title: Expression data in Fhit-negative cell lines

city: Columbus

first: Kay

last: Huebner

address: 460 W. 12th Ave

institute: The Ohio State University

summary:
Characterizing signal pathway alterations that contribute to cellular transformation induced by loss of Fhit protein
Abstract:  The FHIT gene, encompassing an active common fragile site, FRA3B, is frequently silenced in preneoplasia and cancer, through gene rearrangement or methylation of regulatory sequences. Silencing of Fhit protein expression causes thymidine kinase 1 downregulation, resulting in dNTP imbalance, and spontaneous replication stress that leads to chromosomal aberrations, allele copy number variations, insertions/deletions, and single‐base substitutions. Thus, Fhit, which is reduced in expression in the majority of human cancers, is a genome “caretaker” whose loss initiates genome instability in preneoplastic lesions. To follow the early genetic alterations and functional changes induced by Fhit loss that may recapitulate the neoplastic process in vitro, we established epithelial cell lines from kidney tissues of Fhit−/− and +/+ mouse pups early after weaning, and subjected cell cultures to nutritional and carcinogen stress, which +/+ cells did not survive. Through transcriptome profiling and protein expression analysis, we observed changes in the Trp53/p21 and survivin apoptotic pathways in −/− cells, and in expression of proteins involved in epithelial–mesenchymal transition. Some Fhit‐deficient cell lines showed anchorage‐independent colony formation and increased invasive capacity in vitro. Furthermore, cells of stressed Fhit−/− cell lines formed s.c. and metastatic tumors in nude mice. Collectively, we show that Fhit loss and subsequent thymidine kinase 1 inactivation, combined with selective pressures, leads to neoplasia‐associated alterations in genes and gene expression patterns in vitro and in vivo.

overall_design: mouse kidney epithelial cell lines were derived from fhit knockout mice and subcultured with and without carcinogenic and nutritional stress


title: In vivo protein complementation demonstrates direct detection of presynaptic α-synuclein oligomerization and age-dependent accumulation of 8-16mer oligomer species

status: Public on Jul 19 2019

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

type: Expression profiling by high throughput sequencing

summary: Intracellular accumulation of a-synuclein (a-syn) and formation of Lewy bodies are neuropathological characteristics of Parkinson‘s disease (PD), related a-synucleinopathies, and other neurodegenerative diseases. Recent evidence suggests that oligomerization and spreading of a-syn from neuron to neuron are key events contributing to the development of PD. To directly visualize and characterize a-syn oligomerization and spreading in vivo, we generated two independent conditional transgenic mouse models based on a-syn protein complementation assays using both split Gaussia luciferase and split Venus YFP. These inducible, neuron-specific transgenic mice allow to directly assess the quantity and subcellular distribution of a-syn oligomers in vivo. Using these innovative mouse models we demonstrate an age dependent accumulation of a specific subtype of a-syn oligomers and their synaptic localization in vivo. We provide in vivo evidence that although a-syn is found throughout neurons a-syn oligomerization takes place at the presynapse. Furthermore, our new mouse models provide strong evidence for a long distance transsynaptic cell-to-cell transfer of de novo generated a-syn oligomers in vivo.

overall_design: Brain total-RNA profiles of mice were generated by RNA-Seq, in 3/4 replicates, using Illumina Hiseq-2500.

first: Karin

last: Danzer

first: Martin

last: Kiechle


title: Next generation sequencing facilitates the mapping of the transcriptomes of two E3 ligase knock out macrophages

city: Glasgow

first: Jennifer

last: Mitchell

address: Sir Graeme Davies Building, 120 University Avenue

department: Insitute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary: The goal of this study was to compare RNA-seq data generated from WT, Ing4-/- and Socs1-/- RAW 264.7 macrophages. These are two known E3 ligases for the trancription factor NF-kB and so their functional consequences on transcription were explored in this study.

overall_design: 12 samples in total (2 replicates of 6 conditions)

middle: P

first: Ruaidhri

middle: J

last: Carmody


title: Transcriptome as marker for nutrition-related health: added value of time course analyses during challenge tests before and after energy restriction

status: Public on Jul 23 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Phenotypic flexibility is used as a measure for health and can be studied during nutritional challenge tests. Changes in gene expression are early markers and give insight into mechanisms. Energy restriction (ER) has a variety of beneficial health effects and can be used to investigate different health states to study postprandial changes during challenge tests. Objective: We aimed to determine the postprandial effects of a 20% ER diet on whole genome expression profiles of peripheral blood mononuclear cells (PBMCs). Materials and methods: 72 healthy, overweight men and women, aged 50-65, were subjected to an oral glucose tolerance test (OGTT) and a mixed meal test (MMT), before and after a 12 week intervention with either a 20% ER diet or a control diet. Total RNA from PBMCs was isolated at fasting, and at postprandially during the OGTT at 30, 60, and 120 min and during the MMT at 60, 120, 240, and 360 min. RNA of all time points was used to evaluate whole genome gene expression response using Affymetrix microarrays, resulting in a number of 1231 arrays. Results and conclusions: Upon 20% ER, gene sets involved in OXPHOS, cell adhesion, energy metabolism, immune system, cell cycle, and DNA replication were increased. Upon an OGTT, OXPHOS, cell adhesion, and DNA replication gene sets were decreased after ER. Also, some postprandial effects seem to happen in the control group, but at a later stage. We concluded that ER increased phenotypic flexibility by means on increased use of OXPHOS pathways, and that the response to an OGTT seemed faster upon ER than upon a control diet.

overall_design: Microarray analysis was performed on peripheral blood mononuclear cells (PBMC) isolated from 72 healthy overweight men and women that were subjected to an oral glucose tolerance test and mixed meal test  before, and after a 12 week 20% energy restriction or control intervention. A total of 14-18 samples per subject were used for microarray analysis.

first: Inge

last: van Bussel

first: Parastoo

last: Fazelzadeh

first: Gary

last: Frost

first: Lydia

middle: A

last: Afman


title: The expression levels of genes on trisomic chromosomes (chromosome 13, 18 or 21) are increased approximately 1.5-fold on average compared with diploid cells

status: Public on Jul 18 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Phenotypes in chromosome abnormalities do not arise as a mere summation of the specific effects of dosage-sensitive genes, but as a result of the synergistic actions of whole chromosomes. Recent studies on yeast and mammalian cells have demonstrated that aneuploidy exerts detrimental effects on organismal growth and development, regardless of the karyotype, suggesting that aneuploidy-associated stress plays an important role in disease pathogenesis. However, whether and how this effect alters cellular homeostasis and long-term features of human disease are not fully understood. Here, we aimed to investigate cellular stress responses in human trisomy syndromes, using fibroblasts and induced pluripotent stem cells (iPSCs). Dermal fibroblasts derived from patients with trisomy 21, 18 and 13 showed a severe impairment of cell proliferation and enhanced premature senescence. These phenomena were accompanied by perturbation of protein homeostasis, leading to the accumulation of protein aggregates. We found that treatment with sodium 4-phenylbutyrate (4-PBA), a chemical chaperone, decreased the protein aggregates in trisomy fibroblasts. Notably, 4-PBA treatment successfully prevented the progression of premature senescence in secondary fibroblasts derived from trisomy 21 iPSCs. Our study reveals aneuploidy-associated stress as a potential therapeutic target for human trisomies, including Down syndrome.

overall_design: Each of fibroblast cells was assayed as single color experiment.

first: Nobutoshi

last: Nawa

first: Yasuji

last: Kitabatake


title: Chromatin conformation identification by Cut-C

first: Takashi

last: Shimbo

address: 2-2 Yamadaoka

institute: Osaka university

summary: Understanding of the 3D structure of the genome is essential to decipher the detailed regulatory mechanisms of gene expression. Here we present CUT-C, a method that combines the antibody mediated cleavage by tethered nuclease with the chromosome conformation capture technique to identify chromatin interactions mediated by a protein of interest. CUT-C identifies protein-centric chromatin conformation along with the genome wide distribution of target proteins.

overall_design: We developed a method to identify protein centric chromatin conformation based on micro-c. Unlike micro-c, DNA is cleaved by Mnase thethered by target proteins.  Cleaved regions are identified by next generation sequencing.


title: Epigenetic profiling of docetaxel resistance in Breast Cancer

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across 850000 CpGsites in nine different breast cancer PDX models. Docetaxel resistant and residual disease PDX models were also analyzed

overall_design: DNA was isoleted from frozen tumors of different TNBC PDX models sensitive to docetaxel and from docetaxel resistant-derived TNBC PDX models. DNA was quanitifed by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600ng of each sample was performed according to the manufacturer’s recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for the threecontrols that were converted simultaneously with the samples.4ul of bisulfite converted DNA were used to hybridize on Infinium MethylationEPIC BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intesities of the images were extracted with Minfi in Rstudio. Methylation score of each CpG is represented as beta value

first: María

middle: E

last: Calleja-Cervantes

first: J

last: Gómez-Miragaya

first: E

last: González-Suárez


title: Identification of xLEF1 specific target genes in dorsal marginal zone explants of Xenopus laevis

city: Karlsruhe

first: Dietmar

last: Gradl

address: Fritz Haber Weg 2

institute: Karlsruhe Institute of Technology

summary: Lef-1 as nuclear transducer of the canonical Wnt signaling pathway acts as regulator of convergent extension (CE) movements. To identify Lef-1 target genes relevant for CE movements we compared the transcriptome of Lef-1 morphant dorsal marginal zone explants with control morphants.

overall_design: Dorsal marginal zone explants of CO_MO and LEF_MO injected embryos were analysed in three biological replicates.

first: Veronika

last: Wallkamm


title: Comprehensive transcriptomic characterization of hepatic expression signatures affected by guanine nucleotide binding protein (G protein) alpha 12 knockout

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Heterotrimeric guanine nucleotide-binding proteins (G proteins) transmit extracellular signals from cell surface G protein-coupled receptors to intracellular effector molecules. Of the G proteins, Gα12 has attracted particular interest as the gep oncogene in cancer research because it promotes the growth and oncogenic transformation of fibroblasts and is invoked in tumorigenesis. In our findings, Gα12 expression was higher in HCC than surrounding non-tumorous tissue. Results provide information on the role of Gα12 in HCC progression. cDNA microarrays analyses using liver samples obtained from WT and Gα12-knockout mice enabled us to extract the predominant processes affected by a deficiency of Gα12, which include cellular response to stress, cell proliferation, actin cytoskeleton organization, and cellular component biogenesis.

overall_design: Expression profiles of KO mice samples were compared to those of corresponding WT mice and differentially expressed genes were identified.

first: Yoon Mee

last: Yang

first: Chang Yeob

last: Han

first: Tae Hyun


title: RNA-seq analysis of human KMT2A rearranged MV4;11 AML cell line treated with DOT1L and/or EZH2 inhibitor

status: Public on Jul 17 2019

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

country: USA

institute: Children's Hospital of philadelphia

summary: The histone methyltransferases DOT1L (H3K79me1,2,3 KMT, "activating" chromatin mark) and EZH2 (H3K27me1,2,3 KMT, "silencing" mark) have both been shown to be required for growth and survival of KMT2A rearranged AML cells. Both KMTs have been shown to modulate expression of HOXA cluster genes, albeit for EZH2 this has not been shown in the context of KMT2A rearranged AML, but in other subtypes of AML. We asked what transcriptional effects dual inhibition of DOT1L and EZH2 has in KMT2A rearranged AML.

overall_design: MV4;11 AML cells were exposed to the DOT1L inhibitor EPZ5676 at 0.08 and 0.16 uM, and the EZH2 inhibitor GSK126 at 0.3 uM for 7 days. Fresh media and compound were supplied on day 4. RNA was isolated using RNeasy (Quiagen) and submitted for RNA-Seq

first: Michael

last: Xie


title: Comparative study on seasonal hair follicle cycling by analysis of the transcriptomes from cashmere and milk goats

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: Guard hair and cashmere undercoat are developed from primary and secondary hair follicle, respectively. Little is known about the gene expression differences between primary and secondary hair follicle cycling. In this study, we obtained RNA-seq data from cashmere and milk goats grown at four different seasons. We studied the differentially expressed genes (DEGs) during the yearly hair follicle cycling, and between cashmere and milk goats. WNT, NOTCH, MAPK, BMP, TGFβ and Hedgehog signaling pathways were involved in hair follicle cycling in both cashmere and milk goat. However, Milk goat DEGs between different months were significantly more than cashmere goat DEGs, with the largest difference being identified in December. Some expression dynamics were confirmed by quantitative PCR and western blot, and immunohistochemistry. This study offers new information sources related to hair follicle cycling in milk and cashmere goats, which could be applicable to improve the wool production and quality.

overall_design: Examination between cashmere and milk goats in 4 different months.

first: Yanjun

last: Zhang

first: Yi


title: Developmental Exposure to 2,2’,4,4’-Tetrabromodiphenyl Ether Permanently Alters Blood-Liver Balance of Lipids in Male Mice

city: Amherst

first: Alexander

last: Suvorov

state: MA

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

summary: Polybrominated diphenyl ethers (PBDEs) were used as flame-retardant additives starting 1965 and were recently withdrawn from commerce in North America and Europe. Approximately 1/5 of the total U.S. population were born when environmental concentrations of PBDE plateaued at their maximum. Accumulating evidence suggests that developmental exposures to PBDE may result in long-lasting programming of liver metabolism. In this study, CD-1 mice were exposed prenatally or neonatally to 1 mg/kg body weight of 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47), and changes in liver gene histology, transcriptome, and liver-blood balance of triglycerides were analyzed in 10 month old male offspring. In both exposure groups, long-term reprogramming of lipid metabolism was observed, including increased liver triglycerides and decreased blood triglycerides, and altered expression of metabolic genes in the liver. Significant upregulation of lipid influx transporter Cd36 2.3- and 5.7-fold in pre- and neonatal exposure groups respectively was identified as a potential mechanism of blood/liver imbalance of triglycerides. Analysis of our and previously published all-genome gene expression data identified changes in expression of ribosomal protein genes as a transcriptomic signature of PBDE exposure. Further comparison of our new data and published data demonstrate that low doses (0.2 mg/kg body weight) of PBDE induce long-lasting up-regulation of ribosomal genes, suppression of Cd36 in liver and increase circulating triglycerides in blood, while moderated doses (≥ 1 mg/kg body weight) produce opposite long-lasting effects. To conclude, this study shows that an environmentally relevant developmental exposures to BDE-47 permanently alter lipid uptake and accumulation in the liver, with low and moderate doses having opposite effect on liver transcriptomics and triglyceride balance. Similar effects of pre- and neonatal exposures point at hepatocyte maturation as a sensitive window of the liver metabolism programming. These results suggest that PBDE exposure may be an important factor increasing risks of cardio-vascular disease and non-alcoholic fatty liver disease. The translational relevance of these findings for human remain to be studied.

overall_design: Pregnant/lactating CD-1 mice were exposed to tocopherol striped corn oil from pregnancy day 8 till postpartum day 21 (control group) or to 1 mg/kg 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) in corn oil from pregnancy day 8 till  delivery and then to oil only till postpartum day 21 (prenetal exposure group) or to corn oil from pregnancy day 8 till delivery and then to 1 mg/kg BDE-47 till postpartum day 21 (postnatal exposure group). Changes in liver transcriptome were analysed in four individual male animals (affspring of exposed dams) from different litters per group on postnatal day 300.


title: A Novel Factor Associating with Hepatic Insulin Sensitivity in Humans with Nonalcoholic Fatty Liver Disease

city: Otaku

first: Fumika

last: Shigiyama

state: Tokyo

department: Diabetes, Metabolism and Endocrinology

institute: Toho University Graduate School of Medicine

summary: We comprehensively searched for the factors that may attribute to hepatic insulin sensitivity in the patients with NAFLD. Forty-three NAFLD patients were assessed for putative biomarkers in blood and urine, body composition, tissue lipid content, tissue insulin sensitivity by hyperinsulinemic-euglycemic clamp, hepatic histology and gene expressions using liver biopsies, and life styles. In results, the higher levels of plasma adiponectin, muscle insulin sensitivity, and adipose tissue insulin sensitivity positively, but the higher levels of HbA1c, ALT, and log converted high-sensitive CRP negatively correlated with hepatic insulin sensitivity. Interestingly, whole liver volume and hepatic lean volume corrected by body surface area (cm3/m2) showed significant negative correlation with hepatic insulin sensitivity, specifically in patients with T2DM.

overall_design: We comprehensively searched for the factors which significantly associated with hepatic insulin sensitivity assessed by hyperinsulinemic euglycemic clamp test. The 43 NAFLD patients included in this study had been taken liver biopsy and the hepatic gene expressions were also evaluated.


title: NKp46 machinery required for effective NK cell killing

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Comparison of NK1.1 NK cells in WT (B6) and Ly5.1(mut) mice at steady state and in response to tumor challenge

overall_design: Transcriptional profiling of WT and Ly5.1(mut) NK cells at steady-state and response to melanoma

first: Francisca

last: Almeida

first: Yang

last: Liao

first: Gabrielle

last: Belz


title: A comprehensive two-centre RNA-seq study reveals changes in endometrial and blood miRNome at mid-secretory phase in fertile women and in patients with recurrent implantation failure

city: Tallinn

first: Agne

last: Velthut-Meikas

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary:
Study question: Does a comprehensive study involving two different population cohorts and small RNA sequencing from endometrium and blood reveal new endometrial receptivity-related microRNAs (miRNAs) in healthy conditions and in women with recurrent implantation failure (RIF)?
Summary answer: Several annotated miRNAs, not previously associated with endometrial receptivity, as well as one novel miRNA were found as differentially expressed between early secretory vs. mid-secretory phase samples in addition to miRNAs dysregulated in RIF patients.
What is known already: The involvement of miRNAs in mid-secretory endometrial functions has been shown and aberrant expression of miRNAs in RIF has been identified in a few previous studies, but not from whole blood samples. However, as the analysis settings and platforms have been different and a small number of samples has been analysed, there is no consensus about the miRNAs involved in endometrial receptivity and dysfunction.
Participants/materials, setting, methods: A total of 116 endometrial and 114 blood samples were subjected to Illumina small RNA sequencing. Identification of annotated and novel miRNAs from sequencing reads was performed by miRDeep2 algorithm. miRNAs that had significantly altered levels between the study groups in both EST and ESP datasets were considered as differentially expressed. Ingenuity Pathway Analysis was applied for identifying miRNA target genes and respective canonical pathways from the matched mRNA analysis from the same samples. Custom TaqMan Small RNA assay was used for the validation of novel miRNA (chr2_4401) levels from paired early secretory and mid-secretory endometrial samples.
Main results and the role of chance: Among fertile women, 91 differentially expressed miRNAs were identified in mid-secretory vs. early secretory endometrium, while no differentially expressed miRNAs were found in the corresponding blood samples. The comparison of mid-secretory phase samples between fertile women and RIF patients revealed 21 differentially expressed miRNAs from endometrium and one from blood samples. miRNA target gene prediction analysis using our mRNA sequencing data from the matched samples detected several canonical pathways to be involved in mid-secretory endometrial functions, including JAK/STAT signalling, leptin signalling and growth hormone signalling. Moreover, JAK/STAT signalling pathway was also revealed in miRNA target analysis of mid-secretory endometrium from RIF patients when compared to fertile women. Further, our study results highlight the involvement of miR-30 and miR-200 families in endometrial receptivity, and miR-424-5p in the development of endometrial dysfunction. We identified several novel miRNAs, of which miRNA chr2_4401, being 37-fold up-regulated in mid-secretory phase, has a potential role in the mid-secretory endometrial functions. From blood samples we identified miR-30a-5p as a possible marker of infertility related to RIF.

overall_design: Our current study recruited 39 fertile women and 38 infertile RIF patients from Estonia (EST) and Spain (ESP). Paired endometrial and blood samples were collected at early secretory and mid-secretory phases from fertile women and at mid-secretory phase from infertile RIF patients. This is the largest miRNA endometrial receptivity study to date with novel aspects of combining matched samples of endometrium and blood from two different population cohorts.

first: Kadri

last: Rekker

first: Signe

last: Altmäe

first: Marina

last: Suhorutshenko

first: Maire

last: Peters

first: Juan

middle: F

last: Martinez-Blanch

first: Francisco

middle: M

last: Codoñer

first: Felipe

last: Vilella

first: Carlos

last: Simón

first: Andres

last: Salumets


title: Homotypic cooperativity and collective binding are determinants of bHLH specificity and function

city: Saint Louis

first: Christian

last: Shively

state: MO

address: 4523 Clayton Avenue

department: Genetics

institute: Washington University in St Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Eukaryotic cells express transcription factor (TF) paralogues that bind to nearly identical DNA sequences in vitro but bind at different genomic loci and perform different functions in vivo. Predicting how 2 paralogous TFs bind in vivo using DNA sequence alone is an important open problem. Here, we analyzed 2 yeast bHLH TFs, Cbf1p and Tye7p, which have highly similar binding preferences in vitro, yet bind at almost completely non-overlapping target loci in vivo. We dissected the determinants of specificity for these 2 proteins by making a number of chimeric TFs in which we swapped different domains of Cbf1p and Tye7p and determined the effects on in vivo binding and cellular function. From these experiments, we learned that the Cbf1p dimer achieves its specificity by binding cooperatively with other Cbf1p dimers bound nearby. In contrast, we found that Tye7p achieves its specificity by binding cooperatively with three other DNA-binding proteins, Gcr1p, Gcr2p, and Rap1p. Remarkably, most promoters (63%) that are bound by Tye7p do not contain a consensus Tye7p binding site. Using this information, we were able to build simple models to accurately discriminate bound and unbound genomic loci for both Cbf1p and Tye7p. We then successfully reprogrammed the human bHLH NPAS2 to bind Cbf1p in vivo targets and a Tye7p target intergenic region to be bound by Cbf1p. These results demonstrate that the genome-wide binding targets of paralogous TFs can be discriminated using sequence information, and provide lessons about TF specificity that can be applied across the phylogenetic tree.

overall_design: "Calling card" assays for transcription factors, truncated transcription factors, and chimeric transcription factors were performed in S. cerevisiae.

first: Jiayue

last: Liu

first: Xuhua

last: Chen

first: Kaiser

last: Loell

first: Robi

middle: D

last: Mitra


title: Electrophysiological properties of human induced-pluripotent stem cell-derived three-dimensional cerebral organoids

city: Milwaukee

first: Sarah

last: Logan

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: The goal of the study was to compare gene profile between iPSC-derived cerebral organoids, human fetal brain tissue, and human adult brain tissue

overall_design: iPSCs and cerebral organoids were collected at different maturational stages within the differentiation process to assess gene profile

first: Thiago

last: Arzua

first: Yasheng

last: Yan

first: Congshan

last: Jiang

first: Qing-Song

first: Xiaojue

first: Lai-Kang

last: Yu

first: Xiaowen

last: Bai


title: Gene expression profile in porcine ovarian granulosa cells during short-term in vitro culture

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

summary:
The porcine ovarian granulosa cells, when analysed during in vitro cultures, may provide new interesting data on the processes associated with in vitro culture of porcine oocytes, as well as assisted reproduction and in vitro fertilisation processes used in the livestock industry. Porcine ovarian granulosa cells were obtained from 43 crossbred Landrace gilts with a median age of 170 days and weight of 98 kg after slaugheter. The cells were harvested after 0h, 48h, 96h and 144h after begining of culture and submited to RNA isolation and microarray analisys.
In this study, we demonstrated the gene expression profile of short term primary cultured porcine ovarian granulosa cells.

overall_design: Porcine ovarian granulosa cells were obtained from 43 crossbred Landrace gilts with a median age of 170 days and weight of 98 kg, after slaughter. The cells were harvested after 0h, 48h, 96h and 144h after begining of culture and submited to RNA isolation and microarray analysis.

first: Sylwia

last: Ciesiółka

first: Wiesława

last: Kranc

first: Piotr

last: Celichowski

first: Joanna

last: Budna-Tukan

first: Magdalena

last: Kulus

first: Paweł

last: Antosik

first: Dorota

last: Bukowska

first: Małgorzata

last: Bruska

first: Bartosz

last: Kempisty


title: Effects of elicited and pre-existing purified anti-Neu5Gc antibodies on human endothelial cells

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

summary: Human beings are unable to synthetize the glycolylated neuraminidic acid (Neu5Gc) following a mutation of the CMAH gene and diet induced anti-Neu5Gc antibodies develop in the first year of life. However, because humans can absorb Neu5Gc which deposits at low levels on endothelial cells (EC), activation of endothelium by anti-Neu5Gc has been raised. Understanding whether this interaction contributes to EC normal biology or may induce a potentially detrimental EC activation is crucial, particularly in patients  developing  elicited anti-Neu5Gc following introduction of animal derived molecules or bio-devices. Ten EC lines were cultured with immune-affinity purified anti-Neu5Gc from normal sera (diet induced) or sera harvested following  rabbit-IgG infusion (elicited) anti-Neu5Gc. After a 4h-incubation of Neu5Gc loaded ECs at levels close to those of freshly harvested ECs, ECs were stimulated with both anti-Neu5Gc types and with or without human complement. Anti-Neu5Gc induce a differential expression (DE) of 967 out of expressed 12,208 genes, with transcript accumulation in 93%. Most DE transcripts are shared following activation by pre-existing or elicited anti-Neu5Gc. Compared to ATG pre-existing antibodies, elicited anti-Neu5Gc down-regulated 66 genes, involving master genes such as IL8, ICAM1, MAPKINASES or  NFKb1. Furthermore, addition of elicited anti-Neu5Gc to non-heat inactivated sera down-regulated most of the transcripts mobilized by serum alone, including key transcripts involved in apoptosis, fitting with no  increase in apoptotic cells. Altogether, the RNA profiling following culture of human ECs and anti-Neu5Gc suggests that pre-existing anti-Neu5Gc contribute to normal human EC homeostasis rather than to an inflammatory oriented transcriptome. Elicited anti-Neu5Gc do not also skew EC transcriptome toward inflammation either, but trigger the release cytokines or chemokines in culture supernatants.

overall_design:
Ten endothelial cell (EC) lines were cultured with immune-affinity purified anti-Neu5Gc from normal sera (diet induced) or sera harvested following  rabbit-IgG infusion (elicited) anti-Neu5Gc. After a 4h-incubation of Neu5Gc loaded ECs at levels close to those of freshly harvested ECs, ECs were stimulated with both anti-Neu5Gc types and with or without human complement.

NOTE: The raw data for the following samples were not provided:
GSM3272189: Cmplt_C7
GSM3272190: Cmplt_C6

first: Ludmilla

last: Le Berre

first: Hoa

middle: L

last: Mai

first: Jan-Paul

last: Soulillou


title: Genome-wide analysis of T3 and CORT dependent gene expression and hormone synergy in mouse hippocampal neurons (HT-22)

city: Quezon City

first: Pia

middle: Dano

last: Bagamasbad

email: piab@umich.edu, pdbagamasbad@up.edu.ph

state: Metro Manila

address: National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

summary: Analysis of T3 and CORT dependent gene expression tested in the mouse hippocampal neuronal cell line HT-22. The experiment was done to identify genes which are differentially regulated by the two hormones as well as to identify genes which are synergistically regulated by combined T3 + CORT treatment. Results provide an exploratory dataset for studying T3 and CORT regulation in mouse hippocampal neurons.

overall_design: Total RNA obtained from HT22 cells treated with T3, CORT, or T3+CORT compared to HT22 cells treated with the vehicle control.

first: Jose

last: Espina

first: Joseph

middle: R

last: Knoedler

first: Arasakumar

last: Subramani

first: Ariel

last: Harden

first: Robert

last: Denver


title: NK-Exh 72

status: Public on Jul 16 2019

city: Stanford

first: Maite

last: Alvarez

address: CCSR 269 Campus Drive Room 2210

institute: Stanford University

summary:
Long-term in vitro NK cell stimulation results in NK cell exhaustion that can be prevented by inhibition of the DNA damage repair pathway with improvement of NK cell survival
Characterization of the mRNA expresion profile of NK exposed in vitro to IL-2 chronically

overall_design:
Activated NK cells were collected at several time points after in vitro activation with IL-2. mRNA was then extracted and mRNA expression profile was determine using Affymetrix murine Mouse Gene 2.0ST

contributor: Protein and Nucleic Acid Facility (Stanford University)


title: Gene expression analysis in the hippocampus of Tg2576 mice after different treatments with HDAC and PDE inhibitors

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: The goal of this study was the identification of a novel mode of action for this unmet need. Pharmacological tool compounds: suberoylanilide hydroxamic acid (SAHA) and tadalafil, targeting histone deacetylases (HDAC) and phosphodiesterase 5 (PDE5) respectively, were utilized simultaneously for in-vitro and in-vivo Proof-of-Concept (PoC). A synergistic effect was observed in the amelioration of AD signs using the combination therapy in Tg2576 mice. Finally, a therapeutic agent, CM-414, inhibiting simultaneously HDAC2/6 and PDE5 was generated and tested in Tg2576 mice. CM-414 reversed cognitive impairment, reduced amyloid and tau pathology, and rescued dendritic spine density loss in the hippocampus in AD mice. Importantly, the effect obtained was present after a 4-weeks wash-out period.However, to obtain a compound with a safer profile we designed a new compound, CM-695, targeting HDAC6 and PDE9. CM-695 showed similar effect to that of CM-414 after chronic administration to Tg2576 although the effect was not mantained when CM-695 was no longer administered.

overall_design: Comparisson of global gene expression profiling in aged Tg2576 mice hippocampi between diferent treatments and sacrificed 24 hours after the end of the treatment

first: Ana

last: García-Osta

first: Mar

last: Cuadrado

first: Julen

last: Oyarzábal


title: Changes in nuclear and cytoplasmic microRNA distribution following hypoxic stress

city: Kuopio

first: Mikko

last: Turunen

address: Yliopistonranta 1 E

department: A. I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary:
Purpose: MicroRNAs have well characterized roles in cytoplasmic gene regulation by binding mRNA and inhibiting translation. However, besides this post-transcriptional gene silencing, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. The nuclear functions of miRNAs are currently not understood, and there is a paucity of systematic studies of miRNA nuclear-cytoplasmic distribution and fewer still which have investigated this in the context of physiological conditions.
Methods: Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line in hypoxia and characterized the localization of miRNAs using small RNA sequencing.
Results: We show here that there is a broad population of mature miRNAs in the cell nucleus and that it is also altered upon exposure to hypoxia.
Conclusions: Our results strongly imply that miRNAs have extensive regulatory functions in the nucleus and expand potential therapeutic use of small RNA molecules.

overall_design: C166 endothelial cells were treated with hypoxia (NT, 2h and 24h timepoints) and fractionated into nuclear and cytoplasmic samples that were used for sequencing. Samples were done in duplicates.

first: Tiia

last: Laitinen

first: Thomas

middle: C

last: Roberts


title: Changes in rat sperm DNA methylation induced by age and by perinatal exposure to brominated flame retardant flame retardants 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47)

first: Alexander

last: Suvorov

address: 149A - Goessmann,  686 – N. Pleasant Str.

department: Department of Environmental Health Sciences

institute: University of Massachusetts Amherst

summary: Advanced paternal age at fertilization has been suggested to be a risk factor for neurodevelopmental, psychiatric and other disorders in offspring. One emerging hypothesis suggests that altered offspring phenotype is linked with age-related accumulation of epigenetic changes in the sperm of fathers. Given that paternal age is increasing in the developed world, understanding aging-related epigenetic changes in sperm is needed as well as environmental factors that modify such changes. In this study, we characterize age-dependent changes in sperm DNA methylation profiles between young pubertal (postnatal day (PNDs) 65) and mature (PND120) Wistar rats. We also analyze these changes in rats exposed perinatally to 0.2 mg/kg of ubiquitous environmental xenobiotic 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47). Reduced representation bisulfite sequencing (RRBS) libraries were prepared from caudal epididymal sperm DNA and differentially methylated regions (DMRs; ≥ 10x coverage depth, ≥ 3 CpGs per cluster, ≥ 5% methylation change, q < 0.05) were identified via MethPipe package. We identified 21 and 9 exposure-related DMRs in sperm collected on PND65 and PND120, respectively. Two DMRs overlapped between the two time-points. This is the first study to demonstrate that environmentally-relevant perinatal exposure to PBDE results in long-lasting changes in sperm DNA methylation. In control animals, 5,319 age-dependent DMRs were identified, with 99.3% DMRs hypermethylated in mature animals compared to young pubertal rats. These age-related DMRs were enriched for functional categories essential for embryonic development, such as pattern specification, forebrain and sensory organ development, and the Wnt pathway. In BDE-47 exposed rats, sperm DNA methylation was higher in young pubertal and lower in mature animals when compared to controls, which resulted in a significant attenuation in the number of age-dependent DMRs (N = 189) identified in the exposed group. In conclusion, our results indicate that the natural aging process has profound effects on sperm methylation levels and this effect may be modified by environmental exposures. Moreover, our results further support the role of sperm DNA methylation as a likely mechanism by which advanced paternal age is associated with adverse offspring health and development.

overall_design: Seven-week-old Wistar rats were purchased from Charles River Laboratories (Kingston, NY, USA) on the sixth day of pregnancy, housed in a temperature- and humidity-controlled room with a 12-h light cycle and maintained at 23±2 °C. All rats were fed ad libitum with a rodent chow (Prolab Isopro RMH 3000, Cat. # 5P75, LabDiet, St. Louis, MO). Between pregnancy day 8 and postnatal day 21 (PND21) dams were fed daily from the tip of a pipette 0.2 µl/gram body weight of vehicle (tocopherol stripped corn oil, MP Biomedicals, Solon, OH) or same volume of 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) daily (n=6 per exposure group). In the latter group it resulted in exposure level of 0.2 mg/kg body weight BDE-47 per day.  Pups were weaned on PND21. On PND65 and PND120 one male pup was randomly  selected from each litter fasted for 2 hours and euthanized using cervical dislocation.  At each euthanasia both distal cauda epididymis were collected, incised longitudinally and incubated at 37°C for 30 min in 1 ml of sperm wash buffer (Cat. # ART1006, Origio, Denmark) to collect motile spermatozoa via the swim-up procedure. For sperm DNA-methylation analysis we used sperm collected from 6 animals per time-point per exposure group. To remove somatic cells contamination 1.5 ml sperm samples were loaded on top of 1 ml density gradient (40% Isolate, Irvine Scientific, USA) in 15 ml conical tubes and centrifuge for 25 min at 500 g. Pelleted spermatozoa were used to extract DNA. Bisulfite converted libraries were prepared from 100 ng of sperm DNA using Ovation RRBS Methyl-Seq System (Cat. # 0353, NuGEN) and EpiTect Fast DNA Bisulfite Kit (Cat. # 59824, Qiagen) following manufacturers’ protocols. Sequencing of libraries was done on HiSeq 2500 (Illumina) in Deep Sequencing Core Facility of the University of Massachusetts School of Medicine (Shrewsbury, MA).  Differentially methylated regions were analyzed using a MethPipe pipeline. In short, raw reads were processed in accordance with recommended protocol for libraries prepared with Ovation RRBS Methyl-Seq System (NuGEN) and then mapped to rn6 Rattus norvegicus reference genome using Bismark (version 0.16.1) and bowtie-2 (version 2.2.9).  PCR-duplicates were removed using nudup.py (version 2.2). Subsequent analyses were restricted to CpGs with ≥ 10x coverage to comply with ENCODE recommendations and recommendations of MethPipe developers. Differentially methylated regions (DMRs) were identified using MethPipe. All DMR spatial annotations with regard to various genome structures were produced using closest-features (v. 2.4.25) tool from bedOps package.


title: RNA-Seq data from cortex and hippocampus (post novel object recognition test) of rats in a vagus nerve stimulation study

city: Golden

first: Teresa

middle: Hinkle

last: Sanders

state: CO

address: 1510 Quail Court

institute: University of Colorado, Boulder

summary: Vagus nerve stimulation (VNS) has been shown to enhance learning and memory, yet the mechanisms behind these enhancements are unknown. We show that VNS altered the hippocampal, cortical, and blood epigenetic transcriptomes in male Sprague Dawley rats whether or not the rats performed a novelty preference behavioral task. In the hippocampus, novelty preference correlated with decreased histone deacetylase 11 (HDAC11), a transcriptional repressor enriched in CA1 cells important for memory consolidation. In the cortex, the immediate early gene (IEG) ARC was increased in VNS rats and correlated with transcription of plasticity genes and epigenetic regulators, including HDAC3. For rats performing the novelty preference task, ARC correlated with performance. Surprisingly, VNS did not significantly reduce transcription of cortical or hippocampal proinflammatory cytokines. However, TNFRSF11B (osteoprotegerin) correlated with novelty preference as well as plasticity, stress–response signaling, and epigenetic regulation in both hippocampus and cortex. Together, our findings provide the first evidence that VNS induces widespread changes in the cognitive epigenetic landscape and specifically affects epigenetic modulators associated with novelty preference, stress–response signaling, memory consolidation, and cortical neural remodeling.

overall_design: Rats were stimulated with implanted vagus nerve stimulation devices for 30 minutes on 4 consecutive days. A subset of rats performed a 10 minute novelty preference task on days 2-4. For all experiment conditions, matched control rats were implanted with a sham stimulation device. Rats were decapitated immediately following the day 4 stimulation and brains dissected. Hippocampal (for rats performing the novelty preference task) and Cortical RNA was extracted and sequenced.

middle: H


title: A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [ChIP-seq]

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

summary: Estrogen and estrogen receptor alpha (ERα) signaling plays an essential role in ERα-positive breast cancer. ERα mainly occupies on distal enhancers within genome and requires the cooperation of additional co-factors to tune the enhancer activity. Through in vivo proximity-dependent labeling technique BioID, we identified YAP1 and TEAD4 protein as novel co-regulators of ERα. YAP and TEAD are nuclear effectors of the Hippo pathway regulating cell proliferation, organ size and tumorigenesis. Their non-canonical function as transcriptional co-regulators for other signals have been reported but remains under investigated. Our ChIP-seq data in both MCF7 and T47D breast cancer cell lines indicated that YAP1 and TEAD4 co-bind to the strongest estrogen-responsive ERα-bound enhancers, and their bindings are augmented upon E2 stimulation. Knockdown of YAP1 or TEAD4 showed a global effect on the induction of E2/ERα target genes as examined by RNA-seq, also on E2-induced oncogenic growth of ER-positive breast cancer cells. We used Global Run-on sequencing (GRO-seq) assays to test the expression of enhancer non-coding RNAs (eRNAs), which are sensitive markers for estrogen-induced enhancer activation. Our results supported our hypothesis that the recruitment YAP/TEAD to ERα-bound enhancers is required for enhancer activation. Further studies revealed that the binding of YAP1 on ERα enhancers is a prerequisite for the recruitment of the enhancer activation machinery component MED1. These findings indicate that ERα collaborates with YAP1 and TEAD4 to activate or maintain its enhancer activity. Our data reveals a non-canonical function of YAP1 and TEAD4, which is independent of their canonical target genes, in regulating cancer growth, highlighting the potential of YAP1 and TEAD4 as actionable drug targets for ERα-positive breast cancer.

overall_design: Chromatin immunoprecipitation (ChIP) assay followed by high-throughput sequencing (ChIP-seq).

first: Zhang

last: Zhao

first: Zhu

last: Chi

first: Liu

last: Zhijie


title: A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer

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

overall_design: Refer to individual Series


title: A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [RNA-seq]

overall_design: Total RNA extraction followed by high-throughput sequencing (RNA-seq).


title: A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [GRO-seq]

overall_design: Global Run On (GRO) assay followed by high-throughput sequencing (GRO-seq).


title: Propionibacterium acnes and peptidoglycan activate aryl hydrocarbon receptor and modify differentiation of SZ95 sebocytes in vitro

city: Shanghai

first: Ke

last: Cao

address: Pujian Road 160, Shanghai

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

summary: Individual acne comedones can undergo spontaneous remission in association with shrunken sebaceous glands (SGs) containing undifferentiated cells under unknown mechanisms. It is also still controversial whether sebum-induced follicular Propionibacterium acnes（P. acnes）interacts with the SGs. We explored the effects of P. acnes and peptidoglycan (PGN) on the aryl hydrocarbon receptor (AhR) activation, lipogenesis and differentiation in cultured human SZ95 sebocytes in vitro. Both formaldehyde-inactivated P. acnes and PGN upregulated mRNA levels of AhR charachteristic downstream genes CYP1A1, CYP1B1, CYP1A2, as well as significantly induced translocation of AhR protein from cytoplasm into nucleus. GSEA revealed pathways of downregulated lipogenesis and upregulated keratinization. In addition, P.acnes and PGN inhibited linoleic acid(LA)-induced neutral lipid synthesis and expressions of Keratin 7 and Mucin1/EMA (sebocyte markers) and increased the expression of Keratin 10 and involucrin (keratinocyte markers), which were abolished after AhR gene silencing. Moreover, inhibited expressions of lipogenesis-related genes such as SREBP1 were observed. In conclusion, we provide evidence that P. acnes can switch sebocytes into a keratinocyte-like differentiation with reduced lipogenesis via AhR, indicating that follicular P. acnes should not only be considered as acnegenic but also as a factor promoting acne remission through feedback regulation of sebum production.

overall_design: Examination of total RNA from SZ95 sebocytes of three groups:LA,LA+p.acnes,LA+PGN.


title: Transcription as a function of tissue environment

city: South San Francisco

first: Shannon

last: Turley

state: California

address: 1 DNA Way, Building 15, MS 231b

department: Cancer Immunology

institute: Genentech

summary: We are interested in whether fibroblasts (CD45-CD31-Epcam-PDPN+PDGFRA+) cells exhibit unique transcriptional profiles. To this end, we digested tissues and FACS sorted CD45-CD31-Epcam-PDPN+PDGFRA+ fibroblasts CD45-CD31-Epcam-PDPN+PDGFRA- mesothelial cells and compared the transcriptional profiles of these cells. PRJ0014647

overall_design:
Tissues were digested and CD45-CD31-Epcam-PDPN+PDGFRA+ (fibroblasts) or CD45-CD31-Epcam-PDPN+PDGFRA- mesothelial cells were sorted directly into TRIZOL.
RNA from FACS sorted cells sourced from the following mouse tissues: Lymph Node, Spleen, Bone, Pancreas, Omentum, Mesentary, Epididymal, Inguinal Adipose, Brown Adipose Tissue.

first: Matthew

last: Buechler

first: Steve

last: Lianoglou

first: Nicolas

last: Lounsbury


title: Macrophages + Vitamin A

summary: We are interested in whether peritoneal LCM are programmed by omental Wt1+ stroma (identified as PDPN+ cells). To this end, we co-cultured omental PDPN+ cells (purified by MACS by depleting CD45+ and CD31+ cells) with peritoneal exudates in a manner that enables cell:cell contact or inhibited this with a transwell insert or enabled cell:cell contact in the presence of the retinoic acid receptor inverse agonist BMS493. Peritoneal exudates were also cultured alone or with retinoic acid (1uM). After 5-7 days PDPN+ cells and F480+ cells were FACS sorted from cultures directly into RLT Buffer. Ex vivo peritoneal LCM were also FACS-sorted for comparison. PRJ0019587

overall_design: In vitro samples were FACS sorted as either F480+ or PDPN+ directly into RLT Buffer.


title: Transcriptional profiling of individual airway projecting vagal sensory neurons

city: Cambridge

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

summary: Mammalian airways and lungs are richly innervated by bronchopulmonary sensory neurons, the vast majority of which are derived from the vagal sensory ganglia. In the present study we set out to perform high coverage single cell RNA sequencing on a population of identified murine bronchopulmonary sensory neurons collected from the vagal sensory ganglia to better define the molecular expression profiles of these cell types.  Given the importance of P2X2 in differentiating nodose from jugular sensory neurons, we further aimed to investigate the relationship between transcriptional expression of identified genes and P2X2 expression.

overall_design: Bronchopulmonary sensory neurons in the vagal ganglia were identified by retrograde neuronal tracing with the retrograde lipophilic tracer 1,1'-Dioctadecyl-3,3,3',3'-Tetramethylindocarbocyanine Perchlorate (DiI 2%).  Retrogradely labeled neurons were collected individually and cellular mRNA was amplified to obtain enough mRNA for sequencing.  Sequencing was performed on NextSeq 500, single stranded and 76bp read length.

last: Ritchie

first: Alice

last: McGovern

first: Stuart

middle: B

last: Mazzone


title: Finding binding sites for nuclear receptors in S2 Schneider cells

city: Moscow

first: Nadezhda

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: The subject of the current study is the finding of possible molecular partners of drosophila EcR receptor. The whole-genome experiments revealed that the sites of EcR receptor are partially overlapped with ERR binding sites. As ERR receptor specifically binds regulatory regions of glycolytic genes and genes of glycogen metabolism, the presence of EcR on ERR targets signifies involvement of the ecdysone signaling in regulation of carbohydrate metabolism.

overall_design: ChIP-Seqs by anti-3xFLAG antibodies were performed in S2 Scheider cells (control) and S2 Schneider cells stably expressing 3xFLAG-EcR and 3xFLAG-ERR receptors

first: N


city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Regulatory networks including virulence-related transcriptional factors (TFs) determine bacterial pathogenicity in response to different environmental cues. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen of humans, recruits numerous TFs in quorum sensing (QS) system, type III secretion system (T3SS) and Type VI secretion system (T6SS) to mediate the pathogenicity. Although many virulence-related TFs have been illustrated individually, very little is known about their crosstalks and regulatory network. Here, based on chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and transcriptome profiling (RNA-seq), we primarily focused on understanding the crosstalks of 20 virulence-related TFs, which led to construction of a virulence regulatory network named PAGnet (Pseudomonas aeruginosa Genomic integrated regulatory network), including 82 crosstalk targets. The PAGnet uncovered the intricate mechanism of virulence regulation and revealed master regulators in QS, T3SS and T6SS pathways. In particular, GacA and ExsA showed novel functions in QS and nitrogen metabolism. In addition, an online PAGnet platform was provided to analyze these TFs and more virulence factors. Taken together, the present study revealed the function-specific crosstalks of virulence regulatory network, which might provide new strategies for treating infections in P. aeruginosa in the future.

overall_design:
ChIP-seq and RNA-seq analyses of genomic regulators in Pseudomonas aeruginosa
Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample records.

last: Deng


title: Small RNA sequencing reveals new mode of action and potential biomarkers for the mycotoxin Zearalenone

city: Tulln

first: Bertrand

last: Grenier

address: Technopark 1

department: Research Center

country: Austria

institute: BIOMIN

summary:
Purpose: The mycotoxin zearalenone (ZEN) poses a risk to animal health because of its estrogenic effects. Diagnosis of ZEN-induced disorders in animal production remains challenging due to the lack of appropriate non-invasive biomarkers. Thus, we combined untargeted and targeted transcriptomics approaches to investigate the effects of ZEN on the microRNA expression in porcine uterus, jejunum and serum.
Methods: twenty-four piglets received either uncontaminated feed (Control) or feed containing 0.17 mg/kg ZEN (ZEN low), 1.46 mg/kg ZEN (ZEN medium) and 4.58 mg/kg ZEN (ZEN high) for 28 days. microRNA from uterus and jejunum tissues were profiled by next-generation small RNA sequencing. Serum microRNA expression was analyzed by RT-qPCR analysis.
Results: the microRNA expression in the jejunum remained unaffected, while significant changes in the uterine microRNA profile were observed. Importantly, 14 microRNAs were commonly and in a dose-dependent manner affected in both the ZEN medium and ZEN high group, including microRNAs from the miR-503 cluster. Although the effects in the serum were less pronounced, the receiver operating characteristic analysis revealed that several microRNA ratios were able to discriminate properly between non-exposed and ZEN-exposed pigs (e.g. ssc-miR-135a-5p/ssc-miR-432-5p, ssc-miR-542-3p/ssc-miR-493-3p).
Conclusions: This work sheds some new light on the molecular mechanisms of ZEN, and fosters biomarker discovery.

overall_design: Uterus and jejunum microRNA profiles at 28 days post weaned piglets. For each tissue, 6 biological replicates (= 6 pigs) from Control, 4 from ZEN low, 4 from ZEN medium, and 4 from ZEN high were used for library preparation. The final multiplexed (n=18) libraries were sequenced on a NextSeq 500

first: Matthias

last: Hackl

first: Susanna

last: Skalicky

first: Michaela

last: Thamhesl

first: Wulf

last: Moll

first: Roger

last: Berrios

first: Gerd

last: Schatzmayr

first: Veronika

last: Nagl


title: GPRC5A facilitates cell proliferation and bone metastasis of prostate cancer.

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: Prostate cancer is a high frequent disease. Early stage prostate cancer can be cured with high probability by early treatment, but hormone refractory prostate cancer and progressive prostate cancer is poor prognosis. Orphan GPCRs have the potential to become a drug discovery target in various carcinomas, but there are few reports in prostate cancer and there are still many possibilities. By big data analysis, we focused on the biological properties of the prostate cancer cell line and found GPRC5A from Orphan GPCR as one of the regulators of prostate cancer development. GPRC5A knock out by genomic editing in PC3, proliferative ability and bone metastasis was markedly suppressed. In prostate cancer cells, GPRC5A inhibit phosphorylation of CREB and affected the expression of cell cycle related genes. GPRC5A is also involved in the establishment of bone metastases, and correlated with prostate cancer metastasis and prognosis. These dates suggest that GPRC5A facilitates cell proliferation and progression of prostate cancer and can be a target for new prognostic marker or drug discovery of prostate cancer.

overall_design: mRNA profiles of wild type PC3-Luc cells and two GPRC5A knockout PC3-Luc cells were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Yuichiro

last: Sawada


title: Aging-associated gene expression profiling in adipose tissue derived mesenchymal stem cells.

city: Kyoto

first: Taichiro

last: Nishikawa

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Background & Aims: Recently, energy metabolism in adipose tissue has been the subject of renewed interest, because significant energy expenditure can be induced in cells derived from white adipose tissue derived mesenchymal stem cells (Ad-MSCs) as beige adipocytes (BA), in addition to brown adipose tissue. Here we evaluated whether age-related changes in Ad-MSCs affect on impaired energy homeostasis and progressive obesity-related diseases. Materials and Methods: We isolated Ad-MSCs from subcutaneous murine fat tissues fed with control chow (C) or high-fat diet (60% fat; HF) for 12 or 24 weeks (younger or older groups, respectively). After two to three times passage, we performed the cellular characteristics analyses, which included differentiation property, flow cytometric and microarray analyses. Results: Ad-MSCs from older mice showed impaired differentiation capacity into BAs compared to the cells from younger mice. Global gene expression analysis by microarray revealed several genes involved with the browning of white adipose tissue were down-regulated according to aging. Additionally, HF feeding promoted aging-associated characteristic changes in Ad-MSCs. Conclusion: These results indicate the compensation potential of Ad-MSCs on energy homeostasis is affected by aging and dietary factors. A new approach targeting Ad-MSCs might represent a potential strategy for the prevention of obesity-related diseases.

overall_design: Six-week-old male C57BL/6 mice were fed control chow (C) or high-fat diet (60% fat; HF) for 12 or 24 weeks. The Ad-MSC samples were collected from subcutaneous murine fat tissues, and compared global gene expression by AgilentMouse GE  8x60k Microarray.

first: T

first: H

last: Shin-ichi


title: Pattern of miR-31 knockout mouse colon gene expression

city: beijing

first: yongli

last: song

state: china

address: west road2,yuanmingyuan

department: college of life science

institute: china agricultural university

summary: To further understand different gene expression of miR-31 knockout mouse colon and normal colon, we have employed colonic epithelium microarray expression profiling as a discovery platform to identify different genes with miR-31 knockout mouse colon and normal colon.comparision with normal colonic epithelium,upgene is 285 and downgene is 178 in knockout group.

overall_design: 3 control and 3 miR-31 knockout mice colonic epithelium were flow separated into trizol, the samples were taken to lab on ice, mRNA were extracted with trizol, good quality mRNA were choosen as microarrary analysis in capitalBio technology.

first: Jiuzhi

last: Xu

first: Zhengquan

last: Yu


title: RNA-seq for MvfR, RhlR and QscR

first: Xin

last: DENG

summary: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, most notably those with cystic fibrosis or whose immune systems are compromised. As a global regulator, MvfR,RhlR and QscR have been characterized to control a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa, but its detailed molecular regulatory mechanism is largely elusive. To further gain insights into the direct targets of MvfR,RhlR and QscR in viv, this study focused on identifying the potential targets of MvfR,RhlR and QscR directly regulating QS system and other vireulence pathways. We performed a chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) assay that identified 221, 30 and 1 binding sites of MvfR,RhlR and QscR. The direct regulation of these genes by MvfR,RhlR and QscR have been biochemically and genetically verified.  The results indicated that MvfR,RhlR and QscR had direct and profound effects on QS, which provides new cues to better understand the detailed regulatory networks of virulence.

overall_design: RNA-seq for MvfR,RhlR and QscR


title: Ethnicity-specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore

city: Singapore

first: E Shyong

last: Tai

address: 1E Kent Ridge Road

department: Medicine

country: Singapore

institute: National University of Singapore, Yong Loo Lin School of Medicine

summary: Context: Insulin resistance (IR) and obesity differ between ethnic groups in Singapore, with discordant rates of obesity and IR between several ethnic groups. However, the molecular basis underlying these differences are not clear.    Objective: As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity and related traits.   Design, Setting and Main Outcome measures: We integrated transcriptomic, genomic and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study.   Patients: The study contains Chinese (n=63), Malay (n=51) and Asian-Indian (n=42) males, aged 21-40 years, without systemic diseases.  Results: We found remarkable diversity in the SM transcriptome between the three ethnicities with >8,000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences between ethnicities were unique to SM. We identified a network of 46 genes that were specifically down-regulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene-clusters, four of which were also enriched for genes that were found in GWAS of metabolic traits and disease and correlated with variation in IR, obesity and related traits.   Conclusion: We identified extensive gene expression changes in SM between the three Singaporean ethnicities, and report specific genes and molecular pathways that might underpin and explain the differences in IR between these ethnic groups.

overall_design: Total of 214 microarrays were analyzed for 156 samples. 100 of the microarrays were unique samples, 54 samples had technical duplicates and 2 samples had technical triplicates.

first: Ameila Li Min

last: Tan

first: E

middle: S

first: Enrico

last: Petretto


title: miRNA expression profiling of the A375 melanoma cell line and its dabrafenib-resistant A375R sub-line.

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

summary: Altered expression of miRNAs has been demonstrated in tumor tissue and plasma/serum of cancer patients. miRNAs have been shown to have both diagnostic and prognostic significance and to potentially constitute novel targets and therapeutic agents for cancer treatment. Experimental evidences also support a role of miRNAs in tumor cell  response to therapy, including resistance to BRAF inhibitors (BRAFi) in melanoma. In this study, miRNA expression pattern was determined in a BRAFV600E melanoma cell line sensitive to the BRAFi dabrafenib (i.e A375) and in its drug-resistant counterpart (i.e. A375R), derived in vitro by culturing the sensitive cell line with progressively increasing concentrations of dabrafenib (from 8 nM to 1.5 mM).

overall_design: Total RNA was extracted from the melanoma cell line A375 and its dabrafenib-resistant sub-line A375R, and miRNA expression pattern  was determined using Affymetrix GeneChip® miRNA 3.1 microarrays.

first: A

first: U

last: Pfeffer

first: S

last: Caporali

last: D'Atri S


title: Characterization functional of AcoN-like negative regulator protein from Acetoin cluster in Acinetobacter spp. Strains

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: Studies of expression of mechanims of defense of the Acinetobacter sp.5-2Ac.02 from airborne hospital environment under stress conditions, such as SOS response (ROS response, heavy metals resistant mechanisms, peptides), as well as Quorum network (acetoin cluster  and aromatics biodegradation cluster). Characterization functional of AcoN-like as negative regulator protein from acetoin cluster in Acinetobacter spp. Strains

overall_design: We worked with Acinetobacter sp.5-2Ac.02 from airborne (species close to Acinetobacter towneri) which genome of the strain has been sequenced by Barbosa et al. (21) (GenBank accession number. MKQS00000000; Bioproject PRJNA345289). Moreover, we used the Acinetobacter baumannii ATCC17978 (GenBank accession number CP018664.1), as well as two isogenic mutants, A. baumannii 17978ATCCΔacoN which was obtained in this study and A. baumannii 17978ATCCΔabaI from Castañeda-Tamez et al.

first: L

last: Fernandez-Garcia

last: Blasco

last: Ambroa

first: F

last: Fernández-Cuenca

first: I

last: Bleirot

first: B

middle: G

last: Barbosa

first: R

last: Trastoy

first: M

last: López

last: Martinez-Martinez

last: Pascual

last: Tuttobene

last: Mussi

first: G

last: Bou

last: Tomás


title: Long non-coding RNA HOXB-AS3 promotes myeloid cell proliferation and its higher expression is an adverse prognostic marker in myeloid malignancies [AML_normal]

city: Taipei City

first: Huai-Hsuan

last: Huang

state: Taiwan

address: No.7, Chong-Shan South Road, Zhongzheng Dist.

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary:
The mononucleated cells were collected from the bone marrow samples of AML patients and healthy controls.
We compared the expressions between AML patients and the healthy controls.

overall_design: Total RNA were extrated from the mononucleated cells from the bone marrow samples of AML patients and healthy controls. We compared the expressions of AML patients with the healthy donors.


title: Long non-coding RNA HOXB-AS3 promotes myeloid cell proliferation and its higher expression is an adverse prognostic marker in myeloid malignancies [MDS_normal]

summary:
The mononucleated cells were collected from the bone marrow samples of MDS patients and healthy controls.
We compared the expressions between MDS patients and the healthy controls.

overall_design: Total RNA were extrated from the mononucleated cells from the bone marrow samples of MDS patients and healthy controls. We compared the expressions of MDS patients with the healthy donors.


title: Myeloid Skewing in Aging Bone Marrow Depends on Long-lived Plasma Cell Accumulation

city: Los Angeles

first: Kenneth

last: Dorshkind

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

summary: Aging results in a reduction in B lymphopoiesis and an increase in myelopoiesis in mice and humans. We investigated how cellular changes in the aging hematopoietic microenvironment contribute to these alterations in hematopoiesis and found that long-lived plasma cells (LLPCs) increase in number in the bone marrow of old mice. The LLPCs exhibited a Toll Like Receptor activation signal, and their accumulation was partially dependent on inflammatory cytokines. LLPCs were able to stimulate myelopoiesis from hematopoietic stem cells and myeloid progenitors in vitro, and anti-CD138 antibody-mediated depletion of LLPCs or blockade of pro-inflammatory signaling in old mice in vivo resulted in a significant reduction in LLPC number and attenuated myeloid development. However, B lymphopoiesis remained suppressed. These data identify the increase in LLPC number as obligate for age-associated increases in myelopoiesis and provide evidence that, in the context of aging, enhanced myelopoiesis and depressed lymphopoiesis are distinct, independently regulated processes.

overall_design: We isolated bone marrow long-lived plasma cells (LLPCs) as CD45R(B220)- IgD- CD138high TCRb- TCRgd- CD11b- Gr-1- from three independent groups of young (2-3 months, female) and old (17-19 months, male) mice and performed RNA-Seq.

first: Peter

last: Pioli

first: Encarnacion

last: Montecino-Rodriguez

first: David

last: Casero

first: Sherie

last: Morrison


title: HOXB-AS3 expressions promote cell proliferation

summary: We knock down HOXB-AS3 with shRNA in OCI/AML3 cell line to investigate the downstream pathways of HOXB-AS3 in the cell proliferation.

overall_design: We establish four stable cells lines from OCI/AML3. Two are infected with two different shRNAs to knock down HOXB-AS3, and the other two are infected with control shRNA. We compare the differential gene expressions of the cell lines with shHOXB-AS3 with those of the control cell lines.


title: Single Cell RNA-Seq Analysis Reveals  Fate Decision of Human Pre-cDC Determined  by Transcription Factor Competition

city: New York City

first: Kang

last: Liu

state: New York

department: Dept of Microbiology & Immunology

institute: Columbia University

summary: Classic dendritic cells (cDCs) play a central role in the immune system and consist of two major subsets: CD141+ cDC (cDC1) and CD1c+ cDC (cDC2). The pre-cDCs is the immediate precursors to both cDC subsets. Previous studies showed that there were two pre-committed pre-cDC subpopulations. However, the key molecular drivers of pre-commitment in human pre-cDCs were not investigated. To address this question, we performed both single cell and bulk RNA sequencing (RNA-seq) of two cDC subsets and pre-cDCs. We inferred a list of sixteen candidate master regulator transcriptional factors (TFs) that can indeed separate pre-cDCs into two sub-populations, with one close to cDC1 and the other close to cDC2. More importantly, these two pre-cDC sub-populations are correlated with ratio of IRF8 to IRF4 expression level more than their individual expression level. Our results suggest the concept that the ratio of antagonistic TFs and their competition determine cDC subset differentiation fate.

overall_design: mRNA profiles of pre-DCs, DC1 and DC2 in single cell and CDP, pre-DC, DC1 and DC2 in bulk from blood of human healthy donors

first: Yu

middle: J

last: Zhou

first: Wenji

last: Ma

first: Yufeng

last: Shen


title: miR167 limits anther growth to potentiate anther dehiscence

status: Public on Jul 15 2019

city: Chapel Hill

first: Jason

last: Reed

state: NC

address: CB #3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

summary: In flowering plants, anther dehiscence and pollen release are essential for sexual reproduction.  Anthers dehisce after cell wall degradation weakens stomium cell junctions in each anther locule, and desiccation creates mechanical forces that open the locules.  Either effect or both together may break stomium cell junctions.  The microRNA miR167 negatively regulates ARF6 and ARF8, which encode Auxin Response transcription Factors.  Arabidopsis mARF6 or mARF8 plants with mutated miR167 target sites have defective anther dehiscence and ovule development.  Null mir167a mutations recapitulated mARF6 and mARF8 anther and ovule phenotypes, indicating that MIR167a is the main miR167 precursor gene that delimits ARF6 and ARF8 expression in these organs.  Anthers of mir167a or mARF6/8 plants overexpressed genes encoding cell wall loosening functions associated with cell expansion, and grew too large starting at flower stage 11.  Experimental desiccation enabled dehiscence of miR167-deficient anthers, indicating competence to dehisce.  Conversely, high humidity conditions delayed anther dehiscence in wild-type flowers.  These results support a model in which miR167-mediated anther growth arrest permits anther dehiscence.  Without miR167 regulation, excess anther growth delays dehiscence by prolonging desiccation.

overall_design:
The dataset includes experiments from two tissues, stamens or gynoecia.  Arabidopsis thaliana plants were grown in 14:10 h day:night cycles.  Tissue samples for RNA isolation were collected between 1 and 3 hours after dawn, and immediately frozen in liquid nitrogen.  Stage 11 flower buds used for stamen isolation (sample groups F, G, H) were 1.5-1.8 mm long, generally corresponding to 3 to 5 flowers before the first open flower.  Stamens at this stage still appeared green before turning yellow at flower stage 12.  Tissue for the gynoecium experiment (sample groups A, B, C, D, E) was from stage 12 flowers with gynoecia of 0.9 to 1.4 mm long.
For RNA-Seq, RNA was isolated using the Rneasy Plant Mini kit (Qiagen) according to manufacturer’s instructions.  Libraries were constructed with the Truseq mRNA library prep kit (Illumina) according to manufacturer’s instructions.  Samples were bar-coded and multiplexed, and sequenced using an Illumina HiSeq 2000 machine with single-end 50 base reads.  Library construction and sequencing were performed at the UNC-CH high-throughput sequencing facility.
Information on genotypes:
Two different stable transgenic lines carrying the introduced mARF8 transgene are called mARF8 3B and mARF8 4B.  "mARF8 T1s" refers to a pool from several plants carrying the same mARF8 transgene as lines 3B and 4B.  These lines carry a genomic mARF8 gene with the target site for the microRNA miR167 mutated.
pSTK:axr3-1 lines 15-5 and 25-2 were two different transgenic Arabidopsis lines carrying the same introduced pSTK:axr3-1 transgene.  This transgene uses promoter sequences from the SEEDSTICK gene to drive a gain-of-function axr3-1 gene encoding a stabilized AXR3/IAA17 protein.  Col X PSTK:axr3-1 refers to F1 plants from a cross between wild type Columbia and pSTK:axr3-1.

first: Lanjie

last: Zheng

first: Punita

last: Nagpal

first: Gonzalo

last: Villarino

first: Brendan

last: Trinidad

first: Laurina

last: Bird

first: Robert

last: Franks

first: Yubi

middle: W


title: Effect of chemicals in ES cell differentiation

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

country: Japan

institute: Kyoto University Graduate School of Pharmaceutical Sciences

summary: Expression data from ES cell exposed to chemicals

overall_design: RNA from mouse ES cells was extracted and processed for hybridization on Affymetrix microarrays.

first: Tatsuyuki

last: Takada

first: Tomoaki

last: Tanaka

first: Yuriko

last: Ono


title: RNA-sequencing analysis of paternal low-protein diet-induced gene expression change in mouse offspring adipocytes

city: Tsukuba

first: Nhung

middle: Hong

last: Ly

state: Ibaraki

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

institute: Riken

summary: Increasing evidence indicates that parental diet affects the metabolism and health of offspring. It is reported that paternal low-protein diet (pLPD) induces glucose intolerance and the expression of genes involved in cholesterol biosynthesis in mouse offspring liver. The aim of the present study was to determine the effect of a pLPD on gene expression in offspring white adipose tissue (WAT), another important tissue for the regulation of metabolism. RNA-seq analysis indicated that pLPD up- and down-regulated 54 and 274 genes, respectively, in offspring WAT,. The mRNA expression of many genes involved in lipogenesis was down-regulated by pLPD feeding, which may contribute to glucose intolerance. The expression of carbohydrate response element-binding protein β (ChREBP-β), an important lipogenic transcription factor, was also significantly lower in the WAT of pLPD offspring, which may have mediated the down-regulation of the lipogenic genes. By contrast, the LPD did not affect the expression of lipogenic genes in the WAT of the male progenitor, but increased the expression of lipid oxidation genes, suggesting that a LPD reduces WAT mass by activating lipid oxidation, and that LPD may reduce WAT mass using differing mechanisms in parents and offspring. These findings add to our understanding of how paternal diet can regulate metabolism in their offspring.

overall_design: iWAT mRNA profiles of 10-12-week old wild type male mice fed control diet (CD) and low-protein diet (LPD) (F0 generation), in duplicate;  iWAT mRNA profiles of 5-week old wild type (WT) male offspring (F1 generation) from father mice fed CD and LPD were generated by deep sequencing, in triplicate, using NextSeq500 Illumina.

first: N

first: T

last: Maekawa

first: K

last: Yoshida

first: Y

first: M

last: Muratani

first: S

last: Ishii


title: ROCK1 translocates to the nucleus and inhibits human cytomegalovirus propagation

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Rho-associated coiled-coil kinase (ROCK) protein is a central kinase that regulates numerous cellular functions, including cellular polarity, motility, proliferation and apoptosis. Here, we demonstrate that ROCK has antiviral properties and inhibition of its activity results in enhanced propagation of human cytomegalovirus (HCMV). We show that during HCMV infection ROCK1 translocates to the nucleus and concentrates in the nucleolus were it co-localizes with the stress related chaperone, heat shock cognate 71 kDa protein (Hsc70) . Gene expression measurements showed that inhibition of ROCK activity does not affect the cellular stress response. We further demonstrate that inhibition of myosin, one of the central targets of ROCK, also increases HCMV propagation, implying that the anti-viral activity of ROCK might be mediated by activation of the actomyosin network. Finally, we demonstrate that inhibition of ROCK results in increased levels of the tegument protein UL32 and of viral DNA in the cytoplasm, suggesting ROCK activity hinders the efficient egress of HCMV particles out of the nucleus. Altogether our findings illustrate ROCK activity restricts HCMV propagation and suggest this inhibitory effect may be mediated by suppression of capsid egress out of the nucleus.

overall_design: samples of HCMV infected fibroblasts treated with ROCK inhibitor or with DMSO as control, in duplicates

first: Erez

last: Eliyahu

first: Martina

last: Dobesova

first: Michal

last: Schwartz

first: Aharon

last: Nachshon

first: Osnat

last: Tirosh


title: RNA-seq and ribosome profiling of heat shocked wild type and Mettl14 -/- mouse embryonic stem cells

city: New York

first: Ryan

last: Ries

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: N6-methyladenosine (m6A) is a dynamic and reversible nucleotide modification in mRNA. m6A alters mRNA fate, but it is unclear why the effects of m6A can vary in different cellular contexts. Here we show that methylated mRNAs are catalysts for liquid-liquid phase separation of the YTHDF family of m6A-binding proteins. RNAs that contain multiple, but not single, m6A residues recruit multiple YTHDF proteins, causing them to undergo a proximity-induced phase separation. YTHDF proteins show liquid-like properties upon binding polymethylated mRNAs in cells, and partition into endogenous phase-separated compartments, such as P-bodies, neuronal RNA granules, and stress granules. The complexes of YTHDF proteins and polymethylated mRNAs are targeted to different compartments depending on the cell context, leading to different effects on m6A mRNAs. These studies reveal a role for nucleotide modifications in regulating phase separation and indicate that the cellular properties of m6A-modified mRNAs can be explained by liquid-liquid phase separation principles.

overall_design: RNA-seq was performed on wild type and Mettl14 -/- mouse embryonic stem cells. Four replicates were sequenced under non-stressed conditions, after heat shock at 42°C for 30 min, and 1 h after recovery from heat shock stress.

first: Samie

last: Jaffrey


title: RNA-seq analysis of wild type strain at DD12 and DD20

city: Guangzhou

first: Ma

last: Huan

state: Guangdong

address: 132 East Waihuan Rd, Rm 438 Higher Education Mega

institute: Sun Yat-Sen University

summary: Analysis of differentially spliced sites at DD12 and DD20

overall_design: Total RNA obtained from wild type Neurospora crassa strain

first: Huan

last: Ma

first: Jinhu

last: Guo


title: Global transcriptomic changes following carbon limitation and elevated carbon dioxide in Nannochloropsis oceanica IMET1: Illumina sequencing

city: Qingdao

first: Jian

last: Xu

state: Shandong province

address: No.189 Songling Rd, LaoShan District

department: BEGC

institute: QIBEBT-CAS

summary: Limited systems-level understanding of CO2 concentrating mechanism (CCM) and metabolic adaption in response to different CO2-level in wild oleaginous algae has hindered the development of microalgal feedstock and the knowledge of its role in global warming and oceanic acidification. Nannochloropsis are a group of small unicellular microalgae widely distributed in oceans and fresh water, which implies that it plays a crucial role in biogeochemical cycles impinged on global climate change. In addition, Nannochloropsis has been used for flue gas fixation in many large-scale and pilot-scale outdoor cultivation facilities for photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying CCM and metabolic adjustment under different CO2 concentrations in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal CCM and  in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolution transcript change for the complete time-courses of different CO2 concentrations.

overall_design: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2 for preadaption for one hour, and then two samples (from biological replicates) were collected as 0h samples. After the preadaption for one hour, half of them were sequentially grown under 5% in air (High carbon or HC) and other half of them were grown under 0.01% CO2   (Very low carbon or VLC) with 80±5 µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 6h, 12h and 24h. Three biological replicates of algal cultures were established under each of the above “VLC” and “HC” conditions, respectively. Two biological replicates were randomly selected to prepare mRNA-Seq library. In total, 18 samples collected at 5 time points (0h, 3h, 6h, 12h, and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

first: Li

last: Wei


title: Expressional profile of liver of CGMCC No.8730 Eurotium cristatum fermented dark tea fed high-fat diet rats

status: Public on Jul 14 2019

city: Beijing

first: Ting

last: Liu

address: No.4 Road, Future Science and Technology Park, South Beiqijia, Changping District

institute: COFCO Nutrition and Health Research Institute

summary: Microbial fermentation is involved in the processing of a dark tea popular for centuries in Northwest China which has shown many health benefits. This study will examine anti-obesity, hyperlipidemic and hyperglycemic effects of CGMCC No.8730 Eurotium cristatum (EC) fermented dark tea (8730DT).

overall_design: Male SD rats fed with normal or 60% high-fat diet (HFD) were intragastric administrated distilled water, or 8730 dark tea for 9 weeks. Liver was analyzed for gene expression profile. Liver of stilled-water-fed high fat diet rats were used as control. 3 replicates were included in both 8730 dark tea group or control group.

last: Ying

first: Ran

last: Chen

first: Qingjia

last: Meng

first: Song

last: Li

first: Di

first: Junsheng

last: Huo

first: Chunling

last: Wang


title: miRNA Biomarker candidates fo the detection of endometrial atypical hyperplasia

city: rome

first: simona

last: giglio

state: rome

address: via di grottarossa

department: clinical and molecolar medicine

institute: Sapienza university

summary:
in the current study we identified a miRNAs signature able to discriminate between typical and atypical endometrial hyperplasia
the identification of molecular marker that can differentiate between these two distinct pathological conditions is highly considered to be useful for the clinical management of the patients, owing to the fact that hyperplasia with atypical change is associated with higher risk of develop cancer.

overall_design: typical and atypical endometrial hyperplasia were micro or macrodissecate from Formalin fixed paraffine tissue

first: Viviana

last: Annibali

first: Simona

last: Giglio

first: Stefano

last: Volinia


title: Deletion of Cebpa from PreGMs

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

summary: Role of Cebpa in PreGM cells

overall_design: We have sorted PreGMs from 3 Cebpaflox/flox and 3 Cebpaflox/flox;Mx1Cre mice 18 days after pIC injection.

first: Bo

last: Porse

first: Felicia

last: Lauridsen


title: Transcription analysis of recombinant Trichoderma_reesei  strains reveals the molecular basis for fermentation of glucose and xylose

city: nanning

first: jun

last: huang

institute: guangxi sciences academy

summary: In this study, the recombinant Trichoderma reesei strain HJ48 was employed to investigate the differences between anaerobic fermentation of xylose and glucose, through genome-wide transcription analysis. Analysis of the genes induced under fermentation condition has revealed novel features in T. reesei. Our results how that many genes related to ribosome were expressed more highly with xylose than with glucose in HJ48.

overall_design: mRNA profiles of 4-day old of Trichoderma_reesei under fermentation of glucose and xylose condition were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Ribo

last: Huang

first: Jun


title: Histone 3 lysine 27 acetylation profiling reveals its role in the chronic DSS-induced colitis mouse model [RNA-seq]

status: Public on Jul 13 2019

city: Wuhan City

first: Qinglan

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

summary: To investigate whether the H3K27ac is involved in the development of inflammatory bowal disease. We established dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing and Chromatin Immunoprecipitation followed by NGS sequencing for H3K27ac in the mice colon tissues. We find that the global H3K27ac distribution in colon tissue had no significant difference, while on the typical-enhancers specific in the DSS group, H3K27ac signals were significantly enriched when compared with the control. Furthermore, we identified 89 candidate genes which represented the susceptible genes to H3K27ac change and predicted transcription factors (TFs) upon the DSS treatment. Collectively, our study revealed that H3K27ac increase on special typical-enhancers is possibly related to the development of intestinal inflammation by up-regulating adjacent gene expression and shifting TFs networks.

overall_design: We established the dextran sulfate sodium (DSS)-induced chronic colitis and performed RNA-sequencing (RNA-seq) and Chromatin Immunoprecipitation followed by NGS sequencing (ChIP-seq) for H3K27ac in the mice colon tissues to investigate whether the H3K27ac is involved in the development of intestinal inflammation.

first: Meng

last: Cao

first: Yanan

last: Deng

first: Lianyun

first: Qiu

last: Zhao

first: Min

last: Wu

first: Mei

last: Ye


title: RIPK3 activation leads to cytokine synthesis that continues after loss of cell membrane integrity

city: San Francisco

first: Shaun

last: Cullen

state: CA

address: 1435 16th Avenue

country: USA

institute: Genentech

summary: Necroptosis is a form of programmed cell death that is defined by activation of the kinase RIPK3, and subsequent cell membrane permeabilization by the effector MLKL. In addition to triggering cell death, RIPK3 activation can promote immune responses through the production of cytokines and chemokines. How active cytokine production is coordinated with the terminal process of necroptosis is unclear. Here, we report that cytokine production continues within necroptotic cells after cells have lost plasma membrane integrity and irreversibly commited to death. The continued production of inflammatory mediators was dependent on mRNA translation, and required maintanence of endoplasmic reticulum integrity, which remained in tact after plasma membrane integrity was lost. The continued translation of cytokines by cellular corpses contributed to necroptotic cell uptake by innate immune cells, as well as priming of adaptive immune responses to antigens associated with necroptotic corpses. These findings imply that necroptosis may represent a program in which cell death and production of inflammatory mediators are coordinated to optimize the immunogenicity of necroptotic cells.

overall_design: The NIH-3T3 RIPK3-2xFV cell line has been treated with a chemical dimerizer to induce RIPK3-dependent necroptosis. Experiment A (sample 1-12) is a simple timecourse of dimerizer treatment where cell death increases over time. Experiment B (sample 13-24) takes a snapshot at 4 h, taking a polysome RNA fraction for comparison with total cell RNA. TNF is included as a control that will trigger inflammatory gene expression without cell death. Two biological replicates were analyzed for each of 6 conditions, giving 12 samples per experiment.

first: Andrew

last: Oberst

first: Susana

last: Orozco


title: 16s rDNA-sequencing of gastric flora in mice fed with high-salt diets

city: jinan

first: yundong

last: sun

address: wenhua west road 44

country: China

institute: shanda university

summary: There are 10 mice in the experiment, named REC. The mice were fed with high salt diets (5% NaCl) for 4 weeks and then fed with normal salt diets for 4 weeks. Then extracted DNA from mice gastric flora to detect changes in the gastric flora of mice.

overall_design: 16s rDNA-sequencing for 10 samples.

first: Ya

last: Li


title: Identification and validation of GPD1 as an essential cancer stem cell specific target in glioblastoma (Ribosome profiling)

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

summary: Cancer stem cells (CSCs) are attractive targets for cancer therapy, however, little is known about how to target CSCs without affecting the normal stem cell population. Here we report the ribosome-profiling analysis of mouse neural stem cells and brain tumour stem cells (BTSCs), which leads to the identification of glycerol-3-phosphate dehydrogenase 1 (GPD1) as a CSC- specific determinant.  We confirmed that GPD1 is expressed in BTSCs but not in neural stem cells. Intriguingly, expression of GPD1 is only found in the infiltrating dormant BTSCs in vivo and these cells start to divide and drive tumour relapse after chemotherapy. Most importantly, inhibition of GPD1 expression in tumour-bearing mice leads to prolonged survival. Further analysis shows that loss of GPD1 results in widespread changes in important pathways affecting BTSC maintenance. Human patient data analysis suggests that GPD1 is expressed in the dormant infiltrating tumour cells in human glioblastoma and the expression level is associated with a worse prognosis. This study provides an attractive therapeutic target for treating brain tumours and a novel aspect of regulation of CSC dormancy.

overall_design: Two neural stem cell samples and three brain tumor stem cell samples are used in ribosome profiling experiments.

first: Patricia

last: Rusu

first: Chunxuan

last: Shao


title: Gene expression profiles of mouse embryonic neural stem/progenitor cells during astrocyte differentiation

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: We performed a microarray experiment to compare gene expression profiles of neural stem/progenitor cells (NS/PCs) with different culture conditions.

overall_design: NS/PCs were cultured for five days with different conditions (bFGF + EGF or LIF or BMP4 or LIF + BMP4 or FBS).


title: Transcriptomic changes accompanying allopolyploidization are commonly paralleled in Brassica napus.

city: Vancouver

first: David

middle: Christopher

last: Tack

state: B. C.

address: 3529-6720 University Boulevard

department: Botany

country: Canada

institute: Universtiy of British Columbia

summary: Changes to gene expression and splicing are investigated between parental species (B. oleracea and B. rapa) and three resynthesized allopolyploids, as well as a natural B. napus

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea
synthetic construct

overall_design: mRNA seq of first true leaves from B. rapa, B. oleracea, B. napus, and three resynthesized B. napus plants.

first: Keith

last: Adams


title: Neonatal intermittent hypoxia exposure sex-specifically augments rat microglial cytokine expression acutely and long-term

status: Public on Jul 12 2019

city: Madison

first: Jyoti

last: Watters

state: WI

address: 2015 Linden Drive

department: CBS

institute: University of Wisconsin-Madison

summary: We analyzed gene expression via RNA-sequencing in microglia isolated from postnatal day 9 rats exposed to normoxia or intermittent hypoxia, in the presence or absence of lipopolysaccharide

overall_design: P1 sprague dawley rat neonates (three biological replicates per sex and condition) were exposed to one of the following conditions: 1) 8 days of normoxia (21 % O2 followed by 3 hours saline injection (i.p.) 2) 8 days of normoxia followed by 3 hours lipopolysaccharide (LPS) injection (0.1 mg/kg i.p.) 3) 8 days of intermittent hypoxia (2 min cycles between 10.5% O2 and 21% O2 8 hrs/day) followed by vehicle injection and 3) 8 days of intermittent hypoxia followed by 3 hrs LPS injection). Microglia were immunomagnetically isolated following the vehicle or LPS injection and total RNA isolated for sequencing.

first: Elizabeth

middle: A

last: Kiernan


title: Identification and validation of GPD1 as an essential cancer stem cell specific target in glioblastoma (RNA-seq: NSC vs BTSC)

overall_design: Two neural stem cells and two brain tumor stem cells are used in RNA-seq experiments