title: Comparison of circRNA expression profile among the livers of C57BL/6J control mice, high fat diet (HFD) mice and metformin treated mice

status: Public on Jun 21 2018

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

country: China

institute: Peking University

summary: Nonalcoholic fatty liver disease (NAFLD) is a growing worldwide epidemic and an important risk factor for the development of insulin resistance, type 2 diabetes, nonalcoholic steatohepatitis (NASH), and hepatic cellular carcinoma (HCC). Despite the prevalence of NAFLD, lifestyle interventions involving exercise and weight loss are the only accepted treatments for this disease. Over the past years, metformin has been shown to improve NAFLD in preclinical animal models. Several coding and non-coding genes have been suggested to contribute to the metformin treatment mechanism of NAFLD. Circulating RNA (circRNA) is a novel group of non-coding RNAs which may have regulatory role in vivo. This study firstly probe the potential role of circRNA in the treatment of NAFLD by the microarray circRNA expression profiling.

overall_design: Three-week-old wild-type C57BL/6J mice were purchased from the Spfanimals Company (Beijing, China). These mice were divided into three groups: the control group (C), the high fat diet group (H) and the metformin treated (M) group. For the normal control (C) group, the mice were maintained with chow diet for 17 weeks. For the high fat diet (H) and metformin treated (M) group, C57BL/6J mice were fed a high fat diet (HFD, D12451, 45% kcal from fat, Research Diet, USA, http://www.researchdiets.com/opensource-diets/stock-diets) for 17 weeks. Starting at the 15 weeks old of age (i.e. after 12 weeks of high fat diet feeding), the high fat diet (H) and metformin treated (M) group were differentially treated: the mice from metformin treated (M) group were intragastrically treated with 3 mg/kg/day metformin for 5 weeks; while those from the high fat diet (H) group were treated with saline vehicle for 5 weeks. Finally, the liver tissue from different groups of mice were collected respectively at the 20 weeks old of age, and the liver circRNA expression profiles were measured by using CapitalBiotech mouse circRNA v1.0 microarray. Three biological replicates were prepared for each group. It is noteworthy that each biological replicate contains a mixed liver tissue samples collected from four mice of the same group.

first: Jun

last: Guo

first: Yafen

last: Cheng

first: Weiwei

last: Fang

first: Mingxiao

last: Sun

first: Qinghua

last: Cui

first: Jian

last: Li


title: Transcriptomic dynamics provides an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants

status: Public on Jun 27 2018

city: Yangling

first: Ruolin

last: Yang

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

type: Expression profiling by high throughput sequencing

summary: Salinity seriously reduces the yield and quality of crops. Silicon (Si) has been widely reported to have beneficial effects on plant growth and development under salt stress. However, the mechanism is still poorly understood. In an attempt to identify genes or gene networks that may be orchestrated to improve salt tolerance of cucumber plants, we profiled the RNA-seq transcriptomes of both control and salt-stressed cucumber leaves in the presence or absence of added Si. The comparative transcriptome analysis revealed that Si plays an important role in shaping the transcriptome of cucumber: the expression levels of >1,000 genes (differtially expressed genes, DEGs) were changed in response to Si treatment as compared with the control, and these genes were mainly involved in ion transport, hormone and signal transduction, biosynthesis and metabolic processes, stress and defense responses, and antioxidant activity. Under salt stress, many genes functionally associated with metabolic processes and responses to environmental stimuli were strongly up- or down-regulated in their expressions. Si treatment showed a tendency that induced the transcriptomic profile of salt-stressed cucumber back to that of the control with large majority of Na down-regulated DEGs and about half of Na up-regulated DEGs being adjusted back to CT levels. This study provides a novel insight into the mechanism for Si-mediated alleviation of salt stress in plants at the transcriptome level, and it suggests that Si may act as an elicitor to precondition cucumber plants and induce salt tolerance.

overall_design: Transcriptome profiles of both control and salt-stressed cucumber leaves in the presence or absence of added Si were generated by deep sequencing, in triplicates, using Illumina HiSeq 2500.

first: Haijun

last: Gong

first: Yongxing

last: Zhu


title: Small RNA sequencing of cow's peripheral plasma exosomes

city: WUHAN

first: Gan

last: Zhao

state: HUBEI

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
OBJECTIVE: To reveal the miRNA expression profile of placental exosomes by high-throughput sequencing and screen key biomarkers in different pregnancy period to provide new research ideas for the establishment and maintenance of pregnancy in cows and other ruminants.It can also  provide reference for other pregnancy diseases.
METHOD: Exosmal miRNAs were isolated from non-pregnant cows（n=3,Gestation Day(G.D.) 0）,early pregnant cows（n=3,G.D.60）,Middile pregnant cows（n=3,G.D.150）,Late pregnant cows（n=3,G.D.240）, small RNA profiles were generated by deep sequencing, in triplicate, using Illumina Hiseq SE50.
RESULTS: During pregnancy, there was a high quantity of placental exosomes in the peripheral blood of cows, which selectively loaded some miRNAs. The abundance and species of miRNAs various from different stages of pregnancy, suggesting that exosomal miRNAs is involved in the regulation mechanism of pregnancy.

overall_design: The experiment was divided into 4 groups with 3 replicates in each group.

first: Ganzhen

last: Deng


title: Comparison of lncRNA and mRNA expression profile among the livers of C57BL/6J control mice, high fat diet (HFD) mice and metformin treated mice

summary: Nonalcoholic fatty liver disease (NAFLD) is a growing worldwide epidemic and an important risk factor for the development of insulin resistance, type 2 diabetes, nonalcoholic steatohepatitis (NASH), and hepatic cellular carcinoma (HCC). Despite the prevalence of NAFLD, lifestyle interventions involving exercise and weight loss are the only accepted treatments for this disease. Over the past years, metformin has been shown to improve NAFLD in preclinical animal models. However, whether and how the long non-coding RNAs (lncRNAs) were involved in the progression of NAFLD and the mechanism of metformin treatment were not clearly understood. The aim of this study was to identify lncRNAs associated with the regulation of liver lipid metabolism after metformin treatment. We performed computational analysis of the function enrichment of the differentially expressed lncRNAs and mRNAs. Our analysis also suggested significant co-expression between hepatic lncRNAs and their predicted mRNA targets. Our analysis suggests a noticeable role in the etiology and treatment of NAFLD.

overall_design: Three-week-old wild-type C57BL/6J mice were purchased from the Spfanimals Company (Beijing, China). These mice were divided into three groups: the control group (C), the high fat diet group (H) and the metformin treated (M) group. For the normal control (C) group, the mice were maintained with chow diet for 17 weeks. For the high fat diet (H) and metformin treated (M) group, C57BL/6J mice were fed a high fat diet (HFD, D12451, 45% kcal from fat, Research Diet, USA, http://www.researchdiets.com/opensource-diets/stock-diets) for 17 weeks. Starting at the 15 weeks old of age (i.e. after 12 weeks of high fat diet feeding), the high fat diet (H) and metformin treated (M) group were differentially treated: the mice from metformin treated (M) group were intragastrically treated with 3 mg/kg/day metformin for 5 weeks; while those from the high fat diet (H) group were treated with saline vehicle for 5 weeks. Finally, the liver tissue from different groups of mice were collected respectively at the 20 weeks old of age, and the lncRNA and mRNA expression profiles were measured using the CapitalBiotech mouse lncRNA+mRNA v1.0 microarray. Three biological replicates were prepared for each group. It is noteworthy that each biological replicate contains a mixed liver tissue samples collected from four mice of the same group.


title: mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

summary: We performed comparative transcriptomic analysis of the outer membrane vesicles (OMVs) released from B. burgdorferi. We identified a total of ~1200 unique transcripts with at least one mapped read from the bacterial cell and its OMVs.

overall_design: Sequencing of ribosomal depleted Borrelia burgdorferi strain B31 and its OMVs isolated using two methods, ultracentrifugation and size-exclusion chromatography

first: Anjali

last: Malge

first: Vikas

last: Ghai


title: Mefloquine disrupts cancer stem cells by inhibiting lysosomal RAB5/7 mediated mitophagy

status: Public on Jun 20 2018

city: Suita

first: Mitsunbu

last: Takeda

state: Osaka

address: 2-2-E2 Yamadaoka

department: Gastroenterological Surgery

country: Japan

institute: Osaka University Graduate School of Medicine

summary:
BACKGROUND & AIMS
Cancer stem cells (CSCs) establish hierarchy in tumor tissue and a critical role for acquisition of resistance to therapy. Thus, the targeting of CSCs is important. We focused on lysosome which characteristically upregulated in colon CSCs for the aim of CSC targeting and search for new maintenance of CSCs by analyzing the function of CSC targeting drug.
METHODS
Correlation of lysosomal activity and CSC markers was assessed and single sphere formation and limiting dilution assay were performed, to evaluate CSCs property. Additionally, in vitro and vivo, we evaluated that anticancer drugs, antimalarial drugs, antitumor effect by combining them, and changes in cancer stem cell hierarchy. We performed microarray analyses to compare gene expression patterns from the tumors of treated patient derived xenograft mice.
RESULTS
LC3B+ or Lysotracker+ cells were characteristically existed in CD44V9+/ CD133+ CSC fraction as a small cell subpopulation. Single sphere formation assay and limiting dilution assay showed higher sphere formation activity and higher tumorigenic activity of LC3B+ or Lysotracker+ cells compared to LC3B－or Lysotracker－cells. Mefloquine treatment significantly decreased CD44v9+/ CD133+ cell number than representative antimalarial drugs, chloroquine and hydroxychloroquine. Mefloquine demonstrated the synergic effect on oxaliplatin and irinotecan. In Microarray analysis, we elucidated that mefloquine disrupted lysosome pathway by inhibiting Rab5 and Rab7. In patient-derived colon cancer tissue xenografted (PDX) mouse model, combined treatment of mefloquine with oxaliplatin or irinotecan drastically abrogated the tumorigenic activity of cancer cells.
CONCLUSIONS
Lysosomal activity in CSCs is a promising therapeutic target, and repositioning of mefloquine to colon cancer together with conventional chemotherapeutic agent will be a promising strategy for cure of colon cancer.

overall_design: We established xenograft mouse model in which two colon cancer patient-derived tissues were subcutaneously implanted. These models were treated with chloroquine(CQ), MQ (mefloquine) or MQ with L-OHP (trans-l-diaminocyclohexane oxalatoplatinum) .In the PDX models as preclinical model, surgically resected samples from patients were cut into pieces (3–4 mm) and transplanted subcutaneously into the back of 5-week old female NOD/SCID mice. When tumors grew 10 mm, each animal was treated vehicle (PBS with DMSO ,n=2), CQ (25mg/kg, n=2), MQ (25mg/kg, n=2), L-OHP (5mg/kg, n=2), or combination groups (MQ+L-OHP n=2), were injected intraperitoneally or orally administered until day 21. On day 21 from treatment,  we sacrified mice.

first: Takeda

last: Mitsunobu

first: Mori

last: Masaki


title: Zebrafish embryos microinjected with ptGFP1 (control group) or ptGFP1-NOD1 (NOD1 group)

status: Public on Jun 22 2018

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Transcriptional profiling of zebrafish embryos comparing control group microinjected with empty plasmid with NOD1 group microinjected with ptGFP1-NOD1 plasmid.

overall_design: Two-condition experiment:control vs NOD1.Biological replicates: 3 control,3 NOD1-microinjected group.

first: N

middle: N

last: Xue


title: Screening of the target genes of 3miRNAs: has-miR-296-5p, has-miR-324-3p and has-miR-3928-3p.

city: Chiba-shi, Chyuou-ku

first: Sotaro

last: Kanematsu

state: Chiba

address: Nitona-chyo 666-2

department: Division of Genetic Diagnostics

institute: Chiba Cancer Center

summary: To identified the target genes of 3 miRMAs, we performed a screening of differential expression genes analysis between miRNA mimic and mock transfection using expression array.

overall_design: MiRNA mimic mix surppressd the expression of the target genes

first: Endi

last: Xia

last: Kanmematsu

first: Yusuke

last: Suenaga

first: Asmaa

last: Elzawahry

first: Hitomi

last: Kondo

first: Noriko

last: Otsuka

first: Yasumitsu

last: Moriya

first: Toshihiko

last: Iizasa

first: Mamoru

last: Kato

first: Ichiro

last: Yoshino

first: Sana

last: Yokoi


title: Small Molecule PCSK9 Inhibitors: Hit to lead optimization

city: Berkeley

first: Jamie

last: Cate

state: CA

address: 748 Stanley Hall

institute: University of California

summary: Ribosome profiling is used to demonstrate improved selectivity of compounds that promote PCSK9 translational stalling

overall_design: IEC6 cells were treated with 4 µM PF-06446846 (7f), 4  µM PF-06649492 (7l) or vehicle for  60 minutes, and subjected to ribosome profiling.

first: Nathanael

middle: G

last: Lintner

first: Liuqing

last: Wei

first: Jun

last: Xiao

first: Donna

last: Petersen

first: Robert

last: Dullea

first: Kim

middle: F

last: McClure

first: Michael

middle: W

last: Bolt

first: Joseph

middle: S

last: Warmus

first: Steven

middle: B

last: Coffey

first: Chris

last: Limberakis

first: Julien

last: Genovino

first: Benjamin

middle: A

last: Thuma

first: Kevin

middle: D

last: Hesp

first: Gary

middle: E

last: Aspnes

last: Reidich

first: Christopher

middle: T

last: Salatto

first: Jeffrey

last: Chabot

middle: H

first: Spiro

last: Liras

first: David

last: Piotrowski


title: smallRNA NGS revealed the presence of CVA and LCHV1 on apricot in Hungary

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

summary: Fruit trees, as apricots, can be infected by and are constantly exposed to the attack of viruses. As they are propagated on a vegetative way, this risk is present not only at the field, where they exists for decades, but also during propagation. Metagenomic diagnostic methods, based on next generation sequencing, offer unique possibilities to reveal all the presenting pathogens in the investigated sample. Using small RNA NGS, a special fields of this technique, we tested leaf samples of different varieties of apricot in isolator house and at open air stock nursery. As a result, we identified Cherry Virus A (CVA) and Little Cherry Virus1 (LChV1) first time in Hungary. Gained results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral PCR products enabled us to investigate their phylogenetic relationships. Our results demonstrate, that small RNA NGS can offer a sensitive virus diagnostics method, moreover beside obligatory tested viruses we could detect CVA and LChV1. However as these pathogens haven’t been described in our country before, their role in symptom development and modification during coinfection with other viruses requires further investigations.

overall_design: Virus diagnostics of 3 apricot varieties in isolator house (2 libraries) and open air stock nurseries (2 libraries) by Illumina sequencing of the small RNAs

first: Dániel

last: Baráth

first: Nikoletta

last: Czotter

first: János

last: Molnár

first: Tünde

last: Varga

first: Júlia

last: Balássy

first: Luca

last: Szabó

first: Zoltán

last: Kirilla

first: Gábor

last: Tusnády

last: Preininger


title: RNA expression data of inner ear tissues in SOX10 p.R109W mutation pigs with inner ear malformation and wild-type pigs

city: beijing

first: hao

last: qingqing

address: Chinese PLA Medical School, Beijng

institute: Chinese PLA Medical School, China

summary: SOX10 (SRY-box 10) mutation may lead to inner ear deformities. However, its molecular mechanisms on inner ear development are not clear. In this work. The inner ear morphology was investigated at different embryonic stages of the SOX10 mutation miniature porcine model with sensorineural hearing loss, and high-throughput RNA-seq and bioinformatics analyses were applied. Our results indicated that the SOX10 mutation in the miniature pigs led to an incomplete partition of the cochlea, a cystic apex caused by fusion from middle and apical turns, cochlear modiolar defects and a shortened cochlear duct. The model demonstrated 173 DEGs and 185 lncRNAs. The down-regulated DEGs most significantly enriched the inflammatory mediator regulation of the TRP channels, arachidonic acid metabolism, and the salivary secretion pathways, while the up-regulated DEGs most significantly enriched the systemic lupus erythematosus and alcoholism pathways. Based on gene cluster analysis, we selected four gene groups: WNT1, KCNQ4, STRC and PAX6.

overall_design: Otic expression profiles of embryonic 28-day old wild type (WT) and SOX10 p.R109W mutation pigs were generated by high throughput sequencing.

first: Qingqing

last: Hao

first: Liang

last: Li

first: Wei

last: Chen

last: Jiang

first: Fei

last: Ji

last: Sun

first: Hong

last: Wei

first: Weiwei

last: Guo

first: Shiming

last: Yang


status: Public on Jun 19 2018

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Target identification of the cold stress induced sRNA CisR in Lactococcus lactis by CisR overexpression and MAPS technology

overall_design: Two strains, two conditions for CisR overexpression and MAPS

first: S

last: Van der Meulen

first: A

last: de Jong

first: J

last: Kok


title: Transcriptome analysis of females and males following knockdown serine/threonine protein phosphatase 1 catalytic subunit encoding genes(Sj-pp1c) in Schistosoma japonicum

status: Public on Jun 24 2018

first: Lu

last: Zhao

state: Hubei

address: No.1,Shizishan Street ,Hongshan District

department: College of Veterinary Medicine

summary:
Purpose: To obtain the differentially expressed genes based on post-RNAi transcriptional profiling analysis of females and males, which provide a more comprehensive overview about the effects of Sj-pp1c knockdown on schistosoma developmental and reproduction biology at the molecular level.
Methods: Schistosoma japonicum females and males were collected from 21 days post infection worm pairs that untreated (Blank,BLA_FE/M) or treated with combined Sj-pp1c dsRNAs (Sj-pp1c KD,PP1_FE/M) cultured for 7 d in vitro. Total mRNA profiles of females and males were generated by deep sequencing, in triplicate, using Illumina HiSeqTM2000.
Results: 41-51 million reads (average 44 million) were obtained for each sample after quality filtering, and 63-67% reads were mapped to S. japonicum reference genome(WormBase ParaSite, http://parasite.wormbase.org/ftp.html; version 7.0) and identified 15,314 transcripts by Tophat (version v2.0.12) and Cufflinks (Version 2.1.1.). 2291 and 229 transcripts showed differentially expressed in males and females, respectively,between the untreated and Sj-pp1c dsRNAs treated group, with adjust P value <0.05. GO analysis showed differentially expressed genes are mainly function in extracellular matrix structural constituent, proteolysis and collagen trimer.
Conclusions: We performed analysis on transcriptional profiling of females and males following Sj-pp1c-RNAi by RNA-seq, which provided molecular evidence for the pleiotropic roles that Sj-pp1c plays in schistosome biology.

overall_design: Total mRNA profiles of untreated and Sj-pp1c dsRNAs treated female and male Schistosoma japonicum were generated by deep sequencing, in triplicate, using Illumina HiSeqTM2000.

first: Min

last: Hu


title: Microarray profiling of non-coding RNAs and mRNA expression among the livers of C57BL/6J control mice, high fat diet (HFD) mice and metformin treated mice

first: Yuan

last: Zhou

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

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

overall_design: Refer to individual Series


title: Comparison of miRNA expression profile among the livers of C57BL/6J control mice, high fat diet (HFD) mice and metformin treated mice

summary: Nonalcoholic fatty liver disease (NAFLD) is a growing worldwide epidemic and an important risk factor for the development of insulin resistance, type 2 diabetes, nonalcoholic steatohepatitis (NASH), and hepatic cellular carcinoma (HCC). Despite the prevalence of NAFLD, lifestyle interventions involving exercise and weight loss are the only accepted treatments for this disease. Over the past years, metformin has been shown to improve NAFLD in preclinical animal models. Hepatic microRNAs (miRNAs) have been suggested as therapeutic targets because of their involvement in the progression of NAFLD. The aim of this study was to identify miRNAs associated with the regulation of liver lipid metabolism after metformin treatment. We performed computational analysis of the function enrichment and disease association of the differentially expressed miRNAs and their targets. Our analysis may shed light on the novel treatment method for NAFLD.

overall_design: Three-week-old wild-type C57BL/6J mice were purchased from the Spfanimals Company (Beijing, China). These mice were divided into three groups: the control group (C), the high fat diet group (H) and the metformin treated (M) group. For the normal control (C) group, the mice were maintained with chow diet for 17 weeks. For the high fat diet (H) and metformin treated (M) group, C57BL/6J mice were fed a high fat diet (HFD, D12451, 45% kcal from fat, Research Diet, USA, http://www.researchdiets.com/opensource-diets/stock-diets) for 17 weeks. Starting at the 15 weeks old of age (i.e. after 12 weeks of high fat diet feeding), the high fat diet (H) and metformin treated (M) group were differentially treated: the mice from metformin treated (M) group were intragastrically treated with 3 mg/kg/day metformin for 5 weeks; while those from the high fat diet (H) group were treated with saline vehicle for 5 weeks. Finally, the liver tissue from different groups of mice were collected respectively at the 20 weeks old of age, and the liver miRNA expression profiles were measured using the Agilent mouse miRNA 21.0 microarray. Three biological replicates were prepared for each group. It is noteworthy that each biological replicate contains a mixed liver tissue samples collected from four mice of the same group.

first: Jun

first: Yafen

last: Cheng

last: Fang

first: Mingxiao

first: Qinghua

last: Cui

first: Jian


title: Mycosis fungoides

city: Madrid

first: Rebeca

last: Manso

state: Madrid

address: Av. Reyes Católicos, 2

department: Pathology

country: Spain

institute: Fundación Jiménez Díaz

summary: Mycosis fungoides (MF) is the most common and best studied of cutaneous T-cell lymphoma (CTCL). Three clinical cutaneous stages have been described (patch, plaque and tumor) as the disease progress developing also the disease lymph node, peripheral blood or systemic involvement in late stages. Clinical and pathologic diagnosis of early MF stages (patch and plaque) is difficult as its morphologic similarity to inflammatory dermatoses and low proportion of tumoral cells.

overall_design: 14 MF and 15 reactive skin lesions were hybridized on a 8 x 15K human miRNA one-color platform (Agilent) containing probes for 723 human miRNAs.

first: Nerea

last: Martínez-Magunacelaya

first: Socorro

middle: M

last: Rodríguez-Pinilla


title: Gender and strain dependent differences in intestinal immunology correlate with differences in microbiota composition

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University


title: The Impact of Acute Exposure to Cigarette Smoke on Airway Gene Expression

status: Public on Jun 26 2018

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: BACKGROUND: We have previously reported gene expression changes in the bronchial airway epithelium of active chronic smokers. In this study, we investigate the effects of Acute Smoke Exposure (ASE) from cigarettes on airway epithelial gene expression. METHODS: Bronchial airway epithelial cell brushings were collected via fiberoptic bronchoscopy from 63 individuals without recent exposure to cigarette smoke (> 2 days), at baseline and at 24 hours after smoking three cigarettes. RNA from these samples was profiled on Affymetrix Human Gene 1.0 ST microarrays. Differential gene expression was assessed using linear modeling and compared to previous smoking-related gene-expression signatures using Gene Set Enrichment Analysis (GSEA). RESULTS: We identified 91 genes differentially expressed 24-hours after exposure to three cigarettes (FDR < 0.25). ASE induces genes involved in xenobiotic metabolism, oxidative stress, and inflammation; and represses genes involved in cilium morphogenesis, and cell cycle. Genes induced by in vivo ASE are concordantly altered by ASE in vitro. While many genes altered by ASE are altered similarly in the airway of chronic smokers, metallothionein genes were induced by ASE and suppressed among chronic smokers.  Metallothioneins were also suppressed in the bronchial airway of current and former chronic smokers with lung cancer relative to those with benign disease. CONCLUSIONS: Acute exposure to as little as three cigarettes alters gene-expression in bronchial airway epithelium in a manner that largely resembles the changes seen in chronic active smokers.  The difference in the short-term and long-term effects of smoking on metallothionein expression and its relationship to lung cancer requires further study given these enzymes’ role in responding to oxidative stress.

first: Ehab

last: Billatos

first: Yaron

last: Gesthalter

first: Ashley

last: LeClerc

first: Yuriy

middle: O

last: Alekseyev

first: Xiaohui

last: Xiao

first: Gang

last: Liu

first: Nick

last: ten Hacken

first: Dirkje

last: Postma

first: Irene

last: Heijink

first: Wim

last: Timens

first: Corry

last: Brandsma

first: Alen

last: Faiz

first: Maarten

last: van den Berge

first: Avrum

last: Spira

first: Marc

last: Lenburg


title: Gender and strain dependent differences in intestinal immunology correlate with differences in microbiota composition (colon)

first: Guido

last: Hooiveld

summary: A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a gender bias, suggesting gender differences in immune responses and in the intestinal microbiome. We hypothesized that gender differences in immune responses are associated with gender differences in microbiota. We demonstrated mouse strain dependent gender differences in the intestinal microbiome. Interestingly, a cluster of colonic genes (related to humoral and cell-mediated immune responses) correlated oppositely with microbiota species abundant in B6 females and in BALB/c males. This suggests that with different genetic backgrounds, gender associated immune responses are differentially regulated by microbiota. The net result was the same, since both mouse strains showed similar gender induced differences in immune cell populations in the mesenteric lymph nodes. Therefore, host-microbe interactions might be more complicated than assumed, as bacterial-species adaptations might be highly dependent on the genetic make-up of the individual.

overall_design: Male and female wild-type B6 and BALB/c mice were sacrificed by cervical dislocation between an age of 3 and 5 months. Approximately 1 cm of proximal colon was removed for microarray analysis.

first: Marlies

last: Elderman

first: Floor

last: Hugenholtz

first: Clara

last: Belzer

first: Mark

last: Boekschoten

first: Adriaan

last: van Beek

first: Bart

last: de Haan

first: Huub

last: Savelkoul

first: Paul

last: de Vos

first: Marijke

last: Faas


title: Gender and strain dependent differences in intestinal immunology correlate with differences in microbiota composition  (ileum)

overall_design: Male  and female wild-type B6 and BALB/c mice were sacrificed by cervical dislocation between an age of 3 and 5 months. Approximately 1 cm of distal ileum was removed for microarray analysis


title: E. coli transcriptome-level alterations upon antimicrobial peptide exposure

city: Bangalore

first: Deepesh

last: Nagarajan

state: Karnataka

address: FB-04, B-wing, Department of Biochemistry, New Biology Building, IISc

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

summary: E. coli (P1645ec: a clinical isolate) was incubated with differing concentrations of antimicrobial peptides (all at 0.5X MBC)

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

overall_design: E. coli (P1645ec: a clinical isolate) was incubated with differing concentrations of antimicrobial peptides omega76, omega17, and NN2_0018 (all at 0.5X MBC). 3 treated samples (2 biological replicates each) and 1 untreated samples (2 biological replicates) were used in this study. All cultures were grown in 10 ml LB broth at 37C/180rpm for 24 hours before flash-freezing & RNA extraction

first: Sathyabaarathi

last: Ravichandran

first: Nagasuma

last: Chandra


title: Expression data from rice inflorescences of osmads32 mutant and wild type

status: Public on Jun 28 2018

city: Shanghai

first: yun

last: hu

state: Shanghai

address: 800 Dongchuan Road

department: Plant Biology

institute: SJTU

summary:
MADS family genes in rice control flowering and inflorescence development.  In the early flower stages of plant, MADS-box transcripion factors could  form protein-protein interaction complexes with other floral homeotic genes and regulate the expression of downstram genes. OsMADS32 in rice is an important transcription factor in controlling flower development
We used microarrays to detail the expression of downstream genes under the control of OsMADS32 during the early inflorescence stages in rice

overall_design: Rice inflorescence in length of 2 mm is the stage for the initiation of inner floral organ development. 2mm inflorescences in length of rice osmads32 mutant were collected in the paddy field with the control of zhonghua 11 wild type at the same development stage in triple repetition, and total RNA were extracted using Trizol method and hybridized on Affymetrix microarrays. Detailed genes with significant expression change between osmads32 and wild type were analysed to obtain downsteam genes of OsMADS32.

first: Yun

last: Hu


title: Nucleotide resolution genome-wide mapping of 8-oxoG damage

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Single nucleotide resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adduct and mutation patterns in the genome. We coupled the specificity of the repair enzyme with the efficiency of a one-pot click-DNA ligation reaction to insert a readable oligonucleotide code sequence. The biocompatible code enabled high-throughput, base resolution sequencing of the 8-oxoguanine site and thus have named the method click-code-seq. By applying click-code-seq to a eukaryotic (yeast) genome, we uncovered thousands of 8-oxoguanine sites with features and patterns suggesting a potential relationship to chromatin formation and transcription.

overall_design: We sequenced the yeast (BY4741) genome during exponential growth in rich media to generate a nucleotide-resolution background map of 8-oxoG damage.

first: Junzhou

last: Wu

middle: J


title: Expression data from Burkholderia multivorans mucoid and nonmucoid isolates

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: Burkholderia multivorans comprises opportunistic bacteria infecting hosts such as cystic fibrosis (CF) patients. Bcc long-term infection of CF patient airways has been associated with emergence of phenotypic variation including the mucoid-to-nonmucoid colony morphotype. Here we studied three Burkholderia multivorans clonal isolates (mucoid D2095 (BM11L), and nonmucoid D2214G and D2214P) and a laboratory nonmucoid variant (BM11L-nmv1) obtained under prolonged stationary phase. The aim is to identify possible traits associated to the different morphotypes and find possible mechanisms for this morphotypic variation.

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

overall_design: For expression profiling, overnight cultures of the mucoid D2095 and the nonmucoid D2214G, D2214P and D2095R isolates grown in SM medium were diluted to an initial OD640 nm of 0.1 into the same medium. Triplicate samples were cultured at 37ºC with 250 r.p.m. agitation for 17 h and RNA extracted from the two bacterial isolates.

first: Inês

middle: N

last: Silva

first: Jorg

last: Becker


title: RT quantitative PCR analysis of p53 Signaling Pathway related genes in mice choclea after noise exposure.

status: Public on Jun 30 2018

first: Sara

last: Pulido

address: Arturo Duperier, 4.

department: Department of Endocrine and Nervous Systems Pathophysiology

institute: Alberto Sols Biomedical Research Institute (Spanish National Research Council - Autonomous University of Madrid)

summary: Six month-old wild type and Igf1 heterozygous mice were exposed to a violet swept sine noise (frequency range 2–20 kHz) at 110 dB SPL for 30 minutes. Cochlear samples were taken at 2 and 24 hours post-noise exposure to study the evolution of the expression of  inflammation genes by using PCR arrays and RT-qPCR. Six month-old wild type and Igf1 heterozygous mice not exposed to noise were used as control.

overall_design: qPCR gene expression profiling. Cochlea samples from 3 animals per group were analised.  The expression of genes related to inflammation was studied at 2 and 24 hours post-noise exposure.

first: Marta

last: Milo


title: Hierarchal gene master regulators of adenocarcinomic human alveolar basal epithelial cells A549.

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: In previous papers we proved that cancer nodules and surrounding normal tissue are governed by different gene master regulators (GMRs) and that expression manipulation of a cancer GMR can selectively destroy cancer cells with minimal effects on the normal ones. GMR is defined as a coding or non-coding transcript whose strictly controled abundance by the cell homeostatic mechanisms regulates most major cell functional pathways. Here, we determined the gene hierarchy in the standard adenocarcinomic human alveolar basal epithelial cell line A549.

overall_design: One condition, 4 replicas

first: Sanda

first: Katrien

last: Van Roosbroeck

first: George

last: Calin


title: Serum microRNA profile of ADPKD patients

city: Lodz

first: Wojciech

last: Fendler

state: Lodzkie

address: 15 Mazowiecka Str.

department: Department of Biostatistics and Tranalational Medicine

country: Poland

institute: Medical University of Lodz

summary:
From serum samples of non-dialyzed and dialyzed patients with ADPKD and healthy control total RNA was isolated and miRNA expression was evaluated.
Circulating microRNAs (miRNA) are important intercellular communication compounds. We investigated the influence of ADPKD (autosomal dominant polycystic kidney disease) and hemodialysis on the profile of serum miRNAs. We found 37 significant circulating miRNA that differ between ADPKD patients (dialyzed and non-dialyzed) and healthy controls. Bioinformatic analysis revealed strongest connections between those miRNAs and KEGG pathway: MicroRNAs in cancer. We selected 3 miRNAs with highest and 3 with lowest fold change in comparison of dialyzed and non-dialyzed patients and compared their expression in paired pre-/post-dialysis samples. All up-regulated miRNAs (miR-532-3p, miR-320b, miR-144-5p) were not significantly altered by hemodialysis. From down-regulated miRNAs miR-27a-3p was shown to be significantly lower after dialysis in both total and exosomal fraction. MiR-20a-5p was down-regulated after dialysis only in the exosomal fraction whereas miR-16-5p was unaltered by hemodialysis. MiR-16-5p was selected as the best circulating biomarker of ADPKD with miR-22-3p, let-7i-5p and miR-24-3p as following best ones. Circulating representatives of miR-17 family (new drug target of ADPKD (Hajarnis et al. 2017)) sharing the same seed region (miR-20a-5p, miR-93-5p and miR-106a-5p) showed significantly lowered expressed in sera of dialyzed patients vs non-dialyzed ones and their exosomal fraction dropped after hemodialysis. We concluded that serum miRNA among ADPKD patients differ substantially depending on the stage of CKD. These alterations show possible links with cancer. The exosomal fraction of miRNA was more affected by dialysis than total fraction of miRNAs suggesting their dynamically changing functional role.

overall_design: RT-PCR microRNA expression profiling in serum (Exiqon real-time PCR human miRNA arrays I and II (miRCURY LNA)) in 10 patients with ADPKD on hemodialysis treatment, 10 patients with ADPKD without hemodialysis treatment and 10 healthy controls.

first: Beata

last: Malachowska


title: RNAseq of Maize stem at big flare period

city: Hefei

first: Hengsheng

last: Wang

address: Changjiang Rode 130

institute: Anhui Agriculture University

summary: Four samples from the low and high hybrid at big flare period were used for RNA sequencing.

first: Beijiu

last: Cheng


title: Increased AIF-1-mediated TNF-α expression during the implantation phase in IVF cycles with GnRH antagonist protocol

city: shanghai

first: Mingjie

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

summary: Administration of GnRH antagonist in IVF has several advantages. However, studies have shown that GnRH antagonist protocol cycles have lower implantation and clinical pregnancy rates than GnRH agonist long protocol cycles. Endometrial receptivity rather than embryo quality is thought to account for this phenomenon, however the mechanism is still largely unknown. This microarray analysed human endometrium during ‘implantation window phase’ between three groups: 1) untreated control, 2) GnRH agonist long protocol, and 3) GnRH antagonist protocol. The differential gene between groups uncovered the molecular mechanism occurred in endometrium affected by the intake of GnRH agonist or GnRH antagonist. Further study of these differential gene promises to find the reasons for lower endometrial receptivity in patients treated with GnRH antagonist and to improve the implantation rate in GnRH antagonist protocols in IVF.

overall_design: Analysis of 9 human mid-secretory endomtrium samples collected from patients with IVF/ICSI cycles between 2012 and 2014. The recruited patients were divided into three groups (n=3 per group): 1) untreated control, 2) GnRH agonist long protocol, and 3) GnRH antagonist protocol. studies have shown that GnRH antagonist protocol cycles have lower implantation and clinical pregnancy rates than GnRH agonist long protocol cycles. Results provide insight into the effect of  GnRH agonist/ GnRH antagonist on endometrium gene expression changes.

first: Bufang

last: Xu

first: Aijun

last: Zhang


title: Whole fly expression data following DmSTING knockdown and listeria infection

city: Pullman

first: Alan

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

summary:
Parental flies (y1v1;P{TRiP.JF01138}attP2 and y1w*;P{Act5C-GAL4}25FO1/CyO,y+) were mated to obtain progeny with genotypes for ubiquitous DmSTING RNAi and sibling controls. 2-7 day old flies were used for all infections.
23 nl of listeria monocytogenes (strain 10403S) at 1e7 CFU/ml was injected intrathoracically. Mock inoculation was performed with PBS. Whole flies were homogenized 24 h post-infection.

overall_design: We aimed to determine the effect of DmSTING on listeria infection in whole flies.

first: A

middle: G


title: S2 cell expression data following DmSTING knockdown and cyclic ci-GMP transfection

summary:
S2 cells were knocked down for DmSTING by RNAi or using scrambled RNAi. Cyclic di-GMP (Biolog C057) was transfected 72h later. Mock transfection was performed using lipofectamine alone.
Drosophila genome 2.0 Affymetrix arrays were used to perform gene expression analysis.

overall_design: We aimed to determine the effect of DmSTING on c-di-GMP stimulation in S2 cells.

first: Goodman

last: Alan G.


title: The probiotic Escherichia coli strain Nissle 1917 combats the lambdoid bacteriophages stx and λ

status: Public on Jun 14 2018

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

summary: The Escherichia coli strain Nissle 1917 (EcN) is used as a probiotic for the treatment of certain gastrointestinal diseases in several European and non-European countries. In vitro studies showed EcN to efficiently inhibit the production of Shiga toxin (Stx) by Stx producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC). The occurrence of the latest EHEC serotype (O104:H4) responsible for the great outbreak in 2011 in Germany was due to the infection of an enteroaggregative E. coli by a Stx 2-encoding lambdoid phage turning this E. coli into a lysogenic and subsequently into a Stx producing strain. Since EHEC infected persons are not recommended to be treated with antibiotics, EcN might be an alternative medication. However, because a harmless E. coli strain might be converted into a Stx-producer after becoming host to a stx encoding prophage, we tested EcN for stx-phage genome integration. Our experiments revealed the resistance of EcN towards not only stx-phages but also against the lambda phage. This resistance was not based on the lack of or by mutated phage receptors. Rather the expression of certain genes (superinfection exclusion B (sieB) and a phage repressor (pr) gene) of a defective prophage of EcN was involved in the complete resistance of EcN to infection by the stx- and lambda phage. Obviously, EcN cannot be turned into a Stx producer. Furthermore, we observed EcN to inactivate phages and thereby to protect E. coli K-12 strains against infection by stx- as well as lambda-phages. Inactivation of lambda-phages was due to binding of lambda-phages to LamB of EcN whereas inactivation of stx-phages was caused by a thermostable protein of EcN. These properties together with its ability to inhibit Stx production make EcN a good candidate for the prevention of illness caused by EHEC and probably for the treatment of already infected people.

overall_design: Total EcN bacterial RNA was isolated from 3 ml cultures after 16 h of a static incubation period with or without stx phages.

first: Manonmani

last: Soundararajan

first: Susanne

last: Bury

first: Tobias

last: Oelschlaeger


title: The Stat3 target Mettl8 regulates mouse ESCs differentiation via inhibiting JNK pathway

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

summary: The capacity of embryonic stem cells to differentiate into all lineages of mature organism is precisely regulated by cellular signaling factors. STAT3 is a crucial transcription factor that plays a central role in maintaining embryonic stem cells identity. However the underlying mechanism how Stat3 directs differentiation is still not completely understood. Here we show that Stat3 positively regulates gene expression of methyltransferase like protein 8 (Mettl8) in mouse ES cells. We found that Mettl8 is dispensable for pluripotency but affects ESCs differentiation. Subsequently we discovered that Mettl8 interacts with Mapkbp1’s mRNA, which is an intermediate factor in JNK signaling, and inhibits the translation of the mRNA. Thereby, Mettl8 prohibits the activation of JNK signaling and enhances the differentiation of mouse ESCs. Collectively, our study uncovers a Stat3 target Mettl8 which regulates mouse ESCs differentiation via JNK signaling.

overall_design: mRNA profiles of E14 cells transfected with scramble siRNA or Mettl8 siRNA  were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Hao

last: Gu

first: Dang

middle: V

last: Do

first: Xinyu

last: Liu

first: Luang

first: Yixun

last: Su

first: Jie

last: Nah

first: Yuqian

last: Wong

last: Sheng

first: Gebreselassie

last: Addisu Tilaye

first: Henry

last: Yang

first: Huili

last: Guo

first: Xin-Yuan

last: Fu


title: A novel systems immunology approach identifies the collective impact of five miRNAs in Th2 inflammation (microRNA)

status: Public on Jun 18 2018

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signature. The immune response amplifies in self-enforcing loops, promoting Th2-driven cellular immunity and leaving the host unable to terminate inflammation. Posttranscriptional mechanisms, including miRNAs, are pivotal in maintaining immune-homeostasis. Since an altered expression of various miRNAs has been associated with T cell-driven diseases, including asthma, we hypothesized that miRNAs control mechanisms ensuring Th2 stability and maintenance in the lung. We isolated murine CD4+ Th2 cells from allergic inflamed lungs and profiled gene and microRNA expression.

overall_design: Tissue resident Th2 cells were isolated  at two stages of Ovalbumin-induced allergic airway inflammation from lung tissue for RNA extraction and hybridization on Affymetrix microarrays. We obtained live cells by fluorescent-activated cells sorting based on surface marker expression at different stages:  antigen-naive CD4+ T cells from spleens of sham-treated mice, Th2 cells after polarization and recruitment to the inflamed tissue (early Th2), and cells from chronic inflamed tissue (stable Th2). We sought to decipher mechanisms regulating the persistence of chronic allergic inflammation.

first: S

first: A

last: Kılıç


title: Effect of GAGE12I and SPIN4 on the gene expression profile of BGC823 gastric cancer cells

status: Public on Jun 15 2018

city: Jinan

first: Bo

middle: duan

last: Shi

address: Jinan wenhua xi road 44#

institute: Shandong university

summary: To investigate the effect of GAGE12I and SPIN4 on the gene expression profile in gastric cancer cells, genome-wide mRNA changes were analyzed by mRNA microarray upon overexpressing GAGE12I and SPIN4 in BGC823 gastric cancer cells.

overall_design: The BGC823 gastric cancer cells were transfected with PcDNA3.1-GAGE12I, PcDNA3.1-SPIN4 or PcDNA3.1-empty plasmids. Total RNA was extracted 48h after the transfection and the differentially expressed genes were analyzed by mRMA microarray.

first: Gao

last: Peng

first: Shi

last: Duan-bo


title: LncRNA MT1JP Interacts with TIAR to Modulate p53 pathway during Tumorigenesis

city: Beijing

first: Jiao

last: Yuan

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Long non-coding RNAs (lncRNAs) are best known for playing diverse roles at transcriptional level. Here we report a lncRNA MT1JP for its posttranscriptional function as a modulator of tumorigenesis. By associating with RNA-binding protein TIAR, MT1JP favored the translation of vital transcription factor p53, and then regulated a series of p53 involved pathways such as cell cycle, apoptosis, proliferation and so forth. With down-regulation of MT1JP, the protein level of p53 was declined, which in turn accelerated cell deteriorate and tumor formation. Moreover, differential expression of MT1JP in tumor tissues and matched normal tissues suggests that it may be an excellent prognosis and therapy target as a tumor suppressor. Together, our finding identifies MT1JP as a critical lncRNA required for restraining tumorigenesis, which occurs through MT1JP interacting with TIAR to modulate p53 translation.

overall_design: Two siRNAs for MT1JP. For each siRNA, RNAs were collected from cells treated with 24h, 48h and 72h post induction and cells for control. Three independent biological replicates for each sample type.

first: Lihui

first: Haiyan

last: Yue

first: Qinghua

first: Jing

last: Li

first: Guifeng

last: Wei

first: Jianjun

last: Luo

first: Runsheng

last: Chen


title: Retinoid X receptor activation during adipogenesis of female mesenchymal stem cells programs a dysfunctional adipocyte

city: Irvine

first: Bassem

middle: Merit

last: Shoucri

address: 4351 Natural Sciences 2

institute: University of California Irvine

summary:
Early life exposure to endocrine disrupting chemicals (EDCs) is an emerging risk factor for the development of obesity and diabetes later in life. We previously showed that prenatal exposure to the EDC tributyltin (TBT) results in increased adiposity in the offspring. These effects linger into adulthood and are propagated through successive generations. TBT activates two nuclear receptors, the peroxisome proliferator-activated receptor γ (PPARγ) and its heterodimeric partner retinoid X receptor (RXR), that promote adipogenesis in vivo and in vitro. We recently employed a mesenchymal stem cell (MSC) model to show that TBT promotes adipose lineage commitment by activating RXR, not PPARγ. This led us to consider the functional consequences of PPARγ versus RXR activation in developing adipocytes.
We used a transcriptomal approach to characterize genome-wide differences in MSCs differentiated with the PPARγ agonist rosiglitazone (ROSI) or TBT. Pathway analysis suggested functional deficits in TBT-treated cells. We then compared adipocytes differentiated with ROSI, TBT, or a pure RXR agonist IRX4204 (4204). Our data show that RXR activators (‘rexinoids’, 4204 and TBT) attenuate glucose uptake, blunt expression of the anti-diabetic hormone adiponectin, and fail to down-regulate pro-inflammatory and pro-fibrotic transcripts as does ROSI. Finally, 4204 and TBT treatment results in an inability to induce markers of adipocyte browning, in part due to sustained interferon signaling. Taken together, these data implicate rexinoids in the development of dysfunctional white adipose tissue that could potentially exacerbate obesity and/or diabetes risk in vivo. These data warrant further screening and characterization of EDCs that activate RXR.

overall_design: We generated RNA-Seq data in MSCs differentiated in the presence of an adipogenic induction cocktail (0.5 mM isobutylmethylxanthine, 1 uM dexamethasone, 5 ug/mL insulin )treated with DMSO (0.1%), rosiglitazone (ROSI, 500 nM), or tributyltin (TBT, 50 nM) for 14 days. N=4 per treatment --> 12 RNA-Seq samples total.

first: Toshi

last: Shioda

first: Bruce

last: Blumberg


title: Circular RNA CpG Island Hypermethylation-Associated Silencing in Human Cancer

status: Public on Jun 13 2018

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

institute: IDIBELL

summary: Although less than 2% of the human genome code for proteins, most studies in cancer research has focused in this small portion of our DNA. However, it has been recognized in the last years that non-coding RNAs (ncRNAs) also participate in cellular transformation. In this context, microRNAs and long noncoding RNAs (lncRNAs) can act as oncogenes or tumor suppressor genes. Recent work have also demonstrated that ncRNAs with growth-inhibitory functions can undergo promoter CpG island hypermethylation-associated silencing in tumorigenesis. Herein, we wondered whether circular RNAs (circRNAs), a type of RNA transcripts lacking 5’-3´ends and forming closed loops that are gaining relevance in cancer biology, are also a target of epigenetic inactivation in tumors. To tackle this issue, we have used cancer cells genetically deficient for the DNA methyltransferase enzymes in conjuction with circRNA expression microarrays. We have found that the loss of DNA methylation provokes a release of circRNA silencing. We have particularly identified that promoter CpG island hypermethylation of the genes TUSC3 (tumor suppressor candidate 3), POMT1 (protein O-mannosyltransferase 1),  ATRNL1 (attractin-like 1) and SAMD4A (sterile alpha motif domain containing 4A) is linked to the transcriptional downregulation of both linear mRNA and the hosted circRNA. Although a role in the control of the parental gene has been shown for some circRNAs, we did not observe changes in TUSC mRNA levels upon TUSC3 circ104557 overexpression. Most importantly, data mining for 5’-end CpG island methylation of TUSC3, ATRNL1, POMT1 and SAMD4A in a large collection of human cancer cell lines and primary tumors showed that the epigenetic defect was commonly observed among different tumor types, where it was also associated with the diminished expression of the corresponding transcript. Our findings support a role for circRNA DNA methylation-associated loss in human cancer.

overall_design: We compared the circRNA expression profile of 3 DKO and 3 HCT116 cell line replicates by microarray analysis. We also compared the profiles with 3 normal colon patient samples.

first: Humberto

last: Ferreira

first: Manel

last: Esteller


title: Population specific and shared transcriptional responses of fish embryos exposed to PCB153

status: Public on Jun 16 2018

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Killifish (Fundulus heteroclitus) inhabiting the New Bedford Harbor (NBH) Superfund Site have evolved resistance to the toxic and biochemical effects of non-ortho (dioxin-like) polychlorinated biphenyls (DL-PCBs) and other compounds that act via the aryl hydrocarbon receptor (AHR) signaling pathway. However, the majority of PCBs in NBH are ortho-substituted (non-DL) PCBs (o-PCBs), and the impacts of these o-PCBs on fish populations are not well understood.  To determine whether the NBH killifish population has adapted to o-PCBs, we performed a series of experiments involving exposure to killifish embryos and adults from NBH and a reference site (Scorton Creek; SC) to 2,2’,4,4’,5,5’-hexachlorobiphenyl (PCB-153), a model o-PCB. PCB-153 was not acutely embryotoxic to developing F2 killifish embryos (SC or NBH) at concentrations up to 28 µM. RNA-seq showed that SC embryos exposed to PCB-153 (28 µM for 6 hr at 10 days post fertilization) had changes in the expression of genes involved in glucose homeostasis. However, NBH embryos were much less sensitive to these effects of PCB-153.  When adult killifish from SC and NBH were exposed to PCB-153 (20 mg/kg) and sampled 3 days later for gene expression, many more genes were affected in forebrains of SC fish than in NBH fish, in a sex-specific manner. Together, these results demonstrate that NBH killifish have evolved reduced sensitivity to o-PCBs, suggesting complex adaptation to chemical mixtures at a Superfund site.

overall_design: We sequenced 5 pools of killifish embryos (biological replicates) exposed to DMSO and PCB153.

first: Mark

middle: E

last: Hahn

first: Sibel

middle: I

last: Karchner

first: Neelakantewar

first: Eric

last: Reed

first: Stefano

last: Monti

first: Vinay

last: Kartha


title: ERK3 is essential for establishment of epithelial architecture

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

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

overall_design: Refer to individual Series


title: A transcriptomic survey of the impact of environmental stress on response to dengue virus in the mosquito, Aedes aegypti

city: Notre Dame

first: David

middle: Sungin

last: Kang

state: IN

address: 44 Galvin Life Science Center, Department of Biological Sciences, Severson Lab

institute: University of Notre Dame

summary: Here, we present the first whole transcriptome study to address the impact of environmental stress on A. aegypti response to dengue virus. We examined expression profiles of adult females resulting from crowded and optimum reared larvae from the same Trinidad isolate at two critical early time points—3 and 18 hours post dengue virus infected blood meal. We exposed specimens to either a dengue or naïve blood meal, and then characterized the response in ten gene co-expression modules based on their transcriptional associations with environmental stress and time.

overall_design: RNAseq of stressed and optimal dengue and control mosquitoes at 3 and 18 hours post bloodmeal.

middle: S

first: Martin

last: Barron

first: Diane

middle: D

last: Lovin

first: Joanne

last: Cunningham

first: Matthew

middle: W

last: Eng

first: Dave

last: Chadee

first: Jun

last: Li

last: Severson


title: Hepatic gene expression in growth restricted fetal sheep after an acute hyperinsulinemic clamp or saline infusion at 0.9 gestation

city: Aurora

first: Stephanie

middle: R

last: Wesolowski

state: Colorado

address: MS F441

institute: Dr

summary: Here we used gene expresion microarray studies to test the global effect of IUGR on the fetal liver

overall_design: Liver tissue was collected from normal (Control) and intrauterine growth restricted (IUGR) fetal sheep after a hyperinsulinemic-euglycemic clamp (INSULIN) or saline infusion (SALINE) at 0.9 gestation.

first: Amanda

middle: K

last: Jones


title: ERK3 is essential for establishment of epithelial architecture [ERK3 KD vs. TFAP2A KD]

summary:
Establishment and maintenance of epithelial architecture are essential for embryonic development and adult physiology. Here, we show that ERK3, a poorly characterized atypical MAPK, regulates epithelial architecture in vertebrates. In Xenopus embryonic epidermal epithelia, ERK3 knockdown impairs adherens and tight junction protein distribution, as well as tight junction barrier function, resulting in epidermal breakdown. Moreover, in human breast epithelial cancer cells, inhibition of ERK3 expression induces thickened epithelia with aberrant adherens and tight junctions. Microarray results suggest an involvement of TFAP2A, a transcription factor important for epithelial gene expression, in ERK3-dependent gene expression changes. TFAP2A knockdown phenocopies ERK3 knockdown in both Xenopus embryos and human cells, and ERK3 is required for full activation of TFAP2A-dependent transcription. Our findings thus reveal that ERK3 regulates epithelial architecture, possibly in cooperation with TFAP2A.
We used microarrays to compare the changes in ERK3-dependent gene expression profiles with those in TFAP2A-dependent gene expression profiles in Xenopus laevis embryos.

overall_design: Control MO (80 ng), ERK3 MO1/2 (40 ng each of MO1 and MO2), or TFAP2A MO1/2 (40 ng each of MO1 and MO2) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone, and harvested at stage 15. Two independent replicates were prepared. Total RNA was extracted using TRIzol reagent. The quality of the total RNA was assessed using an Agilent 2100 BioAnalyzer. cDNA synthesis and transcriptional amplification were performed using 250 ng of total RNA with the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, #902415). Fragmented and biotin-labeled cDNA targets were hybridized to the GeneChip Xenopus laevis Genome 2.0 Array (Affymetrix) according to the manufacturer's protocol. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned chip images were analyzed with GeneChip Operating Software v.1.4 (GCOS). The probe set signal intensities in the raw data (CEL files) were normalized using a robust multiarray average (RMA) algorithm and Expression Console software.

first: Chika

last: Takahashi

first: Koichi

last: Miyatake

first: Morioh

last: Kusakabe


title: Heterogeneity in early lymphoid compartments [single-cell RT-PCR]

status: Public on Jun 12 2018

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: In order to understand the developmental trajectories of early lymphocyte development it is crucial to prospectively isolate stage and lineage specific cells. It has become clear that early lymphoid progenitor compartments in the bone marrow are molecularly and functionally heterogeneous which warrants further investigation to refine the marker combinations used to isolate these progenitors. An initial antibody screen revealed extensive surface marker heterogeneity amongst early lymphoid progenitors. This heterogeneity was resolved using single cell gene expression assays and single cell in vitro differentiation assays, identifying marker combinations that isolate functionally distinct populations. In addition, using reporter transgenic mice we were able to identify a set of surface markers that can be used alone or in combination with classical targets to identify specific stages of B-cell development. B-cell stages based on transgene expression which were used for screening purposes were verified by RNASeq. The data provides a greater resolution of the complexity of the lymphoid progenitor compartment within the bone marrow than has been understood to date and provides novel tools for the further identification of cell populations in B-lineage development.

overall_design: qPCR gene expression profiling of mouse common lymphoid progenitors (CLPs and FrA). Four 96-well plates with pre-amplified single CLP bone marrow cell cDNA (with 10 and 20 cell controls) were loaded on to a 96.96 Dynamic Array Chip for Gene Expression. Samples Ids follow where SS<X> denotes well ID, and P<X>denoted the plate. Controls include 10 and 20 cell controls. (Fluidigm) with 96 TaqMan assays and analysed on BioMark HD (Fluidigm)

first: Christina

middle: T

last: Jensen

first: Stefan

last: Lang

first: Mikael

last: Sigvardsson


title: ERK3 is essential for establishment of epithelial architecture [ERK3 KD]

first: Eisuke

last: Nishida

summary:
Establishment and maintenance of epithelial architecture are essential for embryonic development and adult physiology. Here, we show that ERK3, a poorly characterized atypical MAPK, regulates epithelial architecture in vertebrates. In Xenopus embryonic epidermal epithelia, ERK3 knockdown impairs adherens and tight junction protein distribution, as well as tight junction barrier function, resulting in epidermal breakdown. Moreover, in human breast epithelial cancer cells, inhibition of ERK3 expression induces thickened epithelia with aberrant adherens and tight junctions. Microarray results suggest an involvement of TFAP2A, a transcription factor important for epithelial gene expression, in ERK3-dependent gene expression changes. TFAP2A knockdown phenocopies ERK3 knockdown in both Xenopus embryos and human cells, and ERK3 is required for full activation of TFAP2A-dependent transcription. Our findings thus reveal that ERK3 regulates epithelial architecture, possibly in cooperation with TFAP2A.
We used microarrays to study the changes in ERK3-dependent gene expression profiles during pronephros and epidermal development in Xenopus laevis embryos.

overall_design: Control MO (80 ng), ERK3 MO1/2 (40 ng each of MO1 and MO2), or ERK3 MO3 (80 ng) were injected into the animal regions of all blastomeres at the 4-cell stage. The animal caps were dissected from the injected embryos at stage 9, cultured alone or in the presence of activin plus retinoic acid (activin/RA), and harvested at stage 15. One experiment was performed. Total RNA was extracted using TRIzol reagent. The quality of the total RNA was assessed using an Agilent 2100 BioAnalyzer. cDNA synthesis and transcriptional amplification were performed using 250 ng of total RNA with the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, #902415). Fragmented and biotin-labeled cDNA targets were hybridized to the GeneChip Xenopus laevis Genome 2.0 Array (Affymetrix) according to the manufacturer's protocol. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned chip images were analyzed with GeneChip Operating Software v.1.4 (GCOS). The probe set signal intensities in the raw data (CEL files) were normalized using a robust multiarray average (RMA) algorithm and Expression Console software.


title: Gene expression in MLE-12 cells transfected with microRNA (miRNA; miR) mimics  upon influenza virus infection

status: Public on Jun 08 2018

city: Madison

first: Tadashi

last: Maemura

state: Wisconsin

address: 575 Science Drive

institute: Influenza Research Institute

summary: To clarify the gene expression profile in MLE-12 cells transfected with microRNA mimics upon influenza virus infection, we transfected microRNA mimics (mmu-miR-483-3p or Negative control miRNA) into MLE-12 cells and infected A/Puerto Rico/8/1934 (PR8) strain at an MOI of 2 at 24 hours post transfection. RNA was isolated from cells at 12 hours post infection. We found that miR-483-3p transfection down-regulated the genes involved in the innate immunity regulation upon influenza virus infection.

overall_design: Each group had three biological replication. MLE-12 cells transfected with control miRNA mimic was used as control. After isolation of total RNA, Gene expression microarray was performed.

first: Satoshi

last: Fukuyama

first: Tiago

middle: J

last: Lopes

first: Yoshihiro

last: Kawaoka


title: Dual bioaugmentation with Desulfitobacterium hafniense Y51 and redox-trained fermenting communities for decontamination of PCE polluted river sediment: a microcosm study

status: Public on Jun 11 2018

city: Wageningen

first: Ye

last: Tian

address: Stippeneng 4

department: AFSG

institute: Wageningen University

summary: The physiology of D. hafniense strain Y51 under close to natural conditions were examined: D. hafniense Y51 was subjected to a variety of limiting conditions (carbon or electron acceptor) or ammonium deprivation, in chemostat. Its physiology was assessed by transcriptomic and proteomic analyses and compared to that in batch culture. Electron donor/acceptor-limited growth conditions cause a switch to alternative metabolic pathways allowing the organism with a capacity to survive in polluted environments and with a readiness to use alternative electron acceptors such as PCE; (ii) nitrogen limitation induces nitrogen fixation implying a robustness vis-a-vis ammonia shortage; (iii) limiting conditions trigger a general stress response that should enable the organism to cope with even more environmental constraints.

overall_design:
A custom-designed array based on the complete genome sequences of D. hafniense DCB-2 and Y51 (NCBI Genbank accession numbers NC_007907 and NC_011830, respectively). The array contains 21905 distinct 45 to-60 oligonucleotides designed with PICKY (Chou et al., 2004; Chou et al., 2009), including two or three probes per target transcript, as well as sense and antisense probes targeting intergenic regions that were larger than 60 oligonucleotides. In total, 11652 probes targeting genes and intergenic regions shared by both genomes. Probes were printed in duplicate on the Agilent 8 x 60 K custom gene expression microarray platform, containing in addition 1319 Agilent control probes.
Expression profiling of:  1) batch culture with 10ml pure hexadecane and 2) river sediment.

first: Raquel

last: Vargas-López


title: mRNA Expression Data from Murine Hearts of Wild type (WT) C57Bl/6 mice housed under a 12h light: 12h dark or 12h light: 4h blue: 8h dark cycle for 4 weeks

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

country: Canada

institute: University of Guelph

summary:
Mice are on a C57Bl/6N background strain, hearts were collected at ZT07, following 4 weeks under a 12h light: 12h dark (LD) or 12h light: 4h blue: 8h dark (LBD) cycle.
The microarray approach allows the investigation of gene expression changes of all genes in WT LD vs. WT LBD hearts.

overall_design: There are a total of 6 samples, 3 from WT LD and 3 from WT LBD. Animals were sacrificed at 7 hours into the light phase.

first: Tami

middle: A


title: mRNA expression data from murine hearts of control or melatonin-treated young wild type (WT) C57Bl/6 mice

summary:
Mice are 4 weeks old on a C57Bl/6N background strain, hearts were collected at ZT15, following 1 week daily administration of melatonin at 4mg/L (human equivalent of 5mg dose) in the drinking water from ZT12-15.
The microarray approach allows the investigation of gene expression changes of all genes in WT control vs. WT melatonin-treated hearts.

overall_design: There are a total of 12 samples, 6 from WT control and 6 from WT melatonin-treated. Animals were sacrificed at 3 hours into the dark phase.


title: mRNA expression data from murine myocardial ischemia/reperfusion (mI/R) hearts following sleeptime or waketime captopril chronotherapy

summary:
Mice are 14 days post-mI/R (10 weeks old) on a C57Bl/6N background strain, hearts were collected at ZT15, following administration of saline placebo, sleeptime captopril (ZT01), or waketime captopril (ZT11) I.P. from day 7-14 post-mI/R.
The microarray approach allows the investigation of gene expression changes of all genes in placebo vs. sleeptime vs. waketime vs. sham hearts.

overall_design: There are a total of 12 samples, 3 sham controls, 3 placebo mI/R, 3 sleeptime captopril-treated mI/R, and 3 waketime captopril-treated mI/R. Animals were sacrificed at 3 hours into the dark phase.


title: Gene regulation in monocytes and CD4+ T cells from low-SES vs. high-SES children with asthma

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: There are marked socioeconomic disparities in pediatric asthma control. To identify the molecular origins of these disparities, we performed genome-wide expression profiling of monocytes and T-helper cells isolated from pediatric asthma patients of lower- and higher socioeconomic status (SES).

overall_design: Microarray-based gene expression profiling was conducted on 98 CD14+ (monocyte) and CD3+/CD4+ (helper T cell) peripheral blood cell samples collected from children diagnosed by a physician with asthma. Children were from lower-SES (household income < $50,000 annually) or higher-SES (household income > $140,000 annually) families. Peripheral blood monocytes and T-helper lymphocytes were isolated, and microarray-based expression profiling was conducted on extracted RNA. Participants were also assessed for background characteristics (age [years], race [Caucasian,Non-hispanic=1/Other=0], body mass index/BMI [kg/m^2]), asthma severity (following guidelines from the National Asthma Education and Prevention Program/Expert Panel Report 2; Bacharier LB, Strunk RC, Mauger D, White D, Lemanske RFJ, Sorkness CA. Classifying asthma severity in children: mismatch between symptoms, medication use, and lung function. Am J Respir Crit Care Med. 2004;170 (4):426-432), use of inhaled corticosteroids (ICS; days used in past week), and use of short-acting beta-adrenergic agonists (SABA; days used in past week). Dichotomous variables were coded 0=no/absent and 1=yes/present.


title: Analysis of miRNA sublocalization in cisplatin-resistant versus parental CAL-27 cells

city: Guangzhou

first: Guokai

last: Pan

address: 107 Yanjiang West Road

department: Department of Oral and Maxillofacial Surgery

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

summary: Chemoresistance frequently leads to therapeutic failure in oral squamous cell carcinoma (OSCC). While miRNA have been widely reported having global regulatory roles in cancer biological properties, yet their localiztion alteration under cisplatin treatment has not been clarified. In this study, to identify the sublocalization characteristics of miRNAs induced by chemotherapy, especially the specific mitochondrial localization of miRNA, we profile the expression of miRNAs in cisplatin-resistant and parental TSCC cells using miRNA microarrays.

overall_design: We investigated the differential localization of miRNA in stable cisplatin-resistant CAL-27 cells and parental CAL-27 cells. Sample labeling and array hybridization were performed by Agilent human miRNA (8*60K) V19.0 microarrays.


title: Differential Expression of LncRNAs of cisplatin-resistant versus parental CAL-27 cells

summary: Chemoresistance frequently leads to therapeutic failure in tongue squamous cell carcinoma (TSCC). Increasing evidence has shown that Long noncoding RNAs (lncRNAs) play pivotal roles in biological properties of cancer. However, the roles and mechanisms of lncRNAs in cisplatin resistance are not well understood. In this study, to identify the lncRNAs induced by chemotherapy, we profile the expression of lncRNAs in cisplatin-resistant TSCC cells using LncRNA microarrays.

overall_design: CAL-27 cells were treated with gradually increased concentration of cisplatin to accquire cisplatin-resistance. RNA from two biological replicates of both cisplatin-resistant and parental CAL-27 cells were collected for microarray analysis.


title: Gene expression after HOS cells treated with DGKZ (diacylglycerol kinase zeta)-silencing by a microarray profiling (Affymetrix)

city: Shanghai

first: Wenxi

last: Yu

state: N/A = Not Applicable

address: No.600, Yishan Road, Xuhui District, 200233 Shanghai, People's Republic of China

institute: Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University

summary:
DGKZ could promote proliferation and inhibit apoptosis in osteosarcoma,both in vivo and in vitro.
To identify downstream molecular mechanism of DGKZ in proliferation of osteosarcoma, we performed a microarray profiling (Affymetrix) in human HOS cells treated with DGKZ knockdown.

overall_design:
Human osteosarcoma HOS cells were treated with DGKZ-silencing, and a microarray profiling (Affymetrix) was conducted to investigate the potential gene expression change.
contributor: Jikai Com.Ltd


title: RNA sequencing of Cryptococcus neoformans H99 treated with eltrombopag

city: Taipei

first: HAO TAI

last: KO

address: No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan(R.O.C)

country: Taiwan

institute: National Taiwan University

summary: The gene expression of C. neoformans H99 treated with eltrombopag

overall_design: C. neoformans H99 cells were grown overnight in liquid YPD at 30°C, washed twice with ddH2O, diluted 1:100 in liquid YPD and grown at 30°C with agitation for 3 h to reach a density of 3 × 10^7 CFU/mL. At this point cultures were equally divided into two aliquots to which either 0.06 μg/mL eltrombopag or same amount of DMSO was added, followed by incubation at 30°C for 90 min. After this treatment, cultures were centrifuged and total RNA was extracted using Trizol reagent and treated with DNase I (Ambion, Thermo Fisher Scientific) to degrade contaminating DNA. mRNAs were enriched with oligo (dT) magnetic beads. Fragmentation buffer allowed the mRNA to be shortened into ~200-base fragments. Then, the first strand of cDNA was synthesized using random hexamer, buffer, dNTPs, and RNase H, and the second strand of cDNA was synthesized by DNA polymerase I. The double-stranded cDNAs were purified with magnetic beads. End preparation and 3' end single nucleotide adenine addition was performed, and sequencing adaptors were ligated to the fragments, which were enriched by PCR amplification. During the quality control step, the Agilent 2100 Bioanaylzer and ABI StepOnePlus RealTime PCR system were used to qualify and quantify the sample library. The library products were sequenced via Illumina NextSeq 500.

first: Hao-Tai

last: Ko

first: Ying-Lien

last: Chen


title: Transcriptional response of porcine skin to sulfur mustard

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary: Sulfur mustard (HD) is a potent alkylating agent that induces cutaneous injury. The molecular mechanisms of cutaneous injury are not completely understood, and the molecular pathways involved in post-exposure wound healing are not well characterized.  To elucidate these molecular pathways for the purpose of identifying potential therapeutic targets, we used oligonucleotide microarrays to identify gene expression profile changes induced by HD in porcine skin, an established animal model of HD injury and wound healing. Female Yorkshire crossbred pigs were exposed to neat HD to generate a superficial dermal (second degree) injury.  Skin punch biopsies were collected at 1 h, 2 h, 4 h, 24 h, 48 h, 72 h, 7 d, 14 d or 21 d post-exposure. Biopsies were scored for histopathology, and RNA extracted from biopsies was used for microarray analysis.  Gene expression profiles were analyzed for significant temporal response to HD by analysis of variance (false discovery corrected p<0.05).  Gene expression profiles were also correlated (Pearson linear correlation |r|>0.7, false discovery corrected p<0.05) to histopathology scores to identify molecular pathways significantly correlated with specific clinical endpoints of injury and repair.  Several pathways linked to aspects of inflammatory response and cell cycle checkpoint regulation were altered by HD exposure through 72 h.  Several of these inflammatory pathways were highly correlated with clinical endpoints assessed through 72 h, including epidermal necrosis and vesicle formation.  Pathways linked to inflammation were also highly correlated with 7-21 d total histopathology scores, suggesting that inflammation is continual through the course of injury and healing.   Specific therapeutic targets were identified within these inflammatory pathways, and potential therapeutics were also identified for future drug screening efforts.

overall_design: Female Yorkshire crossbred pigs were exposured on the ventral surface to sulfur mustard to generate a superficial dermal injury.  An exposure template was used to obtain four uniform 3 cm skin lesions on the ventral abdomen, two sulfur mustard-exposed lesions and two unexposed controls. Sham animals were prepared for exposure but were not exposed to SM. Skin punch biopsies from four animals at each time point (three animals for sulfur mustard exposed and unexposed controls, one animal for sham): 1h, 2h, 4h, 24h, 48h, 72h, 7d, 14d, or 21d post exposure.

first: Christopher

last: Phillips

first: Larry

last: Mitcheltree

first: John

last: Graham


title: Gene expression profiling of juvenile salmon in Pacific Northwest urban streams

city: Tacoma

first: Andrew

middle: Ronald

last: Spanjer

state: WA

address: 934 Broadway STE 300

department: Department of the Interior

institute: US Geological Survey

summary: Stress gene expression profiling of hepatic tissue in wild caught juvenile coho from perenial streams. Stream locations were based on a gradient of urban impact

overall_design: 57 samples were analyzed from 10 different freshwater streams,


title: Comparative analysis of human bone marrow-derived MSCs and corneal stromal cells

city: Edegem

first: Steffi

last: Matthyssen

state: Antwerpen

address: Wilrijkstraat 10, UZA/CCRG U113

country: Belgium

institute: University of Antwerp

summary: Corneal stromal cells from six donors were used and expanded in standard conditions (FBS as a supplement) and xenofree conditions (HPL as a supplement). Bone marrow MSCs from one other donor were used as a comparative control. From the purified RNA, 10ng was used per sample to synthesize cDNA using the iScript Advanced cDNA synthesis kit (Bio-Rad Laboratories, Temse, Belgium) following the protocol supplied by the manufacturer. qRT-PCR assays were prepared in triplicate in 96-well PrimePCR plates for human MSCs (Bio-Rad Laboratories, Temse, Belgium), in which the primers come lyophilized per well. A total of 88 genes was targeted, which account for stemness, differentiation (osteo-, chondro-, adipo-, teno- and myogenesis), MSC-specific, and MSC-related genes. The thermal cycler used to perform the PCR was the CFX96 Real-Time System – C1000 Thermal Cycler (Bio-Rad Laboratories, Temse, Belgium). SsoAdvanced universal SYBR Green supermix was used to quantify double-stranded DNA. Dissociation of double-stranded DNA was assessed in melting curve analysis to determine the specificity. Three reference housekeeping genes were included in the assay plates (TBP, GAPDH and HPRT1) to normalize expression using the ΔΔCq method. The abundance of the transcripts in CS-MSC relative to the control BM-MSC was determined by calculating the relative normalized expression (RNE) or fold change. All analyses were performed using the Bio-Rad CFX Manager software. When gene expression exceeds a more than threefold change compared to BM-MSC it is deemed to be up- or downregulated.

overall_design: qPCR gene expression of 88 genes specific for, related to or associated with MSCs.  Corneal stromal cells from six donors were used and expanded in standard conditions (FBS as a supplement) and xenofree conditions (HPL as a supplement). Bone marrow MSCs from one other donor were used as a comparative control. All plates were run in triplo.

first: Veerle

last: Van Gerwen


title: RNA-Seq of WT and -P treatment

city: Haikou

first: rui

last: xiong

address: Renmin Street

country: China

institute: Hainan University

summary: To further explore the molecular mechanisms of P regulation in banana plants, we used RNA sequencing-based transcriptomic analysis for banana plants subjected to Pi deficit stress for 60 days.We detected 1900 significantly differentially expressed genes (DEGs) in aboveground plant parts and 7398 DEGs in root parts under low P stress. Gene ontology (GO) classification analysis showed that 156,291 GO terms belonging to molecular functions, 53,114 GO terms belonging to cellular components, and 228,544 GO terms belonging to biological processes were enriched in the aboveground and root components. A number of DEGs involved in energy metabolism-related processes, signal transduction, control of rhizosphere P activation, and Pi mobilization were found, which were confirmed by quantitative reverse-transcription PCR (RT-PCR) analysis. At the transcriptomic level, we detected 13 DEGs from different organs and with different functions in the time-course response to phosphorus deficiency stress. These DEGs may include some key genes that regulate the phosphorus network, increasing our understanding of the molecular mechanism of Pi homeostasis in banana.

overall_design: Banana seedling roots and aboveground parts were harvested at 60 days after the start of experimental treatments, and these samples were then frozen immediately using liquid nitrogen and stored at −80 °C before being sent to BGI-Tech(Shenzhen, China) for RNA-seq by Illumina HiSeq2000.

first: Rui

last: Xiong

first: Min

last: Xu

first: Can-Bin

last: Zeng

last: He

first: Yun

last: Peng

first: Zhen

last: Yan

first: Zhao

last: Qi

first: Yu

last: Cheng

first: Shuang-Shuang

last: Wei

first: Jun

last: Xie

first: You-Quan

last: Xia

first: Hua

last: Tang


title: Optimizing Personalized Therapy for Rheumatoid Arthritis Using a Novel Drug Combination of Bioactive Chemical Constituents Derived from a Classic Chinese Herbal Formula

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary:
Personalized therapy of rheumatoid arthritis (RA) based on traditional Chinese medicine cold and hot syndromes is selection of the best treatment for an individual patient. Wutou Decoction (WTD) is one of the classic Chinese herbal formulae which achieve favorable therapeutic response in treating RA-cold syndrome.
Microarray analysis based on the adjuvant induced arthritis model combined with characteristics of RA and cold/hot syndromes was performed to screen RA-cold and RA-hot-syndrome-related genes, as well as WTD effect genes.

overall_design: We aimed to identify bioactive compounds (BACs) of WTD against RA-cold syndrome, and to evaluate the anti-RA effects of the BAC combination by the combination of microarray analysis, network analysis, chemical profiling, absorption-distribution-metabolism-excretion evaluation, molecular docking simulation and in vivo/vitro experimental validation.

last: Lin


title: mRNA Expression Data from Murine Hearts of Transgenic Clock delta 19/delta 19 mice (Clock mice) and Wild type (WT) mice Fed a High-Fat (HFD) or Standard Chow (SC) Diet for 24 weeks

status: Public on Jun 09 2018

first: Dr. Tami

last: Martino

summary:
Mice are on a C57Bl/6J background strain, hearts were collected from Clock and WT mice at ZT07, following 24 weeks on either a HF or SC diet.
The microarray approach allows the investigation of gene expression changes of all genes in Clock HFD vs. Clock SC vs. WT HFD vs. WT SC hearts.

overall_design: There are a total of 16 samples, 4 from Clock HFD, 4 from Wild type HFD, 4 from Clock SC, and 4 from Wild type SC. Animals were sacrificed at 7 hours into the light phase.

first: Tami


title: Toxicogenomic responses of low level anticancer drug exposures in Daphnia magna

status: Public on Jun 06 2018

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

country: USA

institute: UMass Boston

summary: The use of anticancer drugs in chemotherapy is increasing, leading to growing environmental concentrations of imatinib mesylate (IMA), cisplatinum (CDDP), and etoposide (ETP) in aquatic systems. Previous studies have shown that these anticancer drugs cause DNA damage in the crustacean Daphnia magna at low, environmentally relevant concentrations. To explore the mechanism of action of these compounds and the downstream effects of DNA damage on D. magna growth and development at a sensitive life stage, we exposed neonates to low level concentrations equivalent to those that elicit DNA damage (IMA: 2000 ng/L, ETP: 300 ng/L, CDDP: 10 ng/L) and performed transcriptomic analysis using an RNA-seq approach. RNA sequencing generated 14 million reads per sample, which were aligned to the D. magna genome and assembled, producing approximately 23,000 transcripts per sample. Over 90% of the transcripts showed homology to proteins in GenBank, revealing a high quality transcriptome assembly, although functional annotation was much lower. RT-qPCR was used to identify robust biomarkers and confirmed the downregulation of angiotensin converting enzyme (ACE) involved in neuropeptide regulation across all three anticancer drugs and the down-regulation of DNA topoisomerase II by ETP. RNA-seq analysis also allowed for an in depth exploration of the differential splicing of transcripts revealing that regulation of different gene isoforms predicts potential impacts on translation and protein expression, providing a more meaningful assessment of transcriptomic data. Enrichment analysis and investigation of affected biological processes suggested that the DNA damage caused by ETP and IMA influences cell cycle regulation and GPCR signaling.  This dysregulation is likely responsible for effects to neurological system processes and development, and overall growth and development. Our transcriptomic approach provided insight into the mechanisms that respond to DNA damage caused by anticancer drug exposure and generated novel hypotheses on how these chemicals may impact the growth and survival of this ecologically important zooplankton species.

overall_design: Fifteen samples were analyzed in total, including two set of unexposed controls and three replicates per treatment and control, SRA Study:SRP142416 and BioProject:PRJNA453118

first: Chiara

last: Russo

first: Marina

last: Isidori

first: Jessica

last: Deaver


title: RNA-seq and DNA methylomes of germinating rice and developing coleoptiles

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: human serum: Control vs. patients with repeated implantation failure

city: lanzhou

first: lin

last: liu

address: chengguanqu donggangxilu 1 hao

institute: lanzhou university

summary:
microRNAs profiling of human serum comparing control fertile women with women who had experienced  repeated implantation failure after ovarian stimulation and IVF-ET.
Repeated implantation failure was defined as women who had undergone≥3 failed cycles with high-grade embryos were transferred.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two-condition experiment. Biological replicates: 3 control, 3 patients.

first: Lin

last: Liu


title: Metabolomics and transcriptomics identify multiple downstream targets of Paraburkholderia phymatum σ54 during symbiosis with Phaseolus vulgaris

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

summary: RpoN (σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include alpha- and beta-rhizobia. Our previous studies showed that a rpoN mutant of the beta-rhizobial strain Paraburkholderia phymatum formed root nodules on Phaseolus vulgaris that were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by the P. phymatum rpoN Fix- mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix+ and Fix- nodules – combined with a search for RpoN binding sequences in promoter regions of regulated genes – confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also identified additional target genes, whose differential expression was able to explain the observed metabolite changes in a numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype by forming less but heavier nodules on P. vulgaris roots.

overall_design: Unraveling the molecular basis of the nitrogen-fixing symbiosis between P. vulgaris and P. phymatum.

first: Martina

last: Lardi

first: Yilei

first: Gaetano

last: Giudice

first: Christian

middle: H

last: Ahrens

first: Nicola

last: Zamboni


title: RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)

summary: RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.

overall_design: Total RNA was extracted from samples collected at each time point in triplicate. The time points were: 0 h (dry seed), 1 h, 3 h, 12 h, 24 h, 2 days, 3 days and 4 days under aerobic (A) and anaerobic (N) conditions, as well as 3‐day‐old seedlings grown under anaerobic conditions that were switched to air for 1 day.


title: RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (Methyl-Seq)

summary: methylC-seq profiling of seeds, at 0 h and 24 h after imbibition and following 4-d of growth under aerobic and anerobic conditions, as well as following re-oxygenation (3dN1dA) in rice.

overall_design: gDNA was extracted from samples collected at each time point in triplicate. The time points were: 0 h (dry seed), 24 h and 4 days under aerobic (A) and anaerobic (N) conditions, as well as 3‐day‐old seedlings grown under anaerobic conditions that were switched to air for 1 day.


title: Time resolved transcriptome of isolated biofilm cells compared with planktonic cells

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: Most differential expression point to attack and defense strategies, comprising structural and metabolic changes.

overall_design: One strain, four conditions

first: Joaquin

last: Caro-Astorga

first: Elrike

last: Frenzel

first: Oscar

middle: P

last: Kuipers

first: Diego

last: Romero


title: Differential expression analysis of miRNAs expressed in blood and CSF of Huntington's disease [miRNA array]

first: Xianjun

last: Dong

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: Huntington’s disease (HD) is an autosomal-dominant neurodegenerative disorder caused by the CAG expansion in the Huntingtin (HTT) gene. Several studies have shown the potential of microRNAs as biomarkers in neurodegenerative diseases. However, no bona fide microRNAs have been identified as promising diagnostic biomarkers for HD. As part of the PREDICT-HD project, here we performed NanoString on blood samples of 115 pre-manifest HD cases and 111 controls in an effort to provide promising biomarkers for the diagnostic of HD or the disease processes tracking. The results showed that five miRNAs (miR-1252, miR-433, miR-553, miR-138-5p and miR-2053) are significantly differentially expressed in pre-manifest gene-positive HD cases vs. gene-negative controls. We also explored the miRNAs associated with HD severity by correlating the miRNA expression with CAP scores of 115 pre-manifest HD samples and found that 41 and 24 miRNAs are negatively and positively correlated with CAP scores significantly. Furthermore, target gene set of miR-138 and miR-433 , its co-expressed mRNAs in ROSMAP, and differentially expressed mRNAs of HD reveal four overlap genes (CASP7, CNOT6L, TMED and FERMT2). In summary, our study provides new insights into biomarker of Huntington’s disease by analyzing the cross-sectional miRNA expression data in blood.

overall_design: In this study, total RNAs for 233 blood samples, incl. 113 controls and 120 HD, were requested from PREDICT-HD consortium. We then used NanoString to measure the miRNA expression levels of these samples. After normalization and filtering, we called differential expressed miRNAs between control and HD using SVA, after ajusting the covariates.

first: Zhuo

last: Wang

first: Clemens

last: Scherzer