title: Transcriptional analysis of a S. clavuligerus oppA2-deleted mutant

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

institute: University of León

summary:
The objective is to analyze the expression level of a Streptomyces clavuligerus oppA2-deleted mutant
Experiment type  Expression profiling by array

overall_design: Six biological conditions were assayed: one strain (Streptomyces clavuligerus oppA2-deleted mutant), in three culture times (22.5h, 46.5h and 60 h). Two biological replicates were made for each condition.

first: R

last: Alvarez-Alvarez

first: A

last: Rodriguez-Garcia

first: Y

last: Martinez-Burgo

first: J

last: Martin

first: P

last: Liras


title: Effect of ONC201 and its derivatives (ONC206 and ONC212) on glioma cells

status: Public on Sep 25 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

summary: We performed microarray analysis in order to evaluate the effect of ONC201 and its derivatives (ONC206 and ONC212) on gene expression in U87 glioma cells.

overall_design: U87 cells were treated with 200 nM of ONC201, ONC206, or ONC212 in 0.1% DMSO, or with 0.1% DMSO negative control. After 72 hours treatment, total RNA was isolated and analyzed.

first: Chiaki

last: Ishida

first: Markus

last: Siegelin


title: Transcriptome profile of wildtype and Ret homozygote null mouse guts at E10.5 ,E12.5 and E14.5

status: Public on Sep 30 2018

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Total mRNA seq was perfomed on widtype and Ret null mouse embryonic gut at 3 stages of devlopment- E10.5, E12.5 and E14.5

overall_design: Total RNA from 3 replicates each of wildtype and Ret null emryonic gut was converted to cDNA  and run on HiSeq 2000 (75 bp paired end)

first: Aravinda

last: Chakravarti


title: Bolitoglossa ramosi differential expressed genes during limb regeneration

status: Public on Sep 26 2018

city: medellin

first: Jean

middle: Paul

last: Delgado

state: antioquia

department: Biology

country: Colombia

institute: University of Atioquia

summary:
Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-seq to generate transcript sequence data and identify 602 genes that are differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor approximately 180 million years ago. Our study highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders.
All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.

overall_design:
To assembly the reference transcriptome, we sequenced individual samples which had pools of different adult animals we did pools of different animals to get the tissues of controls (three biological replicates, n = 9 animals), gut (one biological replicate, n = 1 animal), skin (one biological replicate, n = 1 animal), blastema 20 dpa (one biological, replicate n = 1 animal), blastema 40 dpa (one biological replicate, n = 2 animals), blastema 60 dpa (two biological replicates, n = 5 animals) and 70 dpa (one biological replicate, n = 3 animals).
All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015, which was delivered by the Ministerio del Medio Ambiente (Ministry of Environment) of Colombia to the Principal Investigator.

first: Claudia

middle: M

last: Arenas

first: Ryan

last: Woodcock

first: Jeramiah

last: Smith

first: Randal

middle: S

last: Voss

middle: P


title: Transcriptome variation among human embryonic stem cell lines impacts on their differentiation

status: Public on Sep 24 2018

city: Shenzhen

first: Changbin

last: Sun

address: Beishan Industrial Zone, Yantian District

country: China

institute: BGI

summary: Human embryonic stem cells (hESCs) have the pluripotency to form any cell type in the body, making them attractive cell sources in drug screening, regenerative medicine, disease and developmental processes modeling. However, not all hESC lines have equal potency to generate desired cell types in vitro, significant variation has been observed for the differentiation efficiency of various human ESC lines, and the precise underpinning molecular mechanism are still unclear. In this work, we compared transcriptome variation of four hESC lines H7, HUES1, HUES8 and HUES9 to find out whether gene expression difference between hESC lines influence their differentiation behavior in vitro. Results demonstrate that different expression genes (DEGs) are significantly enriched in developmental process, such as ectoderm, mesoderm and endoderm development, and the enrichment difference between lines is in accordance with its lineage bias. Among these DEGs, pluripotency factors and genes involved in signaling transduction also show great variation among lines. The Pleiotropic functional role of these genes in hESC identity controlling and early lineage specification, implicate that different hESC lines with distinct differentiation propensity may utilize individual balance mechanism to maintain pluripotent state, whereas the balance broken in a certain environment, gene expression variation between them could impact on their different lineage specification behavior.

overall_design: Examination of  different expression genes in 4 hESC lines.

first: Xi

last: Zhang


title: Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow II

status: Public on Sep 27 2018

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

summary: Today’s diagnostic tests for multiple myeloma (MM) reflect the criteria of the updated WHO classification based on biomarkers and clinicopathologic heterogeneity. To that end, we propose a new subtyping of myeloma plasma cells (PC) by B-cell subset associated gene signatures (BAGS), from the normal B-cell hierarchy in the bone marrow (BM). To do this, we combined FACS and GEP data from normal BM samples to generate classifiers by BAGS for the PreBI, PreBII, immature (Im), naïve (N), memory (M) and PC subsets. The resultant tumor assignments in available clinical datasets exhibited similar BAGS subtype frequencies in four cohorts across 1302 individual cases. The prognostic impact of BAGS was analyzed in patients treated with high dose melphalan as first line therapy in three prospective trials: UAMS, HOVON65/GMMG-HD4 and MRC Myeloma IX with Affymetrix U133 plus 2.0 microarray data available from diagnostic myeloma PC samples. The BAGS subtypes were significantly associated with progression free (PFS) and overall survival (OS) (PFS, P=3.05e−06 and OS, P=1.06e−11) in a meta-analysis of 926 pts. The major impact was observed within the PreBII and M subtypes conferred with significant inferior prognosis compared to the Im, N and PC subtypes. Cox proportional hazard meta-analysis documented that the BAGS subtypes added significant and independent prognostic information to the TC classification system and ISS staging. BAGS subtype analysis identified transcriptome differences and a number of novel differentially spliced genes. We have identified hierarchal subtype differences in the myeloma plasma cells, with prognostic impact. This observation support an acquired reversible B-cell trait and phenotypic plasticity as a hallmark, also in MM.

overall_design: Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow were normalized together with B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells obtained using FACS from mononuclear cells isolated from bone marrow of healthy persons.

first: Julie

last: Bødker

middle: F

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Hans

middle: E

last: Johnsen


title: Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow

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

overall_design: Refer to individual Series


title: Transcriptional profile of human neonatal cord blood and adult peripheral blood dendritic cells

status: Public on Sep 21 2018

city: Paris

first: Sebastien

last: LEMOINE

address: 149 rue de Sèvres, Bat. Hamburger, 5e étage, p507

country: France

institute: Necker Hospial

summary: A phenotypically and functinoally distinct subset of human blood dendritic cells expressing CD11b is specific of the neonatal environment. We have employed whole genome microarray expression profiling to identify the specific gene signature of CD11b+ cord blood dendritic cells as compared to their adult peripheral blood counterparts. Peripheral blood adult cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b- ), neonatal cord blood cDC2 (CD20- CD11c+ CD14- BDCA1+ CD11b-) and neonatal cord blood cDC2b (CD20- CD11c+ CD14- BDCA1+ CD11b+) were FACS purified from BDCA1+ magnetically. Neonatal monocytes (CD11c+ CD14+) and neonatal naive T cells (CD3+ CD4+ CD56- CD25- CD45RO-) were used as controls.

overall_design: Dendritic cell subsets were isolated from 3 peripheral blood donors and 3 cord blood donors. Monocytes were isolated from 3 cord blood donors. Neonatal naive T cells were isolated from 1 peripheral blood donor. Dendritic cells were left unstimulated or were stimulated with either poly I:C + R848, Bacillus Calmette–Guérin (BCG) or Respiratory Syncytial Virus (RSV) for 6h. RNA from 5000 cells was amplified, labeled, and hybridized to an an Agilent Whole Human Genome Oligo Microarrays 8x60K.

last: Lemoine

first: Xiaoming

first: Richard

last: Lo-Man


title: GATA2 monoallelic expression underlies reduced penetrance in inherited GATA2-  mutated MDS/AML

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

summary: Although familial myelodysplasia and acute myeloid leukemia (MDS/AML) is rare, its true prevalence is likely underestimated due to wide variations in the age of onset, disease latency and outcome between and within families, with some mutation carriers remaining asymptomatic into late adulthood. Reduced penetrance is a notable feature of germline GATA2 p.Thr354Met pedigrees. In this study, we demonstrate that silencing of the wildtype (WT) GATA2 allele discriminates between symptomatic and asymptomatic carriers and is linked with allele-specific differences in DNA methylation and H3K4me3 promotor deposition, providing a molecular explanation for the clinical heterogeneity observed within a GATA2-mutated AML family.

overall_design: Bone marrow (BM) and/or peripheral blood (PB) diagnostic samples were obtained from members of the family with written consent and ethical approval (06/Q0401/31) received in accordance with the declaration of Helsinki. Targeted deep sequencing of 33 genes frequently mutated in MDS/AML was used to determine the secondary mutational repertoire in this family. Quantitative real-time PCR was performed to measure global GATA2 expression with Sanger sequencing used to measure allelic GATA2 expression. Allele-specific differences in GATA2 promoter methylation were assessed by bisulphite cloning and sequencing and allele-specific variations in chromatin deposition were assessed by chromatin-immunoprecipitation (ChIP) using either H3K4me3 or H3K27me3 antibodies. RNA-seq was used to analyze transcriptomic differences between GATA2 monoallelic vs. biallelic groups

first: Ahad

last: Al Seraihi

first: Ana

last: Rio-Machin

first: Jude

last: Fitzgibbon


title: Transcriptomic analysis of TDRD9-depleted lung tumor cells

status: Public on Sep 23 2018

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

summary: Tudor domain containing protein 9 (TDRD9) is a RNA helicase normally expressed in the germline. We have shown that TDRD9 is highly expressed in a subset of non-small cell lung carcinomas. Here we determine the transcriptomic changes of a TDRD9-positive lung tumor cells line (NCI-H1993) depleted of TDRD9.

overall_design: NCI-H1993 cells were treated either with siRNA control, siTDRD9-1 or siTDRD9-2 during 72 h. siTDRD9-1 and  siTDRD9-2 are two different siRNAs against the transcript of TDRD9 gene. Triplicated independent cultures were recovered and processed for RNA extraction and hybridization on Affymetrix microarrays.

middle: C

first: Macarena

last: Guijo


title: Global mRNA decay in Gluconobacter oxydans 621H

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

summary: In this study we conducted genome-wide mRNA decay analysis to get further insights into the physiology of Gluconobacter oxydans.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The microarray analysis aimed at the determination of the mRNA level changes in G. oxydans after addition of rifampicin. The analysis was performed three times by independent biological replicates. G. oxydans cells were harvested for isolation of total RNA directly before (t0) and 2 min (t2), 5 min (t5), 10 min (t10) as well as 15 min (t15) after addition of rifampicin. Each sample after addition of rifampicin (tx) was compared to t0 samples.

first: Angela

last: Kranz

first: Andrea

last: Steinmann

first: Ursula

last: Degner

first: Michael

last: Bott


title: mRNA expression profiles in primary microglia cells treated with R848, IFN-α, and R848+ IFN-α

status: Public on Sep 20 2018

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary: Using RNA-seq, we have reported signaling crosstalk between IFN-α and R848 at the level of transcriptomes highlighting synergsitic gene expression dynamics upon different receptors signaling in microglia cells

overall_design: Comparative study of the effects of control versus R848, IFN-α and R848+IFN-α treated PM cells, were generated by deep sequencing on an Illumina HiSeq 2500 (101 cycles PE lane).

first: Young

middle: G


title: PARP1 regulates VSMC phenotypic switch and neointima via Myocardin

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: We applied the transcriptome profiling (RNA-seq) for  high-throughput profiling of genes changes in VSMC dedifferentiation. Rat primary VSMCs were divided into 3 groups, control, PDGF-BB, PDGF-BB+PJ34,and mRNA sequence were performed. We found that PDGF-BB could upregualted the genes involved in cell proliferation and migration, and downregulated the VSMC contractile genes, all of which could be reversed by PARP inhibitor PJ34. Then we knockdowned the co-factor Myocardin in VSMCs, and found the above effects of PJ34 were nearly abolished.Our study  first provided the transcription changes by RNA-seq in VSMC dedifferentiation, and demonstrated the key roles of PARP1 and the PARylation process in VSMC phenotypic switch.

overall_design: Eximination of genes changes in VSMC dedifferentiation

first: Cheng

first: Wenjing

last: Xu

first: Kai

last: Huang


title: Global organization of the B cell genome by the transcription factor Pax5

status: Public on Oct 07 2018

city: Parkville

first: Rhys

last: Allan

state: Victoria

address: 1G Royal Parade

department: Molecular Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research


title: CD24 regulates gene expression in pre-adipocytes in response to IBMX and Dexamethasone stimulation

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

summary: Previous in vitro studies in our lab have shown that CD24, a cell surface receptor, actively regulates lipid accumulation in adipocytes. But how CD24 regulates this process remains unknown. In order to answer this question, we initially tested to determine if CD24 regulates lipid accumulation by regulating glucose uptake in adipocytes in vitro. We observed that instead, CD24 caused the dysregulation of the expression of 134 genes as determined by DNA microarray analysis. We then validated the expression of select four genes, when CD24 is knocked down during the different stages of adipogenesis in 3T3-L1 pre-adipocytes in vitro. To further confirm the role of these genes, we then determined the expression patterns of these four genes in primary cells undergoing adipogenesis that were isolated from the epididymal and inguinal white adipose tissue depots of CD24 knockout mice. Surprisingly, we found that these genes were dysregulated in the inguinal but not the epididymal depot in vitro. Overall, the data presented here suggests that CD24 is necessary for select gene expression, but not glucose uptake, during adipogenesis in vitro.

overall_design: Comparison of 3T3-L1 confluent pre-adipocytes treated with IBMX and Dexamethasone (Dex) for 6 hours if CD24 is knocked-down with siRNA or not. IBMX/Dex samples were compared to vehicle-treated controls.

first: Nicole

last: Smith


title: Cellular metabolism constraints innate immune responses in early human ontogeny

status: Public on Sep 22 2018

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

institute: BC Children's Hospital

summary: We compared LPS responses (5h) between preterm (<30 weeks) neonatal, term neonatal and adult human monocytes at the genome-wide transcriptome level.

overall_design: Total RNA obtained from 8 preterm, 12 term and 12 adults samples (CD14-expressing cells by magnetic bead positive depletion) treated for 5h with LPS, with unstimulated control samples.

first: Bernard

last: Kan

first: Kelsey

last: Lee

first: Fudan

last: Miao

first: Colin

middle: J

last: Ross


title: Gene expression profiling of AC9 overexpression in 393P mice cells

status: Public on Sep 18 2018

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: ADCY9 encodes AC9, which is 1 of 9 transmembrane AC isoforms (AC1-9) that catalyze the synthesis of cyclic AMP from ATP and are regulated primarily by heterotrimeric G-protein-coupled receptors. We ectopically expressed AC9 in 393P cells and found that, relative to empty vector controls, the AC9 transfectants had higher cyclic AMP levels and were more migratory and invasive in Boyden chambers. We examined the prognostic value of an AC9-regulated gene expression signature derived from 393P_AC9 cells and 393P_vector cells. We probed a compendium of 1,586 clinically annotated human lung adenocarcinomas for the manifestation of the AC9 gene signature and found that the manifestation of the signature was correlated with a significantly shorter duration of survival.

overall_design: Gene expression microarray analyses were performed on AC9 overexpression and empty VECTOR in mice 9393P cells.

first: Jon

last: Kurie

first: Fengju

last: Chen


title: Cellular transcriptome upon HSV-1 infection or DUX4 overexpression

status: Public on Sep 19 2018

city: Chicago

first: Michaela

middle: U

last: Gack

state: IL

address: 920 E 58th St

department: Microbiology

institute: The University of Chicago

summary: We found that the germline transcription factor double homeobox 4 (DUX4) is upregulated upon infection with wild-type herpes simplex virus-1 (HSV-1). The goal of this experiment was to compare the cellular transcriptome of HEK293T cells that were infected with HSV-1 (KOS strain), or transfected with a plasmid encoding human DUX4.

overall_design: HEK293T cells remained either untreated (mock), were infected with wild-type HSV-1 (KOS strain) for 18 h, or were transiently transfected with a plasmid encoding untagged human DUX4 (pmkg-DUX4) for 18 h, followed by extraction of total RNA and RNAsequencing.

first: Florian

last: Full

first: Konstantin

last: Sparrer


title: Extensive sex differences at the initiation of meiotic recombination

city: Bethesda

first: Kevin

last: Brick

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Meiotic recombination differs between males and females, however, when and how these differences are established is unknown. We identify extensive sex differences at recombination initiation by mapping hotspots of meiotic DNA double strand breaks in male and female mice. Contrary to past findings in humans, few hotspots are used uniquely in either sex. Instead, grossly different recombination landscapes result from up to 15-fold differences in hotspot use between males and females. Indeed, most recombination occurs at sex-biased hotspots. Sex biased hotspots appear to be partly determined by chromosome structure, and DNA methylation, absent in females at the onset of meiosis, plays a substantial role. Sex differences are also evident later in meiosis as the repair frequency of distal meiotic breaks as crossovers diverges in males and females. Suppression of distal crossovers may help to minimize age-related aneuploidy that arises due to cohesion loss during dictyate arrest in females.

overall_design: Comparison of meiotic DNA double strand break hotspots in mouse testis and ovary

first: Sarah

last: Thibault-Sennett

first: Fatima

last: Smagulova

first: Kwan

middle: W

last: Lam

first: Yongmei

last: Pu

first: Florencia

last: Pratto

first: Rafael

middle: D

last: Camerini-Otero

first: Galina

middle: V

last: Petukhova


title: A comparative miRNA/mRNA analysis in distinct murine liver cancer models reveals miR-193a-5p and NUSAP1 as therapeutic targets in HCC [mRNA]

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
BACKGROUND & AIMS: We performed an integrated analysis to identify microRNAs (miRNAs) and mRNAs with altered expression in liver tumors from 3 mouse models of hepatocellular carcinoma (HCC) and human tumor tissues.
METHODS: We analyzed miRNA and mRNA expression profiles of liver tissues from mice with diethylnitrosamine-induced hepatocarcinogenesis, conditional expression of lymphotoxin alpha and lymphotoxin beta , or inducible expression of a Myc transgene (Tet-O-Myc mice), as well as male C57BL/6 mice (controls). miRNA mimics were expressed and miRNAs and mRNAs were knocked down in human (Huh7, Hep3B, JHH2) hepatoma cell lines; cells were analyzed for viability, proliferation, apoptosis, migration, and invasion. Cells were grown as xenograft tumors in nude mice and analyzed. We combined in-silico target gene prediction with mRNA profiles from all 3 mouse models. We quantified miRNA levels in 146 fresh-frozen tissues from patients (125 HCCs, 17 matched non-tumor tissues, and 4 liver samples from patients without cancer) and published human data sets and tested correlations with patient survival times using Kaplan-Meier curves and the log-rank test. Levels of NUSAP1 mRNA were quantified in 237 HCCs and 5 non-tumor liver samples using the Taqman assay.
RESULTS: Levels of the microRNA 193a-5p (MIR193A-5p) were reduced in liver tumors from all 3 mouse tumor models and in human HCC samples, compared with non-tumor liver tissues. Expression of a MIR193A-5p mimic in hepatoma cells reduced proliferation, survival, migration, and invasion and their growth as xenograft tumors in nude mice. We found nucleolar and spindle associated protein 1 (NUSAP1) to be a target of MIR193A-5p; HCC cells and tissues with low levels of MIR193A-5p had increased expression of NUSAP1. Increased levels of NUSAP1 in HCC samples correlated with shorter survival times of patients. Knockdown of NUSAP1 in Huh7 cells reduced proliferation, survival, migration, and growth as xenograft tumors in nude mice. Hydrodynamic tail-vein injections of a small hairpin RNA against NUSAP1 reduced growth of AKT1-MYC-induced tumors in mice.
CONCLUSIONS: MIR193A-5p appears to prevent liver tumorigenesis by reducing levels of NUSAP1. Levels of MIR193A-5p are reduced in mouse and human HCC cells and tissues, leading to increased levels of NUSAP1, associated with shorter survival times of patients. Integrated analyses of miRNAs and mRNAs in tumors from mouse models can lead to identification of therapeutic targets in humans.

overall_design: Control, non-tumorous and tumor liver samples from three different mouse models were subjected to gene expression profiling.

first: Sanchari

last: Roy

first: Christoph

last: Roderburg

first: Tom

last: Luedde


title: A comparative miRNA/mRNA analysis in distinct murine liver cancer models reveals miR-193a-5p and NUSAP1 as therapeutic targets in HCC [miRNA]

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: qPCR miRNA expression profiling. miRNA expression was profiled in three pathogenically distinct murine hepatocellular carcinoma models


title: High-throughput single cell transcriptome analysis and CRISPR screen identify key β cell-specific disease genes

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

summary: Pancreatic endocrine cells orchestrate the precise control of blood glucose levels, but the contribution of each cell type to diabetes or obesity remains elusive. Here we used a massively parallel single-cell RNA-seq technology (Drop-Seq) to analyze the transcriptome of 26,677 pancreatic islets cells from both healthy and type II diabetic (T2D) donors. We have analyzed cell type-specific gene signatures, and detected several rare α or β cell subpopulations with high sensitivity. We also developed RePACT, a sensitive single cell analysis algorithm to identify genes associated with rare disease causing cells, or to capture the subtle disease-relevant cellular variation. We successfully identified both common and specific signature genes of obesity and T2D with only a small number of islet samples. We also performed an unbiased genome-wide CRISPR screen and mapped these Drop-Seq signature genes to the core insulin regulatory network in β cells. Notably, our integrative analysis discovered a β cell-specific function of the cohesin loading complex in regulating insulin gene transcription, and a previously unrecognized role of the NuA4/Tip60 histone acetyltransferase complex in regulating insulin release. These data demonstrated that single-cell trancriptomics is necessary to dissect the heterogeneity, disease state, and functionality of islet β cells and other cell types.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell sequencing (Drop-seq) for Human Pancreatic islet from 9 individuals respectively. Including 6 Healthy donor and 3 Type II diabetes patient donor. 4 Chipseq for further validation.

first: Fulai

last: Jin

first: Leina

last: Lu


title: Internally Calibrated ChIP-seq (ICeChIP-seq) using a large panel of antibodies against H3K4 methylations to measure genome-wide histone modification density in mammalian cells

first: Rohan

middle: Nishant

last: Shah

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

summary: Post-translational modifications (PTMs) on histone proteins regulate genome accessibility and are frequently studied using chromatin immunoprecipitation (ChIP). In ChIP, an antibody putatively specific towards a histone PTM is used to map its genomic locations. ChIP experiments assume perfect antibody-epitope specificity, an assumption previously shown to be problematic, largely through peptide array studies. Among the most well-studied histone PTMs are the mono-, di-, and tri-methylation states of histone H3 lysine 4 (H3K4). While each state has been ascribed different biological functions, the methylation state specificity of antibodies used in these studies has not been systematically interrogated. Here, we use internally calibrated ChIP (ICeChIP) to comprehensively define the specificities of 52 commercially available antibodies marketed to distinguish the three methylation states of H3K4, allowing identification of both high- and low-specificity antibodies. We then conduct ICeChIP-seq with 18 such antibodies of varying specificity. We further find that the sum of H3K4me1 and H3K4me2 across enhancers contacting a promoter correlates strongly with gene expression for all genes, including housekeeping genes, and note that use of low-quality antibodies yields materially different biological interpretations. These results illustrate the way by which variable specificity of commercial antibodies contributes to the “reproducibility crisis” in biological research and demonstrates the need to carefully validate antibodies with techniques appropriate for the intended applications.

overall_design: Semi-synthetic nucleosome standards are spiked into ChIP experiments to conduct internally calibrated ChIP-seq (ICeChIP-seq) with 17 anti-H3K4 methylation antibodies of varying specificities in K562 cells and one anti-H3K4me1 antibody in WT and dCD MLL3/4 R1 mESC cells.

middle: N

first: Adrian

middle: T

last: Grzybowski

first: Evan

last: Cornett

first: Andrea

last: Johnstone

first: Bradley

last: Dickson

first: Brandon

middle: A

last: Boone

first: Marcus

last: Cheek

first: Martis

last: Cowles

first: Danielle

last: Maryanski

first: Matthew

last: Meiners

first: Rochelle

last: Tiedemann

first: Robert

last: Vaughan

first: Neha

last: Arora

first: Zu-Wen

last: Sun

first: Scott

middle: B

last: Rothbart

first: Michael-Christopher

last: Keogh

first: Alexander

last: Ruthenburg


title: Transient expression of T-bet epigenetically imprints the Ifng locus for its expression in a distinct Tfh cell subset

status: Public on Sep 17 2018

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: T follicular helper (Tfh) cells, which reside in the B cell follicles and help Ig class switching, express the master transcription factor BCL-6 and signature cytokine IL-21. Tfh cells are also capable of expressing IFN-g, however, whether IFN-g-producing Tfh population represents a unique Tfh subset and how they develop are unknown. While T-bet is the master regulator for IFN-g production in Th1 cells, Tfh cells express no or very low levels of T-bet. Here, by using a T-bet-fate-mapping mouse strain, we report that all the IFN-g-producing Tfh cells identified after immunization have previously expressed T-bet. DNase I hypersensitivity analysis indicates that the Ifng gene locus is partially accessible in this ‘ex-T-bet’ population but inaccessible in Tfh cells without a history of T-bet expression. Furthermore, multi-color tissue imaging shows that some “ex-T-bet” Tfh cells reside in germinal centers and express IFN-gin situ. Finally, IFN-g-expressing Tfh cells are absent in T-bet-deficient mice and the Ifng gene is inaccessible in T-bet-deficient Tfh cells. Thus, transient expression of T-bet epigenetically imprints the Ifng locus for cytokine production in Tfh cells. Our results also indicate that Tfh cells are composed of different subsets and they may use genetic programs similar to those of classical non-Tfh T helper cells in order to acquire unique cytokine producing capacity.RNA-Seq analysis of gene expression in splenic CD4+CD44highCD25- T cell subsets. RNA-Seq analysis of gene expression in antigen-specific Tfh cells and non-Tfh cells that have a history of T-bet expression. DNase 1-Seq of T-bet expressed and un-expressed Tfh cells and non-Tfh cells.

overall_design: RNA-Seq analysis of gene expression in splenic CD4+CD44highCD25- T cells from naive mice that are either expressing T-bet or have a history of T-bet expression. RNA-Seq analysis of gene expression in antigen (AS15)-specific Tfh and non-Tfh cell subsets that were separated based on their history of T-bet expression. scDNase-seq analysis of antigen (AS15)-specific Tfh and non-Tfh cell subsets that were separated based on their history of T-bet expression. AS15-specific cells from draining lymph nodes of AS-15/CFA-immunized mice on day 16 were identified by tetramer staining. All the cell subsets were harvested by cell sorting after staining.

first: Difeng

last: Fang

first: Kairong

last: Cui

first: Kairui

last: Mao

first: Rao

last: Li

first: MingZhu

last: Zheng

first: Nicolas

last: Riteau

first: Steven

last: Reiner

first: Alan

last: Sher

first: Keji

last: Zhao

first: Jinfang

last: Zhu


title: Expression data from EBV+ and EBV- plasmablastic lymphomas

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary:
We produced and analyzed the transcriptomic profiles of agressive plasmablastic lymphomas to describe their "immune escape" profile, depending on their viral status (HIV, EBV, ...). We used microarrays to compare the global gene expression profile between EBV+ and EBV- PL subtypes. This analysis unveiled the interest of treating EBV+ PL patients by immune checkpoint blockade strategies.
Plasmablastic lymphoma (PL) is a subtype of diffuse large B-cell lymphoma occurring frequently in HIV-positive individuals and most often associated with Epstein Barr Virus infection. Despite recent therapeutic progress, PL still is an aggressive lymphoma with adverse prognosis. The aim of this study was to investigate whether the emerging strategies of immune checkpoint blockade could be efficient for PL patients. Here, we produced and analyzed the transcriptomic profiles of such tumors to address this question. Unsupervised hierarchical analysis of PL samples showed that PL segregated according to their EBV-status. Moreover, we report that EBV+ PL displayed a significant association with abundant leucocyte infiltrate and selective T-cell activation signatures, together with high level of inhibitory receptors and immune checkpoint markers. We propose that EBV infection induced an anti-viral cytotoxic immunity which progressively exhausted and promoted the tolerogenic tumor microenvironment of PL. Hence, most EBV+ PL patients presenting an early stage of cancer immune-editing process appear eligible for ICB immunotherapies.

overall_design: Frozen biopsies of diagnosed plasmablastic lymphomas were selected for RNA extraction and hybridization on GeneChip® Human Gene 2.0 ST microarrays.

first: Camille

last: Laurent


title: Role of transcription complexes in the formation of the basal methylation pattern in early development

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

summary: Following erasure in the blastocyst, the entire genome undergoes de novo methylation at the time of implantation, with CpG islands being protected from this process.  This bimodal pattern is then preserved throughout development and the lifetime of organism.  Using mouse embryonic stem cells as a model system, we demonstrate that the binding of an RNA polymerase complex on DNA prior to de novo methylation is predictive of it being protected from this modification, and tethering experiments demonstrate that the presence of this complex is, in fact, sufficient to prevent methylation at these sites.  This protection is most likely mediated by the recruitment of enzyme complexes that methylate histone H3K4 over a local region and in this way prevent access to the de novo methylation complex.  The topological pattern of H3K4me3 that is formed while the DNA is as yet is unmethylated provides a strikingly accurate template for modeling the genome-wide basal methylation pattern of the organism.  These results have far-reaching consequences for understanding the relationship between RNA transcription and DNA methylation.

overall_design: ChIP-seq of H3K4me3 in ICM and ChIP-seq of H3K4me3 and RNAP II in ES cells and TKO cells

first: Alon

last: Goren

first: Howard

last: Cedar


title: Epigenomic analysis of micro-dissected human liver reveals principles of zonated morphogenic and metabolic control

status: Public on Sep 13 2018

city: Dresden

first: Alexander

last: Herrmann

address: Fetscherstraße 74

department: Clinic of Internal Medicine I

institute: Technical University Dresden, University Hospital Carl Gustav Carus

summary: To investigate the underlying molecular principles of metabolic and morphogenic zonation of the human liver lobule, we generated an integrated epigenetic map across three zones (pericentral, intermediate and periportal) by methylation and transcriptomic analysis of hepatocytes captured by laser micro-dissection. We observe a deep link between epigenetic zonation of human liver and a zonated expression of metabolic and morphogenic pathways: Key transcriptionally zonated enzymes in xenobiotic and glutamine metabolism show a strong anticorrelated methylation gradient indicating that zonal expression of these genes is partly controlled by epigenetic programs. Zonated DNA-methylation at binding sites of uniformly expressed transcription factors such as HNF4A and RXRα points to an epigenetic layer in regulatory networks and a zonated activity of their nuclear ligands and drugs such as fibrates and bile acids. The same holds for genes of the wnt morphogen pathway whose expression show a zonated methylation at binding sites of TCF4L2. A strong pericentral expression of LGR5 and AXIN2 and a corresponding expression gradient of the liver progenitor marker TBX3, indicates a predominant pericentral source of hepatocyte regeneration under steady-state conditions in humans. Conversely, the periportal expression of NOTCH and EPCAM at the border to the biliary tree as source of regeneration under injury conditions. Overall our data provide a deep understanding of molecular control of the zonal organisation in the human liver.

overall_design: The study comprises 19 human liver biopsy donors divided into the groups normal control (NC = 7012, 7173, 7194, 7279), healthy obese (HO = 6758, 6922, 7213, 7230, 7252), bland steatosis (STEA = 6967, 7137, 7172, 7181, 7251) and early NASH (EARLY = 6610, 7041, 7157, 7188, 7344). Hepatocytes captured by laser microdissection were obtained from three hepatic zones (pericentral, intermediate and periportal) and subjected to reduced representation bisulfite sequencing and RNA-seq resulting in 114 sequencing libraries. Liver samples were obtained intraoperatively in patients in whom an intraoperative liver biopsy was indicated on clinical grounds such as during scheduled liver resection, exclusion of liver malignancy during major oncologic surgery, or assessment of liver histology during bariatric surgery. NASH was defined by the NAFLD activity score (NAS) PMID: 15915461 Samples were frozen immediately in liquid nitrogen ensuring an ex vivo time of less than 40 seconds in all cases. Patients with evidence of viral hepatitis, hemochromatosis, or alcohol consumption greater than 20 g/day for women and 30 g/day for men were excluded. All patients provided written informed consent. The study protocol was approved by the institutional review board (Ethikkommission der Medizinischen Fakultät der Universität Kiel, D425/07, A111/99), before study commencement. A single pathologist, blinded to the molecular analyses, performed standardized histopathologic assessment.

first: Mario

last: Brosch

first: Kathrin

last: Kattler

first: Witigo

last: von Schönfels

first: Karl

last: Nordström

first: Daniel

last: Seehofer

first: Georg

last: Damm

first: Thomas

last: Becker

first: Sebastian

last: Zeissig

first: Sophie

last: Nehring

first: Fabian

last: Reichel

first: Vincent

last: Moser

first: Gustavo

last: Baretton

first: Christoph

last: Röcken

first: Michael

last: Muders

first: Madlen

last: Matz-Soja

first: Andreas

last: Dahl

first: Clemens

last: Schafmayer

first: Jörn

last: Walter

first: Jochen

last: Hampe


title: Genomewide identification of LHY binding targets

city: Coventry

first: Isabelle

last: Carre

address: Gibbet Hill

department: School of Life Sciences

institute: University of Warwick

summary: The plant circadian clock enables plants to adjust their physiology and modulate their developmental responses in anticipation of diurnal and seasonal changes in environmental conditions. Thus, it makes an important contribution to overall fitness. The complex regulatory network underlying the oscillatory mechanism of the clock is now well characterized, but we still know relatively little about how downstream processes are controlled. In order to investigate this question we identified genes that are under direct control of one of the oscillator components, a MYB transcription factor known as LATE ELONGATED HYPOCOTYL (LHY).

overall_design: The Columbia (Col-0) samples were extracted at 2 hours after dawn, corresponding to the time of the day at which LHY is maximally expressed. Chromatin immunoprecipitation experiments were carried out using an antibody to the full-length LHY protein. Input DNA was used as control in ChIP experiments.

first: Sally

last: Adams

first: Siren

last: Veflingstad

first: Nigel

last: Dyer


title: Role of BET proteins in YAP/TAZ-dependent transcription [RNA-seq 2]

status: Public on Sep 15 2018

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: We compared the impact of small molecules on the transcriptional profile of triple negative breast cancer cells.

overall_design: Transcriptional profiling by RNA-seq of MDA-MB-231 cells treated with different epigenetic inhibitors.

first: Mattia

last: Forcato

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Role of BET proteins in YAP/TAZ-dependent transcription

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

overall_design: Refer to individual Series


title: Expression data from lung and spleen natural killer cells of WT and Kras mice

status: Public on Sep 14 2018

city: Hefei

first: Shu

last: Zhu

address: 443 Huangshan Road, Hefei, Anhui, China

institute: University of Science and Technology of China

summary:
Natural killer (NK) cells are gradually induced into a dysfunctional state, and increasingly lose their antitumor effect during lung cancer development. To gain mechanistic insights into these findings, we performed unsupervised bioinformatic analyses by microarrays.
We used microarrays to identify a pivotal molecule involved in NK cell dysfunction.

overall_design: WT and Kras mice (6-8 weeks old) were intranasally infected with Lenti-Cre for induction of lung cancer. At Stage 3 (16 weeks after Lenti-Cre delivery), NK cells were isolated from spleens and lungs of WT and Kras mice.

first: Jingjing

last: Cong

first: Haiming

last: Wei


title: A comparative miRNA/mRNA analysis in distinct murine liver cancer models reveals miR-193a-5p and NUSAP1 as therapeutic targets in HCC

first: Guido

last: Hooiveld

type:
Expression profiling by array
Expression profiling by RT-PCR


title: Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate [Bisulfite-Seq]

city: Barcelona

first: Thomas

last: Graf

address: c/Dr. Aiguader, 88. PRBB Building

department: Gene Regulation, Stem Cells and Cancer

institute: CRG (Center for Genomic Regulation)

summary: Studies of DNA hydroxy-methylation and chromatin state dynamics during highly-efficient somatic cell reprogramming

overall_design: DNA hydroxy-methylation profiling of B cell reprogramming to (induced) pluripotent stem cells using Bis-Seq and oxBS-seq

first: Jose

last: Sardina

first: Samuel

last: Collombet

first: Antonio

last: Gomez


title: A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

institute: University of Washington

summary: When DNA is unwound during replication, it becomes overtwisted and forms positive supercoils in front of the translocating DNA polymerase. Unless removed or dissipated, this superhelical tension can impede replication elongation. Topoisomerases, including gyrase and topoisomerase IV in bacteria, are required to relax positive supercoils ahead of DNA polymerase, but may not be sufficient for replication. Here, we find that GapR, a chromosome structuring protein in Caulobacter crescentus, is required to complete DNA replication. GapR associates in vivo with positively supercoiled chromosomal DNA, and our biochemical and structural studies demonstrate that GapR forms a dimer-of-dimers that fully encircles overtwisted DNA. Further, we show that GapR stimulates gyrase and topo IV to relax positive supercoils, thereby enabling DNA replication. Analogous chromosome structuring proteins that locate to the overtwisted DNA in front of replication forks may be present in other organisms, similarly helping to recruit and stimulate topoisomerases during DNA replication.

overall_design: Sequencing experiments from Caulobacter crescentus CB15N wild-type, GapR-3xFLAG, and GapR-depleted cells. (i) RNA-seq after GapR depletion, (ii) GapR-3xFLAG ChIP-seq, (iii) cell-cycle DNA-seq after GapR depletion.

first: Diane

last: Haakonsen

first: Wenjie

last: Zeng

first: Maria

last: Schumacher

first: Michael

last: Laub


title: Effects of temperature on specificity and efficiency of a bacterial regulatory RNA

status: Public on Sep 12 2018

city: Cambridge

first: Erel

last: Levine

address: 52 Oxford St

department: Physics

institute: Harvard University

summary: Bacterial small RNAs (sRNAs) are post-transcriptional regulators of stress response, virulence and more. The activity of sRNAs must be maintained across diverse environmental conditions, including the range of temperatures that defines the thermal niche of the species.  Here we characterize the effects of temperature on the specificity and efficiency of sRNA regulation in E. coli. By measuring the activity of a large-scale library of sRNA variants at different temperatures, we found that many mutations have a significant but temperature-independent effect. We identified temperature-sensitive sequence elements using measurements that break from this dominant trend. Features associated with the specificity of sRNA regulation are more sensitive to mutations at high temperatures, and we confirm that specificity is more stringent at these temperatures. In contrast, many mutations in the region responsible for interactions with other targets have a stronger negative impact at low temperatures. Together, our results suggest that sRNAs may be structured such that variation in temperature may enhance their evolutionary plasticity.

overall_design: Sort-seq assays across a range of bacterial growth temperatures from 21 C to 37 C

first: N

last: Peterman


title: Fezakinumab (anti-IL-22) treatment in adults with moderate-to-severe atopic dermatitis

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: We conducted a randomized, double-blind, placebo-controlled trial in adults with moderate-to-severe AD unresponsive to conventional topical or systemic treatment. Fezakinumab (ILV-094; anti IL-22 monoclonal antibody) monotherapy was administered for 12 weeks (primary endpoint), and clinical responses were followed until week 20. AD transcriptome significantly improved at week 12 in fezakinumab vs. placebo (p<1E-18).

overall_design: We conducted a phase IIa, randomized, double-blind, placebo-controlled, multi-center clinical trial to evaluate efficacy and safety of fezakinumab in patients with moderate-to-severe AD (clinicaltrials.gov #NCT01941537). Patients were randomly assigned to receive either intravenous fezakinumab or placebo (2:1 randomization to drug and placebo, respectively), with a loading dose of 600mg at baseline (day 0), followed by 300mg at weeks 2, 4, 6, 8, and 10. Primary outcome measures were assessed at week 12. Patients were followed up until week 20. Patients were enrolled at two sites in New York City, NY, USA. Biopsy specimens (lesional and non-lesional skin) were obtained before the first dose (day 0), and at weeks 4 and 12.

first: Emma

last: Guttman-Yassky

first: Patrick

middle: M

last: Brunner

first: Avidan

last: Neumann

first: Saakshi

last: Khattri

first: Kunal

last: Malik

first: Giselle

last: Singer

first: Danielle

last: Baum

first: Patricia

last: Gilleaudeau

first: Mary

last: Sullivan-Whalen

first: Sharon

last: Rose

first: Shelbi-Jim

last: On

first: Xuan

last: Li

first: Judilyn

last: Fuentes-Duculan

first: Yeriel

last: Estrada

first: Sandra

last: Garcet

first: Claudia

last: Traidl-Hoffmann

first: Mayte

last: Suárez-Fariñas

first: James

last: Krueger

first: Mark

last: Lebwohl


title: Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands (HTS)

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

institute: Aix-Marseille Université

summary: The plant Topoisomerase VI complex has been implicated in a wide array of biological processes but little is known about its precise molecular role. In this study, we provide evidence that Topo VI acts as a chromatin barrier between chromatin territories by interacting with methionine adenosyltransferases (MAT), which produce the universal donor of methyl groups S-adenosyl-methionine (SAM). We first show that pericentromeric transposable elements (TEs) are awakened whereas  euchromatic island genes (EIGs) within heterochromatin are downregulated in mutants of the Topo VI complex. Consistent with this, the level of repressive H3K9me2 marks increases at EIGs loci while it decreases at TEs in a hypomorphic Topo VI mutant. We demonstrate that the Topo VI complex can interact with the SAM synthase MAT3 and drives it to TEs. A deficiency of Topo VI induces relocation of MAT3 from TEs to EIGs islands, leading to the levelling of the H3K9me2 mark and hence heterochromatin spreading.

overall_design: The transcriptome analysis of the caa39 mutant comprises three biological replicates for mutant and WT genotypes. The ChiPseq analysis of H3K9me2 includes a comparison of a pool of two biological replicates for caa39 and wt. This was done in duplicate for H3K27me3. In addition, an input chromatin control comprising a pool of two biological replicates was used for both genotypes. In total, we analyzed 6 RNAseq samples, and 6 ChIP samples and 2 input chromatin samples.

first: Louis-Valentin

last: Méteignier

first: Cécile

last: Lecampion

last: Vriet

first: Michel

last: Térèse

first: Martin

last: Rougée

first: Christian

last: Breuer

first: Ludivine

last: Soubigou-Taconnat

first: Keiko

last: Sugimoto

first: Frédy

last: Barneche


title: Methylation of structured RNA by the m6A writer METTL16 is essential for mouse embryonic development

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved and widely used means of gene expression control. METTL16 is an m6A writer but how it recognizes its RNA targets and its physiological roles remain unknown. Here we describe the crystal structure of human METTL16 to reveal a classical methyltransferase domain but with an extra N-terminal module that is essential for catalysis. Together, they form a deep-cut groove lined by highly conserved positively charged residues that are essential for RNA binding and methylation activity. When given a random pool of RNAs, METTL16 selects structured RNAs for m6A methylation. We demonstrate that mouse Mettl16 is essential for early embryonic development, and acts via regulation of the SAM synthetase Mat2a mRNA. Our results highlight the pivotal role of an m6A RNA methyltransferase in facilitating early developmental decisions via regulation of SAM availability.

sample_organism:
Mus musculus
synthetic RNA

platform_organism:
Mus musculus
synthetic RNA

overall_design: RNA sequencing was used to identify transcript abundance differences between Mettl16 mutant and control in E2.5 and E3.5 mouse embryos.   In vitro RNA methylation assay with METTL16 followed by m6A immunoprecipitation and sequencing was used to identify METTL16 preferred targets.

first: Mateusz

last: Mendel

first: Kuan-Ming

last: Chen

first: David

last: Homolka

first: Pascal

last: Gos

first: Radha

middle: R

last: Pandey

first: Andrew

last: McCarthy


title: Leydig cell transcripts from adult mouse stage synchronized testis array

city: Pullman

first: Estela

middle: Jasmin

last: Jauregui

address: 1770 NE Stadium Way

department: School of  Molecular Biosciences

institute: Washington State University

summary:
Leydig cell gene expression across the different stages of the seminiferous epithelium of mice with Synchronized spermatogenesis by WIN18,446/RA treatment combined with the RiboTag methodology
Microarray analysis was used to identified Leydig cell-specific transcripts across the different stages of the seminiferous epithelium.

overall_design: Leydig cell mRNA and total testis mRNA were collected from ten different groups of synchronized adult mouse testis samples (N=2 per group) and were analyzed using GeneChip ST 1.0 Arrays

first: Michael

last: Griswold


title: SUMOylation regulates nucleo-cytoplasmic shuttling  of LKB1 in liver cancer

status: Public on Sep 11 2018

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Even though liver kinase B1 (LKB1) is commonly described as a tumor suppressor, we and others have shown that LKB1 is augmented in liver cancer. In agreement, LKB1 modulation in human hepatoma cells and mouse livers induces changes in cell proliferation and the appearance of liver neoplastic lesions in association with disruptions of energetic metabolism. After LKB1 overexpression, a surprising uncoupling between LKB1 and its downstream kinase AMP-activated protein kinase is observed as well as activation of the oncogenic Ras pathway, driven by the direct or indirect binding of LKB1 to the promoter region of the Ras activator, RASGRP3. Under these circumstances, LKB1 SUMOylation at Lys178 by SUMO-2, the main SUMO paralogue present in liver, promotes LKB1 nuclear localization, fueling hepatoma cell proliferation. Overall, SUMO-2 mediated modification of LKB1 at Lys178 is suggested as a bona fide oncogenic driver in liver cancer by regulating the nucleo-cytoplasmic shuttling of LKB1.

overall_design: Genome-wide changes in gene expression of normal mice (N=4)  and mice where LKB1 was overexpresssed after tail vein injection of LKB1 WT plasmid once a week for 8 weeks (N=6)

first: T

last: Cardoso

first: J

first: M

last: Martínez-Chantar


title: Metabolic and Molecular Framework for the Enhancement of Endurance by   Intermittent Fasting

status: Public on Sep 10 2018

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Evolutionary considerations suggest that the body has been optimized to perform at a high level in the fasted state when fatty acids and their ketone metabolites are a major fuel source for muscle cells. Because fasting is the most potent physiological stimulus for ketosis, we designed a study to determine the impact of intermittent fasting during endurance training on performance, and to elucidate the underlying cellular and molecular mechanisms.   Male mice were randomly assigned to either ad libitum feeding or alternate-day fasting (AF) groups, and half of the mice in each diet group were trained daily on a treadmill for 1 month (45 minutes of running with increasing speed or incline each week).  A run to exhaustion endurance test performed at the end of the training period revealed superior performance in the mice maintained on AF during training compared to mice fed ad libitum during training.  VO2max was increased similarly by treadmill training in mice on AF or ad libitum diets, whereas respiratory exchange ratio (RER) was reduced in AF mice on fasting days and during running. Analyses of gene expression in liver and soleus tissues, and metabolomics analysis of blood suggest that the metabolic switch invoked by AF and potentiated by exercise strongly modulate molecular pathways involved in mitochondrial biogenesis, metabolism and cellular plasticity.  Our findings demonstrate intermittent fasting engages metabolic and cellular signaling pathways that result in increased metabolic efficiency and endurance capacity.

overall_design: Six month-old male C57BL/6J mice were randomly assigned to one of four groups: a sedentary control group fed ad libitum (CTRL); a sedentary group on alternate-day fasting (AF); a group with daily treadmill running exercise fed ad libitum (EX); and a group that ran every day on a treadmill while on AF (EXAF)  during a 4-week study period.

first: Krisztina

last: Marosi

first: Keelin

last: Moehl

first: Ignacio

last: Navas-Enamorado

first: Sarah

last: Mitchell

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: Miguel

last: Aon

first: Sonia

last: Cortassa

first: Kevin

last: Becker

first: Mark

middle: P

last: Mattson


title: Promoter bivalency favors an open architecture of the stem cell genome

first: Enrique

last: Blanco

address: Dr. Aiguader 88

institute: Center for Genomic Regulation (CRG)

summary: In embryonic stem cells (ESCs), bivalency characterizes the chromatin state of developmental gene promoters, simultaneously modified by Mll2 and Polycomb complexes. Despite its essential role in embryogenesis, the function of bivalency is currently unclear. Here we show that Mll2 plays a central role in stem cell genome organization. We generate a catalog of bona-fide bivalent genes in mESCs and demonstrate that loss of Mll2 leads to increased Polycomb occupancy. Consequently, promoters lose accessibility and long-range interactions become redistributed, affecting ESC differentiation. We propose that bivalency balances accessibility and long-range connectivity of promoters to modulate developmental gene expression.

overall_design:
List of ChIPseq samples (Mll2 wt and mutant), ATACseq samples (Mll2 wt and mutant) and RNAseq samples (differentiation in embryoid bodies, day0, day3, day6 and day9).
List of new ChIPseq samples and PROseq samples (Mll2 wt and mutant).
List of HiC samples. Conditional MLL2 KO samples: OH means WT and TAM means KO. Catalytic inactive MLL2 samples: WT means WT and CD means Catalytic Dead.

first: Gloria

last: Mas

first: Marc

last: Marti-Renom

first: Luciano

last: DiCroce


title: Microarray analysis of Human Epidermal Keratinocytes, neonatal (HEKn)  exposed to solar-simulated visible and ultraviolet radiation with and without sunscreen protection.

status: Public on Sep 07 2018

city: Ottawa

first: Sami

middle: Shaker

last: Qutob

state: Ontario

address: 775 Brookfiled Rd.

department: Consumer and Clinical Radiation Protection Bureau

institute: Health Canada

summary: Kertinocyte cultures grown in 60 mm petri dishes were placed 186 mm from the solar simulator source (Solar-simulated ultraviolet radiation 1600W Xenon short arc lamp with an Oriel  Air Mass 1 Direct Filter, (AM1:D:B; model 81074) and KG2 Short Pass Filter. irradiance 9.84 mW/cm² for UVA (98.3%), 0.174 mW/cm² for UVB (1.7%) and 10 mW/cm² (0.017 mW/cm² erythemally-weighted) for the total UVR irradiance) and received a dose of either 0, 10, 20 and 150 kJ/m2 of unweighted ultraviolet radiation and 0, 10 and 150 kJ/m2 of unweighted ultraviolet radiation with SPF 15 sunscreen filtration (Homosalate 3%, Octisalate 4%, Avobenzone 2%, Titanium dioxide 0.66%) (2 mg/cm2 sandwiched between two 5x5 inch quartz plates) and were temperature controlled at 37oC using a customized water-bath. Six and Twenty-four hours post-exposure cells were harvested and RNA was extracted and subjected to microarray analysis.

overall_design: Expression profiling by array analysis-Sample set, 0, 10, 20 and 150 kJ/m2 of UVR and 0, 10 and 150 kJ/m2 UVR with sunscreen filtration, analysed 6 h and 24 h post exposure, for HEKn cells (n=6).


title: IFIT1 exerts opposing regulatory effects on the inflammatory and interferon gene programs in LPS-activated human macrophages

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Activation of the TLR4 signaling pathway by LPS leads to induction of both inflammatory and interferon-stimulated genes, however, the mechanisms through which these coordinately activated transcriptional programs are balanced to promote an optimal innate immune response remain poorly understood. In a genome-wide siRNA screen of the LPS-induced TNF- response in macrophages, we identified the interferon-stimulated protein IFIT1 as a negative regulator of the inflammatory gene program. Transcriptional profiling further identified an unexpected positive regulatory role for IFIT1 in type I interferon expression, implicating IFIT1 as a reciprocal modulator of LPS-induced gene classes. We demonstrate that these effects of IFIT1 are mediated through modulation of a Sin3A-HDAC2 transcriptional regulatory complex at LPS-induced gene loci. Beyond the well-studied role of cytosolic IFIT1 in restricting viral replication, our data demonstrate an unappreciated function for nuclear IFIT1 in differential transcriptional regulation of separate branches of the LPS-induced gene program.

overall_design: Wild type THP1 and IFIT1 shRNA cells were transfected with NT siRNA and IFIT1 siRNA respectively in 24-well plates, and differentiated with 10 ng/ml PMA for 72 hours. Cells were stimulated with 100 ng/ml LPS for 0h, 1h, 2h, 4h, 6h and 24h. All but two of the conditions were tested in two biological replicates

first: Sinu

last: John

first: Jing

last: Sun

first: Rebecca

last: Carlson

first: Binh

last: Cao

first: Jian

last: Song

first: Iain

last: Fraser


title: lncRNA and mRNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients

city: Guangzhou

first: Yaoyao

last: Zou

state: Guangdong

address: No. 58 Zhongshan Road 2

institute: The First Affiliated Hospital, Sun Yat-sen University

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

summary: Fibroblast-like synoviocytes (FLSs) are critical for synovial aggressiveness and joint destruction in rheumatoid arthritis (RA).The role and expression patterns of long noncoding RNAs (lncRNAs) in RA are largely unknown. We performed lncRNA and mRNA microarrays to identify differentially expressed lncRNAs and mRNAs in fibroblast-like synoviocytes from rheumatoid arthritis patients compared with fibroblast-like synoviocytes from trauma patients.

overall_design: FLSs were isolated from synovial tissues and cutured until passage 4. Total RNA was extracted from FLSs with Trizol and subjected to microarray assay.

first: Xu

last: Hanshi

first: Xiao

last: Youjun

first: Zou

last: Yaoyao


title: Proteogenomic landscape of medulloblastoma subgroups [methylation]

status: Public on Sep 09 2018

city: Orsay

first: Olivier

last: Ayrault

address: Institut Curie / CNRS UMR 3347 / INSERM U1021 Bldg. 110 – Centre Universitaire

institute: Institut Curie

type: Methylation profiling by genome tiling array

summary: Extensive high-throughput sequencing led to the characterization of four main medulloblastoma subgroups. However, to date these analyses have not attained a global comprehension of their dynamic network complexity. Wishing to get a comprehensive view of all medulloblastoma subgroups, we employed a proteomic analysis to integrate accurate protein activity. In this study we present the first analysis regrouping genomic and methylation status, whole-transcriptome sequencing and quantitative proteomics. First, our proteomic analysis clarified medulloblastoma subgroup identity. Second, analysis of proteome and phosphoproteome highlighted disregulated signalling pathways that have not been predicted by transcriptomic analysis. Altogether, combined multi-scale analyses of medulloblastoma have allowed us to identify and prioritize novel molecular drivers involved in human medulloblastoma.

overall_design: 44 human medulloblastoma samples were profiled on IlluminaHumanMethylation450k array

first: Antoine

last: Forget

first: Sébastian

last: Brabetz

first: Marcel

last: Kool

first: Stefan

last: Pfister

first: Stéphanie

last: Puget

first: Michael

last: Taylor


title: Proteogenomic landscape of medulloblastoma subgroups


title: Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: Suppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to polarize Meis2 expression along the PD axis. With mathematical modeling and simulation, we propose that PcG factors are required to adjust the threshold for RA-related signaling to regulate Meis2 expression. Finally, we show that a variant Polycomb repressive complex 1 (PRC1), incorporating PCGF3 and PCGF5, represses Meis2 expression in the distal limb bud. Taken together, we reveal a previously unknown link between PcG proteins and downregulation of RA-related signals to mediate the phase transition of Meis2 transcriptional status during forelimb patterning.

overall_design: ChIP-seq analysis of RAR and H3K27me3 in the proximal and distal forelimb buds at mouse E11.5

first: N

first: H

last: Koseki


title: Gene expression profiles of SKOV3 tumor cells that could form heterotypic spheroids with high grade serous ovarian cancer derived cancer-associated fibroblasts, and those remaining individual SKOV3 cells in non-adherent (NAD) coculture condition.

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

summary:
Interaction between stromal cells and the tumor greatly influences tumor initiation and progression. Cancer-associated fibroblasts (CAFs) are the major component of tumor stroma and play a key role in ovarian cancer (OC) cells adhesion and metastasis. CAFs were found abundantly in primary tumor and metastases, as well as in malignant ascites of high grade serous OC patients, underscoring that CAFs modulate OC cells phenotype and facilitate disease exacerbation along OC progression. Studies of CAFs exertion on OC mainly focused on the influence of CAFs conditioned medium (CM) influence of tumor cells phenotype, while ignoring the fact that CAFs are supposed to be in intimate contact with neoplastic cells in tumor mass, and that CAFs also form compact heterotypic spheroids with ascitic tumor cells in malignant ascites. We hypothesized that uncovering the underlying molecules that mediate tumor cells binding with CAFs could aid in developing measures destroying the pro-carcinogenic heterotypic spheroids in malignant ascites. In this study, gene expression profiling was completed for individual SKOV3, and magnetic sorted SKOV3 cells that form heterotypic spheroids with 4 cases of high grade serous OC derived CAFs. By comparing the expression data of SKOV3 cells in individual group with that in spheroid group, we identified a set of differential expressed genes. This study revealed the heterogeneity of ascitic tumor cells and raised potent therapeutical targets in destroying of the heterotypic spheroids in malignant ascites of OC.
We used microarrays to profile the mRNA expression of SKOV3 tumor cells that could or not form heterotypic spheroids with CAFs, in order to identify molecules that potentially mediate the combination between tumor cells and CAFs.

overall_design: Transcriptome profiling analyses were performed on 7 samples of SKOV3 cells, including 3 samples in the individual group and 4 samples of SKOV3 cells isolated from developed spheroids with primary CAFs in suspension coculture.

first: Qinglei

last: Gao


title: HTS-Seq analysis of wild type (WT; Col-0), npr1-1, and hac1/5

city: Seoul

first: Hongshi

last: Jin

address: Gwanak_599 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Genome-wide maps of histone H3 acetylation (H3Ac) in wild type (WT; Col-0), npr1-1, and hac1/5

summary: Genome-wide H3Ac maps of WT (Col-0), npr1-1, and hac1/5 leaves were generated by chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP seq) to understand the role of HATs in the reprogramming of the epigenome during immune response.

overall_design: Examination of H3Ac levels in WT (Col-0), npr1-1, and hac1/5 leaves

first: Yoo-Sun

last: Noh

first: Bosl

first: Sun-Mee

last: Choi

first: Min-Jeong

last: Kang

first: Se-Hun

last: Yun

first: Dong-Jin

last: Kwon


title: RNA-seq study of transcriptiona factor FleQ in Pseudomonas putida KT2442

status: Public on Sep 06 2018

city: Wuxi

first: Yuzhou

last: Wang

state: Jiangsu

address: 1800 Lihu Avenue

department: School of Biotechnology

institute: Jiangnan University

summary: We constructed fleQ mutant strain and analyzed its regulation role through gene expression profile compared to the wild-type KT2442.

overall_design: The Pseudomonas putida KT2442 in-frame deletion fleQ mutant and wild-type KT2442 were analyzed by RNA-seq. All samples were cultivated in LB medium until reaching an OD600 of 1.3 or 3.5.  Cultures were pooled for RNA extraction, library preparation and sequencing. qRT–PCR validation was performed using SYBR Green assays.

first: Xiaoyuan


title: Transcriptomic RNAseq drug screen in cerebrocortical cultures; towards novel neurogenetic disease therapies.

first: Hualin

last: Xi

state: MA

address: 1 portland st

institute: Pfizer

summary: Rare monogenic diseases affect millions worldwide; although over 4,500 rare disease genotypes are known, disease-modifying drugs are available for only 5% of them. The sheer number of these conditions combined with their rarity precludes traditional costly drug discovery programs. An economically viable alternative is to repurpose established drugs for rare diseases. Many genetic diseases result from increased or decreased protein activity and identification of clinically approved drugs which moderate this pathogenic dosage holds therapeutic potential. To identify such agents for neurogenetic diseases, we have generated genome-wide transcriptome profiles of mouse primary cerebrocortical cultures grown in the presence of 218 blood brain barrier penetrant clinic-tested drugs. RNAseq and differential expression analyses were used to generate transcriptomic profiles; therapeutically relevant drug-gene interactions related to rare neurogenetic diseases identified in this fashion were further analyzed by qRT-PCR, western blot and immunofluorescence. We have created a transcriptome-wide searchable database for easy access to the gene expression data resulting from the cerebrocortical drug screen (Neuron Screen) and have mined this data to identify a novel link between thyroid hormone and expression of the peripheral neuropathy associated gene Pmp22. Our results demonstrate the utility of cerebrocortical cultures for transcriptomic drug screening, and the database we have created will foster further discovery of novel links between over 200 clinic-tested blood brain barrier penetrant drugs and genes related to diverse neurologic conditions.

overall_design: mRNA differential expression profiles of mouse primary cortical cultures treated individually with 218 clinic-tested drugs and 9 vehicle treated samples, 1 replicate performed per drug.

first: Jeremiah

last: Hadwen

first: Sarah

last: Schock

first: Alan

middle: J

last: Mears

first: Robert

first: Philippe

last: Charron

first: Liying

last: Zhang

first: Alex

middle: E

last: MacKenzie


title: Gene expression profiles from corpus callosum brain tissue obtained from cuprizone-treated mice

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
Mouse cuprizone (CPZ ) model of experimental de- and remyelination was applied to mimic demyelination pathology of multiple sclerosis. The aim of the study was to profile whole genome expression to identify differentially expressed genes during the demyelinisation and after discontinuation of cuprizon treatment, during rapid remyelinisation in affected areas of mouse corpus callosum. Control mice were kept on a normal diet.
The following groups representing de- and remyelinisation pathology in corpus callosum of CPZ-treated mice were compared: Partial demyelination: 2weeks CPZ (dem_2w); Complete demyelination: 4weeks CPZ (dem_4w); Remyelination: 4weeks CPZ + UNTREATED (rem); and UNTREATED control (C). The experiments were performed using 3-4 animals per groups.

overall_design: Nellie,A,Martin

first: Arkadiusz

last: Nawrocki

last: Molnar

first: Maria

middle: L

last: Elkjaer

first: Eva

middle: K

last: Thygesen

first: Miklos

last: Palkovits

first: Peter

last: Acs

first: Tobias

last: Sejbaek

first: Helle

middle: H

last: Nielsen

first: Zoltan

last: Hegedus

first: Finn

last: Sellebjerg

first: Eudes

last: Barbosa

first: Nicolas

last: Alcaraz

first: Ferenc

last: Gallyas

first: Asa

middle: F

last: Svenningsen

first: Jan

last: Baumbach

first: Hans

last: Lassmann

first: Martin

last: Larsen

first: Zsolt

last: Illes


title: Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm [Junction Arrays]

status: Public on Sep 05 2018

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

country: USA

institute: 10x Genomics

summary: In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. Common results and discrepancies between both technologies were validated or resolved by more than 200 PCRs.

overall_design:
Three different triple negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, SUM 149) treated with CX4945 and DMSO with 5 replicates. A total of 30 samples
This submission represents 'junction arrays' component of study.

first: María

last: Ortiz-Estévez

first: Ander

last: Muniategui

first: Soraya

last: Carrancio

first: Fernando

last: de Miguel

last: Carazo

first: Luis

last: Montuenga

first: Matthew

last: Trotter

first: Remco

last: Loos

first: Rubén

last: Pío

first: Angel

last: Rubio


title: Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm


title: 4week organoid VS 54week organoid

status: Public on Sep 08 2018

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Transcriptional profiling of mouse intestinal organoids comparing  4 week mouse with 54 week mouse

overall_design: Two-condition experiment, 4 week intestinal organoids vs. 54 week intestinal organoids of mouse . Biological replicates: 1 4 week, 1 54 week

first: Ryoei

last: Uchida


title: Minipuberty and Thymic Sexual Dimorphism in the Infant Human Thymus [puberty miRNA]

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: AIRE expression in thymus is downregulated by estrogen after puberty, what probably renders women more susceptible to autoimmune disorders. Here we investigated the effects of minipuberty on male and female infant human thymic tissue in order to verify if this initial transient increase in sex hormones - along the first six months of life - could affect thymic transcriptional network regulation and AIRE expression. Gene co-expression network analysis for differentially expressed genes and miRNA-target analysis revealed sex differences in thymic tissue during minipuberty, but such sex differences were not detected in thymic tissues from donors aged 7-18 moths of age, the non-puberty group. AIRE expression was essentially the same in both sexes in minipuberty and in non-puberty groups, as assessed by genomic and immunohistochemical assays. However, AIRE-interactors networks showed several differences in all groups regarding gene-gene expression correlation. Therefore, minipuberty and genomic mechanisms interact in shaping thymic sexual dimorphism along the first six moths of life.

overall_design: Thymus miRNA transcriptomic profiles of patients undergoing minipuberty (aged up to 6 months) comparing male versus female infants in order to identify differentially expressed transcripts.

first: Silvia

middle: Y

last: Bando

first: Fernanda

last: Bertonha

first: Leandro

last: Ferreira

first: Christiana

last: Vinhas

first: Lucila

last: Oliveira

first: Maria

middle: C

last: Zerbini

first: Glaucio

last: Furlanetto

first: Paulo

last: Chacur

first: Antonio

last: Coutinho

first: Madga

last: Carneiro-Sampaio


title: Chromatin state changes in HOXA9/MEIS1 leukemia cells [ChIP-Seq]

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

summary: Aberrant expression of homeobox transcription factor HOXA9 is a central component of the leukemogenic program driven by diverse oncogenes. Here we show that HOXA9 overexpression in myeloid progenitor cells and pro-B cells leads to significant rearrangement of the epigenetic landscape with prominent emergence of cancer-specific de novo enhancers. HOXA9 acts as a pioneer factor at the de novo enhancers and is required for recruitment of transcription factor CEBP/ and the histone H3K4 methyltransferase MLL3/MLL4 complex. The HOXA9 function at de novo enhancers is distinct from its physiological role at enhancers during normal hematopoietic development. The MLL3/MLL4 complex physically interacts with HOXA9 and is required both for the active enhancer signatures at de novo enhancers and HOXA9/MEIS1-mediated leukemogenesis.  The findings suggest that therapeutic targeting of HOXA9-dependent histone methylation could be an effective therapeutic strategy in acute leukemia associated with HOXA9 over expression.

overall_design: Untransformed myeloid progenitors (MP), HOXA9/MEIS1-transformed myeloblasts (HMM), HMM cells with HOXA9 inactivation (HOXA9in) were subjected to ChIP-seq for analysis of their chromatin states and epigenetic regulator binding. Differentially regulated genomic regions were tested for chromatin state changes and HOXA9/MEIS1-transformed proB lymphoblasts (HMB cells)

first: Yuqing

last: Sun

first: Jay

last: Hess


title: Chromatin state changes in HOXA9/MEIS1 leukemia cells [4C-Seq]

summary: Aberrant expression of homeobox transcription factor HOXA9 is a central component of the leukemogenic program driven by diverse oncogenes. Here we show that HOXA9 overexpression in myeloid progenitor cells and pro-B cells leads to significant rearrangement of the epigenetic landscape with prominent emergence of cancer specific de novo enhancers. HOXA9 acts as a pioneer factor at the de novo enhancers and is required for recruitment of transcription factor CEBP/a and the histone H3K4 methyltransferase MLL3/MLL4 complex. HOXA9 function at the de novo enhancer is distinct from its physiological role at distal enhancers during normal hematopoietic development. Genetic deletion of MLL3/4 specifically affects the active enhancer signatures at de novo enhancers and inhibits HOXA9/MEIS1-mediated leukemogenesis. Our study reveals a previously uncharacterized role of HOXA9 and the MLL3/4 complex in leukemogenesis and provide mechanistic insights in epigenetic deregulation during malignant transformation.

overall_design: Untransformed myeloid progenitors (MP), HOXA9/MEIS1-transformed myeloblasts (HMM cells) and HMM cells with HOXA9 inactivation were subjected to ChIP-seq, RNA-seq and 4C-seq for assessment of their chromatin states and transcriptomes. Untransformed pro-B cells and HOXA9/MEIS1-transformed proB lymphoblasts (HMB cells) were subjected to ChIP-seq for analysis of their chromatin states.


title: Genome-wide profiling of siRNA targeting EWS-FLI1 in TC32 Ewing sarcoma cell line

first: Suntae

last: Kim

address: Bldg 37, room 6128

department: Genetics Branch

institute: CCR, NCI, NIH

summary: Identification of genes and pathways that were influenced by knock-down EWS-FLI1 in TC32 Ewing sarcoma cell line.

overall_design: TC32 Ewing sarcoma cell line were transfected with control siNeg or siRNA corresponding EWSR1 or FLI1 gene. Two samples in each group were analyzed.

first: Sen

last: Nirmalya

first: Natasha

last: Caplen


title: Influenza virus infection causes global RNAPII termination defects

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: Viral infection perturbs host cells and can be used to uncover host regulatory mechanisms controlling both cell response and homeostasis. Here, using cell biological, biochemical and genetic tools, we reveal that influenza virus infection induces global transcriptional defects at the 3’-end of active host genes and RNA polymerase II (RNAPII) run-through into extragenic regions. This effect induces the biogenesis of aberrant RNAs (3’-extensions and host gene fusions) which ultimately causes global transcriptional downregulation of physiological transcripts, an effect that impacts antiviral response and virulence. We show that this phenomenon occurs with multiple strains of influenza virus and it is dependent on influenza NS1 protein expression. Mechanistically, pervasive RNAPII run-through can be modulated by SUMOylation of an intrinsically disordered region (IDR) of the NS1 expressed by the 1918 pandemic influenza virus. SUMOylation increases NS1 partitioning in nuclear granules and interference with the host transcriptional apparatus which result in augmentation of termination defects and a concomitant increase in global host gene shut off. Our data identify a general strategy used by influenza virus to suppress host gene expression and indicate that polymorphisms in IDRs of viral proteins, along with human genetic variation in enzymes that metabolize post-translational modifications, can determine the outcome of an infection. We thus propose that analysis of strain-specific determinant of pathogenesis can shed light on the molecular basis of virulence.

overall_design:
We performed directional RNA-Seq profiling (Illumina TruSeq protocol) of uninfected A549 cells, and at 6 and 12 hours after infection with wild-type H1N1 Influenza A/Puerto Rico/8/1934 (PR8-NS1) or PR8-NS1-SUMO Influenza A virus. In the NS1-SUMO virus we fused a SUMO domain to the C-terminus of the NS1 protein.

We also performed RNA-Seq of A549 cells transfected with empty vector, or a vector expressing GFP or SUMO. Additionally, cells transfected with empty vector or a vector expressing SUMO were infected with PR8∆NS1 virus and RNA-Seq was performed at 4 hours post-infection.

Finally, we performed RNA-Seq of uninfected A549 cells depleted for Ubiquitin Conjugating Enzyme E2 (siUBE2I) and control (siCtrl).

All experiments were performed in duplicate.

first: Ivan

last: Marazzi

last: Zhao

first: Vittorio

last: Sebastiano

last: Moshkina

first: Nacho

last: Mena

first: Judd

last: Hultquist

first: David

last: Jimenez-Morales

first: Alex

last: Rialdi

first: Randy

last: Albrecht

first: Romain

last: Fenouil

middle: T

last: Sánchez-Aparicio

first: Juan

last: Ayllon

first: Sweta

last: Ravisankar

first: Bahareh

last: Haddad

first: Sook-Yiun

last: Ho

first: Diana

last: Low

first: Jian

last: Jin

first: Yurchenko

last: Vyacheslav

first: Rab

last: Prinjha

first: Alexander

last: Tarakhovsky

first: Ernesto

last: Guccione

first: Terrence

last: Tumpey

first: Nevan

last: Krogan

last: van Bakel

first: Benjamin

last: Greenbaum

first: Adolfo

last: García-Sastre


title: Minipuberty and Sexual Dimorphism in the Infant Human Thymus

status: Public on Sep 04 2018

first: Carlos

last: Moreira-Filho

summary:
AIRE expression in thymus is downregulated by estrogen after puberty, what probably renders women more susceptible to autoimmune disorders. Here we investigated the effects of minipuberty on male and female infant human thymic tissue in order to verify if this initial transient increase in sex hormones - along the first six months of life - could affect thymic transcriptional network regulation and AIRE expression. Gene co-expression network analysis for differentially expressed genes and miRNA-target analysis revealed sex differences in thymic tissue during minipuberty, but such sex differences were not detected in thymic tissues from donors aged 7-18 moths of age, the non-puberty group. AIRE expression was essentially the same in both sexes in minipuberty and in non-puberty groups, as assessed by genomic and immunohistochemical assays. However, AIRE-interactors networks showed several differences in all groups regarding gene-gene expression correlation. Therefore, minipuberty and genomic mechanisms interact in shaping thymic sexual dimorphism along the first six moths of life.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Thymus transcriptomic profiles of patients undergoing minipuberty comparing male versus female infants in order to identify differentially expressed transcripts.

Refer to individual Series


title: Pharmacologic inhibition of STAT5 in AML

status: Public on Sep 03 2018

city: Vienna

first: Tobias

last: Suske

state: Vienna

address: Veterinärplatz 1

department: Functional Cancer Genomics

country: Austria

institute: University of Veterinary Medicine

summary: The transcription factors STAT5A and STAT5B are essential downstream mediators of many tyrosine kinases, particularly in hematopoietic cancers. As such, STAT5 is activated by FLT3-ITD, which is a constitutively active tyrosine kinase driving the pathogenesis of acute myeloid leukemia (AML). Since STAT5 is a critical mediator of diverse malignant properties of AML cells, direct targeting of STAT5 function is of significant clinical value. Here, we describe the novel small molecular weight inhibitor AC-4-130 that directly binds to the phosphotyrosine (pY)-binding pocket of the STAT5 SH2 domain, thereby disrupting STAT5 activation, dimerization, nuclear translocation, and STAT5-dependent induction of gene transcription. AC-4-130 substantially impaired the proliferation and clonogenic growth of human AML cell lines and primary FLT3-ITD+ AML patient cells in vitro and in vivo. Importantly, AC-4-130 synergistically increased the cytotoxicity of the JAK1/2 inhibitor Ruxolitinib and the p300/pCAF inhibitor Garcinol. In summary, we report the development and preclinical evaluation of a novel, potent STAT5 SH2 domain inhibitor that can efficiently block pathological levels of STAT5 activity in AML. The synergistic effects of AC-4-130 tyrosine kinase inhibitors as well as emerging treatment strategies provide new opportunities for combinatorial treatment of leukemia and potentially other cancers.

overall_design: MV4-11 and MOLM-13 cells were treated in triplicates with 5 µM AC-4-130 or DMSO (Ctrl)

first: Richard

last: Moriggl

first: Bettina

last: Wingelhofer

first: Anna

last: Orlova

first: Frank

last: Ruge


title: Single-cell RNA-seq of human airway epithelial cells

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

overall_design: We have made scRNA-Seq from human airway epithelial cells after 14 days of Air-Liquid-Interface (ALI) differentiation and sequenced each cell to ~120,000 reads/cell.

first: S

last: Ruiz-Garcia

first: M

last: Deprez

first: A

last: Paquet

first: K

first: N

last: Pons

first: L

last: Zaragosi

first: P

last: Barbry


title: PAX5 transduction of Pax5-/- pro-B cells

status: Public on Sep 01 2018

city: Toulouse

first: Eric

last: DELABESSE

address: 1 avenue Irène Joliot-Curie

institute: Institut Universitaire de Cancérologie de Toulouse, site Oncopôle CHU de Toulouse

summary: After 5 days in culture with 2ng/ml of IL7, Pax5-/- transduced pro-B cells with PAX5A or PAX5B cDNA were sorted according to their EGFP positivity and total RNA was extracted.

overall_design: 2 controls (MIE), 3 PAX5A, 3 PAX5B

first: Nais

last: PRADE


title: BDE-47 Transcriptomic Alterations in Human Primary Villous Cytrophoblasts

city: SAN FRANCISCO

first: Joshua

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Transcriptomic characterization of BDE-47 exposed cultured primary human cytrophoblasts (2nd trimester) undergoing differentiation in vitro.

overall_design: Transcriptome of human villous cytotrophoblasts exposed to BDE-47 or vehicle for 24h.

first: J

last: Kapidzic

last: Fisher


title: Characterization of gene expression profile during the implantation phase in IVF cycles in endometrium of women with recurrent implantation failure

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

country: China

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

summary: With the rapid development of assisted reproductive techniques (ART), the number and quality of embryos have been optimized, but the embryo implantation rate has not been significantly improved yet. Recurrent implantation failure (RIF), a condition that is typically diagnosed in patients who fail to achieve clinical pregnancy after having undergone at least 3 times of embryo transfers (including a total of ≥4 good-quality embryos), is a challenging problem in ART treatment. Previous studies about RIF are limited to clinical trials and the detection of limited biomarkers within peripheral blood, but few about gene expression within local endometrial tissue and RIF, the key factors involved in RIF remain unclear. Our study was designed with an aim to compare the gene expression profile of RIF women with that of healthy proven fertile controls to explore the influence factors of endometrial receptivity and the mechanisms of RIF.

overall_design: Two groups of 6 women were selected: women with RIF (n=3) and fertile control women (n=3). Patients were suffering from tubal obstruction (tubal obstruction factor on hydrosalpinx, salpingitis, etc. were excluded) or unexplained infertility. Women recruited in the RIF group had a history of implantation failure from at least three consecutive IVF attempts (including a total of ≥ 4 good-quality embryos). Specimens were obtained via pipe suction curettage from the patients on day LH + 7. Tissue samples were washed thoroughly with sterile normal saline to remove excess blood and mucous and then snap-frozen in liquid nitrogen for microarray analysis.

first: Feng

last: Guo

first: Chenchen

last: Si

first: Bufang

last: Xu

first: Aijun

last: Zhang


title: Transcriptome profiling of liver samples from WT and AKAP12 KO mice after inducing fibrosis resolution

first: Hye Shin

last: Lee

department: College of pharmacy

summary: AKAP12 KO mice showed reduced fibrosis resolution in DDC-induced hepatic fibrosis and resolution model. To compare gene expression profile between genotypes, transcriptome was analyzed by RNA sequencing.

overall_design: age matched, weight matched WT and AKAP12 KO mice were fed 0.1% DDC-containing diet for 3 weeks followed by normal diet for another 2 weeks. Liver transcriptome was analyzed by RNA sequencing. Three mice per genotype were applied for analysis

first: Hye

middle: S

first: Kyu-Won

last: Kim

first: Taekwon

last: Son


title: Comparison of gene expression profiles for heat-shocked and non-heat shocked stationary phase samples from heat tolerant isolates R1-0006 and R1-0007 and reference strain SL476

city: West Lafayette

first: Andrea

last: Ray

state: IN

address: 745 Agriculture Mall Drive

department: Food Science

institute: Purdue University

summary: Salmonella Heidelberg is currently the 9th common serovar and has more than twice the average incidence of blood infections in Salmonella. A recent Salmonella Heidelberg outbreak in chicken infected 634 people during 2013-2014, with a hospitalization rate of 38% and an invasive illness rate of 15%. While the company’s history suggested longstanding sanitation issues, the strains’ characteristics which may have contributed to the outbreak are unknown. We hypothesized that the outbreak strains of S. Heidelberg might possess enhanced stress tolerance or virulence capabilities. Consequently, we obtained nine food isolates collected during the outbreak investigation and several reference isolates and tested their tolerance to processing stresses, their ability to form biofilms, and their invasiveness in vitro. We further performed RNA-sequencing on three isolates with varying heat tolerance to determine the mechanism behind our isolates’ enhanced heat tolerance. Ultimately, we determined that (i) many Salmonella Heidelberg isolates associated with a foodborne outbreak have enhanced heat resistance (ii) Salmonella Heidelberg outbreak isolates have enhanced biofilm-forming ability under stressful conditions, compared to the reference strain (iii) exposure to heat stress may also increase Salmonella Heidelberg isolates’ antibiotic resistance and virulence capabilities and (iv) Salmonella Heidelberg outbreak-associated isolates are primed to better survive stress and cause illness. This data helps explain the severity and scope of the outbreak these isolates are associated with and can be used to inform regulatory decisions on Salmonella in poultry and to develop assays to screen isolates for stress tolerance and likelihood of causing severe illness.

sample_organism: Salmonella enterica subsp. enterica serovar Heidelberg

overall_design: 3 isolates, 2 conditions (heat stress at 56C and control of stationary-phase culture at 37C), with three biological replicates for each condition per isolate; R1-0006 and R1-0007 are heat-tolerant outbreak-associated isolates, while SL476 is the Salmonella Heidelberg reference strain with average heat tolerance.

last: Etter

first: Haley

last: Oliver


title: mRNA expression profiling in human brain glioblastoma cell line U251 after stable knockdown the expression of linc01116

status: Public on Aug 31 2018

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

institute: changzheng hospital

summary: The expression profiling of a total of 34181 mRNAs in 3 paired U251 cell line, which had been stable knockdown the expression of LINC01116.

overall_design: In the study presented here, 3 paired U251 cell which had been stable knockdown the expression of LINC01116 were used to acquire expression profiles of a total of 34181 mRNAs, leading to the successful construction of supervised

first: Chun

last: Luo

first: Jingliang

last: Ye