to identify early biomarkers of Bronchiolitis Obliterans Syndrome (BOS), the main form of CLAD. Microarray experiments performed from 80 patients (40 stable (STA) and 40 BOS) identify 47 genes differentially expressed between STA and BOS recipients. An independent set of patients (13 STA, 11 BOS) was then used for external validation by qPCR. POU Class 2 Associating Factor 1 (POU2AF1), T-cell leukemia/lymphoma protein 1A (TCL1A) and B-cell lymphocyte kinase (BLK) genes were identified and validated as predictive markers of BOS more than 6 months before diagnosis with AUCs of 0.83, 0.77 and 0.78 respectively. These genes allow stratifying upon CLAD risk (log-rank test p<0.01) and could provide clinicians with new tools to improve follow-up and adapt treatment of patients likely to develop BOS.

overall_design: This dataset represents gene expression profiling of periphal blood samples collected in PAXgene from 80 patients (40 stable (STA) and 40 BOS) using Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarrays.

first: Pierre-Joseph

last: Royer

first: Sophie

last: Brouard

first: Antoine

last: Magnan


city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Molecular Cytogenetics, Medical Research Institute

institute: Tokyo Medical and Dental University

summary:
To explore malignant phenotype related genes in Panc-1-CTC, we performed gene expression array analysis with Panc-1-CTC and Panc-1-Parent (Panc-1-P).  As a result, TGFBI upregulation emerged as highly malignant feature for pancreatic ductal adenocarcinoma.
Identification of malignant phenotype related genes in pancreatic ductal adenocarcinoma

overall_design: Extraction of difference of gene expression level between highly malignant subline (Panc-1-CTC) and low malignant subline (Panc-1-P)

first: Tomoki

last: Muramatsu

first: Minoru

last: Tanabe

first: Johji

last: Inazawa


title: Resident macrophage enhances an autoimmune lesion in Sjögren's syndrome

status: Public on Feb 21 2018

city: Tokushima

first: Aya

last: Ushio

state: Tokushima

address: Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University

summary: Macrophages are critical regulators of immune responses, and link innate immunity to acquired immunity. The precise mechanism of the pathogenesis of autoimmune diseases through tissue-resident macrophage is unclear. The role of the tissue-resident macrophages in the onset or development of autoimmunity was investigated using a murine model for Sjögren’s syndrome.

overall_design: We focused on chemokine gene expression of salivary glands macrophages (sMΦs) of SS model mice to define a key role of different two subsets, CD11bhigh and CD11blow F4/80+ sMΦs, in the formation of autoimmune lesions. Chemokine mRNA gene expression was comprehensively compared between CD11bhigh and CD11blow F4/80+ sMΦs in SS model mice by qPCR gene expression profiling.Data are representative of 4 mice in each group.

first: Rieko

last: Arakaki

first: Naozumi

last: Ishimaru


title: Affymetrix SNP array data for samples of 9 members of a FNMTC family

status: Public on Dec 31 2017

city: Tianjin

first: Liu

last: Chang

address: 94 Weijin Road

department: College of Life Science

institute: Nankai University

summary: Familial nonmedullary thyroid cancer (FNMTC) is a disease with the inheritance pattern is autosomal dominant with incomplete penetrance, but the causative gene is not clear. To identify the disease related locus in the FNMTC family, whole-genome SNPs of nine family members (five affected and four unaffected) were genotyped. We analyzed the SNP data with a novel method and mapped the disease-causing gene to several regions on the whole genome.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Yang

last: Yu

first: Chang

last: Liu


title: Long non-coding RNAs have age-dependent diurnal expression that correlates with age-related changes in genome-wide facultative heterochromatin

status: Public on Jan 30 2018

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey


title: Ivy Glioblastoma Atlas Project (SNP)

status: Public on Dec 01 2017

first: Ralph

middle: B.

last: Puchalski

address: 550 17th Ave., Suite 570

institute: Swedish Neuroscience Institute

summary: The Ivy Glioblastoma Atlas Project (Ivy GAP) is a detailed anatomically based transcriptomic atlas of human glioblastoma tumors.  As collaborators, the Ivy Foundation funded the Allen Institute and the Swedish Neuroscience Institute to design and create the atlas.  The Paul G. Allen Family Foundation also supported the project.  This resource consists of a viewer interface that resolves the manually- and machine-annotated histologic images (H&E and RNA in situ hybridization) at 0.5 µm/pixel, a transcriptome browser to view and mine the anatomically-based RNA-Seq samples, an application programming interface, help documentation that describes the methods and how to use the resource, as well as SNP array data and the supporting longitudinal clinical information and MRI time course data.  The resource is made available to the public without charge as part of the Ivy GAP (http://glioblastoma.alleninstitute.org/) via the Allen Institute data portal (http://www.brain-map.org), the Ivy GAP Clinical and Genomic Database (http://ivygap.org/) via the Swedish Neuroscience Institute (http://www.swedish.org/services/neuroscience-institute), and The Cancer Imaging Archive (https://wiki.cancerimagingarchive.net/display/Public/Ivy+GAP).  The Ivy GAP processed data at GEO includes normalized RNA-Seq FPKM files used for analysis in "An anatomic transcriptional atlas of glioblastoma,” which is under review.  Other processed data files as well as sample and donor meta-data and QC metrics are available at http://glioblastoma.alleninstitute.org/static/download.html. The raw RNA-Seq and SNP array data will be submitted to dbGaP.

overall_design:
Copy number analysis was performed using Affymetrix GenomeWideSNP_6 platform. A total of 35 samples were used from 34 GBM patients’ and 1 glioma patient’s surgical resections.
--------------------------------
Authors state "Raw files will be made available through dbGaP."

first: Nameeta

last: Shah

middle: B

first: Jeremy

last: Miller

first: Michael

middle: J

last: Hawrylycz


title: Affymetrix SNP-array data for splenic diffuse red pulp lymphoma samples

status: Public on Dec 23 2017

city: Barcelona

first: Alba

last: Navarro

address: Villaroel, 170

institute: IDIBAPS - Hospital Clínic

summary:
Deep characterization of a large series of splenic diffuse red pulp lymphomas
DNA from 5 tumor samples, corresponding to 4 cases, were analyzed with Affymetrix SNP 6.0 platform for copy number alteration study.

overall_design: Affymetrix SNP-arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood or splenic samples

first: Sílvia

last: Beà


title: Description of the microRNA repertoire of leucocytes of patients suffering from atypical myeloproliferative syndromes

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

institute: Bordeaux University

summary: Atypical Myeloproliferative Neoplasms (aMPN) share characteristics of MPN and Myelodysplastic Syndromes (MDS). Although anomalies of tyrosine-kinases or proteins involved in cytokine signaling are common in MPN, the pathophysiology of atypical MPN is still elusive. Since deregulation of microRNAs has been involved in the biology of various cancers, we screened the miRNome of aMPN compared to CML or reactive hyperleukocytosis (RHL) states. The study highligths the overexpression of miR-10a in the aMPN group

overall_design: We analysed the microRNA repertoire of blood leukocyte RNA from patients with aMPN (n=16), CML (n=10) or reactive hyperleukocytosis (n=4)

last: Cardinaud

first: Eric

last: Lippert


title: The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [human SNP array]

status: Public on Nov 30 2017

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

summary: T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. To address its incomplete molecular concept, we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identified novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor / cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM towards a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.

overall_design: Purified T-cells from 98 T-PLL patients (Supplementary Data1 for additional information) were analyzed using various high-throughput profiling platforms (overlap indicated): Affymetrix SNP 6.0 arrays (n=83 cases) for analysis of somatic copy-number alterations (sCNAs). For sCNA profiling patient-derived germline control DNA from 13 t/g pairs of the 83 cases) were used as a pooled reference alone or in combination with publically available HapMap data sets (http://hapmap.ncbi.nlm. nih.gov/).


title: In vitro transformation of human bronchial epithelial cells by diesel exhaust particles

city: OSLO

first: Steen

last: Mollerup

address: Gydas vei, 8

department: Department of Chemical and Biological Work Environment

country: Norway

institute: National Institute of Occupational Health

summary: The potential of diesel exhaust particles (DEP) to transform human bronchial epithelial cells (HBEC3) was investigated and a stably transformed cell line (T2-HBEC3) was established. Short-term DEP exposure experiments adds information of immunomodulatory effect markers and differences in susceptibility between normal and sensitized bronhial epithelial cells of the human lung.

overall_design: Total RNA obtained from HBEC3 and T2-HBEC3 exposed to DEP in dose-response  and time-course experiments.

first: Iselin

last: Rynning

first: Jiri

last: Neca

first: Kristyna

last: Vrbova

first: Helena

last: Libalova

first: Pavel

last: Rossner Jr

first: Jørn

last: Holme

first: Kristine

last: Gützkow

first: Anani

middle: K

last: Afanou

first: Yke

last: Arnoldussen

first: Eva

last: Hruba

first: Øivind

last: Skare

first: Aage

last: Haugen

first: Jan

last: Topinka

first: Miroslav

last: Machala


title: Long non-coding RNAs have age-dependent diurnal expression that correlates with age-related changes in genome-wide facultative heterochromatin (ChIP-Seq data set)

first: William

last: Belden

country: USA

summary: The circadian rhythm controls timed choreography of gene expression to maintain normal cell physiology and metabolism. The predominant regulatory mechanism of the circadian rhythm is a transcriptional negative feedback loop that facilitates, and is facilitated by, circadian-regulated facultative heterochromatin. The long-term consequence of disrupted diurnal rhythm, or mutations in core clock genes, cause accelerated aging and an increased incidence in age-related diseases. To understand chromatin dynamics underlying age-related changes to circadian transcription, we performed a combined RNA-seq and ChIP-seq at two diurnal time-points for three different age groups. Our analysis focused on uncovering relationships between long non-coding RNA (lncRNA) and age-related changes to heterochromatin. We determined that the core clock genes maintain rhythmic expression regardless of age, but circadian output, including numerous lncRNAs, changes dramatically with age. In addition, there is both diurnal and age-related changes in Histone H3 lysine 9 tri-methylation (H3K9me3) that correlate with the changes in gene expression. Collectively, the data suggest a model where age-related changes in diurnal gene expression occur, in part, due to age-related redistribution of rhythmic facultative heterochromatin. Alterations in heterochromatin appear to be mediated by changes in diurnal lncRNA expression creating an interlocked circadian-chromatin regulatory network that undergoes age-dependent metamorphosis.

overall_design: H3K9me3 ChIP-seq of brain tissues from three different ages (4M, 12M and 20M) at two time points (ZT4 and ZT16) in triplicates

first: Jinhee

last: Park


title: Application of the transcriptomic biomarker, TGx-DDI, in genotoxicity screening

status: Public on Nov 21 2017

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

summary: Cell-based application of a transcriptomic biomarker, TGx-DDI, in addressing potentially irrelevant positive findings in chromosome damage assays

overall_design: This experiment examined the whole genome transcriptional response of TK6 cells exposed to 45 compounds of the responsive concentration for 4 hours.

first: Heng-Hong

first: Renxiang

last: Chen

first: Albert

last: Fornace Jr


title: Genome wide transcriptional profiles of biopsies collected from non-IBD control subjects

status: Public on Nov 11 2017

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

overall_design: Transcriptional profiles of N=27 pinch biopsies from non-IBD control subjects, for comparison with transcriptional profiles of biopsies collected from IBD patients (GSE96665).

first: Mei

middle: S

first: Jacqueline

last: Leung

first: Uma

last: Gundra

first: P'ng

last: Loke


title: Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells

status: Public on Nov 12 2017

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

overall_design: Refer to individual Series


title: Genome-wide analysis of differential gene expression in MDA-MB-231 cells after GRMI silencing

status: Public on Oct 25 2017

city: Detroit

first: David

middle: H

last: Gorski

state: MI

address: 840.2 HWCRC

department: Surgery

institute: Wayne State University School of Medicine

summary: MDA-MB-231 cells were used to determine genes differentially regulated by metabotropic glutamate receptor-1 (GRM1)

overall_design: MDA-MB-231 cells were transduced with GIPZ Lentiviral vectors expressing either GRM1 shRNA or a control non-silencing vector and differientially expressed genes were determined by microarray analysis after stable transduction

first: Cecilia

middle: L

last: Speyer


title: Clinical and molecular characterization of splenic diffuse red pulp lymphomas

first: Alba

last: Navarro

type: Genome variation profiling by genome tiling array


title: Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

summary: The Affymetrix Genome-Wide Human SNP 6.0 and CytoScan HD arrays are high-resolution SNP platforms for studying copy number variations in the human genome.  It is widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed this platform to investigate the burden of clinically relevant rare (<0.1% in population controls) CNVs in individuals with schizophrenia, stratified by IQ group. We genotyped 540 unrelated probands with schizophrenia and applied rigorous methods to detect genome-wide CNVs. All rare CNV >500 kb and all rare exonic CNV >100 kb were adjudicated for clinical relevance following the American College of Medical Genetics guidelines for CNV interpretation. Our results revealed that burden of pathogenic CNVs is significantly greater for individuals with schizophrenia and low IQ compared to those with normal to superior IQ

overall_design: All samples met the Affymetrix quality control cut-offs. We only included CNVs that were >10 kb, identified by at least two CNV calling algorithms (two of ChAS, iPattern, or Genotyping Console for the CytoScan HD array and two of iPattern, Birdsuite or Genotyping Console for the Affymetrix 6.0 array), spanning 10 consecutive array probes, and overlapping <75% of segmental duplications. We defined the ancestry and relatedness of the samples using PLINK.

first: Anne

last: Bassett

first: Chelsea

last: Lowther


title: Specific normalization of urinary mRNAs reveals genome-wide patterns associated with renal allograft subclinical injury

status: Public on Sep 01 2017

city: Paris

first: Pierre

last: Galichon

address: 4 rue de la Chine

department: Hopital Tenon - Urgences Nephrologiques et Transplantation Renale

institute: Assistance Publique - Hopitaux de Paris

summary:
urinary mRNA quantification using an Agilent 60k microarray in 26 stable kidney transplant patients with or without renal partial Epithelial to Mesenchymal Transition
Subclinical pathological features on the 3-month biopsy of renal allografts predict a poor prognosis, but it is unclear whether surveillance biopsies are beneficial. Non-invasive biomarkers are wanted, and urinary pellet RNA quantification of selected candidate genes has been used with some success do detect overt rejection. We performed a mRNA microarray study using different normalization methods on the urinary cell pellet to evaluate the feasibility of using urine to detect renal partial epithelial mesenchymal transition of the renal allograft (renal pEMT) non-invasively in a group of 26 stable transplanted patients. We found that, when using a novel method of normalization by Upk1a mRNA, renal pEMT of the renal allograft was associated in urine with differential expression of genes belonging to predefined gene sets of kidney-expressed genes and epithelial mesenchymal transition genes. An unbiased pathway analysis revealed that the immune response was the main urinary biological process associated with pEMT in the kidney. In urine from patients with pristine biopsies, pEMT was not associated with inflammation, but with reduced metabolic functions. Thus, we show that pEMT translates into specific UPK1a-normalized mRNA patterns in urine and use genome-wide analyses to characterize underlying molecular patterns, i.e. increased inflammation and decreased metabolic functions.

overall_design: 12 pateins without renal partial Epithelial to Mesenchymal Transition and 14 patients with renal partial Epithelial to Mesenchymal Transition