title: Transcriptome profiling of differentially expressed genes from floral buds and flowers of male sterile and fertile lines in watermelon

status: Public on Jan 04 2016

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

institute: Seoul National University

summary: Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs).

overall_design: This study employed tophat and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 2 tissues obtained from 2 different breeds of watermelon

first: Gungpyo

last: Lee

first: Sun-Ju

last: Rhee


title: MicroRNA expression profile in non-alcoholic fatty liver disease

status: Public on Jan 01 2016

city: Yonago-city

first: Kinya

last: Okamoto

state: Tottori

address: 36-1, Nishi-cho

department: Second Dept. Internal Medicine

country: Japan

institute: Tottori University

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

summary: Simple steatosis (SS) and non-alcoholic steatohepatitis (NASH) are subtypes of non-alcoholic fatty liver disease. The difference in pathogenesis between SS and NASH is still not clear. MicroRNAs (miRNAs) are endogenous, non-coding short RNAs that regulate gene expression. The aim of this study was to examine the relationship of miRNA expression profiles with SS and NASH in animal models and humans.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Animal models  DD Shionogi (DS), Fatty Liver Shionogi (FLS Wild; W), and FLS ob/ob mice were subjected as the normal control, SS model and NASH model, respectively. Male DS mice (Riken BRC No. 03706) were provided by Riken bio-resource center through the national bio-resource project of Japan. Male FLS W and male FLS-ob/ob mice were obtained from Shionogi research laboratories (Shiga, Japan). Animals were housed in a room maintained at a controlled temperature of 24 ± 2 ˚C under a 12-h light-dark cycle. Animals were provided ad libitum access to water and standard pellet feed.   Five male mice of every strain (24 weeks old; mean body weight of DS, FLS W and FLS-ob/ob were 31.1 ± 1.1g, 38.4 ± 3.4g and 56.0 ± 5.0g, respectively) were sacrificed under pentobarbital anesthesia by whole blood collection from the right ventricle. The livers were cut into about 200 mg pieces and fixed in 10% formalin for histological analysis or fresh-frozen in liquid nitrogen and stored at -80 °C in a freezer until use.   miRNA expression analysis  Total RNAs in mouse liver were isolated using TrizolReagent (Life Technologies, California, USA) as described the manufacturer’s protocol. The quality of total RNA samples was checked by applying the RNA Integrity Number (RIN) which is calculated by a proprietary algorithm of the Agilent 2100 Bioanalyzer expert software (Agilent technologies, CA, USA). Only high quality RNA, with RNA integrity number (RIN) greater than 8 and A260/280 and A260/230 greater than 1.8, will be considered for microarray analysis. TaqMan® Array Rodent MicroRNA A Card v2.0 (Thermo Fisher Scientific, MA, USA) was used to assess 375 miRNA expression profiles in mouse liver tissue.

first: Toshiaki

first: Takumi

last: Onoyama

first: Kenichi

last: Miyoshi

first: Manabu

last: Kishina

first: Jun

last: Kato

first: Shiho

last: Tokunaga

first: Taka-aki

last: Sugihara

first: Yuichi

last: Hara

first: Masahiko

last: Koda

first: Keisuke

last: Hino

first: Yoshikazu

last: Murawaki


title: Repressive Histone Marks Renewal Impedes Replication Fork Progression and Contributes To Late Replication in Drosophila

status: Public on Jan 10 2016

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Quantitative analysis of chromatin interactions upon copy number variation at mouse 4E2

city: Cold Spring Harbor

first: Cinthya

middle: J

last: Zepeda-Mendoza

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

type: Expression profiling by high throughput sequencing


title: Quantitative analysis of chromatin interactions upon copy number variation at mouse 4E2 [RNA-seq]

summary: The three-dimensional organization of chromatin has a critical impact on the regulation of gene expression. However, little is known about the effect of DNA copy number variants (CNVs) on chromatin organization. We performed an allele-specific chromatin conformation and gene expression analysis of wild-type (WT) mouse chromosome 4 and an engineered 4.3Mb chromosome 4 deletion in mouse embryonic fibroblasts. A newly developed quantitative framework for the analysis of paired-end 4C-seq data revealed a number of significant differentially interacting regions (DIRs) and higher-order chromatin compaction changes present in the deletion chromosome. Selected DIRs were validated by 3D DNA FISH experiments. We discovered a significant enrichment of CTCF and Smc1 binding sites within DIRs, as well as differentially expressed genes determined by RNA-Seq. Together, our findings highlight the complex effects of a 4E2 CNV on chromatin structure and function, both locally in the deletion chromosome and globally in the WT copy.

overall_design: Examination of chromatin contacts and gene expression in wild type chromosome 4 and a 4.3Mb deletion in chromosome 4 in mouse

first: David

middle: L

last: Spector


title: A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

city: athens

first: panagiotis

last: georgiadis

state: Greece

address: 48 vas costantinou

department: IBMCB

country: Greece

institute: NHRF

type: Methylation profiling by genome tiling array

summary: High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic and analytical pipelines for an efficient systems level analysis and interpretation. In the present study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the -established in transcriptomic microarrays- logarithmic ratio of the Methylated versus the Unmethylated signal intensities, quoted as M-value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures based on coefficient variation measurements of DNA methylation between control and case samples alleviate the impact of technical variation. The results presented here are juxtaposed to those derived by applying classical pre-processing and statistical selection methodologies. Overall, in comparison to traditional approaches, the introduced framework's superior performance in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies.

overall_design: Bisulphite converted DNA from the samples were hybridized to the Illumina Infinium  HumanMethylation450 BeadChip

first: Soterios

middle: A

last: Kyrtopoulos

first: Panagiotis

last: Georgiadis

first: Aristoteis

last: Chatzionnou

first: Emmanouil

last: Sifakis

first: Ioannis

last: Valavanis


title: Luteinizing hormone induces ovulation via tumor necrosis factor α-dependent increases in prostaglandin F2α in a nonmammalian vertebrate

status: Public on Dec 31 2015

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

summary: Ovulation is induced by the preovulatory surge of luteinizing hormone (LH) that acts on the ovary and triggers the rupture of the preovulatory ovarian follicle by stimulating proteolysis and apoptosis in the follicle wall, causing the release of the mature oocyte. In mammals, the pro-inflammatory cytokine tumor necrosis factor α (TNFα) and prostaglandin F2α (PGF2α) are known to be involved in the control of ovulation but their role mediating the pro-ovulatory actions of LH has not been established. Here we show that Lh induces PGF2α synthesis through its stimulation of Tnfα production in trout, a primitive teleost fish. Importantly, trout recombinant Tnfα (rTnfα) and PGF2α recapitulate the stimulatory in vitro effects of salmon Lh (sLh) on contraction, proteolysis and loss of cell viability in the preovulatory follicle wall and, finally, ovulation. Furthermore, all pro-ovulatory actions of sLh are blocked by inhibition of Tnfα secretion or PG synthesis and those of rTnfα are blocked by PG synthesis inhibitors. Therefore, we provide evidence that the Tnfα–dependent increase in PGF2α production is necessary for the pro-ovulatory actions of Lh in a teleost fish. The results from this study shed light onto the mechanisms underlying the pro-ovulatory actions of LH in vertebrates and may prove important in clinical assessments of female infertility.

overall_design: Preovulatory follicles from brook trout from four different females (n = 4) were isolated and incubated in the absence or presence of salmon LH. Total RNA of control and LH-treated preovulatory follicles from each of the four females was analyzed.


title: Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)

status: Public on Dec 30 2015

city: wuhan

first: Fei

last: Guo

address: shizishan

country: China

institute: Huazhong Agricultural Univesity

summary: To gain new insight into the underlying mechanism that may be involved in carotenoid biosynthesis, global gene expression at the transcriptional level was also investigated by RNA-seq analysis. The comparative analysis revealed extensive changes in the gene expression level of the orange-pericarp mutant (MT), which resulted in the down-regulation of 168 genes and the up-regulation of 135 genes. Gene ontology (GO) and KEGG pathway analysis indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids.

overall_design: Total six sample pools: the pericarp of WT and MT in ripe stage, each three biological replicates. The orange-pericarp mutant accumulates large amounts of β-carotene in the pericarp.

first: Xiuxin

last: Deng


title: Oviductal expression data from wild type and Wt1 heterozygous mice

status: Public on Dec 12 2015

city: Jena

first: Abinaya

last: Nathan

address: Beutenberg Str. 11

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: Comparison of gene expression in wild type and Wt1 (Wilms tumor suppressor gene 1) heterozygous knockout mice. Background: in Wt1+/- mice (MF1 strain) litter sizes are significantly smaller than in wild type animals. In addition, we observe retarded embryonic development of pre-implantation embryos that are still within the oviduct. By gene expression analysis we want to elucidate the molecular basis for these phenomena.

overall_design: 3 wild type and 3 heterozygous RNA samples

first: A

first: P

last: Reinhardt

last: Habenicht

first: C

last: Englert


title: Fucoidan alleviates high-fat diet-induced dyslipidemia and atherosclerosis in ApoEshl mice deficient in apolipoprotein E expression

status: Public on Dec 29 2015

city: Kawasaki

first: takashi

last: yokota

address: 1-396,Kosugi-cho, Nakahara-ku

institute: Nippon medical shool

summary:
Fucoidan, a sulfated polysaccharide extracted from brown seaweeds, possesses many biological activities including anti-inflammatory and anti-oxidant activities. We aimed to investigate the protective
effects of fucoidan on dyslipidemia and atherosclerosis in apolipoprotein E-deficient mice (ApoEshl mice) and to elucidate its molecular targets in the liver by using a transcriptomic approach. For 12 weeks,
ApoEshl mice were fed a high-fat diet (HFD) supplemented with either 1% or 5% fucoidan. Fucoidan supplementation significantly reduced tissue weight (liver and white adipose tissue), blood lipid,
total-cholesterol (TC), triglyceride (TG), non-high density lipoprotein-cholesterol (Non-HDL-C), and glucose levels in HFD-fed ApoEshl mice but increased plasma lipoprotein lipase (LPL) activity and HDL-C levels.
Fucoidan also reduced hepatic steatosis levels (liver size, TC and TG levels, and lipid peroxidation) and increased white adipose tissue LPL activity. DNA microarray analysis and quantitative reverse
transcription-polymerase chain reaction demonstrated differential expression of genes encoding proteins involved in lipid metabolism, energy homeostasis,  and insulin sensitivity, by activating Ppara
and inactivating Srebf1. Fucoidan supplementation markedly reduced the thickness of the lipid-rich plaque, lipid peroxidation, and foaming macrophage accumulation in the aorta in HFD-fed ApoEshl mice.
Thus, fucoidan supplementation appears to have anti-dyslipidemic and anti-atherosclerotic effects by inducing LPL activity and inhibiting the effects of inflammation and oxidative stress in HFD-fed ApoEshl mice.

overall_design: Fucoidan were ingested by fed a high-fat diet supplemented with either 1% or 5% fucoidan. lipid and carbohydrate metabolism related gene expression profile in liver of ApoEshl mice was analyzed by DNA microarray.

first: Takashi

last: Yokota

first: Koichi

last: Nomura

first: Mikio

last: Nagashima

first: Naomi

last: Kamimura


title: Quantitative analysis of chromatin interactions upon copy number variation at mouse 4E2 [4C-seq]

first: Cinthya

last: Zepeda-Mendoza

first: David

last: Spector


title: genome-wide profiling of microRNA in PTSD with comorbid depression (PTSD&Dep)

status: Public on Dec 01 2015

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

type: Non-coding RNA profiling by high throughput sequencing

summary: We aimed to examine genome-wide differential expression profiles of miRNA in PTSD&Dep cases versus controls

overall_design: Examined differential expression of miRNAs in 16 cases of PTSD&Dep versus 7 controls with no PTSD and no depression

first: Kerry

last: Ressler


title: Expression data from pancreatic ductal adenocarcinoma (PDAC) cell lines AsPC1, BxPC3 and their cisplatin-resistant derivatives AsPC1-R and BxPC3-R

status: Public on Nov 30 2015

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary:
Cisplatin is a broad-spectrum anticancer drug, which is estimated to be administered to 40-80% of patients undergoing chemotherapy. However, its clinical utility is often limited due to factors that include acquired resistance of cancer cells to cisplatin. Because cisplatin is currently evaluated as a prospective agent for combined chemotherapy of pancreatic ductal adenocarcinoma (PDAC), we have investigated mechanisms involved in the acquired resistance of PDAC cells to cisplatin using gene expression study of two different parental-resistant pairs of PDAC cell lines.
We have developed cisplatin-resistant cell lines AsPC1-R and BxPC3-R from their parental PDAC cell lines AsPC1 and BxPC3, respectively, by culturing them in medium with step-wise increasing concentration of cisplatin. Parental and resistant pairs of PDAC cells were analyzed by whole-transcript gene expression analysis.

overall_design: Cells from adherent subconfluent cultures of parental cell lines AsPC1, BxPC3, and their cisplatin-resistant derivatives AsPC1-R and BxPC3-R (3 replicates per cell line) grown in the absence of cisplatin were harvested and processed for isolation of total cell RNA.


title: Gene expression analysis to characterize similarities and differences in T. canis- or T. cati-induced neurotoxocarosis

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Larvae of Toxocara canis and T. cati show affinities to different tissues within the paratenic host. T. canis preferably migrates to the CNS whereat T. cati prefers muscle tissue. As both species share many characteristics like antigen fractions, reasons for this behaviour as well as underlying pathomechanisms or host reactions towards the respective parasite are unknown. Therefore, it was aimed to characterize the general pathogenesis as well as the respective host's reaction on the transcriptional level to identify similarities and differences between T. canis- and T. cati-infected brains.

overall_design: Transcriptional changes in cerebra as well as cerebella of T. canis- and T. cati-infected C57Bl/6J mice were analysed 42 days post infection. In each infection group, 3 animals were included and 4 animals in the uninfected control.

first: Elisabeth

last: Janecek

first: Esther

last: Wilk

first: Klaus

last: Schughart

first: Christina

last: Strube


title: Genome wide host gene expression analysis in chicken lungs infected with avian influenza viruses

status: Public on Jan 02 2016

city: bhopal

first: Anamika

last: Mishra

state: Madhya Pradesh

address: Anand Nagar

department: Animal Genetics

country: India

institute: NIHSAD

summary: The mechanisms responsible for the molecular pathogenesis of the highly pathogenic avian influenza virus (HPAIV) or low pathogenic avian influenza virus (LPAIV) in avian species remain poorly understood. Thus, global immune response of chickens infected with HPAIV H5N1 (A/duck/India/02CA10/2011) and LPAIV H9N2 (A/duck/India/249800/2010) viruses was studied using microarray to identify crucial host genetic components responsive to these infection. HPAIV H5N1 induced excessive mRNA expression of cytokines (IFNA, OASL, MX1, RSAD2, IFITM5, GBP 1, IL1B, IL18, IL22, IL13, IL12B, CCL4, CCL9, CCL10, CX3CL1 etc) in lung tissues. This excessive cytokine response (cytokine storms) may cause tissue damage and high mortality in chickens. In contrast, the expression levels of most of the cytokines remained unchanged in the lungs of LPAIV H9N2 virus infected chickens. This study indicated the relationship between host cytokines response and their roles in pathogenesis in chickens infected with HPAIVs.

overall_design: Agilent Custom Chicken Gene Expression 8X60k (AMADID: G4102A_059389) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Pradip

middle: B

last: Ranaware

first: Ashwin

last: Raut

first: Diwakar

middle: D

last: Kulkarni

first: Periyasamy

last: Vijayakumar


title: Gene expression profiles in comorbid PTSD and depression

summary: This is a genome-wide differential gene expression survey of cases of comorbid PTSD and depression versus controls

overall_design: We compared genome-wide gene expression profiles of cases of comorbid PTSD and depression to those of controls, adjusting for sex, age, and ancestry via genotypic principal components

middle: P

first: Lynn

last: Almli

first: Bekh

last: Bradley

last: Binder


title: The effects of aging on circadian patterns of gene expression in the human prefrontal cortex

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

institute: University of Pittsburgh

summary: With aging, significant changes in circadian rhythms occur, including a shift in phase toward a “morning” chronotype and a loss of rhythmicity in circulating hormones. However, the effects of aging on molecular rhythms in the human brain have remained elusive. Here we employed a previously-described time-of-death analyses to identify transcripts throughout the genome that have a significant circadian rhythm in expression in the human prefrontal cortex (Brodmann’s areas (BA) 11 and 47). Expression levels were determined by microarray analysis in 146 individuals. Rhythmicity in expression was found in ~10% of detected transcripts (p<0.05). Using a meta-analysis across the two brain areas, we identified a core set of 235 genes (q<0.05) with significant circadian rhythms of expression. These 235 genes showed 92% concordance in the phase of expression between the two areas. In addition to the canonical core circadian genes, a number of other genes were found to exhibit rhythmic expression in the brain. Notably, we identified more than one thousand genes (1186 in BA11; 1591 in BA47) that exhibited age-dependent rhythmicity or alterations in rhythmicity patterns with aging. Interestingly, a set of transcripts gained rhythmicity in older individuals, which may represent a compensatory mechanism due to a loss of canonical clock function. Thus, we confirm that rhythmic gene expression can be reliably measured in human brain and identified for the first time significant changes in molecular rhythms with aging that may contribute to altered cognition, sleep and mood in later life.

overall_design:
Using the resources of the University of Pittsburgh’s Brain Tissue Donation Program, 210 subjects were identified. Samples were obtained after consent from next-of-kin during autopsies conducted at the Allegheny County Medical Examiner’s Office (Pittsburgh, USA). The absence of lifetime psychiatric disorders was determined by an independent committee of experienced clinical research scientists using information from clinical records, toxicology results and a standardized psychological autopsy. Subjects of unwitnessed death were removed from the study. A total of 146 individuals with the following characteristics were analyzed in this study: mean (range) age of 50.7 (16-96) years, 78% male, 85% Caucasian, mean postmortem interval (PMI) for brain collection 17.3 (4.8-28) hours, mean pH 6.7 (5.8-7.6) and RNA integrity number (RIN) 8.0 (5.9-9.6).
For each subject, the right hemisphere was blocked coronally, frozen and stored at -80C. Blocks containing  Brodmann area 11 (BA11) or  Brodmann area 47 (BA47) of the orbital PFC were cut on a cryostat, and cortical gray matter was collected for RNA extraction as previously described. All procedures were approved by the University of Pittsburgh’s Institutional Review Board for Biomedical Research and Committee for Research Involving the Dead.


title: Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus

status: Public on Nov 26 2015

city: Wuhan

first: Jingyin

last: Yu

address: No.2, Xudong Second Road, Wuchang District

department: Department of Genomics and Molecular Biology

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

summary: Background: The fertile and sterile plants are derived from the self-pollinated offspring of the F1 hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus, which possess the identical cytoplasmic genetic material arising from Nsa CMS line. As far as the nuclear genetic background is concerned, both fertile and sterile plants have the complete set of chromosomes from Brassica napus, except one or two members of the added Sinapis arvensis chromosome pair in the fertile plant. To elucidate gene expression and regulation caused by the A and C subgenomes, the alien chromosome and cytoplasm from S. arvensis during the development of young floral buds, we performed genome-widely high-throughput transcriptomic sequencing between young floral buds of sterile and fertile plants.  Results: In this study, equal amount of RNA taken from young floral buds of sterile and fertile plants were sequenced using Illumina/Solexa platform. A total of 4,415,866 and 4,244,140 raw tags were obtained in sterile plant (Ste) and fertile plant (Fer) libraries, respectively. After filtering out low quality data, a total of 2,760,574 and 2,714,441 clean tags remained from the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. To identify the genes corresponding to the distinct tags in each library, all distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. Many genes showed substantial differences in expression between the two libraries. In total, there were 3231 genes of B. rapa and 3371 genes of B. oleracea which were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further understand the biological functions of differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor mapped to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and confirmed their expression levels by quantitative RT-PCR, fourteen of the fifteen genes showed expression patterns consistent with the digital gene expression (DGE) data.  Conclusions: A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specially expressed in Fer will help to dig those genes with desirable agronomic traits from wild species.

overall_design: mRNA profiles of fertile buds (Fer) and sterile buds (Ste) were generated by deep sequencing.

first: Xiaohong

last: Yan


title: Signaling through MyD88 in bone marrow-derived cells promotes gastric tumorigenesis by inducing the TLR2/CD14 pathway in tumor cells

status: Public on Dec 15 2015

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

institute: kanazawa university

summary: Gan mice express Wnt1, Ptgs2, and Ptges, which develop inflammation-associated gastric tumors (Oshima et al, Gastroenterology 131: 1086, 2006). We examined the role of MyD88 in tumorigenesis by construction of Myd88-/- Gan mice and bone marrow transplantation into Gan mice from Myd88-/- mice.

overall_design: Total RNA was prepared from wild-type normal glandular stomach (n=3: WT 1–WT 3),  B6 C2mE mice (n=3: C2mE 1–C2mE 3), B6 Gan mice (n=3: Gan1–Gan3), B6 Gan MyD88-/- mice (n=3: Gan 1 (MyD88-/-)–Gan 3 (MyD88-/-)), and B6 bone marrow transplanted Gan mice from Myd88-/- mice (n=3: BMT-Gan 1 (from MyD88-/-)–BMT-Gan 3 (from MyD88-/-)). We used Illumina HiSeq 2000, and examined expression profiles.

first: Yusuke

last: Maeda

first: Kanae

last: Echizen

first: Yoichi

last: Yamada

first: Masanobu

last: Oshima


title: TCDD-induced hepatic transcriptomic responses in transgenic AHR-variant mice

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

summary: The aryl hydrocarbon receptor (AHR) mediates most of the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, TCDD toxicity phenotypes vary widely between species, strains and even between sexes within a strain. While the exact reasons for this variation remain unclear, it is thought to be related to differences in the structure of the AHR. Previous studies comparing the downstream effects of TCDD exposure between animals with different AHR isoforms have been confounded by the genetic differences between these model systems. To address this issue conclusively, we evaluated three transgenic mouse lines, each of which express a different rat AHR isoform (rWT, DEL, and INS) from two strains of rat with highly divergent TCDD-susceptibilities, within identical genetic backgrounds. Here we profile hepatic transcriptomic responses following exposure to TCDD, and use these to identify transcripts associated with toxicity. We have confirmed that the variation in toxicity is inherent to the AHR isoform. Additionally, we note the enhanced activity of the modified transactivation domain of the DEL isoform, relative to the INS isoform, and provide further evidence that the INS isoform is responsible for the high resistance to TCDD observed in H/W rats. We also uncover several candidate genes that were consistently differentially expressed in TCDD-sensitive mice and rats.

overall_design: Adult male transgenic mice were treated by gavage with 0, 125, 250, 500, or 1000 µg/kg TCDD dissolved in corn oil vehicle. Mice were euthanized 4 days following treatment and liver tissue was harvested for analysis. RNA was isolated and the transcriptome for each animal assayed on separate microarrays.

first: Aileen

last: Lu

first: Cindy

middle: Q

last: Yao

first: John

last: Watson

first: Raimo

last: Pohjanvirta

first: Paul

middle: C

last: Boutros


title: Rhizoctonia solani AG8 infection of wheat seedling roots

status: Public on Nov 04 2015

city: Bentley

first: James

last: Hane

state: WA

address: Kent Street

department: Environment and Agriculture

country: Australia

institute: Curtin University

summary: Rhizoctonia solani is a nectrotrophic fungal pathogen that causes billions of dollars of damage to agriculture worldwide and infects a broad host range including wheat, rice, potato and legumes.  In this study we identify wheat genes that are differentially expressed in response to the R. solani isolate, AG8-1, using microarray technology.  A significant number of wheat genes identified in this screen were involved in ROS production and redox regulation.  Levels of ROS species were increased in wheat root tissue following R. solani infection as determined by NBT, DAB and titanium sulphate measurements/stainings.  Pathogen/ROS related genes from R. solani were also tested for expression patterns upon wheat infection.  TmpL, a R. solani gene homologous to a gene associated with ROS regulation in Alternaria brassicicola, and OAH, a R. solani gene homologous to oxaloacetate acetylhydrolase which has been shown to produce oxalic acid in Sclerotinia sclerotiorum, were highly induced in R.solani when infecting wheat.  We speculate that the wheat germin-like protein (GLP) is induced to inactivate the oxalic acid that is produced by the R. solani OAH.

overall_design: infected vs mock-infected seedlings, 3 biological replicates

first: Rhonda

last: Foley

first: Brendan

middle: N

last: Kidd

middle: K

first: Jonathan

last: Anderson

first: Karam

last: Singh


title: TLR4/NF-κB-responsive microRNAs in a mouse model of skeletal muscle ischemia-reperfusion injury

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
TLR4/NF-κB signaling plays a central mediator in response to danger signals released in the muscle ischemia-reperfusion injury (IRI). This study was designed to profile TLR4/NF-κB-responsive microRNAs (miRNAs) in the skeletal muscles following IRI.
Following 2 h of ischemia and subsequent reperfusion for indicated times (0 h, 4 h, 1 d, and 7 d) of the isolated thigh skeletal muscles based on femoral artery perfusion of C57BL/6, Tlr4–/–, and NF-κB–/–mice, the muscle specimens were analyzed with an miRNA array to detect the TLR4/NF-κB-responsive miRNAs.

overall_design: Male C57BL/6 mice (10–12 weeks of age, 22–35 g) were purchased from BioLasco (Taiwan). Tlr4–/– (C57BL/10ScNJ) and NF-κB–/– (B6.Cg-Nfkb1tm1Bal/J) mice were purchased from Jackson Laboratory (Bar Harbor, ME, USA). All housing conditions were established and surgical procedures, analgesia, and assessments were performed in an AAALAC-accredited, SPF facility following national and institutional guidelines. Animal protocols were approved by the IACUC of Chang Gung Memorial Hospital. Mice were anesthetized with an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine, given as an intraperitoneal injection (0.01 ml/g body weight). After the induction of anesthesia, the mice were restrained in a supine position on a heating pad to maintain body temperature at 37°C. The quadriceps muscle perfused based on the femoral artery of the mouse was carefully isolated away from the femoral bone and the underlying adductor muscle group. In the ischemic group, ischemia was induced by placing a microvascular clamp carefully across the proximal site of vascular pedicle for 2 h and then the microvascular clamp was removed. Good vascular inflow and outflow through the pedicle was verified under direct magnified vision. In the sham-operated control group, the muscle was isolated without microvascular clamp being applied. The incision wound was closed with interrupted sutures (4-0 nylon) and the animals were allowed to awaken in the remaining periods of reperfusion. The harvested muscles were frozen in isopentane chilled in liquid nitrogen and stored at -80°C. For the miRNA array experiments, the isolated skeletal muscles of C57BL/6 mice after 2 h of ischemia and 0 h, 4 h, 1 d, and 7 d of reperfusion as well as of Tlr4–/–and NF-κB–/– mice after 2 h of ischemia and 1 d of reperfusion were used in 3 replicate experiments.

first: Johnson

last: Yang

first: Shao-Chun

last: Wu

first: Cheng-Shyuan

last: Rau


title: Targeted mRNA gene expression profiling of primary tumors and lung metastases using a mouse model of spontaneous metastatic mammary carcinoma

status: Public on Nov 02 2015

city: Frederick

first: David

last: Salomon

state: MD

address: 1050 Boyles Drive, Bldg. 560 Room 1246

department: NCI

institute: NIH

summary: In this study, we explored the molecular basis of site-specific metastasis of breast cancer to the lungs in a clinically relevant model based on the JygMC(A) cell line. In this dataset, we include expression data from JygMC(A) primary mammary tumors (carcinoma and EMT-like areas), lung metastases, normal mammary glands and normal lung parenchyma.

overall_design: In total, 36 laser microdissected samples were analyzed. We built a customized NanoString nCounter® Gene Expression Codeset of 104 genes and controls that contained significant embryonic core stem cell genes and EMT-MET markers. This customized assay was performed to target gene expression profiling on the following samples: primary tumor carcinoma, primary tumor EMT, lung metastasis, normal mammary gland and normal lung parenchyma.

first: Nadia

last: Pereira de Castro

first: Anand

last: Merchant

first: Natalie

last: Abrams


title: Global gene expression profiling of primary tumors and lung metastases using a mouse model of spontaneous metastatic mammary carcinoma

summary: In this study, we explored the molecular basis of site-specific metastasis of breast cancer to the lungs in a clinically relevant model based on the JygMC(A) cell line. In this dataset, we include expression data from JygMC(A) primary mammary tumors, lung metastases, normal mammary glands and normal lung parenchyma.

overall_design: In total, 28 samples were analyzed. We generated the following pairwise comparisons using Partek Genomic Suite 6.6 (PGS, Version 6.6, Partek Inc.): PT vs. NMG; PT vs. LM; LM vs. NL; LM vs. NMG. Genes with an FDR-adjusted p-value < 0.05 and a fold-change > 2 were selected.


title: Investigation of signaling requirements underlying cardiac induction of human pluripotent stem cells

status: Public on Nov 12 2015

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

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

overall_design: Refer to individual Series


title: Expression data from the kidney tissue of Han:SPRD rats

status: Public on Dec 02 2015

city: Zurich

first: Meliana

last: Riwanto

address: Winterthurerstrasse 190

department: Nephrology

country: Switzerland

institute: University of Zurich

summary:
Han:SPRD rats carry a missense mutation in Anks6 (also called Pkdr1), leading to an R823W substitution in SamCystin, a protein that contains ankyrin repeats and a sterile alpha motif (SAM). Han:SPRD Cy/+ rats develop a slowly progressing form of PKD which resembles phenotypically human ADPKD.
We used microarrays to examine alterations in the renal gene expression in a rodent model of PKD, namely the Han:SPRD rat.

overall_design: We performed microarray gene expression analysis on mRNA transcripts from kidney tissues from ten-week old heterozygous Han:SPRD Cy/+ and wild-type +/+ male rats.

first: Rudolf

last: Wuethrich


title: Genome-wide screening of mRNA expression in leprosy patients

status: Public on Oct 30 2015

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

summary:
In this study, a comprehensive assessment of human mRNA was performed on leprosy skin lesions using DNA chip microarrays, which included the entire spectrum of the disease along with its reactional states. Sixty-six samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) and nine skin biopsies from healthy
individuals were used as controls (CC) (ages ranged from 06 to 83 years, 48 were male and 29 female). The evaluation identified differentially expressed mRNAs [Fold Change (FC)≥2.0, p<0.05] in disease lesions versus healthy controls or between them. Some of these genes were validated by RT-PCR and/or immunohistochemistry.

overall_design: The sequence of events for this study followed the order below. Patients who were treated for leprosy were examined by leprologists and submitted to two biopsy procedures. One biopsy was processed for histopathological analysis, bacilloscopy and immunohistochemistry (IHC), the other was immediately stored in RNAlater® solution (Ambion) for further RNA extraction. Sixty-eight samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) were selected for analysis. In addition, nine skin biopsies from healthy individuals were usedas controls (CC). Differentially expressed genes identified in the cDNA microarray assay were validated by quantitative RT-PCR and IHC.

first: Andrea

middle: F

last: Belone

first: Patrícia

middle: S

last: Rosa

first: Ana-Paula

last: Trombone

first: Luciana

last: Fachin

first: Cássio

last: Guidella

first: Somei

last: Ura

first: Jaison

last: Barreto

first: Mabel

middle: G

last: Pinilla

first: Dirce

middle: M

last: Carraro

first: Fernando

last: Soares

first: Cleverson

middle: T


title: mRNA-Seq Expression profiling of human post-mortem BA9 brain tissue for Huntington's Disease and neurologically normal individuals

status: Public on Dec 08 2015

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary: Huntington’s Disease (HD) is a devastating neurodegenerative disorder that is caused by an expanded CAG trinucleotide repeat in the Huntingtin (HTT) gene. Transcriptional dysregulation in the human HD brain has been documented but is incompletely understood. Here we present a genome-wide analysis of mRNA expression in human prefrontal cortex from 20 HD and 49 neuropathologically normal controls using next generation high-throughput sequencing. Surprisingly, 19% (5,480) of the 28,087 confidently detected genes are differentially expressed (FDR<0.05) and are predominantly up-regulated. A novel hypothesis-free geneset enrichment method that dissects large gene lists into functionally and transcriptionally related groups discovers that the differentially expressed genes are enriched for immune response, neuroinflammation, and developmental genes. Markers for all major brain cell types are observed, suggesting that HD invokes a systemic response in the brain area studied. Unexpectedly, the most strongly differentially expressed genes are a homeotic gene set (represented by Hox and other homeobox genes), that are almost exclusively expressed in HD, a profile not widely implicated in HD pathogenesis. The significance of transcriptional changes of developmental processes in the HD brain is poorly understood and warrants further investigation. The role of inflammation and the significance of non-neuronal involvement in HD pathogenesis suggest anti-inflammatory therapeutics may offer important opportunities in treating HD.

overall_design: 20 Huntington's Disease and 49 neurologically normal control samples from post-mortem human subjects

first: Richard

last: Myers

first: Andrew

last: Hoss


title: Comparison of gene expression changes in Streptococcus pyogenes in the presence of zinc

city: St Lucia

first: Cheryl-lynn

middle: Yanwen

last: Ong

state: QLD

address: Cooper Road, Building 76, Rm 125

department: School of Chemistry and Molecular Biosciences

institute: The University of Queensland

summary:
Manuscript title: Zinc disrupts central carbon metabolism and capsule biosynthesis in Streptococcus pyogenes.

Macrophages and neutrophils release free zinc to eliminate phagocytosed bacterial pathogens. The study investigates the effect of how zinc toxicity affects Streptococcus pyogenes. Therefore, a microarray analysis was performed in S. pyogenes cells to determine gene expression changes when exposed to high levels of zinc. We discovered that a pathway involved in tagatose-6-phosphate metabolism was upregulated when the cells are under zinc stress.

overall_design: 3 biological replicates of each condition tested were performed.

first: Mark

last: Walker

first: Alastair

last: McEwan


title: Expression data from Bama minipig hearts - high-fat, high-sucrose diet

status: Public on Oct 31 2015

city: beijing

first: Jihan

last: Xia

state: beijing

address: No. 2 Yuanmingyuan West Road, Beijing,

institute: Chinese academy of agrigultural sciences

summary:
In order to study the heart disorder that the long term, high energy diet caused, Bama miniature pigs were fed a high-fat, high-sucrose diet for 23 months. These pigs developed symptoms of metabolic syndrome and showed cardiac steatosis and hypertrophy with a greatly increased heart weight (1.82-fold, P<0.05) and heart volume (1.60-fold, P<0.05) compared with the control pigs.
To understand the molecular mechanisms of cardiac steatosis and hypertrophy, nine pig heart cRNA samples were hybridized to porcine GeneChips.

overall_design: The control group consisted of 6 Bama pigs fed a control diet, and the HFHSD group comprised 6 pigs that were induced with a HFHS diet, which included 37% sucrose, 53% control diet and 10% pork lard. The pigs were fed twice every day and provided water ad libitum for 23 months. The pigs were fasted for 12 hours and euthanized with ketamine and xylazine. Pig hearts from the HFHSD group pigs (120, 126, 138, 140, 144, and 146) and three control group pigs (157, 159, and 161)  were sampled and preserved in liquid nitrogen and then for RNA extraction and hybridization on Affymetrix microarrays.

first: Shulin

last: Yang

first: Li

last: Kui


title: Whole genome transcriptomic experiments in mice heart development system

status: Public on Nov 17 2015

city: Chicago

first: Xinan

middle: Holly

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

summary: In order to understand genes expressed during posterior second heart field (pSHF) development, we performed microdissections of the region for transcriptomic analysis at mouse embryonic day 9.5.

overall_design: RNA-sequencing of microdissected posterior second heart field samples at mouse embryonic day 9.5 from 5 wildtype samples.

middle: H

first: Jeffrey

last: Steimle

first: Junghun

last: Kweon

first: Ivan

last: Moskowitz


title: Combinatorial effects of estrogen with progestogens or androgen in the breast cancer cell line ZR-75-1

status: Public on Oct 18 2015

city: Woodville South

first: Eleanor

last: Need

state: SA

address: 28 Woodville Rd

department: Discipline of Surgery

institute: The University of Adelaide

summary: Cells were cotreated with dihydrotestosterone, progesterone or medroxyprogesterone acetate and estrdiol to assess the combinatorial effects of hormone exposure in breast cancer cells

overall_design: Cells were plated in hormone stripped media for 56h, followed by treatment for 16h with 10nM of the nominated hormone(s)

first: Grant

last: Buchanan


title: Modulation of the transcriptional response to TNF-alpha in the human melanoma cell line MZ7 by MITF

status: Public on Oct 29 2015

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital Bonn

summary:
We analyzed the transcriptional response of the human melanoma cell line MZ7 to TNF-alpha (24 hours) in a dose-dependent manner (TNF-alpha 10U/ml, 100U/ml, 1000U/ml) either transfected with control siRNA (siNT = non-targeting siRNA) or transfected with siRNAs (pool of 4 active and independent siRNAs) against the melanocytic transcription factor and lineage oncogene MITF. (Microphthalmia-associated transcription factor).
The experiment was performed as biological duplicate. As MITF is critical for melanoma cell state control, we aimed to explore how MITF expression intersects with inflammation-induced plasticity pathways in melanoma.

overall_design: Total RNA was obtained from siRNA/TNF-treated MZ7 melanoma cell lines at various conditions and global gene expression profiling was done using the Illumina Human HT12 v4 platform.

first: Stefanie

last: Riesenberg

last: Hölzel


title: microRNA miR-142-3p induced expression changes in MDA-MB-231 breast cancer cells

status: Public on Nov 16 2015

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

summary: MicroRNAs (miRNAs, micro ribonucleic acids) are pivotal post-transcriptional regulators of gene expression. These endogenous small non-coding RNAs play significant roles in tumorigenesis and tumor progression. miR-142-3p expression is dysregulated in several breast cancer subtypes. We aimed at investigating the role of miR-142-3p in breast cancer cell invasiveness. Supported by transcriptomic Affymetrix array analysis and confirmatory investigations at the mRNA and protein level, we demonstrate that overexpression of miR-142-3p in MDA-MB-231, MDA-MB-468 and MCF-7 breast cancer cells leads to downregulation of WASL (Wiskott-Aldrichsyndrome-like, protein: N-WASP), Integrin-aV, RAC1, and CFL2, molecules implicated in cytoskeletal regulation and cell motility. ROCK2, IL6ST, KLF4, PGRMC2 and ADCY9 were identified as additional targets in a subset of cell lines. Decreased matrigel invasiveness was associated with the miR-142-3p-induced expression changes. Confocal immunofluorescence microscopy, nanoscale atomic force microscopy and digital holographic microscopy revealed a change in cell morphology as well as a reduced cell volume and size. A more cortical actin distribution and a loss of membrane protrusions were observed in cells overexpressing miR-142-3p. Luciferase activation assays confirmed direct miR-142-3p-dependent regulation of the 3'-untranslated region of ITGAV and WASL. siRNA-mediated depletion of ITGAV andWASL resulted in a significant reduction of cellular invasiveness, highlighting the contribution of these factors to the miRNA-dependent invasion phenotype. While knockdown of WASL significantly reduced the number of membrane protrusions compared to controls, knockdown of ITGAV resulted in a decreased cell volume, indicating differential contributions of these factors to the miR-142-3p-induced phenotype. Our data identify WASL, ITGAV and several additional cytoskeleton associated molecules as novel invasion-promoting targets of miR-142-3p in breast cancer.

overall_design: Biological triplicates of the human breast cancer cell line MDA-MB-231 were transiently transfected with miR-142-3p precursors (ABI) or a control miRNA. miRNA was prepared 72h after transfection, reverse transcribed, and analyzed by Affymetrix GeneChip Human Gene 1.0 ST arrays. Expression changes in selected targets significantly regulated in the Affymetrix screening were confirmed independently in miR-142-3p-transfected MDA-MB-231, MDA-MB-468 and MCF-7 cells by qPCR and Western blotting. Significantly regulated targets included WASL, ITGAV, RAC1, CFL2, IL6ST, PGRMC2, ROCK2, KLF4 and ADCY9.

first: M

last: Goette

first: A

last: Schwickert

first: E

last: Weghake

first: K

last: Brueggemann

last: Engbers

first: B

last: Brinkmann

last: Kemper

first: J

first: C

last: Stock

last: Ebnet

first: L

last: Kiesel

last: Riethmueller


title: Identification of c-Jun dependent genes downstream of acute MITF loss in the context of inflammatory signals in the human melanoma cell line Ma-Mel-15

summary:
Ma-Mel-15 human melanoma cell cultures were transiently transfected (RNAiMax, Lipofectamin) with control siRNA, siRNA against MITF (pool of 4 siRNAs), siRNA against c-JUN (pool of 4 siRNAs) or combinations of siMITF and siJUN. Cells were then either treated with TNF-alpha (1000U/ml) for 24 hours or left untreated.
The experiment was performed as biological duplicates. We aimed to determine how c-JUN cooperates with acute MITF-loss in human melanoma cells to increase inflammatory responsiveness and cell plasticity.

overall_design: Total RNA was obtained from siRNA/TNF-treated Ma-Mel-15 melanoma cell lines and global gene expression profiling was done using the Illumina Human HT12 v4 platform.


title: Cardiac differentiation time-courses of human ES cells using distinct initial induction conditions

status: Public on Nov 13 2015

first: Boris

last: Greber

summary: A simultaneous stimulation of the Activin / FGF, BMP, and WNT pathways is required for promoting most efficient mesoderm induction in human embryonic stem cells, as well as for subsequent differentiation into cardiomyocytes. To reveal the contributions of three of these signaling pathways to mesoderm formation and cardiac induction, comparative differentiation time-courses were recorded, varying the combinations of signaling factors administered to the cells during the first day of differentiation: FGF (F) + BMP (B) + WNT (W) treatment during the first 24 hours, or FGF + BMP, or BMP + WNT, or FGF + WNT

overall_design: Total RNA isolated from differentiating in-vitro samples at the indicated time-points and of undifferentiated human ES cells before the induction of differentiation

first: Greber

last: Boris


title: The developmental transcriptome of Dictyocaulus viviparus

status: Public on Oct 09 2015

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

institute: McDonnell Genome Institute at Washington University

summary:
Purpose: The goal of this study was to track fluctuations in gene expression across all defined life cycle stages of the cattle lungworm Dictyocaulus viviparus.
Methods: Batches of worms from a Hannover, Germany strain were harvested in duplicate as eggs, L1, L2, L3, L4, hypobiotic L5, mixed-sex L5, male L5, female L5, mature males and mature females. RNA was isolated, reverse transcribed and sequenced on the Illumina platform. Finally, reads were mapped to the D. viviparus draft genome assembly and read counts associated with each feature were used to estimate gene expression levels and predict differential gene expression at various transitional points across the life cycle.
Results: Principal component analyses indicated that major gene expression shifts occur upon hatching, infection of the bovid host, and sexual maturation.

overall_design: Gene expression was assessed at various timepoints in the D. viviparus life cycle by high throughput sequencing, in duplicate, using Illumina HiSeq technology.  Raw data for this experiment was submitted as the SRA Study accession SRP007900 (BioProject accesion: PRJNA72587)

first: Christian

last: Strube


title: Next Generation Sequencing Facilitates Quantitative Analysis of oocyte, sperm, 2PN embryos derived from WT, Dicer cKO and Drosha cKO small non-coding RNAs

status: Public on Oct 08 2015

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare small non-coding RNA profiling (snRNA-seq) in WT oocyte, sperm and 2PN stage embryos to those sperm and 2PN stage embryos derived from WT, Dicer cKO and Drosha cKO. We further study the roles of sperm-borne small RNA on fertilization and pre-implantation embryonic development.
Methods: Small RNA profiles of adult wild-type (WT) oocytes, adult WT sperm, 2PN stage embryos, adult Dicer cKO/Drosha cKO sperm, 2PN stage embryos were generated by deep sequencing in duplicate, using Ion Torrent Proton. The sequence reads that passed quality filters were analyzed at the small RNA level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 small RNA (miRNA and endo-siRNA) in the oocyte, sperm and 2PN stage of WT and Dicer cKO/Drosha cKO mice with BWA workflow and 34,115 transcripts with TopHat workflow.  Approximately 47% of the miRNAs showed differential expression between the WT and Dicer cKO sperm, ~52% of miRNAs were shown dysregulated in Drosha cKO sperm compared to those in WT sperm with a fold change ≥2.0 and p value <0.05. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of small non-coding RNAs (miRNAs) in sperm and demonstrated that sperm-borne small RNAs are important for fertilization and early embrynic develoment, with biologic duplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of small RNAs profiles in mouse sperm, oocytes and 2PN stage of embryos. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of small RNA contents within sperm or oocytes/embryos. We conclude that RNA-seq based small RNAs characterization in gametes would expedite genetic network analyses and permit the dissection of complex biologic functions during fertilization and embryonic development.

overall_design: Small non-coding profiles of oocytes, sperm and 2PN stage of embryos derived from adult WT and Dicer cKO/Drosha cKO mice were generated by deep sequencing, in duplicate, using Ion Torrent Proton.

first: Shuiqiao

last: Yuan

first: Chong

last: Tang

first: Tian

last: Yu


title: miRNA gene expression profiling of primary tumors and lung metastases using a mouse model of spontaneous metastatic mammary carcinoma

first: David

last: Salomon

summary: Expression profiling of a total of 566 miRNA genes and controls in 24 laser microdissected samples (normal lung parenchyma, normal mammary glands, lung metastases, primary tumor carcinoma and primary tumor EMT) and Jyg MC (A) GFP/Luc cells and spheres

overall_design: Laser-capture microdissection combined with NanoString gene expression assays  of microRNAs  revealed overexpression of either epithelial or mesenchymal markers in epithelial and spindle-like cell regions, respectively

first: Nadia

last: Pereira de Castro

first: Anand

last: Merchant

first: Natalie

last: Abrams


title: Rapamycin induces chromosome reorganization and increases cytokine production in normal human fibroblasts

status: Public on Oct 15 2015

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

institute: University of Saskatchewan

summary: We report the effects of Rapamycin treatment on the transcriptome of normal human dermal fibroblasts isolated from foreskin (designated 2DD). We sequenced mRNA from 2 replicates of proliferative (PRO) quiescent (QUI, serum starved) or treated with 500nM Rapamycin for 5 days (RAP). Comparative analyses with PRO transcripts a baseline indicate that genes that changed expression from Rapamycin treated fibroblasts are significantly different from those of quiescence cells. Rapamycin treated cells showed a significant enrichment for cytokines from the Il-6 cascade.

overall_design: Examination of mRNAs from proliferative, quiescent (serum starvation) and Rapamycin (5oonM, 5days) treated 2DD normal human dermal/foreskin fibroblasts.

middle: A

last: Mitchell

middle: E


title: DNA Methylation Sequencing of Prostate Tumors Reveals Possible Molecular Mechanisms for Cancer Aggressiveness

status: Public on Nov 01 2015

city: Houston

first: Angela

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: A major challenge in the clinical management of prostate cancer is the inability to definitively diagnose indolent versus aggressive cases. Contributing to this challenge is a lack of basic science understanding of the molecular basis behind aggressiveness subtypes in prostate cancer. DNA methylation is the epigenetic addition of a methyl group to the DNA base cytosine and has been found to regulate cell proliferation and environmental adaptation. We hypothesized that DNA methylation changes are a mechanism by which an aggressive cancer attains phenotypes that distinguish it from indolent cases via disruption of regulatory networks. This hypothesis was tested by comparing DNA methylation between benign prostate and both low grade (Gleason score 6) and high grade (Gleason score 8 to 10) groups. Methylome-wide next generation sequencing was performed on formalin-fixed paraffin embedded (FFPE) samples from radical prostatectomy cases using MBD-isolated genome sequencing (MiGS). This technique uses a DNA methylation binding protein (MBD) to purify fragments from a genomic library with a high level of CpG DNA methylation. These fragments were then sequenced via next generation sequencing, the reads were aligned to a reference genome, and then the reads were counted within non-overlapping 50bp windows genome wide. Statistical analysis was then performed on these windowed counts to produce differentially methylated regions (DMRs).

overall_design: MBD-isolated Genome Sequencing (MiGS) for groups of benign prostate (from cystoprostatectomy), low grade prostate cancer (from radical prostatectomy with Gleason Score 6), and high grade prostate cancer (from radical prostatectomy with Gleason Scores 8 to 10) in both European Americans and African Americans

first: Jeffrey

last: Bhasin

first: Lars

last: Matkin

first: Margaret

last: Taylor

first: Byron

last: Lee

first: Cristina

last: Magi-Galluzi

first: Eric

last: Klein

first: Bo

last: Hu

first: Yaomin

last: Xu


title: Evolution of robustness to protein mistranslation by accelerated protein turnover

status: Public on Nov 06 2015

city: Aveiro

first: Ana

middle: Rita

last: Bezerra

address: Campus Universitário Santiago

department: Health Sciences

country: Portugal

institute: University of Aveiro

summary: To investigate how organisms mitigate the deleterious effects of mistranslation during evolution, a mutant tRNA was expressed in S. cerevisiae. The expression of Candida Ser-tRNACAG from a low copy plasmid in S. cerevisiae promoted mistranslation events by random incorporation of both serine and leucine at CUG codons. As mistranslation causes an overload of the protein quality pathways, it disrupts cellular protein homeostasis leading to a major fall in fitness. Laboratory evolutionary experiments were performed to study whether the fitness cost of mistranslation can be lowered. We also wanted to identify the cost-reduction strategy: reducing the frequencies of errors (mitigation), or increasing tolerance to errors (robustness), either by global or local activities.

overall_design: Gene expression was measured in the ancestor (non-evolved) lineage in two different situations: 1) carrying an empty vector and 2) expressing the mutant Ser-tRNACAG. Gene expression was also measured in three ambiguously evolved lineages (B3, D11, H9) in both situations (carrying an empty vector and expressing the mutant tRNA). Three independent experiments were performed for each lineage. Non-evolved strain with empty vector was used as control sample.

middle: R

first: Dorottya

last: Kalapis

first: Manuel

last: Santos

first: Csaba

last: Pal

first: Zoltán

last: Farkas

first: Peter

last: Horvath

last: Bódi

first: Andreea

last: Daraba

first: Béla

last: Szamecz

first: Ivo

last: Gut

first: Mónica

last: Bayes


title: Gene-profile comparison of wt and Ifnb–/– cerebellar granular neurons

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

summary:
Interferon-b (IFN-b) belongs to the type I interferon family of cytokines and via binding to its receptor, interferon-a/b-receptor (IFNAR), it exerts immunoregulatory effects such as anti-viral and anti-inflammatory properties, and clinical benefits for patients with the CNS disease multiple sclerosis.
To compare differentially regulated genes in neurons of interferon-beta knock out mice (Ifnb–/–), we conducted a microarray analysis on cerebellar granular neurons (CGNs) from wt (Ifnb+/+) and Ifnb-/- mice with or without treatment with recombinant IFN-b.

overall_design: Cerebellar granular neurons from wt and Ifnb-–/– mice were cultured in triplicates with or without treatment with IFN-beta and processed for RNA extraction and hybridization on Affymetrix microarray. Thus, 4 types of samples were analysed in triplicates. Our aim was to analyse genes regulated by IFNb in neurons and because CGNs provide a high purity of neuronal cells, this type of neuron culture was choosen.

first: Junyang

last: Wang


title: Cotreatment effects of estrogen with progestogens or dihydrotestosterone in the breast cancer cell line T-74D

first: Eleanor

last: Need

summary: Cells were cotreated with estrogen and dihydrotestosterone, progesterone or medroxyprogesterone acetate to assess the combinatorial effects of progestogens or androgens with estrogen in T47D breast cancer cells

first: Grant

last: Buchanan


title: Expression data from human osteosarcoma cells treated with CDK11 siRNA

status: Public on Oct 07 2015

first: Yong

last: Feng

address: 100 Fruit St

institute: Massachusetts General Hospital

summary: The U-2OS and KHOS osteosarcoma cell lines where seeded onto the 100mm cell culture plate, then treated with CDK11 siRNA (40nM) or nonspecificsiRNA (40nM).  Change with regular medium 24 hour later. Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter  and  Qlucore were used to analyze the microarray data (http://www.genesifter.net/web/; http://www.qlucore.com). Fold change in expression between CDK11 siRNA treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

overall_design: Evalutate the effect of CDK11 siRNA regulaed gene expression in osteosarcoma cells

first: Zhenfeng

last: Duan


title: Can High Grade Serous Ovarian Cancer TCGA Gene Expression Signatures be seen in High Grade Endometrioid or Clear Cell Ovarian Cancer?

status: Public on Oct 01 2015

city: Santa Monica

first: Habib

last: Hamidi

state: CA

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

summary: The goal of the study was to examine the transcriptional profile of ovarian cancer cancers in order to develop validated clinically useful prognostic signatures with the potential to guide therapy decisions.  Fresh frozen samples were prospectively collected from a series of 107 consecutive women with high-grade serous ovarian, primary peritonial, or fallopian tube cancer as well as high grade clear cell and endometrioid cancer who underwent surgery by a gynecologic oncologist at Mayo Clinic between 1994 and 2005. All patients received postoperative chemotherapy with a platinum agent, and 75% received a taxane. All patients signed an Institutional Review Board approved consent for bio-banking, clinical data extraction and molecular analysis. Median follow-up time was 35 months (range, 1-202 months). Fourteen patients (8%) were included in the TCGA study.

overall_design: High grade serous, clear cell and endometrioid ovarian tumors (n=107) were compared to a reference pool of 106 ovarian samples. Mixed reference includes normal, benign, borderline, and malignant sample of various histolgies.

first: Boris

last: Winterhoff

first: Chen

first: Kimberly

last: Kalli

first: Brooke

last: Fridley

first: Judy

last: Dering

first: Hsiao-Wang

last: Chen

first: William

last: Cliby

first: He-Jing

first: Sean

last: Dowdy

first: Gary

last: Keeney

first: Ellen

middle: L

last: Goode

first: Gottfried

last: Konecny


title: Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development

status: Public on Oct 06 2015

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: Here we profile the expression of circRNA in 6 different brain tissues at up to 6 different time-points during fetal porcine development, constituting the first report of circRNA in a large animal. An unbiased analysis reveals a highly complex regulation pattern of thousands of circular RNAs, with a distinct spatio-temporal expression profile. The amount and complexity of the circRNA expression was most pronounced in cortex day 60 from gestation. Here we find 4,634 unique circRNAs expressed from 2,195 genes out of a total of 13,854 expressed genes. These data demonstrate that circRNAs are highly abundant and dynamically expressed in a spatio-temporally manner in porcine fetal brain, suggesting important functions during mammalian brain development.

overall_design: Sequencing of rRNA depleted total RNA from 14 embryonic porcine brain samples, no replicates were done

last: Venø

first: Jørgen

last: Kjems


title: Asthma III

status: Public on Oct 27 2015

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

institute: University of Pittsburgh

summary: Bronchial Epithelial Cells were isolated processed as described (Chu et al., 2002 and Zhao et al., 2011). The objective of the study was to identify differentially expressed genes between normal control (NC), mild-moderate asmathic (notSA) and severe asthmatic (SA) patients.   For demographics data, contact Dr. Sally Wenzel (wenzelse@upmc.edu)

overall_design: Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).  Bronchial alveolar lavage fluids were spun down on 4000 g for 10 minutes. 0.5- 1X10^6 cells were stored in Trizol for RNA extraction. RNA in Trizol solution was extracted using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.

first: Sally

last: Wenzel

first: Naftali

last: Kaminski


title: Identification of MITF-regulated genes in the human melanoma cell line Ma-Mel-15

first: Michael

last: Holzel

summary:
We analyzed the transcriptional response of the human melanoma cell line Ma-Mel-15 either transfected with control siRNA (siNT = non-targeting siRNA) or transfected with siRNAs (pool of 4 active and independent siRNAs) directed against the melanocytic transcription factor and lineage oncogene MITF (Microphthalmia-associated transcription factor).
The experiment was performed as biological duplicates and RNA was isolated 48 hours after siRNA transfection. We aimed to determine novel markers and pathways of melanoma cell plasticity.

overall_design: Total RNA was obtained from siRNA-treated Ma-Mel-15 melanoma cell lines and global gene expression profiling was done using the Illumina Human HT12 v4 platform.

first: Stefanie

last: Riesenberg

last: Hölzel


title: Estrogen priming of breast cancer ZR-75-1 cells results in a unique response to a timecourse of progesterone and medroxyprogesterone acetate exposure

first: Eleanor

last: Need

summary: A timecourse assessment of the response of ZR-75-1 breast cancer cells to progestogens in cells pretreated with estrogen.  P4 treatment in cells pretreated with E2 results in a unique transcriptional response, including upregulation of ErbB growth factor pathways and alteration of the intrinsic subtype of the breast cancer cells.

overall_design: Cells were plated in 10nM estrogen or vehicle for 72h, followed by an overlay treatment for 4, 8 or 16h in triplicate with 10nM progesterone, 10nM medroxyprogesterone acetate, or equivalent vehicle (ethanol). 16hr samples were also treated with 10nM estrogen plus 10nM progesterone or 10nM estrogen plus medroxyprogesterone acetate. RNA was isolated for each sample and hybridised to Affymetrix Human Gene 1.0ST chips.

first: Grant

last: Buchanan


title: Gene expression changes during serum starvation-induced quiescence in human fibroblasts

first: Christopher

last: Eskiw

summary:
We report a comparison of gene expression profiling microarray datasets generated from proliferating and serum-starved quiescent human normal diploid fibroblasts. 4 biological replicates of proliferative and quiescent fibroblasts were subjected to 4 individual dye-swap experiments. Data from these arrays were used in a publication to compare reproducibility between microarrays and RNA-seq; RNA-seq (2 replicates of each proliferative and quiescent fibroblasts) are available through the GEO (accession #: GSE65145). Correlations between both the microarrays and the RNA-seq dataset showed only moderate concordance (r =0.42) in genes exhibiting a ≥5-fold change.
Examination of gene expression profiles from prolfierating and quiescent normal human fibroblasts using microarray technology

overall_design: Analysis used proliferative expression as a baseline and quiescent samples were compared against this. Four independent arrays were used with dye swaps to make direct comparisions between quiescent and prolfierative gene expression levels.

first: C


title: Reprogramming of Polycomb-mediated gene silencing in embryonic stem cells by the miR-290 family and the methyltransferase Ash1l

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Genome-wide analysis of Jarid2, Suz12 and  H3K27me3 profiling in DCR-/- and DCRfl/fl ESCs performed by ChIP-seq and transcriptome analysis by RNA-seq

overall_design: Examination of Jarid2, Suz12 and H3K27me3 changes between DCR-/- and DCRfl/fl ESCs.

first: Chryssa

last: Kanellopoulou

middle: J

last: Lenardo

first: Stefan

last: Muljo


title: Lactobacillus rhamnosus CNCMI-4317 modulates Fiaf/Angptl4 in intestinal epithelial cells and impacts host metabolism

status: Public on Oct 16 2015

city: jouy en josas

first: elsa

last: jacouton

address: Allée de Vilvert

department: MICA

country: France

institute: INRA

summary: Background & Objectives: Identification of news targets for metabolic diseases treatment or prevention was required. In this context, FIAF/ANGPTL4 appeared as a crucial regulator of energy homeostasis. Lactobacilli are often considered to display beneficial effect for their hosts, acting on regulatory pathway. The aim of the present work was to study the effect of several lactobacilli strains on Fiaf gene expression in human intestinal epithelial cells (IECs) and on mice tissues to decipher the underlying mechanisms.  Subjects & Methods: Nineteen lactobacilli strains have been tested on HT-29 cells for their ability to regulate Fiaf gene expression by RT-qPCR. In order to determine regulated pathways, we analyzed the whole genome transcript of IECs. We then validate in vivo bacterial effect using C57BL/6 mono-colonized mice fed with normal chow.   Results: We identified one strain (L. rhamnosus CNCMI-4317, p<0,001) modulating Fiaf expression in IECs. This regulation relies potentially on bacterial surface-exposed molecules and seems to be PPAR-γ independent and PPAR-α dependent. Functional analysis revealed that most of the significant different expressed genes affected by this strain were involved in cellular function and maintenance, lymphoid tissues structure and development or lipids metabolism. The regulation of immune system and lipids and carbohydrates metabolism was also confirmed by overrepresentation of Gene Ontology terms analysis. In vivo, the strain increased FIAF protein (p<0,05) in the serum and tend to up regulate it in distal small intestine (p=0,14). Moreover, the observed induction of IL-7 (p<0,05) suggested a role on immune cells regulation.  Conclusion: We showed that the strain induce Fiaf expression in human IECs and in mice intestine. This bacterial effect is accompanied by modulation of immune response and metabolism providing such a bacterial strain an interesting candidate to modulate metabolic and low grade inflammation disorders.

overall_design: A total of 28 microarrays were analysed: 8 independent cultures of HT-29 cells at different passage number for L. rhamnosus CNCMI-4317 treatment, rosiglitazone (positive control) and DMEM (negative control) and four replicates for L. rhamnosus CNCMI-2493. We used the Illumina human genome microarrays (HumanHT-12 v4 Expression BeadChip Kit, SanDiego,USA).  For each sample, 750ng of labeled cDNA was synthesized from total RNA using Ovation PicoSL WTA System v2 and Encore BiotinIL Module kits (Nugen Technologies, Inc. Leek, The Netherlands).

first: Elsa

last: Jacouton

first: Nuria

last: Mach

first: Julie

last: Cadiou

first: Karine

last: Clëment

first: Joël

last: Doré

first: Johan

last: van Hycklama Vlieg

first: Tamara

last: Smokvina

first: Hervé

last: Blottière


title: Prior infection with Type A Francisella tularensis antagonizes the pulmonary transcriptional response to an aerosolized TLR4 agonist

status: Public on Sep 30 2015

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Prior aerosol exposure to F. tularensis subsp. tularensis, but not the live attenuated strain (LVS) of F. tularensis subsp. holarctica or F. novicida, significantly antagonized the transcriptional response in the lungs of infected mice exposed to aerosolized TLR4 ligand E. coli LPS.

overall_design: The ability of a Toll-like receptor 4 (TLR4) agonist to induce a pulmonary inflammatory response in Francisella-infected animals was examined to distinguish between these two possible mechanisms, and also to investigate potential differences between three Francisella strains that exhibit varying levels of virulence in humans.

first: Kathie-Anne

last: Walters

first: Shawn

last: Skerrett

first: Adrian

last: Ozinsky


title: MEF_OSK_O_KS_T20

status: Public on Sep 17 2015

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

summary:
Next Generation Sequencing with differdent pluripotent transcript factor overexpression in MEF
Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by defined factors. The low efficiency of reprogramming limited the potential application of iPSCs. Here we found that knockdown LSD1 , which demethylates histone H3 Lys 4 or 9 , could increase iPSCs generation. It has been reported that LSD1 interaction with Oct4 which is the core factor of reprogramming. So we try to find out the different of overexpression Oct4 or Kllf4/Sox2 in MEF and LSD1 inhibitor.

overall_design:
Retrovirus-mediated different pluripotent transcript factor overexpression in MEF cells after 4 days collect mRNA profiles processing with Illumina MiSeq;
MEF, Mouse Embryonic Fibroblast
O, MEF infected with Oct4
KS,MEF infected with Klf4 and Sox2
OSK, MEF infected with Oct4 Klf4 and Sox2
T20, MEF infected with Oct4 Klf4 and Sox2 and treated with 20nm LSD1 inhibitor Tranylcypromine

first: Hui

last: Zheng


title: Mononuclear phagocytes in muscle after notexin injury in C57Bl/6, Cx3cr1-/-, Ccl2-/-,Cx3cr1-/-Ccl2-/- mice

status: Public on Sep 29 2015

city: Paris

first: Helene

last: Perrin

address: 91 boulevard de l'hopital

institute: INSERM

summary: Muscle injury triggers inflammation in which infiltrating mononuclear phagocytes are crucial for tissue regeneration. The interaction of the CCL2/CCR2 and CX3CL1/CX3CR1 chemokine axis that guides phagocyte infiltration is incompletely understood. Here, we show that CX3CR1 deficiency promotes muscle repair and rescues Ccl2-/- mice from impaired muscle regeneration as a result of altered macrophage function, not infiltration. Transcriptomic analysis of muscle mononuclear phagocytes reveals that Apolipoprotein E (ApoE) is up-regulated in mice with efficient regeneration. ApoE treatment enhances phagocytosis by mononuclear phagocytes in vitro, and restores phagocytic activity and muscle regeneration in Ccl2-/- mice. Because CX3CR1 deficiency may compensate for defective CCL2-dependant monocyte recruitment by modulating ApoE-dependent macrophage phagocytic activity, targeting CX3CR1 expressed by macrophages might be a powerful therapeutic approach to improve muscle regeneration.

overall_design: Mgl1lo, Mgl1Hi, Ly 6c Hi and F4/80 lo mononuclear phagocyte subsets were isolated from muscles 4 days post Notexin injection;  Mgl1lo and Mgl1Hi mononuclear phagocyte subsets were isolated from untreated muscles of 4 mice strains: C57Bl/6 (WT), Cx3cr1-/-, Ccl2-/-,Cx3cr1-/-Ccl2-/- (pool of 3 mice per strain and per condition).

first: Ludovic

last: Arnold

first: Camille

last: Baudesson de Chanville

first: Marielle

last: Saclier

first: Patricia

last: Hermand

first: Lucie

last: Poupel

first: Elodie

last: Guyon

first: Fabrice

last: Licata

first: Wassila

last: Carpentier

first: José

last: Vilar

first: Remi

last: Mounier

first: Benedicte

last: Chazaud

first: Nora

last: Benhabiles

first: Alexandre

last: Boissonnas

first: Behazine

last: Combadiere

first: Christophe


title: nc886, a noncoding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: nc886 is a 101 nucleotides long non-coding RNA that is also known as a precursor microRNA or a vault RNA. nc886 has been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s). In order to understand potential roles of nc886 in gastric cancer, we performed the knockdown of nc886 in nonmalignant HFE-145 cells and identified and analyzed genes whose expression is activated by nc886 knockdown in gastric cancer.

overall_design: Pre-clinical study

first: Yong-Sun

last: Lee

first: Hyun-Sung

first: Ju-Seog


title: Cancer cell-endothelial intercellular transfer alters the endogenous miRNA profile and phenotype of recipient endothelial cells

status: Public on Sep 04 2015

city: Boston

first: Yamicia

last: Connor

address: 38 Dix Street Unit 1

institute: MIT

summary: Metastasis is a major cause of mortality, and remains a final frontier in the search for a cure for cancer. While there has been much research on the ‘seed’ (metastatic tumor cells) and the ‘soil’ (colonized host tissue), interactions between metastatic cancer cells and stromal endothelial cells, which occur at multiple stages during metastasis, are less well understood. Here we report a dynamic regulation of the endothelium by cancer cells through the formation of nanoscale intercellular membrane bridges, which act as physical conduits for intercellular communication in vitro and in vivo, including horizontal transfer of microRNAs (miRNA). The communication between the tumor cell and the endothelium upregulates markers associated with pathological endothelium, which is reversed by pharmacological inhibition of these nanoscale conduits. These results lead us to define the notion of “metastatic hijack”: cancer cell-induced transformation of healthy endothelium into pathological endothelium via horizontal communication through the nanoscale conduits. Pharmacological perturbation of these nanoscale membrane bridges decreases metastatic foci in syngeneic- and human xenograft-breast cancer models. Targeting the formation of these nanoscale membrane bridges may potentially emerge as a new therapeutic opportunity in the management of metastatic cancer.

overall_design: A miRNA microarray was used to evaluate the transport of endogenous microRNAs. The intercellular transfer-ve and intercellular transfer+ve samples were sorted from the same endothelial cell population with the only difference being the occurrence of intercellular transport. The heat map shows potential miRNA candidates for exogenous transfer on two independent biological replicates. These miRNA candidates were significantly up-regulated in the cells receiving transfer of intercellular contents. HUVECs that were not exposed to cancer cells were used as a baseline control.

first: Sarah

last: Tekleab

first: Shyama

last: Nandakumar

first: Cherelle

last: Walls

first: Yonatan

first: Thomas

last: Reiberger

first: Amjad

last: Husain

first: Or

last: Gadish

first: Venkata

last: Sabbisetti

first: Shelley

last: Kaushik

first: Seema

last: Sehrawat

first: Ashish

last: Kulkarni

first: Harold

last: Dvorak

first: Bruce

last: Zetter

first: Rakesh

middle: K

last: Jain

first: Elazer

last: Edelman

first: Shiladitya

last: Sengupta


title: Capturing the dynamic RNA landscape of the malaria parasite P. falciparum

city: University Park

first: Heather

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we establish a new methodology in Plasmodium falciparum that enables biosynthetic labeleing and capture of sub-population mRNA. As a proof of principle for this novel method, we examine the mRNA dynamics of early gametocyte commitment.

overall_design: Plasmodium falciparum strains 3D7, E5, and F12 were highly synchronized and, at 36 hours post invasion, incubated with 40um 4-TU for 12 hours followed immediately by Trizol total RNA extraction. Total RNA from each timepoint was then biotinylated via a thiol-group on any transcript that incorporated a thiol-modified UTP. Biotinylated transcripts were then separated from total RNA by Streptavidin magnetic beads resulting in a Labeled sample. Any mRNA that was not bound to the beads resulted in an Unlabeled sample. Every 12 hours, two samples were analyzed by Agilent P. falciparum DNA microarray, Unlabeled and Labeled, resulting in 48 individual DNA microarrays (4 for each sample type).

first: Manuela

last: Carrasquilla

first: Manuel

last: Llinás


title: Novel JAZ co-operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection

status: Public on Aug 28 2015

city: Exeter

first: ZhengRong

last: Yang

address: Stocker Road

country: United Kingdom

institute: Exeter University

summary: Pathogens target phytohormone signalling pathways to promote disease. Plants deploy salicylic acid (SA) mediated defences against biotrophs. Pathogens antagonise SA immunity by activating jasmonate signalling, e.g. Pseudomonas syringae pv. tomato DC3000 produces coronatine (COR), a jasmonate (JA) mimic. This study found unexpected dynamics between SA, JA and COR and co-operation between JAZ jasmonate repressor proteins during DC3000 infection. JA did not accumulate until late in the infection process and was higher in leaves challenged with coronatine deficient P. syringae or in the more resistant JA receptor mutant coi1. JAZ regulation was complex and coronatine alone was insufficient to sustainably induce JAZs.

overall_design: RNA was extracted from leaves of wild type Col-0 or the jaz5/10 mutant plants from leaves 6, 8, 12 or 16 hours after challenged with Pseudomonas syringae pv. tomato DC3000.

first: Marta

last: de Torres

first: Bing

last: Zhai

first: Siddharth

last: Jayaraman

first: Garoufalia

last: Eleftheriadou

first: Rebecca

last: Winsbury

first: Ron

first: William

last: Truman

first: Orkun

last: Soyer

first: Saijung

last: Tang

first: Nicholas

last: Smirnoff

first: Murray

last: Grant


title: Transcriptome analysis of Dop1R2 RNAi in Drosophila melanogaster

status: Public on Sep 01 2015

city: Chestnut Hill

first: Kimberly

last: Regna

state: Massachusetts

address: 140 Commonwealth Avenue

department: Biology

institute: Boston College

summary: The process of metamorphosis relies on choreography of temporal and spatial cues that mediate, in which inappropriate activation of many of these genes results in growth defects, developmental delay and death.  Using RNA interference, we have unraveled an essential role for the insect specific dopamine 1(D1)-like receptor Dop1R2 at the late larval/prepupal stage.  We used microarrays to evaluate differentially expressed genes during the early/pale pupal stage and identified up-regulation of families of functionally related genes, including ecdysone induced genes, stress and defense/immune response genes, and those that underlie tissue morphogenesis.

overall_design: Drosophila Dop1R2 RNAi or w1118 control early/pale pupae were collected from crosses maintained at 29C.  These tissues were processed for hybridization on Affymetrix microarrays (DrosGenome1).  Results were used to assess differential expression of genes in Dop1R2 RNAi verses control flies.

first: Peri

last: Kurshan

first: Benjamin

middle: N

last: Harwood

first: Adam

last: Jenkins

first: Chao

middle: Q

last: Lai

first: Marc

last: Muskavitch

first: Alan

last: Kopin

first: Isabelle

last: Draper


title: Expression data from lung tissues of IPF patients and Normal Control

status: Public on Aug 15 2015

city: Beijing

first: Huaping

last: Dai

address: No. 8 Gongren Tiyuchang South Road

institute: Beijing Chao-Yang Hospital-Beijing Institute of Respiratory Medicine, Capital Medical University

summary:
Idiopathic pulmonary fibrosis (IPF) is a progressive lethal interstitial lung disease of unkown etiology with limited effective therapies. The pathogenic mechanisms of IPF remain unkown. Emerging evidences indicate that abnormal behaviors of fibroblasts in IPF are associated with a variety of genetic alterations and aberrant reactivation of developmental signaling pathways.
We compared gene expression profiles in fibrotic lung tissues from IPF patients and normal lung tissues from patients with primary spontaneous pneumothorax using cDNA microarray to examine the mechnisms involved in the pathogenesis of IPF.

overall_design: Lung tissues were obtained from 5 IPF patients and 3 normal control subjects (patients with primary spontaneous pneumothorax). Gene expression profiling was performed using GeneChip Human Transcriptome Array 2.0.

first: Jing

last: Geng


title: Early innate lymphoid cell progenitor

status: Public on Aug 17 2015

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

summary:
We identified a new type of bone marrow progenitors termed early innate lymphoid cell progenitor (EILP) using TCF-1 GFP reporter mice.
We compared the transcriptomes of early innate lymphoid cell progenitors (EILP) with other early progenitors, including HSC, LMPP, CMP, CLP, ETP and DN3.

overall_design: Bone marrow EILP, HSC, LMPP, flt3+ CMP, flt3- CMP, CLP, and thymic ETP and DN3  were obtained by flow cytometric cell sorting. To obtain sufficient numbers of cells for micro-array analysis, we pooled cells from long-term bone marrow chimeric mice. Chimeric mice were constructed by intravenous inoculation of donor bone marrow cells from TCF-1 GFP reporter mice into lethally irradiated (900 rads) CD45-congenic (B6 CD45.1) recipient mice, and were used at 12 weeks of reconstitution. RNA was extracted by Trizol (Qiagen), amplified by Nugene PicoV2 kit (Nugene), and hybridized with Affymetrix Mouse Gene 2.0 ST Array.

first: Q

first: H

last: Xue

first: A

last: Bhandoola


title: Effects on gene expression of nuclear export inhibitor in control and TP53-knockdown cell line of mantle cell lymphoma

status: Public on Aug 18 2015

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: The TP53 wild-type cell line JVM2, representing mantle cell lymphoma (MCL), was transduced to create control or TP53 knockdown (KD) forms. These were then either left untreated or treated with KPT-185, a selective inhibitor of nuclear export (SINE) by XPO1, for gene expression profiling (GEP). Consistent with the observation that KPT-185 was equally toxic to both forms, the majority of gene expression changes resulting from KPT-185 treatment were similar for both forms, even though TP53 is known to be one of the cargo proteins of XPO1. GEP showed downregulation of genes involved in proliferation, consistent with findings of cell cycle analysis and supported by Western blot results. Quantitative proteomics revealed repression of ribosomal biogenesis to be a major TP53-independent effect of KPT-185.

overall_design: GEP data were used for comparison to similarly-prepared B-cell depleted fractions of follicular lymphoma samples.

first: Yoko

last: Tabe

first: Kensuke

last: Kojima

first: Shinichi

last: Yamamoto

first: Michael

last: Andreeff

first: Zhiqiang

last: Wang

first: R

last: Davis


title: Next Generation Sequencing Facilitates Quantitative Analysis of Physcion and Chrysophanol on cucumber powdery mildew Transcriptomes

status: Public on Aug 14 2015

first: Yanping

last: Li

address: No 38 Xueqing Road, Haidian Distric

institute: Novogene institue

summary: We generated 17.6 Gb of high-quality sequencing data (~2 Gb per sample) and catalogued the expression profiles of 12,293 annotated cucumber genes in each sample. The analysis showed differences of transcriptomes between physcion and chrysophanol alone treatment and combination treatment as well as revealed that the combination treatment the most defence-related genes induced expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and defence-related genes that were highly differentiated between the physcion and chrysophanol alone treatment and combination treatment. These genes have known or potential roles in defense response and were enriched in functional gene categories potentially responsible for cucumber resistance. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to defense response.

overall_design: cucumber leaves mRNA profiles of physcion and chrysophanol alone treatment and combination treatment were generated by deep sequencing, in two or triplicate, using Illumina HiSeq2000.

first: Hanwen

last: Ni


title: Regulatory Rewiring Confers Serotype-Specific Hyper-Virulence in the Human Pathogen Group A Streptococcus

status: Public on Aug 24 2015

city: Reno

first: Eric

middle: W

last: Miller

state: Nevada

address: 1664 N Virginia St

department: Microbiology and Immunology

institute: University of Nevada Reno

summary: We sequenced mRNA transcripts from three isogenic M3 serotype GAS strains, parental (MGAS10870), complement (10870::rocAM1), and deletion (10870ΔrocA).  There were no significant changes between the parental and revertant strain.  Comparison of the parental and complemented strain revealed several virulence factors were up-regulated in the parental strain where RocA function was diminished.  We concluded that RocA, through direct or indirect mechanisms, is able to control numerous virulence genes and this lack of RocA regulation increases expression of virulence factors, which contributes to the hyper-virulent state of serotype M3 GAS.

overall_design: GAS strains were grown to mid-exponential phase, total RNA isolated, rRNA depleted, cDNA libraries synthesized, and libraries analyzed using Illumina MiSeq and CLC Genomics Workbench version 7.5.1 RNA-seq software.

first: Paul

last: Sumby


title: Whole rye consumption improves blood and liver n-3 fatty acid profile and gut microbiota composition in rats

status: Public on Aug 06 2015

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

institute: EA-CIDAM 4678

summary: This study in rats was designed to investigate whether whole rhye (WR) can influence the metabolism of n-3 and n-6 long-chain fatty acids (LCFA) and gut microbiota composition. For 12 weeks, rats were fed a diet containing either 50% WR or 50% refined rye (RR). Total bacterial DNA was extracted from fecal and cecal samples (n=5 per group). 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. Amplified DNA was purified and labelled with either Cy3 or Cy5 dye and hybridized on the microarray.

overall_design: A 15 chip study was realized, each corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from either mice fecal and cecal samples. Each probe (4441) was synthetized in three replicates.

first: Fayçal

last: Ounnas

first: Florence

last: Privé

first: Patricia

last: Salen

first: Nadia

last: Gaci

first: William

last: Tottey

first: Luca

last: Calani

first: Letizia

last: Bresciani

first: Noelia

last: López-Gutiérrez

last: Hazane-Puch

first: François

last: Laporte

first: Camilla

last: Melegari

first: Jean-François

last: Brugère

first: Daniele

last: Del Rio

first: Christine

last: Demeilliers

first: Michel

last: de Lorgeril


title: In situ Staphylococcus aureus gene expression in a human prosthetic joint infection

city: Aalborg East

first: Yijuan

last: Xu

address: Fredrik Bajers vej 7H

department: Department of biotechnology, chemistry and environmental engineering

institute: Aalborg University

summary: Little is known about regulation of gene activity of the major pathogen Staphylococcus aureus during actual human infection. Here we characterize the transcriptome using deep RNA sequencing and the metabolome using NMR of S. aureus infected joint fluid derived from an acute human prosthetic joint infection, and compare them with the genome, transcriptome and metabolome of an isolate obtained from the sample grown in vitro (LB medium). The transcriptome indicated that the bacterial infection sustained on a versatile human-cell-based diet consisting of amino acids, glycans and nucleosides, since significant upregulation of genes involved in the catabolic degradation pathways of these compounds were observed in situ. This is consistent with metabolite analysis of the infected joint fluid and of S. aureus culture supernatants where the concentration of most amino acids and some amino sugars were found to be higher in the joint fluid, whereas the concentration of glucose was higher in culture supernatant. Furthermore, presumably because of oxygen limitations in the joint fluid, transcriptomic evidence for fermentation was observed, consistent with the presence of fermentation products (ethanol) in situ. Moreover, many, but not all, of the known virulence factor genes were upregulated in situ as well as the nine genes encoding the iron uptaking siderophore synthesis system.

overall_design: Staphylococcus aureus differential gene expression between growth in situ (infected prosthetic joint fluid, single sample) and in vitro (LB medium, triplicate)

first: Raluca

middle: G

last: Maltesen

first: Lone

last: Larsen

first: Henrik

middle: C

last: Schønheyder

first: Jeppe

last: Nielsen

first: Per

first: Trine

last: Thomsen

first: Kåre