title: Exploring Listeria monocytogenes transcriptomes in correlation with divergence of lineages and virulence measured in Galleria mellonella

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

summary: For bacteria in general and Listeria monocytogenes in particular, little is known about transcriptome diversity in comparison to the copious data on intraspecific genome diversity. The current study employed RNA sequencing to investigate the variation of transcript levels of conserved single copy genes from several perspectives including differences between lineages and correlation with previous classification of the virulence potential of clonal complexes based on epidemiological MLST data. Infection of G. mellonella, a surrogate host, also allowed a correlation analysis with virulence data experimentally determined in vivo.

overall_design: The study encompasses 66 samples corresponding to 2 biological replicates (independent cultures) for 33 Listeria monocytogenes isolates belonging to the two major phylogenetic lineages, grown in an optimal in vitro culture condition.

first: Bo-Hyung

last: Lee

first: Cyprien

last: Guérin

first: Björn

last: Rotter

first: Pascal

last: Piveteau


title: AML subtype is a major determinant of the association between prognostic gene expression signatures and their clinical significance.

status: Public on Sep 10 2019

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Relapse in acute myeloid leukemia (AML) may result from variable genetic origins or convergence on common biological processes. Exploiting the specificity and sensitivity of regulatory DNA, we analyze patient samples of multiple clinical outcomes covering various AML molecular subtypes. We uncover regulatory variation between patients translating into a transcriptional signature that predicts relapse risk. In addition, we find clusters of co-expressed genes within this signature selectively link to relapse risk in distinct patient subgroups defined by molecular subtype or AML maturation. Analyzing these gene clusters and the AML subtypes separately enhances their prognostic value substantially and provides insight in the mechanisms underlying relapse risk across the distinct patient subgroups. We propose that prognostic gene expression signatures in AML are valid only within patient subgroups and do not transcend these subgroups.

overall_design: ChIP-sequencing for H3K27ac and RNA-sequencing of pediatric AML patient samples.

first: C

middle: R

last: Wiggers

first: M

middle: L

last: Baak

last: Bartels


title: Seminal fluid compromises visual perception in honeybee queens reducing their survival during additional mating flights

city: Lausanne

first: Joanito

last: Liberti

address: Biophore

country: Switzerland

institute: University of Lausanne

summary: Queens of social insects make all mate-choice decisions on a single day, except in honeybees whose queens can conduct mating flights for several days even when already inseminated by a number of drones. Honeybees therefore appear to have a unique, evolutionarily derived form of sexual conflict: a queen’s decision to pursue risky additional mating flights is driven by later-life fitness gains from genetically more diverse worker-offspring but reduces paternity shares of the drones she already mated with. We used artificial insemination, RNA-sequencing and electroretinography to show that seminal fluid induces a decline in queen vision by perturbing the phototransduction pathway within 24-48 hours. Follow up field trials revealed that queens receiving seminal fluid flew two days earlier than sister queens inseminated with saline, and failed more often to return. These findings are consistent with seminal fluid components manipulating queen eyesight to reduce queen promiscuity across mating flights.

overall_design: Two subsequent RNA-seq experiments, each with three treatment groups. Each treatment consisted of three biological replicates. Each biological replicate was a pool of three brains of honeybee queens after they were artificially inseminated with either semen, seminal fluid or mock-inseminated (first experiment), or semen, seminal fluid and Hayes saline (second experiment). RNA-seq libraries were sequenced on Illumina HiSeq 2500 (single-end 120 bp reads).


title: Analyses of lncRNA profiling during the development from pre-receptive to receptive phases in goat endometrium

city: Yangling District

first: Lei

last: Zhang

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: In the present study, RNA-seq technique was used to compare the expression profiles of lncRNAs from goat endometrium samples at gestational day 5 (pre-receptive endometrium, PE) and day 15 (receptive endometrium, RE). This yielded 18 gigabases (Gb) of sequence, representing approximately seven times the size of the genome (2.66 Gb). A total of 120 million raw reads were produced from the Illumina HiSeq 2500 platform. After discarding adaptor sequences and low-quality sequences, 90 to 97 million clear reads per sample were obtained, and the percentage of clean reads among raw tags in each library ranged from 75.79–81.03 %. A total of 668 lncRNAs were found to differ significantly in terms of expressional levels (P< 0.05) between the PE and RE libraries,98.35% of the DELs were mapped to “u” (Unknown, intergenic transcript).Our results included 76,844 lncRNAs that corresponded to 42,933 protein-coding genes within a range of 1-100 kb. It deserved to note that 783 target genes of the 200 DELs that were annotated to 153 GO terms meeting our designated criteria of P-values< 0.05, KEGG pathway annotation showed 242 target genes of the DELs were annotated for 146 KEGG pathways.

overall_design: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study. The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium). Endometrium samples from 10 goats at gestational day 5 and 10 goats at gestational day 15 were obtained from the anterior wall of the uterine cavity.

first: Bin-yun

last: Cao


title: Age- and Nicotine-Associated Gene Expression Changes in the Hippocampus of APP/PS1 Mice

city: chongqing

first: jie

last: yang

address: 1 Youyi Road

institute: Chongqing Medical University

summary: The etiology of Alzheimer's disease (AD) has been intensively studied. However, little is known about the molecular alterations in early-stage and late-stage AD. Hence, we performed RNA sequencing and assessed differentially expressed genes (DEGs) in the hippocampus of 18-month and 7-month-old APP/PS1 mice. Moreover, the DEGs induced by treatment with nicotine, the nicotinic acetylcholine receptor agonist that is known to improve cognition in AD, were also analyzed in old and young APP/PS1 mice. When comparing old APP/PS1 mice with their younger littermates, we found an upregulation in genes associated with calcium overload, immune response, cancer, and synaptic function; the transcripts of 14 calcium ion channel subtypes were significantly increased in aged mice. In contrast, the downregulated genes in aged mice were associated with ribosomal components, mitochondrial respiratory chain complex, and metabolism. Through comparison with DEGs in normal aging from previous reports, we found that changes in calcium channel genes remained one of the prominent features in aged APP/PS1 mice. Nicotine treatment also induced changes in gene expression. Indeed, nicotine augmented glycerolipid metabolism, but inhibited PI3K and MAPK signaling in young mice. In contrast, nicotine affected genes associated with cell senescence and death in old mice. Our study suggests a potential network connection between calcium overload and cellular signaling, in which additional nicotinic activation might not be beneficial in late-stage AD

overall_design: Examination of nicotine modifications in early and late stage of Alzheimer’s disease

first: Jie

last: Yang

first: Guo-Jun

last: Chen


title: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

summary: High throughput RNA sequencing (RNA-seq) using cDNA has played a key role in delineating transcriptome complexity, including alternative transcription initiation, splicing, polyadenylation and base modification. However, the reads derived from current RNA-seq technologies are usually short and deprived of information on modification during reverse transcription, compromising their potential in defining transcriptome complexity. Here we applied a direct RNA sequencing method with ultra-long reads from Oxford Nanopore Technologies (ONT) to study the transcriptome complexity in C. elegans. We sequenced native poly-A tailed mRNAs by generating approximately six million reads from embryos, L1 larvae and young adult animals, with average read lengths ranging from 900 to 1,100 bps across stages. Around half of the reads represent full-length transcripts, judged by the presence of a splicing-leader or their full coverage of an existing transcript. To take advantage of the full-length transcripts in defining transcriptome complexity, we devised a novel algorithm to predict novel isoforms or group them with exiting isoforms using their mapping tracks rather than the existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. Intriguingly, stage-specific expression at the level of gene and isoform demonstrates little correlation. Finally, we observed an elevated level of modification in all bases in the coding region relative to the UTR. Taken together, the ONT long reads are expected to deliver new insights into RNA processing and modification and their underlying biology.

overall_design: Animals of different stages, i.e., embryo, L1 larva and young adult, were collected and total RNAs were extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. Approximately 100 µg total RNAs were extracted for each sample. Around 900 ng of poly-A tailed mRNAs was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) based on the user’s manual for each library preparation. Nanopore sequencing libraries were constructed using Direct RNA sequencing kit (cat# SQK-RNA001). The libraries were loaded onto Nanopore R9.4.1 flow cell (cat# FLO-MIN106) and sequenced on MinION acquired from Oxford Nanopore Technologies. The software used for sequencing was MINKNOW 2.1 with base-caller, Albacore (v2.0.1).

first: Zhongying

last: Zhao


title: Genome-wide enhancer profiling identifies novel Shh regulated gene targets in the developing cochlear duct

status: Public on Sep 09 2019

city: Philadelphia

first: Douglas

middle: J

last: Epstein

state: PA

address: 415 Curie Boulevard

country: USA

institute: University of Pennsylvania

summary: The development of the mammalian inner ears is a highly dynamic process that is dependent on the interplay of multiple signaling molecules. Previous studies demonstrated the role of Shh in the initiation and outgrowth of the cochlea. However, the gene targets of Shh in the cochlea largely remain unknown. We show in this study, Shh responsive genes that are loss in the cochlea of Smoecko mutant (Smo null) and upregulated in Shh-P1 mutant embryos through comparative RNA-seq profiling. We performed a genome-wide cis-regulatory element (cRE) study (via ATAC-seq and Gli2 ChIP-seq) and identified potential cREs that are targets of the Shh signaling pathway in   the cochlea. Our data unravel novel Shh signaling regulated gene targets that have important functional roles in the development of the cochlea.

overall_design: 1) Examination of genome wide gene expression in 2 different inner ear mutants at E11.5, 2) Examination genome wide of open chromatin regions using ATAC-seq in E11.5 inner ear, 3) Examination of genome wide Gli2 binding site in the E10.5 embryonic head


title: Accurate detection of m6A RNA modifications in native RNA sequences [Yeast]

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

summary: The field of epitranscriptomics has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using Oxford Nanopore Technologies, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide resolution, in individual RNA molecules.

overall_design: Total RNA from meiotic SK1 yeast cells was extracted. Enrichment of polyadenylated RNA from total RNA was performed using Oligo(dT) dynabeads. Purified PolyA RNA was sequenced with Direct RNA Nanopore Sequencing. Three biological replicates were performed for each strain .

first: Eva

middle: M

first: Huanle

last: Liu

first: Oguzhan

last: Begik


title: An ultra effective method of generating extra multipotent cells from human fibroblasts via ultrasound-directed instant chromatin remodeling

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

summary: We have developed an ultra effective method of generating extra multipotent (xpotent) cells which have differentiation potential more than limited cell types, by the mechanism of ultrasound-directed permeation of environmental transition-guided cellular reprogramming (Entr).

overall_design:
Ultrasound stimulus treated x/Entr cells and control HDF cells

The HDF_control sample (GSM2308280) is identical to GSM2308274.

first: Yong

middle: S

first: Hyejung

last: Heo

first: Jonghwan

first: Ki-Sung

last: Hong

first: Sung

middle: U

last: Moon

first: Hana

last: Gu

middle: K

last: Park

first: Woon

middle: Y

last: Jung

first: Min

middle: G

first: Seung-Hun

last: Oh

first: Soonhag

last: Kim


title: High-density spatial transcriptomics arrays for in situ tissue profiling

city: Cambridge

first: Sanja

last: Vickovic

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

summary: Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.

overall_design: Three sections of the main olfactory bulb from adult C57BL/6J mice

first: Ludvig

last: Bergenstråhle


title: An ultra effective method of generating extra multipotent cells from human fibroblasts via ultrasound-directed instant chromatin remodeling [MBD-seq]

type: Methylation profiling by high throughput sequencing

overall_design: MBD-seq on ultrasound stimulus treated x/Entr cells and, control cells were HDF cells and ES cells


title: Downregulation of Uhrf1 activity by TGF-β signaling controls Foxp3 methylation and iTreg cell differentiation

status: Public on Sep 08 2019

city: Shanghai

first: Xiang

last: Sun

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, SIBS, CAS

summary: Foxp3+ regulatory T cells (Treg cells) are essential for immune system homeostasis and suppression of excessive immune responses. Both TGF-β signaling and epigenetic modifications are important in the regulation of Foxp3 induction, but whether TGF-β signaling participates in the epigenetic regulation of Foxp3 has not been fully clarified. Here, we show that Uhrf1, which is induced by TCR stimulation and regulated by TGF-β signaling, controls Foxp3 methylation and iTreg cell differentiation. T cell-specific ablation of Uhrf1 led to Treg-biased differentiation in naïve T cells, with DNA hypomethylation upon TCR stimulation, and these Foxp3+ T cells had suppressive function. Uhrf1 maintained Foxp3 DNA methylation by recruiting Dnmt1 during cell division upon TCR stimulation. TGF-β treatment led to passive demethylation of the Foxp3 promoter to initiate its expression. Mechanistically, Uhrf1 was phosphorylated upon TGF-β stimulation and largely sequestered in the cytoplasm. Phosphorylated Uhrf1 underwent proteasomal degradation through inhibition of Usp7-mediated deubiquitination. Collectively, our study reveals a novel epigenetic mechanism of TGF-β-mediated iTreg cell differentiation regulated by Uhrf1 and reveals the differential role of active and passive demethylation in Foxp3 induction and stability.

overall_design: Wild-type (WT) and Uhrf1-/- mice T lymphocytes were analysed for: gene expression by RNA-seq, DNA methylation by whole-genome bisulfite sequencing (WGBS)

first: Yu

last: Cui

first: Haiyun

last: Feng

first: Haifeng

first: Xiaolong


title: Pathogenomic study of Clostridium difficile strains

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: In the present study we conducted a gene-wide analysis from nine couples of C. difficile strains. Each couple is composed of a high potential virulence (HPV) strain associated with its control (CON) strain. The HPV strains were chosen using two clinical criteria: prevalence and severity. The prevalent strains, defined in this study by an overrepresentation in European hospital, were associated with phylogenetically close control strain but rarely found in hospital. In other hand, the severe strains sampled on patient with very serious symptoms were associated with phylogenetically identical strain but that gave mild symptoms in another patient. The aim of this work was to determined if we could explain at least a part of the clinical criteria differences between these nine couples of strains in the light of their genomic and transcriptomic differences.

overall_design: Total RNA was extracted from one sample of each of the 17 C. difficile strains of the study.

first: Marc

last: Monot

first: Bruno

last: Dupuy


title: Elucidating the microRNA-203 specific biological processes in glioblastoma cells from comprehensive high-throughput RNA-sequencing transcriptome profiling

status: Public on Sep 07 2019

city: Chicago

first: Sajani

last: Lakka

state: IL

address: 909 S Wolcott,, College of Medicine Research Building

department: Medicine

institute: The University of Illinois at Chicago

summary: We report the application of high-throughput RNA-sequencing Profile of miR-203 expressing glioma U251 cells. Glioblastoma (GBM) is the most common primary malignant intracranial adult brain tumor. Allelic deletion on chromosome 14q plays an essential role in GBM pathogenesis, and this chromosome 14q site was thought to harbor multiple tumor suppressor genes associated with GBM, a region that also encodes microRNA-203 (miR-203). This study was conducted to identify whole transcriptome profile changes associated with miR-203 expression by high-throughput NGS-RNA sequencing. Total RNA samples are quantified using Nanodrop and qualified by agarose gel electrophoresis. The mRNA  is enriched by oligo(dT) magnetic beads or the total RNA is depleted of rRNAs by Arraystar rRNA Removal  Kit if the RNA sample is degraded or is of prokaryotic origin. We use Illumina kits for the RNA-seq library  preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA  synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library  PCR amplification. Finally, the prepared RNA-seq libraries are qualified using Agilent 2100 Bioanalyzer and  quantified by qPCR absolute quantification method. The sequencing is performed using Illumina Hiseq 4000.

overall_design: Examination of miR-203 specific biological processes in U251 cells using high-througput RNA-sequencing transcriptome profiling

first: Bhaevsh

last: Ahir


title: Impact of high fat diet and hepatocyte nuclear factor four alpha loss on hepatic gene expression in mice.

city: Houston

first: Kristin

last: Eckel-Mahan

state: TX

address: 1825 Pressler St., SRB 437B

department: Institute of Molecular Medicine

institute: UT Health Sciences Center at Houston

summary: The transcription factor hepatocyte nuclear factor four alpha (Hnf4a) has various isoforms, one of which (P1-Hnf4a) is expressed in adult liver, where it functions as a tumor suppressor by providing circadian restrains at genes promoting cell proliferation and epithelial to mesenchymal transition. High fat diet feeding promotes the loss of nuclear P1-Hnf4a activity and a gain in the pro-proliferative P2-Hnf4a isoform, which does not function as a tumor suppressor, nor provide similar circadian restraint at cell cycle-promoting genes. P2-Hnf4a is found in all Hnf4a-positive hepatocellular carcinoma. Purpose: To determine whether inducible loss of hepatic Hnf4a followed by high fat feeding predisposes a liver to hepatocellular carcinoma. Methods: Hepatic Hnf4a was inducibly knocked out in mice at six weeks of age ("H4LivKO") followed by vivarium chow ("H4LivKOVC") or high fat feeding ("H4LivKOHF")at 8 weeks of age. Control, littermate wild-type mice  (WT) were also treated with tamoxifen at six weeks of age, but since they lacked the Cre transgene, Hnf4a expression remained intact. Control mice were divided into the same feeding groups as H4LivKO mice ("WTVC" and "WTHF"). Livers were harvested at 38 weeks of age and liver tissue was flash frozen in liquid nitrogen. RNA was extracted from frozen liver tissue using Trizol, and purified RNA was submitted to Novogene for quality control and RNA-seq analysis using a 250-300 bp insert cDNA library and Illumina Platform sequencing.

overall_design:
Three biological replicates were used for each of the four conditions, resulting in 12 samples.
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The authors state "we cannot find the FASTQ files associated with our study".

first: Baharan

last: Fekry


title: West Nile virus infection of human monocyte-derived dendritic cells

status: Public on Sep 06 2019

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

summary: West Nile virus (WNV) is a neurotropic flavivirus and the leading cause of mosquito-borne encephalitis in the United States. Recent studies in humans have found that dysfunctional T cell responses strongly correlate with development of severe WNV neuroinvasive disease. However, the contributions of human dendritic cells (DCs) in priming WNV-specific T cell immunity remains poorly understood. Here, we demonstrate that human monocyte derived DCs (moDCs) support productive viral replication following infection with a pathogenic strain of WNV. Antiviral effector gene transcription was strongly induced during the log-phase viral growth, while secretion of type I interferons (IFN) occurred with delayed kinetics. Activation of RIG-I like receptor (RLR) or type I IFN signaling prior to log-phase viral growth significantly diminished viral replication, suggesting that early activation of antiviral programs can block WNV infection. In contrast to the induction of antiviral responses, WNV infection did not promote transcription or secretion of pro-inflammatory (IL-6, GM-CSF, CCL3, CCL5, CXCL9) or T cell modulatory cytokines (IL-4, IL-12, IL-15). There was also minimal induction of molecules associated with antigen presentation and T cell priming, including the co-stimulatory molecules CD80, CD86, and CD40. Functionally, WNV-infected moDCs dampened allogenic CD4 and CD8 T cell activation and proliferation. Combined, we propose a model where WNV subverts human DC activation to compromise priming of WNV-specific T cell immunity.

overall_design: Human monocyte-derived DCs moDCs were generated from 5 donors and  treated with innate immune agonists for 12hr (RIG-I, MDA5, or IFNβ) or infected with WNV (12hpi and 24hpi). Time matched mocks were left untreated and collected at 12 and 24 hours post-treatment. RIG-I agonist- 100 ng RNA derived from the 3'UTR of Hepatitis C virus, MDA5 agonist- 100 ng high molecular weight poly-I:C, IFN- 100 IU/ml IFNb and West Nile virus(WNV)-TX lineage 1 strain.

first: Matthew

last: Zimmerman

first: James

last: Bowen

first: Circe

last: McDonald

first: Bali

last: Pulendran


title: Non-immune niche analysis in breast tumour derived lung metastasis

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

summary: We used our novel Cherry-niche system to specifically isolate cells from the metastatic niche of 4T1 lung metastasis and compared their profile with the one obtained isolating lungs cells distal from the tumour growth.

overall_design: Labelling-4T1 were injected intravenuosly and lungs collected 7 days post-injection. From the dissociated tissue cells were collected via FACS and single cell RNA seqeuncing was performed.

first: Emma

last: Nolan

first: Luigi

last: Ombrato


title: Exposure to a low-dose pollutant mixture does not trigger obesity in female mice but results in metabolic disturbances showing both common and specific features as compared to a high-fat diet challenge

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: In order to identify pollutants effects on liver metabolism in mice, 12 weeks old female mice were submitted to 3 differents diets. Either a standard diet or a high fat diet containing or not a mixture of 4 pollutants. Mice were fed with these diets from preconception to 12 weeks old. Mice were sacrificed and livers were taken and immediately snap frozen until further processing. Microarrays analysis were performed in order to identify direct pollutants effects.

overall_design: 12 weeks old female mice were submitted to 3 differents diets. Either a standard diet (ST) or a high fat diet (HFHS) containing (+ pollutants) or not (+ vehicule) a mixture of 4 pollutants.

first: Emmanuel

last: Labaronne

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

first: Brigitte

last: Le magueresse


title: Genome-wide transcription analysis of whole blood prior to rituximab treatment in relation to clinical response

city: Amsterdam

first: Saskia

last: Vosslamber

address: de Boelelaan 1118

institute: VU University medical center

summary: B cell depletion therapy is efficacious in RA patients failing on TNF blocking agents. However, approximately 40-50% of the rituximab-treated RA patients have a poor response. We investigated wheter baseline gene expression levels can discriminate between clinical nonresponders and responders to rituximab

overall_design: Whole blood total RNA is isolated from PAXgene tubes obtained prior to start of rituximab treatment

first: C

last: Verweij

first: S


title: Coordination of neuron production in mouse and human cerebral cortex by the homolog of Drosophila Mastermind protein

city: New Haven

first: Albert

middle: E.

last: Ayoub

state: CT

address: 333 Cedar St. SHM C317

department: Neurobiology

institute: Yale University

summary: The coordination of progenitor self-renewal, neuronal production and migration is essential to the normal development and evolution of the cerebral cortex. Numerous studies have shown that the Notch, Wnt/beta-catenin and Neurogenin pathways contribute separately to progenitor expansion, neurogenesis, and neuronal migration, but it is unknown how these signals are coordinated. In vitro studies suggested that the mastermind-like 1 (MAML1) gene, homologue of the Drosophila Mastermind, plays a role in coordinating the afore-mentioned signaling pathways, yet its role during cortical development remains largely unknown. Here we show that ectopic expression of dominant-negative MAML (dnMAML) causes exuberant neuronal production in the mouse cortex without disrupting neuronal migration. Comparing the transcriptional consequences of dnMAML and Neurog2 ectopic expression revealed a complex genetic network controlling the balance of progenitor expansion versus neuronal production. Manilpulation of MAML and Neurog2 in cultured human cerebral stem cells exposed interactions with the same set of signaling pathways. Thus, our data suggest that evolutionary changes that affect the timing, tempo and density of successive neuronal layers of the small lissencephalic rodent and large convoluted primate cerebral cortex depend on similar molecular mechanisms that act from the earliest developmental stages.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq after disruption of Notch and Neurognin2 signaling in human fetal glia in vitro and after in utero electroporation in the mouse dorsal cortex. Tissue was laser-microdissected. Cells propagated in vitro were magnetically seperated.

middle: E

first: Pasko

last: Rakic


title: RNAseq analysis of ESRP regulated splicing events in prostate cancer

city: Newcastle upon Tyne

first: David

last: Elliott

address: International Centre for Life

institute: Institute of Genetic Medicine

summary: Progression of prostate cancer -the most frequent cancer in men- is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription in prostate cancer cells by stimulating androgen receptor (AR) activity, but also control pre-mRNA splicing through less clear mechanisms. Here we examine whether androgens regulate splicing through AR-mediated transcriptional control of splicing regulator proteins. Supporting this mechanism we find AR controls ESRP2, which encodes a key epithelial-specific splicing regulator. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer, and slow growth of prostate cancer xenografts in mice. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including a key splicing switch in the metastatic regulator FLNB which is associated with disease relapse after treatment. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, FLNB splicing was reciprocally switched by the AR antagonist Casodex®. Our data reveal a new mechanism of splicing control in prostate cancer with important implications for disease progression.

overall_design: LNCaP cells (passage 19) were treated with either control siRNAs or siRNAs targeting ESRP1 and ESRP2 for 72 hours (samples prepared in triplicate)

first: Jennifer

last: Munkley

first: Simon

last: Cockell

first: Kathleen

last: Cheung


title: Next Generation Sequencing Facilitates Quantitative Analysis of Listeria monocytogenes Transcriptomes

city: Changsha

first: Zhipeng

last: Gao

address: Nong da road 1#

institute: Hunan Agriculture University

summary: RNA-Seq was used to unravel the potential antimicrobial mechanism of linalool against Listeria monocytogenes.

overall_design: we compared the RNA-Seq data between L. monocytogenes without the treatment of linalool (control group) and with the treatment of linalool for 8 h at 1×MIC (treated group).

first: Jiajing

last: Guo


title: Gene expression in murine amygdala, cortex, hippocampus and hypothalamus of Pianp-deficient mice

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Pianp (also known as Leda-1) is a type I transmembrane protein with preferential expression in the mammalian central nervous system.
We used microarrays to analyze the programme of gene expression in murine brain regions amygdala, cortex, hippocampus and hypothalamus of Pianp deficient mice.

overall_design: Amygdala, cortex, hippocampus and hypothalamus of Pianp-deficient and control mice were microdissected for RNA extraction and hybridization on Affymetrix microarrays.

first: Manuel

last: Winkler


title: The effects of di-butyl phthalate exposure from medications on human sperm RNA among men

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Endocrine disruptors, such as phthalates, are suspected of affecting reproductive function. The Mesalamine and Reproductive Health Study (MARS) was designed to address the physiological effect of in-vivo phthalate exposure on male reproduction in patients with Inflammatory Bowel Disease (IBD). As part of this effort, sperm RNA profiles as an effect of exposure to DBP were longitudinally assessed using a cross-over cross-back design of binary, high or background, levels of DBP. As the DBP level was altered, numerous sperm RNA elements were differentially expressed, and suggest that exposure to or removal from high DBP produces effects that require longer than one spermatogenic cycle to resolve.  In comparison, small RNAs are minimally affected by DBP exposure. While initial study medication (high or background) implicates different biological pathways, initiation on the high-DBP condition activated oxidative stress and DNA damage pathways. Using ejaculated sperm, this work provides insight into the male germline’s response to phthalate exposure.

overall_design: Total RNA from purified ejaculated spermatozoa was sequenced as a long RNA (>200 bp) fraction and small RNA (<200 bp) fraction.

first: Russ

last: Hauser

first: Feiby

last: Nassan

first: Alan

last: Moss

first: Stephen

middle: A

last: Krawetz


title: Epigenome analysis of normal and myelodysplastic sundrome (MDS) bone marrow derived mesenchymal stromal cells (MSCs)

city: Singapore

first: Zhiyong

last: Poon

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

summary:
Methylation data for MDS bone marrow derived MSCs before and after 5-Azacitidine treatment. Methylation profiles were measured using the Infinium Human MethylationEPIC BeadChip (Illumina).
There are 5 healthy MSC and 8 high-risk MDS-MSC samples, untreated and treated with 5-Azacitidine in vitro.

overall_design: Subconfluent MSCs at P1 - P2 were treated with 1 µM AZA (Sigma-Aldrich) for up to 48 h. After exposure to AZA, cells were washed with PBS and replaced with drug free media. The drug-treated MSCs were then maintained in AZA free media for further experimentation.

first: William

last: Hwang


title: Dissecting human endoderm development through a genome-wide CRISPR screen in human embryonic stem cells

city: NEW YORK

first: Qing

last: Li

address: 1275 YORK AVE

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Combining human ES cell differentiation with the CRISPR/Cas technology, we have conducted a genome-wide knockout screen for genes that cell-autonomously regulate the
formation of human definitive endoderm (DE), which gives rise to most of the cells in respiratory
and gastrointestinal organs including the lung, pancreas and liver. Our screen identified
previously known as well as unknown regulators of endoderm differentiation. We further report
that the MEKK1-MKK4/7-JNK1-JUN signaling axis acts as a previously unrecognized inhibitory
pathway that constrains endoderm formation.

overall_design: Genomic DNA from sorted SOX17GFP+/- cells were extracted by using Qiagen Maxi Kit (Qiagen 13362). Two-step PCR method was used to amplify the gRNA sequence and prepare Hi-seq library.

last: Xiang


title: GDE3 regulates oligodendrocyte precursor proliferation via release of soluble CNTFRα

city: Baltimore

first: Shanthini

last: Sockanathan

address: 725 North Wolfe St.

institute: The Solomon H. Snyder Department of Neuroscience Johns Hopkins University School of Medicine

summary: Oligodendrocyte development is tightly controlled by extrinsic signals; however, mechanisms that modulate cellular responses to these factors remain unclear. Six-transmembrane glycerophosphodiester phosphodiesterases (GDEs) are emerging as central regulators of cellular differentiation via their ability to shed glycosylphosphatidylinositol (GPI)-anchored proteins from the cell surface. We show here that GDE3 controls the pace of oligodendrocyte generation by negatively regulating oligodendrocyte precursor cell (OPC) proliferation. GDE3 inhibits OPC proliferation by stimulating ciliary neurotrophic factor (CNTF)-mediated signaling through release of CNTFRα, the ligand-binding component of the CNTF-receptor multiprotein complex, which can function as a soluble factor to activate CNTF signaling.  GDE3 releases soluble CNTFRα by GPI-anchor cleavage from the plasma membrane and from extracellular vesicles (EVs) after co-recruitment of CNTFRα in EVs. These studies uncover new physiological roles for GDE3 in gliogenesis and identify GDE3 as a key regulator of CNTF-dependent regulation of OPC proliferation through release of CNTFRα.

overall_design: Spinal cords from P0.5 pups were dissected and the OPCs were isolated and cultured for 16 hours in proliferative media

first: Mateusz

last: Dobrowolski


title: Transcriptional Profiling of a high glucose tolerance Saccharomyces cerevisiae stain by RNA-Seq

city: NanNing

first: Chen

last: Ying

address: Daxuedaling street, number 98

institute: Guangxi academy of science

summary: Using RNA-Seq, the transcriptomes of saccharomyces cerevisiae wild-type MF02 and UV mutant strain UV02_HG were compared under high sugar conditions. Based on this analysis, we found that different expressions between two strains mainly  focus on the transport and modification of proteins and metabolism of carbon

overall_design: mRNA profiles of mid-exponential phase cells under 40%(W/V) glucose growth condition were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

first: Ribo

last: Huang

first: Ying

last: Chen


title: RTEL1 modulates H3 occupancy in heterochromatic regions and acts synergistically with MET1/DDM1 to maintain genome integrity

city: Beijing

first: Jinkui

last: Cheng

address: No.2 Yuanmingyuan West Road

institute: China Agricultural University

summary: RTEL1 mainly mediates histone H3 occupancy in heterochromatic regions and functions in parallel with DDM1 and MET1 to maintain genome integrity.

overall_design: Examine DNA methylation, histone modification and gene expression changes by whole-genome bisulfite sequencing; RNA sequencing; H3K27me3-, H3K4me3-, H3K9me2-, H3-ChIP-sequencing in L119 and rtel1-3 mutant

first: Xiaowen

last: Zhao

first: Jingyi

last: Wang

first: Jingjing

last: Meng

first: Dan

last: Jin

first: Xinjie

first: Jian-Kang

last: Zhu

first: Zhizhong

last: Gong


title: FoxO Transcription Factors Are Critical Regulators of Diabetes-Related Muscle Atrophy

status: Public on Sep 05 2019

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Insulin deficiency and uncontrolled diabetes lead to a catabolic state with decreased muscle strength, contributing to disease-related morbidity. FoxO transcription factors are suppressed by insulin and thus are key mediators of insulin action. To study their role in diabetic muscle wasting, we created mice with muscle-specific triple knockout of FoxO1/3/4 and induced diabetes in these M-FoxO-TKO mice with streptozotocin (STZ). Muscle mass and myofiber area were decreased 20-30% in STZ-Diabetes mice due to increased ubiquitin-proteasome degradation and autophagy alterations, characterized by increased LC3-containing vesicles, and elevated levels of phosphorylated ULK1 and LC3-II. Both the muscle loss and markers of increased degradation/autophagy were completely prevented in STZ FoxO-TKO mice. Transcriptomic analyses revealed FoxO-dependent increases in ubiquitin-mediated proteolysis pathways in STZ-Diabetes, including regulation of Fbxo32 (Atrogin1), Trim63 (MuRF1), Bnip3L, and Gabarapl. These same genes were increased 1.4- to 3.3-fold in muscle from humans with type 1 diabetes after short-term insulin deprivation. Thus, FoxO-regulated genes play a rate-limiting role in increased protein degradation and muscle atrophy in insulin-deficient diabetes.

overall_design: Muscle-specific FoxO1, FoxO3, and FoxO4 triple knockout (M-FoxO-TKO) mice were generated using ACTA1-Cre (stock number 006149; The Jackson Laboratory) and FoxO1/3/4 triple floxed mice, provided by Dr. Domenico Accili, Colombia University Medical Center. Littermate controls were used for all experiments, as the mice are on a mixed background containing C57Blk6, C57Blk6J, and 129 strains. For STZ treatments, mice were fasted overnight and then injected intraperitoneally with a single high dose of STZ (150 mg/kg) (S0130; Sigma) dissolved in 100 mmol/L citrate buffer (pH 4.5) or injected with citrate buffer alone as a control, then immediately given access to food. Female mice were given a 150 mg/kg dose followed by a 75 mg/kg dose of STZ on day 3, since female mice are less responsive to STZ (24). Mice were monitored for hyperglycemia on days 3, 7, 12, and 15, and only mice in which random blood glucose remained >300 mg/dL for the following 9–12 days were used for experiments.

first: Brian

middle: T

last: O’Neill

first: C

last: Kahn


title: Rectal cancer sub-clones respond differentially to neoadjuvant therapy

city: Ann Arbor

first: Karin

last: Hardiman

state: Michigan

address: 2922F Taubman Center

department: General Surgery

institute: University of Michigan

summary:
Unique sub-clones within rectal tumors may harbor mutations which contribute to inter-patient variation in response to neoadjuvant chemoradiotherapy (nCRT). Analysis of the influence of nCRT on the extent and nature of intra-tumoral genetic heterogeneity in rectal cancer may provide insights into mechanisms of resistance.
Ten locally advanced rectal cancer patients underwent pre-treatment biopsies. At the time of surgery, tissue from the treated tumor was obtained and analyzed. Pre- and post-treatment specimens were subjected to whole exome and confirmatory deep sequencing for somatic mutations. Copy number variation was assessed using OncoScan SNP arrays. In total, data from 32 pre/post-treatment samples are provided. The provided data include the pre/post tumor samples and the Affymetrix OncoScan SNP arrays.

overall_design: ThermoFisher (Affymetrix) OncoScan v3 arrays were run on all samples. The assay detects copy number change by generating data at 50-100kb resolution across a set of 891 cancer genes and 300-400kb across the rest of the genome.  Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (ThermoFisher, Waltham, Massachusetts) and processed using the standard Affymetrix reference control files, based on sample type (normal or FFPE).

first: P

last: Ulintz

first: K


title: Gene expression from MS5 stroma cells co-cultured with normal human hematopoietic progenitors/stem cells (HSPCs) and AML

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

institute: Francis Crick Institute

summary:
Acute myeloid leukemia remodels the bone marrow non-hematopoietic microenvironment which disrupts niche archiecture and normal hematopoiesis The precise interactions underlying this process are not well understood
We used microarrays to detail the global programme of gene expression underlying the interactions between healthy mesenchymal stroma cells and normal hematopoietic progenitors/stem cells (HSPCs) and AML

overall_design: In the first dataset (0611_DoB(5)) MS5 murine mesenchymal stroma cells (MSCs) were cultured either alone or with AML cell lines in myelocult H5100 from STEM CELL TECHNOLOGIES. In the second dataset (0610_DoB(2) and 0910_DoB(2)) MS5 mesenchymal stroma cells were either cultured alone, with human cord blood CD34+ or AML patient samples AML7 and AML8.  After 7 days the MSCs were FACS-sorted, followed by RNA extraction and hybridization on Affymetrix microarray.

first: Ashley

last: Hamilton


title: Disrupted gene networks in subfertile hybrid mice

city: Bath

first: Katy

last: Morgan

address: Milner Centre for Evolutionary Biology

department: Department of Biology and Biochemistry

institute: University of Bath

summary: The Dobzhansky-Muller model provides a widely accepted mechanism for the evolution of reproductive isolation: incompatible substitutions disrupt interactions between genes. To date, few candidate incompatibility genes have been identified, leaving the genes driving speciation mostly uncharacterized. The importance of interactions in the Dobzhansky-Muller model suggests that gene coexpression networks provide a powerful framework to understand disrupted pathways associated with postzygotic isolation. Here, we perform Weighted Gene Coexpression Network Analysis (WGCNA) to infer gene interactions in hybrids of two recently diverged European house mouse subspecies, Mus mus domesticus and M. m. musculus, which commonly show hybrid male sterility or subfertility. We use genome-wide testis expression data from 467 hybrid mice from two mapping populations: F2s from a laboratory cross between wild-derived pure subspecies strains and offspring of natural hybrids captured in the Central Europe hybrid zone. This large data set enabled us to build a robust consensus network using hybrid males with fertile phenotypes.  We identify several expression modules, or groups of coexpressed genes, that are disrupted in subfertile hybrids, including modules functionally enriched for spermatogenesis, cilium and sperm flagellum organization, chromosome organization and DNA repair, and including genes expressed in spermatogonia, spermatocytes and spermatids. Our network-based approach enabled us to hone in on specific hub genes likely to be influencing module-wide gene expression and hence potentially driving Dobzhansky-Muller incompatibilities. A total of 67 (24.4%) of these genes lie in sterility loci identified previously in these mapping populations, and represent promising candidate barrier genes and targets for future functional analysis.

overall_design: A total of 499 samples were analyzed. Raw microarray data was taken from two previous studies (Turner et al. 2014 and Turner and Harr, 2014). The raw microarray data was normalized using the quantile method and batch corrected using Combat (Johnson et al. 2007).

first: Leslie

last: Turner


title: The impact of stanniocalcin 1 on the transcriptome of human cord blood stem/progenitors

summary: Purpose: Stanniocalcin 1 (STC1) is a secreted glycoprotein expressed in mesenchymal stroma cells (MSCs). STC1 expression is upregulated in response to acute myeloid leukemia (AML) co-culture. Recombinant STC1 has proliferation limiting effects on human hematopoietic stem/progenitors cells (HSPCs) and facilitiates the preservation of HSCs ex vivo. We hope to gain insight into the mechanism by exploring the transcriptome of stem/progenitors exposed to STC1.

overall_design: Human umbilical cord blood CD34+CD38- HSPCs and  CD34+CD38+ hematopoietic progenitors cells (HPCs) from three independent donors were FACS-isolated and independently co-cultured on bone marrow MSCs in myelocult H5100 media supplemented with 100 ng/ml STC1 or PBS as control. After 48h HSPCs, HPCs and MSCs were FACS-sorted into lysis buffer.

first: Alexander

last: Waclawiczek

first: Manuel

last: Garcia Alboroz

first: Nourdine

last: Bah


title: DJ-1 is dispensable for human stem cell homeostasis

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: our data showed that the absence of DJ-1 had no adverse effects on proliferation, differentiation, and oxidative stress responses of human stem cells such as hNSCs and hMSCs as well as hVECs, suggesting that loss of DJ-1 function alone is insufficient to disrupt the homeostasis of these human cells. In addition, we found that CHCHD2 was upregulated upon DJ-1 deficiency, which may account for the absence of severe phenotypes in various types of DJ-1-deficient cells. For the first time, our study revealed the 'see-saw' expression pattern of two Parkinson’s disease-associated genes, providing potential clues for understanding the mechanisms of DJ-1- and CHCHD2-associated Parkinson’s disease.

overall_design: Transcriptional profiles of DJ-1-deficient  and WT hMSCs and hNSCs.

first: Guang

middle: H


title: Discovery and verification of liver cancer marker genes and variable scission based on second-generation sequencing data analysis

city: Changchun

first: Mengqi

last: Cui

address: 5368 Renmin Street

institute: National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University

summary: The RNA-seq technique was used to sequence the liver cancer tissues and paracancerous tissues of 6 clinical patients, aiming to find differentially expressed genes and transcripts, and to verify the expression level and function of the expression. To improve the accuracy of gene discovery, we used two methods to analyze the sequencing data.

overall_design: Liver mRNA profile of liver cancer tissue and paracancerous tissue of 6 clinical patients


title: Effects of lidocaine on the expression of rat spinal cord

city: Xi'an

first: Hailiang

last: Du

state: Shaanxi

address: 277 West Yanta Road

department: Anesthesiology

institute: The First Affiliated Hospital of Xi'an Jiaotong University

summary:
This study aimed to explore the possible mechanism of lidocaine-induced neurotoxicity. A total of 40 rats were randomly assigned to 4 groups (n = 10 per group): control group; sham group, received only intrathecal catheter insertion; saline group, received an intrathecal injection of saline; and lidocaine group, received an intrathecal injection of 10% lidocaine. Neurobehavioral tests were performed on rats in each group before injection and 1, 2, 3, and 4 days after the intrathecal injection. On the fourth day, after completing neurobehavioral tests, the spinal cords of all rats from L2 to L6 were removed and immediately stored in liquid nitrogen. In the control and lidocaine groups, parts of the spinal cord tissues of three rats were selected for gene microarray analysis.Based on the results of the gene chip analysis,Five rats in each group underwent real-time quantitative polymerase chain reaction (PCR) and five Western blot analysis to verify Differentially expressed genes at the mRNA transcription and protein levels.
The aim of gene chip analysis is to screen potential genes involved in lidocaine-induced neurotoxicity.

overall_design: In the control and lidocaine groups, parts of the spinal cord tissues of three rats were selected for gene microarray analysis.In the control group, the spinal cord tissue markers were CON_1, CON_2, CON_3 and lidocaine group: TEST_1, TEST_2 and TEST_3.

first: Yaomin


title: DNA damaging agent doxorubicin induces the expression of myotonic dystrophy kinase protein in tumor suppressor p53 dependent manner

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Tumor suppressor p53 plays an integral role in DNA damage-induced apoptosis, which is one of the biological processes to protect against tumor progression. Cell shape is dramatically changed undergoing apoptosis, which is often associated with actomyosin contraction; however, it remains entirely elusive how p53 regulates actomyosin contraction in response to DNA-damaging agent. We here show that p53 controls expression of myotonic dystrophy protein kinase (DMPK), which is known to upregulate actomyosin contraction. To identify a novel p53 regulating gene encoding the modulator of myosin, we performed a DNA microarray and then found that, in response to DNA-damaging agent doxorubicin, DMPK expression was increased in a p53-dependent manner.

overall_design: Gene expression analysis of p53+/+ (wild-type: WT) and p53−/−  mouse embryonic fibroblasts (MEFs) in the absence and presence of doxorubicin was performed using Agilent Mouse Gene Expression 4x44K v2 Microarray as one color experiments.

first: Keiko

last: Kawauchi


title: RNAseq of human monocyte cell line (U937-Cas9) WT or IRF2KO

city: Lyon

first: Thomas

last: Henry

address: 21 avenue Tony Garnier

department: CIRI

institute: INSERM

summary: We analyzed the transcriptional effect of IRF2 in the U937 human monocyte cell line. The major findings of the study is the regulation of CASP4 by IRF2

overall_design: RNAseq human monocyte cell line (U937-Cas9) WT or IRF2KO

first: T

first: A

last: Corbin


title: Chronically elevated androgen and/or consumption of a Western-style diet impairs oocyte quality and granulosa cell function in the nonhuman primate periovulatory follicle.

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

summary: Purpose: To investigate the impact of chronically-elevated androgens in presence and absence of an obesogenic diet on oocyte quality in the naturally-selected primate periovulatory follicle.   Methods: Rhesus macaques were treated using a 2-by-2 factorial design (n=10/treatment) near onset of menarche  with implants containing either cholesterol (C) or testosterone (T; 4-5 fold increase above C) and a standard or “Western-style” diet alone (WSD), or in combination (T+WSD). Following ~3.5 years of treatment, females underwent controlled ovulation (COv; n=7-10/treatment) cycles, and contents of the naturally-selected periovulatory follicle were aspirated. Follicular fluid (FF) was analyzed for cytokines, chemokines, growth factors, and steroids. RNA was extracted from luteinizing granulosa cells (LGCs) and assessed by RNA-seq.     Results: Only healthy, metaphase (M) I/II-stage oocytes (100%) were retrieved in the C group, whereas degenerated oocytes were prevalent in other groups (33-43%; overall effect of WSD and T, p=0.1). Levels of two chemokines and one growth factor were reduced (p<0.04) in FF of follicles with a MI/MII oocyte in WSD+T (CCL11) or T and WSD+T groups (CCL2 and FGF2) compared to C and/or WSD. Intrafollicular cortisol was elevated in T compared to C follicles (p<0.02). Changes in expression pattern of 640+ gene products were detected in LGC samples from follicles with degenerated oocytes versus MI/MII-stage oocytes. Pathway analysis on RNAs altered by T and/or WSD found enrichment of genes mapping to steroidogenic and immune cell pathways.  Conclusions: Female primates experiencing hyperandrogenemia and/or consuming a WSD exhibit an altered intrafollicular microenvironment and reduced oocyte quality/competency, despite displaying menstrual cyclicity.

overall_design: Biological Replicates

middle: V

first: Taylor

last: Reiter

first: David

middle: W

last: Erickson

first: Carol

middle: B

last: Hanna

first: Brittany

last: Daughtry

first: Shawn

last: Chavez

first: Jon

middle: D

last: Hennebold

first: Richard

last: Stouffer


title: AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia

city: Houston

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Rho Guanine Nucleotide Exchange Factor ARHGEF10 is a putative tumor suppressor in pancreatic ductal adenocarcinoma

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

summary: Our study has shown that ARHGEF10 is a putative tumor suppressor in pancreatic ductal adenocarcinoma. To determine its functional mechanism, we perfomed microarray gene expression analysis of two pancreatic cancer cell line models of ARHGEF10 expression : MiaPACA2 cells in which ARHGEF10 was stably overexpressed, and Hs766T cells in which ARHGEF10 expression had been stably knocked down by short hairpin RNAs.

overall_design: Profiling changes in gene expression after overexpression of ARHGEF10 in MiaPACA2 cells, and shRNA knockdown of ARHGEF10 expression in Hs766T cells. Total RNA from Hs766T cells expressing two independent shRNAs targeting ARHGEF10 were pooled for this study.

first: Joella

last: Joseph

first: Quan

last: Li


title: AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: RNA-seq

summary: Altered metabolism fuels two hallmark properties of cancer cells, unlimited proliferation and differentiation blockade. AMP-activated protein kinase (AMPK) is a master regulator of bioenergetics crucial for glucose metabolism in acute myeloid leukemia (AML) and its inhibition delays leukemogenesis, but whether the metabolic function of AMPK alters AML epigenome remains unknown. Here, we demonstrate that AMPK maintains the epigenome of MLL-rearranged AML by linking acetyl-CoA homeostasis to BET bromodomain protein recruitment to chromatin. AMPK deletion reduced acetyl-CoA and histone acetylation, displacing BET proteins from chromatin in leukemia-initiating cells (LICs). In both mouse and patient-derived xenograft AML models, treating with AMPK and BET inhibitors synergistically suppressed AML. Our results provide a therapeutic rationale to target AMPK and BET for AML therapy.

overall_design: RNA-seq of sorted AMPK WT or KO leukemia-GMP cells, with three replicates of each.

first: Yajian

last: Jiang

first: Kevin

last: Hoegenauer


title: AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: ChIP-seq

first: Daisuke

overall_design: ChIP-seq of sorted AMPK WT or KO leukemia-GMP cells, with three replicates of each condition, per each of three different antibodies and one input.


title: The transcriptome analysis of Treg subset

city: La Jolla

first: Bi-Huei

last: Yang

address: 9500 Gilman Dr

institute: UCSD

summary:
The transcriptome analysis of WT and Tcf7/Lef1 double knockout (dKO) Treg subset

CD4+ Foxp3+ T regulatory (Treg) cells are key players in preventing lethal autoimmunity and deleterious tissue inflammation. To fulfill these roles, Treg cells undergo activation and differentiate processes to acquire diverse functional properties. However, how Treg’s functional specifications are regulated during their differentiation remains poorly understood. Here we show that two TCF/LEF family transcription factors (TFs), TCF1 and LEF1 act redundantly as checkpoint regulators in peripheral Treg homeostatic differentiation and functional subset specification. We find that gradient expression of TCF1 and LEF1 distinguishes Treg cells into three distinct subsets. Sustained expression of TCF1/LEF1 retains Treg at their resting stage. Conversely, conditional knockout of TCF1 and LEF1 promotes the effector-like phenotype in bulk Treg cells, but surprisingly renders the mice susceptible to early onset of systemic autoimmunity. This uncoupling between Treg effector phenotype and their function in suppressing autoimmunity is attributed by two TCF1/LEF1-centered mechanisms. First, the ablation of TCF1 and LEF1 in Treg cells abolishes the generation of T follicular regulatory (Tfr) cells, leading to unrestrained T follicular helper (Tfh) and germinal center B cell responses. Second, TCF1 and LEF1 are required for Treg survival under competitive conditions. Thus, TCF1 and LEF1 play critical roles in Treg homeostatic maintenance and Tfr generation.

overall_design:
ex vivo CD62L+/-TCF1-GFP+/- Treg(CD4+Foxp3-Thy1.1+) subsets were sorted from Foxp3Thy1.1TCF7GFP reporter mice.
WT or dKOTreg sorted from Foxp3creYFP/wt mice using YFP

first: Wenxian

last: Fu


title: Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem


title: Effect of NF90 knock-down on whole gene expression in Beta-TC-6 cells, a pancreatic beta cell line

status: Public on Sep 04 2019

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

summary:
We found that knock down of NF90 and its binding factor, NF45, complex leads to retardation of growth in Beta-TC-6 cells, a pancreatic beta cell line.
To uncover molecular mechanisms for the growth retardation in Beta-TC-6 cells depleted of NF90-NF45, we performed comprehensive analysis of gene expression using microarray.

overall_design: RNAs were extracted from Beta-TC-6 cells depleted of either NF90 or a non-targeting control. The RNAs were hybridized with GeneChip Mouse Gene 2.1 ST Array Strip which is an Affymetrix microarray

first: Sylvia

last: Lai


title: Effect of NF45 knock-down on whole gene expression in Beta-TC-6 cells, a pancreatic beta cell line

overall_design: RNAs were extracted from Beta-TC-6 cells depleted of either NF45 or a non-targeting control. The RNAs were hybridized with GeneChip Mouse Gene 2.1 ST Array Strip which is an Affymetrix microarray


title: Regulation of pre-mRNA splicing by m6A through the low-complexity protein hnRNPG and co-transcriptional pausing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Co-transcriptional processing of nascent transcripts is coupled with transcription through the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). The mRNA modification N6-methyladenosine (m6A) occurs co-transcriptionally and impacts pre-mRNA processing. How alternative splicing of pre-mRNA is co-transcriptionally regulated in an m6A-dependent manner is not well understood. Furthermore, splicing regulation through RNAPII pausing has been frequently suggested but the underlying control mechanism remains unclear. Here, we show that the m6A reader protein hnRNPG directly binds to the phosphorylated CTD of RNAPII using Arg-Gly-Gly (RGG) motifs in its low-complexity region. This RGG-phospho-CTD interaction and nascent RNA binding by hnRNPG enables its co-transcriptional association with RNAPII, resulting in transcriptome-wide regulation of alternative splicing and transcript abundance. m6A sites near exon splice sites in nascent mRNA further modulate hnRNPG binding and exon splicing. Exon inclusion is associated with RNAPII pausing downstream of the m6A site. Our results reveal an integrated nuclear mechanism of m6A-mediated gene regulation, in which an m6A reader protein regulates gene expression by using RGG motifs to co-transcriptionally interact with both RNAPII and m6A-modified nascent pre-mRNA, while the interplay between hnRNPG binding and RNAPII pausing modulates alternative splicing regulation.

overall_design:
HEK293T cells were transfected with hnRNPG siRNA and either pCMV3-Flag plasmid (NCV) or wild-type or mutant pCMV3-Flag-hnRNPG plasmid (WT, RRMmut, RGG1mut, or RGG2mut), with 3 biological replicates for each of the 5 different plasmid transfections. mRNA sequencing libraries were prepared using the Tru-Seq Stranded mRNA LT Sample Prep Kit (RS-122-9005DOC, Illumina). The WT replicates were used as the reference when analyzing for changes in transcript abundance or exon expression.

To investigate the hnRNPG effect on alternative splicing through its binding to nascent mRNA, we performed hnRNPG PAR-CLIP with the chromatin fraction to sequence only the chromatin-bound mRNAs that were crosslinked to hnRNPG. To investigate whether hnRNPG affects RNAPII pausing, we performed quantitative chromatin-immunoprecipitation followed by sequencing (ChIP-seq). We first knocked down hnRNPG protein using two different siRNA, followed by building ChIP-seq libraries (Figure S7E) using individual antibodies for RNAPII, the S2-phosphorylated CTD (S2P), and the S5-phosphorylated CTD (S5P). Each sample was spiked-in with a same amount of the Drosophila chromatin and Drosophila-specific antibody to enable cross-sample comparison of RNAPII densities.

first: Katherine

middle: I

last: Zhou

first: Hailing

last: Shi

first: Ruitu

last: Lyu

first: Chuan

last: He

first: Żaneta

last: Matuszek

first: Jessica

middle: N

first: Marc

last: Parisien


title: Differential gene expression in Glis2 knckdown  tubular cells

city: Iowa City

first: Massimo

last: Attanasio

state: IA

address: 285 Newton Road

department: Internal medicine

institute: University of Iowa Carver College of Medicine

summary: Immortalized kidney tubular cells were obtained from immortomice. The gene Glis2 was knocked down by adenoviral-mediated infectipon of specific shRNAs

overall_design: Biallelic mutation in the gene GLIS2 cause progressive kidney cystic degeneration and fibrosis in humans and mice. We performed unbiased differential gene expression analysis in mouse immortalized kidney tubular cells in which Glis2 was stably knocked down by Glis2-targeting shRNA or GFP-targeting as a control. Cells were harvested 7 days after lentiviral infection and tested for knockdown efficiency (> 80%). Samples and controls were run in triplicates.


title: RNA-seq analysis of gene expression profile in PTEN WT and KO LN229 glioblastoma multiforme (GBM) Xenograft tumor Transcriptomes

city: Nanjing

first: Chao

last: Chen

address: 101 Longmian Road

institute: Nanjing Medical University

summary: The goal of this study is to compare gene expression profiles of PTEN WT and KO GBM cells when they are growing in vivo. Isogenic PTEN WT or KO LN229 GBM cells were subcutaneously implanted into Balb/c nude mice (two in each group) to form tumor. At the 30th day tumors were harvested and total RNA was isolated. RNA-seq analysis was performed to examine the differential express pattern of the two type of xenografts.

overall_design: Xenograft GBM tumor mRNA profiles of  PTEN wild type (WT) and KO were generated by deep sequencing, in triplicate, using BGISEQ-500.

first: C

first: F

last: Lin


title: The human box C/D snoRNA U3 is a miRNA source

city: Göttingen

first: Nicolas

last: Lemus-Diaz

state: Lower Saxony

address: Humboldtalle 23, 37073 Goettingen, Germany

institute: Goettigen University Medical Center

summary:
small RNA seq form Hek 293 using IonTorrent Sequencing;
To assess the general expression of snoRNA derived miRNA like fragments in Hek293. Three independent small RNA libraries were sequenced, aligned and subset for snoRNA (C/D, H/ACA, Small Cajal bodies); analysis of read-length for individual snoRNAs was used to define fragments, then to define coherent processing or degradation of the fragments the location of individual reads over the snoRNA annotation was define.

overall_design: Analysis of small RNA derived from Hek293 cells

first: Jens

last: Gruber


title: TGFβ1 determines the fate of human adipose-derived stromal cells by restraining their immaturity and white/beige adipocyte potentials

city: TOULOUSE

first: Frederic

last: Deschaseaux

state: HAUTE-GARONNE

address: 4 BIS AVENUE HUBERT CURIEN, BATIMENT INCERE

department: Research

institute: EFS-Occitanie, Inserm U1031

summary:
Human adipose-derived stem/stromal cells (hASCs) can differentiate into a large broad of specialized cell types to ensure homeostasis of tissues. Thus, they are drawing increasing attention in cell therapy and regenerative medicine. However, culture conditions are still critical to ensure their regenerative capabilities. Here we compared Standard conditions (αMEM containing 10% fetal bovine serum) and Endothelial cell Growth Medium 2 (EGM2) containing few serum (2% v/v) for expansion of hASCs. Both types of hASCs were exhaustively characterized by high throughput studies, Gene Set Enrichment Analyses (GSEA) and differentiation potentials experiments. EGM2-hASCs showed enhanced multipotency and their phenotype was more immature than Standard-hASCs. The adipogenic potential of EGM2-hASCs was clearly more extented, including toward the thermogenic beige adipocyte fate. Data from microarray and GSEA highlighted Transforming Growth Factor β1 (TGFβ1) as upstream factor influencing the becoming of Standard-hASCs which is consistent with higher TGFβ1 content in Standard medium. This was associated with nuclear SMAD3 localization and higher expression of its active form in Standard-hASCs. Moreover, these cells were primed into osteoblast, chondroblast and Vascular Smooth Muscle (VSM) lineages at the expense of their adipogenic potential. Their treatment with TGFβ1 receptor inhibitors resulted in a cytoplasmic re-localization of SMAD3 and a decrease of VSM and osteoblastic lineages markers, increasing in turn their beige adipogenic potential. Therefore, TGFβ1 is a key factor committing hASCs toward osteo-chondroblastic and VSM lineages at the expanse of their beige adipogenic potential. Thanks to low TGFβ1 content, EGM2 medium improves the maintenance of uncommitted hASCs with strong beige adipocyte potential.
We used microarrays to unravel differential gene expressions between human ASCs cultured in standard conditions or in EGM2 medium.

overall_design: We cultured cells extracted from human subcutaneous adipose tissue in two types of medium: standard (MEM complemnted by 10% FBS plus 1ng/mL FGF2) or EGM2. After passage 1, whole mRNAs were extracted and subjected for high throughput study by using affimetrix 1ST microchips.

first: Hélène

last: Leménager

first: Loïc

last: Fievet

first: Fabien

last: Guilloton

first: Abderrahim

last: Naji

first: Narufumi

last: Suganuma

first: Benoît

last: Chaput

first: Louis

last: Casteilla

first: Audrey

last: Carrière

first: Luc

last: Sensebé

first: Frédéric


title: RNAseq data comparing iKPC cells overexpressing WT-USP21 and ED-USP21

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

summary: USP21 belongs to ubiquitin specific protease (USP) family. To dissect the molecular mechanisms that regulated by USP21 overexpression in PDAC cells, we conducted RNA-seq analysis of iKPC PDAC cells overexpressing wild-type USP21 (WT-USP21) and enzyme dead USP21 (ED-USP21).

overall_design: Four iKPC cell lines were used as biological replicates with overexpression of WT-USP21 or ED-USP21.

first: Jun

last: Li


title: Transcription differences in DLBCL cell lines U2932, DOHH2 on treatment with TK compound compared to DMSO

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: These experiments were designed to investigate the effectiveness of TK compound in treating DLBCL. Ets family transcription factors frequently have a role in driving DLBCL, and as this compound is known to prevent interactions with Ets family members, we wanted to determine whether this would be an effective treatment strategy by evaluating the effect of treatment on Ets target genes.

overall_design: DOHH2 and U2932 cell lines were treated with TK or DMSO for 18H or 8H. Samples were collected in duplicate or triplicate.

first: Filipo

last: Spriano

first: Luciano

last: Cascione

first: Francesco

last: Bertoni


title: Transcriptional state of T-cells from Atm-proficient and Atm-deficient mice in response to B-cell lymphoma

city: Cologne

first: Filippo

last: Beleggia

address: Kerpener Str. 62

institute: University Hospital Cologne

summary: CD4 and CD8 murine T-cells from Atm-deficient mice show marked transcriptional changes compared to T-cells from wt mice and respond differently to the transplantation of B-cell lymphoma

overall_design: a total of 24 samples were sequenced (3 replicates * 2 cell types [CD4 / CD8] * 2 genotypes [Atmwt/wt / Atm-/-] * 2 conditions [with / without transplantation of B-cell lymphoma])

first: Arina

last: Riabinska

first: Christian

last: Reinhardt


title: Transcriptomic analysis of Sh2d2a knockout regulatory T cells following a time-course of anti-CD3 stimulation

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: We report that the T cell specific adaptor protein (TSAd, encoded by the Sh2d2a gene) serves as a critical cell intrinsic molecule in CD4+Foxp3+ regulatory T cells to regulate cellular activation responses, mitochondrial translocation of  Lymphocyte-specific protein tyrosine kinase (Lck) and immunoregulation following solid organ transplantation

overall_design: CD4+CD25high regulatory T cells were FACS-sorted from Sh2d2a knockout and wild type mice and activated with 1 µg/ml anti-CD3 (clone: 145-2C11) for 2, 8 and 24 hours. Experiments were performed in duplicate conditions.

first: David

middle: M

last: Briscoe

first: Sek

last: Kong


title: Target Gene Repression Based on Dismissal of Polymerase II from Estrogen Receptor Trans-bound Enhancers Is Associated With Clinical Outcome in Human Breast Cancer

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

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

Keywords: Genome binding/occupancy profiling by high throughput sequencing


title: Single cell RNA sequencing CD45+ TIL samples from melanoma mouse model treated with leptin expressing vaccinia virus.

status: Public on Sep 03 2019

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5115 Center Ave

institute: University of Pittsburgh

summary: We report the analysis of tumor infiltrating lymphocytes from a mouse melanoma model that were treated with PBS, CTRL virus or leptin expressinb vaccina oncolytic virus

overall_design: 3 conditions, PBS treated, Control vaccinia virus, leptin expressing virus

first: Aditi

last: Kulkarni

first: Dayana

last: Rivadeneira


title: Transcriptomic profiling of vegfc(hy-/-);vegfd(-/-) mutant hearts reveals that vegfc/d signaling and lymphatics vasculature play a role in cardiac metabolism [fresh tissue]

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

summary: Recent studies have suggested that promoting lymphangiogenesis enhances cardiac repair following injury, but it is unknown whether lymphangiogenesis is required for cardiac regeneration. Here, we describe the anatomical distribution, regulation and function of the cardiac lymphatic network in a highly regenerative zebrafish model system using transgenic reporter lines and loss-of-function approaches.To understand the transcriptional profile of  the model, we performed RNA-seq on cardiac ventricles from control and mutant (vegfc(hy-/-);vegfd(-/-)) ventricles. Overall, vegfc(hy-/-;vegfd-/-) mutant ventricles were characterized by an up-regulation of pathways related to sphingolipid and phospholipid metabolism, translation, protein maturation and nonsense mediated decay compared to control hearts. Our findings suggest that lymphatics vasculature play a role in lipid transport and when lymphatic function is compromised in vegfch(y-/-;vegfd-/-) mutant, there are consequences to sphingolipid and phospholipid metabolism. Vegfc(hy-/-;vegfd-/-) mutant ventricles were not characterized by an enrichment of genes pathways implicated in pathological hypertrophy. This finding suggests that the absence of cardiac lymphatics induced a physiological rather than pathological cardiac hypertrophy.

overall_design: Transcriptional analysis of hearts from 2 different zebrafish lines.

middle: R

first: Choon

last: Sim


title: Transcriptomic profiling of non-regenerative vegfc(hy-/-);vegfd(-/-) mutant hearts reveals a marked inflammatory response [fixed tissue]

summary: To determine whether lymphangiogenesis is required for cardiac regeneration, vegfc(hy-/-);vegfd(-/-) double mutants and control hearts were collected and analyzed at 180 days after cryoinjury, this corresponds to a time point when the regenerative response is normally completed in wild-type zebrafish. Surprisingly, the vast majority (~70%) of vegfc(hy-/-);vegfd(-/-) mutants, which completely lack cardiac lymphatics, were able to mount a complete regenerative response without any signs of fibrosis. We found that the cardiac regenerative response was impaired only in a subset (3/8) of vegfc(hy-/-);vegfd(-/-) mutants, which were characterized by large deposits of fibrotic scar tissue present at the injury site. To profile vegfc/d-dependent genetic pathways contributing to lymphangiogenesis in cardiac regeneration, we performed RNA-seq on cryosections from control and mutant ventricles at 180 days following cryoinjury. Overall, vegfc(hy-/-);vegfd(-/-) mutant ventricles were characterized by an up-regulation of pathways related to metabolism, inflammation, hemostasis, negative regulation of FGFR signaling, translation, protein maturation and nonsense mediated decay compared to control hearts. These findings are consistent with the cardiac hypertrophy phenotype in vegfc(hy-/-);vegfd(-/-) mutants. To determine the molecular basis of the regenerative capacity within the mutant fish population, we next compared the transcriptional profiles of vegfc(hy-/-);vegfd(-/-) mutant hearts that did not regenerate (n=3) with the profiles of mutant hearts which recovered completely (n=5) at 180 days post cryoinjury. The subset of vegfc(hy-/-);vegfd(-/-) mutant hearts that failed to regenerate were characterized by an enrichment of inflammatory pathways, in particular TRAF6-mediated IRF7 activation, interferon alpha beta signaling and regulation of IFNA signaling. These findings suggest that loss of the vegfc/d signaling axis causes a sustained and pronounced inflammatory response following injury. This change in the cardiac micro-environment seems to favor adverse conditions which impair the regenerative process.

overall_design: Transcriptional analysis of hearts from 2 different zebrafish lines following cryoinjury.


title: Transcriptome Clarifies Mechanisms of Lesion Genesis Versus Progression in Models of Ccm3 Cerebral Cavernous Malformations [RNA-seq]

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary:
Cerebral cavernous malformations (CCMs) are dilated capillaries causing epilepsy and stroke.
Inheritance of a heterozygous mutation in CCM3/PDCD10 is responsible for the most aggressive familial form of the disease.
Here we studied the differences and commonalities between the transcriptomes of microdissected lesional neurovascular units (NVUs) from acute and chronic in vivo Ccm3/Pdcd10ECKO mice, and cultured brain microvascular endothelial cells (BMECs) Ccm3/Pdcd10ECKO.
We identified 2409 differentially expressed genes (DEGs) in acute and 2962 in chronic in vivo NVUs compared to microdissected brain capillaries, as well as 121 in in vitro BMECs with and without Ccm3/Pdcd10 loss (fold change ≥ |2.0|; p < 0.05, false discovery rate corrected).
A functional clustered dendrogram generated using the Euclidean distance showed that the DEGs identified only in acute in vivo NVUs were clustered in cellular proliferation gene ontology functions.
The DEGs only identified in chronic in vivo NVUs were clustered in inflammation and immune response, permeability, and adhesion functions.
In addition, 1225 DEGs were only identified in the in vivo NVUs but not in vitro BMECs, and these clustered within neuronal and glial functions.
One miRNA mmu-miR-3472a was differentially expressed (FC = -5.98; p = 0.07, FDR corrected) in the serum of Ccm3/Pdcd10+/- when compared to wild type mice, and this was functionally related as a putative target to Cand2 (cullin associated and neddylation dissociated 2), a DEG in acute and chronic lesional NVUs and in vitro BMECs.
Our results suggest that the acute model is characterized by cell proliferation, while the chronic model showed inflammatory, adhesion and permeability processes.
In addition, we highlight the importance of extra-endothelial structures in CCM disease, and potential role of circulating miRNAs as biomarkers of disease, interacting with DEGs.
The extensive DEGs library of each model will serve as a validation tool for potential mechanistic, biomarker, and therapeutic targets.

overall_design: Examined the differences and commonalities between the transcriptomes of microdissected lesional neurovascular units from acute and chronic in vivo Ccm3/Pdcd10ECKO mice, cultured brain microvascular endothelial cells Ccm3/Pdcd10ECKO and circulating miRNAs from Ccm3/Pdcd10+/- mice.

first: Janne

last: Koskimäki

first: Dongdong

last: Zhang

first: Laleh

last: Saadat

first: Thomas

last: Moore

first: Rhonda

last: Lightle

first: Sean

middle: P

last: Polster

first: Julián

last: Carrión-Penagos

first: Seán

last: Lyne

first: Hussein

last: Zeineddine

first: Changbin

last: Shi

first: Robert

last: Shenkar

first: Sharbel

last: Romanos

first: Kenneth

last: Avner

first: Abhinav

last: Srinath

first: Le

last: Shen

first: Matthew

last: Detter

first: Daniel

last: Snelling

first: Ying

last: Cao

first: Miguel

last: Lopez-Ramirez

first: Gregory

last: Fonseca

first: Alan

last: Tang

first: Pieter

last: Faber

first: Jorge

last: Andrade

first: Mark

last: Ginsberg

middle: L

last: Kahn

first: Douglas

last: Marchuk

first: Romuald

last: Girard

first: Issam

last: Awad


title: Transcriptome Clarifies Mechanisms of Lesion Genesis Versus Progression in Models of Ccm3 Cerebral Cavernous Malformations [miRNA-seq]

first: Yan

last: Li

first: Janne

last: Koskimäki

first: Dongdong

last: Zhang

first: Laleh

last: Saadat

first: Thomas

last: Moore

first: Rhonda

last: Lightle

first: Sean

last: Polster

first: Julián

last: Carrión-Penagos

first: Seán

last: Lyne

first: Hussein

last: Zeineddine

first: Changbin

last: Shi

first: Robert

last: Shenkar

last: Romanos


title: Cross-species co-analysis of prefrontal cortex chronic ethanol transcriptome responses in mice and monkeys

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary: Despite recent extensive genomic and genetic studies on behavioral responses to ethanol, relatively few new therapeutic targets for the treatment of alcohol use disorder have been validated. Here we describe a cross-species genomic approach focused on identifying gene networks associated with chronic ethanol consumption. To identify brain mechanisms underlying a chronic ethanol consumption phenotype highly relevant to human alcohol use disorder, and to elucidate potential future therapeutic targets, we conducted a genomic study in a nonhuman primate model of chronic open-access ethanol consumption. Microarray analysis of RNA expression in anterior cingulate and subgenual cortices from rhesus macaques was performed across multiple cohorts of animals. Gene networks correlating with ethanol consumption or showing enrichment for ethanol-regulated genes were identified, as were major ethanol-related hub genes within these networks. A subsequent consensus module analysis was used to co-analyze monkey data with expression data from a chronic intermittent ethanol vapor-exposure and consumption model in C57BL/6J mice. Ethanol-related gene networks conserved between primates and rodents were enriched for genes involved discrete biological functions, including; myelination, synaptic transmission, chromatin modification, Golgi apparatus function, translation, cellular respiration, and RNA processing. The myelin-related network, in particular, showed strong correlations with ethanol consumption behavior and displayed marked network reorganization between control and ethanol-drinking animals. Further bioinformatics analysis revealed that these networks also showed highly significant overlap with other ethanol-regulated gene sets. Altogether, these studies provide robust primate and rodent cross-species validation of gene networks associated with chronic ethanol consumption. Our results also suggest potential novel focal points for future therapeutic interventions in alcohol use disorder.

overall_design: Tissue samples of monkey anterior cingulate and subgenual cortex (Brodmann areas 24, 25, and 32) from 43 (32 ethanol drinking, 11 control) adult male rhesus macaques (Macaca mulatta), aged 5 to 11 years, were used in this study. These animals, individually housed at the Oregon National Primate Research Center, were induced to drink ethanol by schedule-induced polydipsia per previously published methods (Grant et al. 2008, Helms, Park, and Grant 2014), and were then allowed 22 hours per day of ad libitum access to water and 4% (w/v) ethanol in water for a period of one year. Control animals were given daily maltose dextran solution (calorically matched to an ethanol drinker) and had access to water during all portions of the experiment.

first: James

last: Bogenpohl

first: Maren

last: Smith

last: Farris

first: Catherine

last: Dumur

first: Marcelo

middle: F

last: Lopez

first: Howard

middle: C

last: Becker

first: Kathleen

last: Grant


title: RNA-sequencing of paired normal-adjacent and liver tumor tissue from WT and Liver MPC-knockout mice

first: Eric

last: Taylor

address: 169 Newton Rd

department: Biochemistry

institute: University of Iowa

summary:
Purpose: Liver-specific MPC-knockout (Mpc1-/-, LivKO) mice develop less liver tumors than wild-type (Mpc1+/+) mice when given a DEN/CCl4 hepatocarcinogenesis protocol. The goals of this study are to compare transcriptome changes (RNA-seq) between liver tumor and normal-adjacent tissue in WT and Mpc1-/- mice.
Methods: Total RNA was collected from tumor and paired normal-adjacent liver samples using the Qiagen miRNeasy kit. RNA from four samples each of wild-type tumor (WT-Tumor), paired wild-type normal-adjacent (WT normal adjacent), Mpc1-/- (MPC LivKO) tumor (MPC LivKO-Tumor), and paired MPC LivKO normal-adjacent (MPC LivKO normal adjacent) tissue was isolated. Each tumor and its paired normal-adjacent tissue were analyzed in a paired manner. Library preparation and sequencing were performed using the Illumina mRNA-Seq workflow. For data normalization, the raw number of reads for each transcript was converted to Fragments Per Kilobase of transcript per Million mapped reads (FPKM). FPKM values were log transformed, and unsupervised clustering was performed on samples based on normalized expression of genes with variation in Euclidean distance among samples of at least 2.5 standard deviations using Cluster 3 software.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (buildmm10) and identified 15,777 transcripts in the liver tissue samples of WT an Mpc1-/- (MPC LivKO) with Illumina workflow. FPKM values were log transformed, and unsupervised clustering was performed using Cluster 3 software. Unsupervised clustering analysis identified six gene expression groups: (1) increased gene expression in both WT and LivKO tumors, (2) increased gene expression in WT tumors, (3) increased gene expression  in MPC LivKO tumors, (4) decreased gene expression down in both WT and LivKO tumors, (5) decreased gene expression in WT tumors, and (6) decreased gene expression in MPC LivKO tumors.
Conclusions: Our study is the first on Mpc1-/- liver tumors. The HCC markers Alpha-fetoprotein (Afp) and Glypican-3 (Gpc3) were in the cluster of genes upregulated in both WT and MPC LivKO tumors. In the cluster of 14 genes up-regulated in only WT tumors were two GSTs: Gsta1 and Gstp2. In the cluster of 108 genes down-regulated in only MPC LivKO tumors were three GSTs: Gsta2, Gsta3, and Mgst1. That same cluster contained Gpx1, glutathione peroxidase (Gpx1). Thus, we concluded WT tumors increased but MPC LivKO tumors decreased expression of glutathione metabolizing genes.

overall_design: Liver tumor and NormAdj mRNA profiles of 24 week-old wild type (WT) and Mpc1-/- mice treated with a  DEN/CCl4 chemical hepatocarcinogenesis protocol were generated by deep sequencing using Illumina HiSeq 4000-275.

last: Tompkins


title: Transcriptome Clarifies Mechanisms of Lesion Genesis Versus Progression in Models of Ccm3 Cerebral Cavernous Malformations

first: Yan

last: Li

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

overall_design: Refer to individual Series


title: Characterization of an Immortalized Human Small Airway Basal Stem/Progenitor Cell Line with Airway Region-specific Differentiation Capacity

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College


title: Genome-wide characterization of REST binding regions in LNCaP prostate cancer cells

city: Copenhagen

first: Diego

last: Iglesias-Gato

address: Univesitetsparken 2

country: Denmark

institute: Unoversity of Copenahgen

summary: Transcriptional regulator REST plays a key role in repressing neuronal specific genes in prostate cancer and other non-neuronal tissues. Moreover, loss of REST is observed in neuroendocrine prostate tumors. Here, we use ChIP-seq analysis to study genome–wide REST occupied regions in the prostate cancer cell line, LNCaP. REST occupied regions were then correlated to gene expression changes occurring between prostate adenocarcinoma and neuroendocrine prostate tumors in vivo.

overall_design: Examination of REST binding region in LNCaP cell in duplicates.

last: Igleisas-Gato

first: Amilcar

last: Flores-Morales

first: Mads

last: Lerdrup

first: Charlotte

last: Lavallee


title: The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice

city: Shanghai

first: Jian-Kang

last: Zhu

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology

summary: The widespread agricultural problem of pre-harvest sprouting (PHS) could potentially be overcome by improving seed dormancy. Here, we report that miR156, an important grain yield regulator, also controls seed dormancy in rice. We found that mutations in one MIR156 subfamily enhance seed dormancy and suppress PHS with negligible effects on shoot architecture and grain size, whereas mutations in another MIR156 subfamily modify shoot architecture and increase grain size but have minimal effects on seed dormancy. Mechanistically, mir156 mutations enhance seed dormancy by suppressing the gibberellin (GA) pathway through de-represssion of the miR156 target gene Ideal Plant Architecture 1 (IPA1), which directly regulates multiple genes in the GA pathway. These results provide an effective method to suppress PHS without compromising productivity, and will facilitate breeding elite crop varieties with ideal plant architectures.

overall_design: High-depth paired-end RNA-seq from Nipponbare (the wild type), mir156abckl, mir156defghi and mir156abcdfghikl mutant rice. Each sample contains 3 biological replicates.

first: Chunbo

last: Miao

first: Zhen

last: Wang


title: Evaluation of gene expression changes in wild type (C57BL/6) vs Angelman syndrome (AS) model mice

city: Wako

first: Xiaoxi

last: Liu

state: Saitama

address: Hirosawa 2-1

department: Brain Science Institute

institute: RIKEN

summary:
We aimed to identify differentially expressed genes in hippocampus of AS mice compared with that of WT mice. The analysis revealed  around 120 genes were significantly affected at the mRNA levels in AS mouse brain.
We found that immune-related genes were enriched in genes that were upregulated in AS. Particularly, the genes downstream of an anti-virus transcription factor, IRF family, were affected in AS brain, suggesting that IRF-dependent transcription is regulated by UBE3A

overall_design: By microarray analysis, we measured the gene expression changes in hippocampi of four pairs of Angelman syndrome (AS) model mice and wild type mice.

first: Ryohei

last: Furumai

first: Kota

last: Tamada

first: Toru

last: Takumi


title: Transcriptomic profiling of vegfc(hy-/-);vegfd(-/-) mutant hearts reveals that vegfc/d signaling and lymphatics vasculature play a role in cardiac metabolism

first: Enzo

last: Porrello


title: Host resistance to pulmonary infection with Mycobacterium tuberculosis is mediated by IL-1alpha.

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Background: M.tuberculosis is one of the most prevalent and deadly human pathogens. The molecular mechanisms determining the outcomes of an infection with M.tuberculosis, that range from resistance to an active progressive disease, remain incompletely understood. Here we provide the evidence that IL-1alpha plays a critical and non-redundant role in enabling host resistance to pulmonary M.tuberculosis infection in mice that develop functional pathogen-specific adaptive immunity. Mechanistically, IL-1alpha-deficient mice fail to control M.tuberculosis replication in vivo at a level of individual infected cells and succumb to progressive disease at the late phase of infection. Furthermore, we show that IL-1alpha from hematopoietic compartment through IL-1RI operates upstream of TNFRI-signaling pathway and the lack of IL-1alpha leads to the continuous influx of monocytes that acquire a hyper-inflammatory phenotype and contribute to pathology, rather than to a pathogen control. Cell-type-specific restoration of IL-1alpha expression in CD11c+ subsets of lung leukocytes resulted in reduced levels of inflammatory marker expression on lung cells and improved survival IL-1alpha-deficient mice after M.tuberculosis infection. In humans, genetic analysis of single nucleotide polymorphisms in 14 genes implicated in IL-1-IL-1R signaling pathway revealed association of genetic variations in IL-1alpha and IL-1RAP genes with human susceptibility to pulmonary tuberculosis. Our results implicate IL-1alpha as a principal factor of host resistance to M.tuberculosis and IL-1alpha-driven cell-cell crosstalk as a key step in triggering M.tuberculosis control mechanisms that are critical for host survival.

overall_design: Two pools of CD11c+ cells from three mice each were prepared for WT and Il1a-/- experimental groups.

first: Richard

last: Beyer

first: Nelson

last: DiPaolo

first: Shahin

last: Shafiani

first: Tracey

last: Day

first: Thalia

last: Papayannoupoulou

first: Yoichiro

last: Iwakura

middle: A

last: Flavell

first: Theodor

middle: K

last: Bamler

first: David

last: Russell

first: Sarah

middle: J

last: Dunstan

first: Thomas

last: Hawn

first: Amber

last: Burt

first: Brian

last: Browning

first: Gail

last: Jarvik

last: Sherman

first: Kevin

last: Urdah

first: Dmitry

last: Shayakhmetov