title: Synergy from Gene Expression and Network Mining (SynGeNet) method predicts genotype-specific synergistic drug combinations in melanoma

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: The Ohio State Univ

summary: Using our computational method SynGeNet to evaluate genomic and transcriptomic data characterizing four major genomic subtypes of melanoma, we selected the top ranked drug combination for BRAF-mutation melanoma for subsequent validaiton. Here we present drug-induced gene expression data from the BRAF-mutant A375 melanoma cell line in response to four treatment conditions: vehicle control (DMSO), vemurafenib alone, tretinoin (ATRA) alone and vemurafenib+tretinoin combination.

overall_design: Gene expression profiles of A375 melanoma cells were generated by RNAseq (Illumina HiSeq 4000) under the following treatment conditions: vehicle control (DMSO),  vemurafenib, tretinoin and vemurafenib + tretinoin combination.

last: Regan-Fendt


title: SOX9 is dispensable to initiate epigenetic remodeling and activation of marker genes at the onset of chondrogenesis (ChIP-Seq)

status: Public on Jul 02 2018

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

country: USA

institute: Cleveland Clinic Lerner Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using whole-transcriptome and whole-epigenome sequencing approaches for wild-type and Sox9-deficient mouse embryo limb buds, we here identify genes specifically expressed and likely involved in precartilaginous condensation. We show that SOX9 directly upregulates these genes and well-known early-cartilage markers, and that its actions in chondrogenic cells have little impact on neighboring cell types. Intriguingly, we find that SOX9 helps remove epigenetic signatures of transcriptional repression and establish active-promoter and active-enhancer marks at precartilage- and cartilage-specific loci, but is not absolutely required to initiate these changes and activate transcription. Altogether, these findings widen our current knowledge of SOX9 targets in early chondrogenesis and call for new studies to identify the pioneer and transactivating factors that act upstream of or along with SOX9 to prompt chromatin remodeling and specific gene activation at the onset of chondrogenesis and other processes.

overall_design: ChIP-seq for histone modifications were carried out using E11.5 and E12.5 control and Sox9-deficient embryonic mouse limb buds

first: Veronique

last: Lefebvre


title: Comparison of the transcriptomic profiles of two human glioma cell lines, U87 and Glio6.

status: Public on Jul 01 2018

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

summary: Using Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array, we compared the gene expression profiles between the glioma cell lines U87 and Glio6, cultured at 3% of oxygene.

overall_design: Seven independent biological samples were analysed, U87 cell cultures (n=4) and Glio6 cell cultures (n=3).

first: Ulysse

last: Gimenez

first: Adriana-T

last: Perles-Barbacaru

first: Michele

last: El Atifi

first: Florence

last: Appaix

first: Didier

last: Wion

first: François

last: Berger

first: Boudewijn

last: Van der Sanden

first: Hana

last: Lahrech


title: RNA-seq analysis of miR-324-5p overexpression upon H5N1 infection in A549 cells

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

type: Expression profiling by high throughput sequencing

summary: The goals of this study are to compare NGS-derived whole transcriptome profiles (RNA-seq) of H5N1 infected A549 cells overexpressing either negative control mimic or miR-324-5p mimic

overall_design: A549 cells were either mock transfected or transfected with either negative control or mir-324-5p mimic. After 12 hours cells were either mock infected (mock transfected cells) or infected with A/duck/India/02CA10/2011 - H5N1 virus (negative control and miR-324-5p overexpressing cells)


title: Skeletal muscle satellite cells, endothelial cells and single muscle fibers

city: Minneapolis

first: Mayank

last: Verma

state: MN

address: 2001 6th st se

department: Stem Cell Institute

institute: University of Minnesota

summary: There is considerable crosstalk between satellite cells, endothelilal cells and muscle fibers. Transcriptome analysis from freshly isolated cells from each compartment should help elucidate these pathways.

overall_design: 2-3 replicates for each group are provided

first: Atsushi

last: Asakura


title: SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [Bulk RNA-Seq]

city: Cold Spring Harbor

first: Molly

last: Hammell

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the SMART-seq/Fluidigm and 10x Genomics platforms were analyzed to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance

overall_design: Two Melanoma cell lines were treated with BRAF inhibitor for 6 weeks to derived a parental and resistant cell states. Bulk and single-cell RNA-Seq were generated using Illumina Hiseq 2000 to study cell response after drug treatment.

middle: G

first: Yu-Jui

last: Ho


title: RRBS in Smchd1 control and Smchd1 deleted male and female neural stem cells.

status: Public on Jun 30 2018

city: Parkville

first: Marnie

last: Blewitt

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

type: Methylation profiling by high throughput sequencing

summary: We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq,  chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

overall_design: Neural stem cells were generated from Smchd1 del/fl Xist 129-KO/Xist WT-Cast E14.5 embryos, as previously described (Chen et al., 2015 PNAS). After these lines were established, they were split in two - half were transduced with a retrovirus carrying Cre recombinase and a puromycin selection cassette (MSCV-Cre-puro), half were retained untransduced as controls. 24h post transduction puromycin was added to select transduced cells, and 7 days following transduction cells were harvested for genomic analyses.

first: Natasha

last: Jansz


title: In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells. [II]

overall_design: n=2 Smchd1del/del vs n=2 Smchd1fl/fl male neural stem cell lines analysed by in situ Hi-C


title: SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [Fluidiam scRNA-Seq]

overall_design: Two Melanoma cell lines were treated with BRAF inhibitor for 6 weeks to derived a parental and resistant cell states. Bulk and single-cell RNA-Seq were generated using Illumina NextSeq to study cell response after drug treatment.


title: Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27ac]

overall_design: n=3 Smchd1del/del vs n=3 Smchd1del/fl female neural stem cell lines analysed by RNA-seq.


title: A widespread alternate form of cap-dependent mRNA translation initiation

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

summary: We report the application of polysome profiling sequencing technology for high-throughput transcriptomics and translatomics in mammalian cells. We compare reduction of Dap5 to control in metastatic breast cancer cells in transcription and polysome enriched translation using RNA sequencing. Genome-wide transcriptomic and translatomic analyses indicate that DAP5 is required for translation of many transcription factor and receptor capped mRNAs and their mRNA targets involved in cell survival, motility, DNA repair and translation initiation, among other mRNAs.

overall_design: Examination of transcriptomics and translatomics in breast cancer cells.

first: Amanda

middle: W

last: Ernlund

first: Columba

last: de la Parra


title: Chromatin binding of NRF1 after exposure to proteasome inhibitor

city: Sendai

first: Hiroki

last: Sekine

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer (IDAC)

country: Japan

institute: Tohoku University

summary: NRF1 was localized at promoter regions of almost all proteasome subunit genes

overall_design: Chromatin occupancy of NRF1 under MG132-treated condition were generated by deep sequencing, in duplicate

first: Fumiki

last: Katsuoka

first: Hozumi

last: Motohashi


title: Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27me3]


title: Nutrient deprivation elicits a transcriptional and translational inflammatory response coupled to decreased protein synthesis

city: Boston

first: Paulo

middle: A.

last: Gameiro

state: MA

address: 240 Longwood Ave., Building C2, Room 325

institute: Harvard Medical School

summary:
Purpose: The goal of this study is to examine gene expression regulation at the transcriptional and translational levels in response to various forms of nutrient deprivation, and whether there are differences between isogenic transformed and non-transformed cells.
Mehods: We apply high-throughput sequencing of ribosome footprints (ribosome profiling) and poly(A) RNA (RNA sequencing) in an isogenic pair of transformed (tamoxifen-treated) and non-transformed (ethanol control) MCF10A-ER-Src cells subjected to the metabolic stresses that differentially affect global protein synthesis (Figure 1): deprivation of glutamine (for 30min and 4 hours), glucose (4hours), cysteine/cystine (4hours) or leucine/isoleucine/valine (brach-chain aminoacids - BCAA) (4hours).  The same experiments were also performed in transformed ER-Src MCF10A treated with torin1 (500nM) for 4 hours.
Results: Genome-wide translational profiling of glutamine deprived ER-Src MCF10A cells (for 30 minutes) shows increased translation of uORFs-containing mRNAs and down-regulation of ribosomal protein mRNAs, which is followed by increased translation and transcription of cytokine and inflammatory mRNAs (after 4 hours of glutamine deprivation). The transcription and translation of inflammatory and cytokine mRNAs is also stimulated in response to 4 hours deprivation of glucose, cysteine/cystine and BCAA, with the extent of stimulation correlating with the i) decrease in global protein synthesis and ii) down-regulation of all translationally-repressed mRNAs or ribosomal protein mRNAs.
Conclusions: Pro-inflammatory gene expression is associated with translational repression in response to short-term nutrient deprivation.

overall_design: Ribosome occupancy and mRNAs levels in transformed and non-transformed cells cultured for i) 30 minutes under complete (Ctrl) or glutamine-free (NoQ) DMEM medium, and ii) 4 hours under complete (Ctrl),  glucose-free (NoG), glutamine-free (NoQ), cysteine/cystine-free (NoCys) or leucine, isoleucine, valine (NoBCAA)-free DMEM medium. The translation efficiency (TE) was calculated as the log2 ratio of RPKM measured by ribosome profiling over RPKM measured by RNA-seq. Differences in ribosome occupancy (RO) and TE between the metabolic stress condition and the reference sample (either TAM or EtOH cells grown in complete DMEM) were used to examine the transcriptional and translational changes, respectively. The ribosome profiling and RNA sequencing experiments were performed in duplicate with the exception of RNA-seq at 30 minutes (single experiments), ribosome profiling in cysteine/cystine-deprived EtOH cells (triplicate experiments), and the Torin1 ribosome profiling and RNA-seq (single experiment).  The complete dataset comprises the raw (.fastq) and processed (RPKM) files of all 57 high-throughput sequenced samples.

middle: A

first: Kevin

last: Struhl


title: RNA-seq in Smchd1 wild-type and Smchd1 null presomitic mesoderm from E9.5 embryos

summary: We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq,  chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loci. Smchd1 deletion in differentiating ES cells results in failed Hox gene silencing and Smchd1 null E9.5 embryos show altered Hox gene expression.. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers.  We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

overall_design: n=3 Smchd1 wild-type and n=3 Smchd1 MommeD1/MommeD1 (null) presomitic mesoderm samples from E9.5 embryos


title: Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.


title: RNA-seq in Smchd1 wild-type and Smchd1 deleted differentiating male ES cells.

summary: We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq,  chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loci. Smchd1 deletion in differentiating ES cells results in failed Hox gene silencing. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

overall_design: n=2 Smchd1del/del vs n=2 Smchd1fl/fl male ES cell lines differentiated to neuromesodermal progenitors over an 8 day period, samples taken at day 0, 5 and 8 of differentiation, and comparisons made between Smchd1 deleted and control samples over time.


title: ChIP-seq for Smchd1 in male and female neural stem cells.

overall_design: n=2 Smchd1 GFP/GFP vs n=2 Smchd1+/+ female neural stem cell lines +  Whole cell extract controls, to test binding of Smchd1 to the inactive X, using long sonication to release the inactive X heterochromatin. n=1 Smchd1GFP/GFP female + n=1 Smchd1 GFP/GFP male NSCs vs n=1 Smchd1+/+ female and n=1 Smchd1+/+ male neural stem cell lines plus whole cell extract controls, using MNase digestion for fragmentation, to assess autosomal binding of Smchd1.


title: ATAC-seq in Smchd1 wild-type and Smchd1 deleted neural stem cells.

overall_design: n=3 Smchd1del/del vs n=3 Smchd1fl/fl female neural stem cell lines + n=2 Smchd1del/del vs n=2 Smchd1fl/fl male neural stem cell lines, ATAC-seq in all. Comparisons made between del/del and fl/fl for females alone, or females+males together.


title: In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells.

overall_design: n=3 Smchd1del/del vs n=3 Smchd1fl/fl female neural stem cell lines analysed by in situ Hi-C


title: RNA-seq in Smchd1 control and Smchd1 deleted male and female neural stem cells.

overall_design: n=4 Smchd1del/del vs n=5 Smchd1del/fl female neural stem cell lines analysed by RNA-seq.


title: Gene expression in PANC1 cells treated with Rakicidin

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

summary: Cells were treated with Rakicidin A or an analogue compound BE-43547 or DMSO (control) in three replicates.

overall_design: three groups in triplicates.

middle: M

first: Kristian

last: Jakobsen

first: Jakob

middle: S

last: Pedersen

first: Thomas

middle: B

last: Poulsen


title: Gene expression profiling of 786-O cells with ZHX2 and p65 knockdown

city: Chapel Hill

first: Qing

last: Zhang

state: NC

address: 450 West Dr.

institute: Lineberger Cancer Center

summary: We are examining the regulatory pathway of ZHX2 and p65 in clear cell renal cell carcinoma cell line 786-O

overall_design: 786-O cells were infected with Scr (scrambled), ZHX2 shRNA (44), ZHX2 shRNA (45), Ctrl (Control) shRNA or p65 shRNA . All of these samples were prepared in two replicates.

first: Q

first: J


title: Smchd1 in neural stem cells.

first: Marnie

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

overall_design: Refer to individual Series


title: Aalysis of replication timing in the RPE1 and HCT116 cell line

city: Edinburgh

first: Lora

last: Boteva

state: City of Edinburgh, Midlothian

address: Crewe Road

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Mapping replication timing in the RPE1 and HCT116 cell lines revealed differences in replication dynamics and replication domain structures in the two cell lines

overall_design: Asynchronously growing cell populations were pulsed with the thymidine analogue 5-Ethynyl-2'-deoxyuridine (EdU) and sorted inot an early, mid and late - S phase fraction. Nascent DNA was isolated from each fraction and sequenced. RPE 1 experiments were performed in duplicate.

first: Nick

last: Gilbert


title: miRNA sequencing in ccRCC

city: Bergen

first: Hans-Peter

last: Marti

address: Jonas Liesvei 65

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

type: Non-coding RNA profiling by high throughput sequencing

summary: Full miRNA next generation sequencing in 24 samples (normal and tumor pairs) from 12 ccRCC patients

overall_design:
Tumor vs adjacent tissue (normal) in nephrectomy specimens

The authors state "Based on Norwegian legislation we are not able to upload patient raw sequencing FASTQ files. The files have to be at our Hospital server only."
Thus, this submission is incomplete.

first: Christian

last: Beisland


title: A multiplexed homology-directed DNA repair assay reveals the impact of over 1,000 BRCA1 missense substitution variants on protein function

status: Public on Jun 29 2018

city: Seattle

first: Lea

last: Starita

state: WA

department: Genome Sciences

institute: University of Washington

summary: Here we describe a multiplex HDR reporter assay to concurrently measure the effects of hundreds of variants of BRCA1 for their role in DNA repair. Using this assay, we characterized the effects of 1,056 amino acid substitutions in the first 192 residues of BRCA1.

overall_design: Multiplex HDR reporter assays for BRCA1 amino acids 2-96 and 97-192, each in 4 replicates.

first: Muhtadi

last: Islam

first: Tapahsama

last: Banerjee

first: Aleksandra

last: Adamovich

first: Justin

last: Gullingsrud

first: Stanley

last: Fields

first: Jay

last: Shendure

first: Jeffrey

middle: D

last: Parvin


title: AffymetrixHuman Gene 2.0 ST Array

city: Toulouse

first: VALERIE

last: GOUAZE-ANDERSSON

address: 2 avenue Hubert Curien, CS 5317

department: Glioblastoma radioresistance: from signaling pathways to clinical trials

institute: CRCT

summary:
Gene expression in glioblastoma cells from patients before treatment. The cells were inhibited or not for FGFR1.
Glioblastoma are known to be aggressive and therapy-resistant tumors, due to the presence of glioblastoma stem cells (GSC) inside this heterogeneous tumor. We investigate here the involvement of FGFR1 in glioblastoma stem-like cells (GSLC) radioresistance mechanisms. We first demonstrated that the survival after irradiation was significantly diminished in FGFR1-silenced (FGFR1-) GSLC compared to control GSLC. The transcriptome analysis of GSLCs FGFR1(-) showed that FOX family members are differentially regulated by FGFR1 inhibition, particularly with an upregulation of FOXN3 and a downregulation of FOXM1.  GSLC survival after irradiation was significantly increased after FOXN3 silencing and decreased after FOXM1 inhibition, showing opposite effects of FGFR1/FOX family members on cell response to ionizing radiation. Silencing FGFR1 or FOXM1 downregulated genes involved in mesenchymal transition such as GLI2, TWIST1, and ZEB1 in GSC. It also dramatically reduced GSLC migration, strongly suggesting that FGFR1/FOXM1 pathway which regulates GSLC radioresistance. Databases analysis confirmed that the combined expression of FGFR1/FOXM1/MELK/GLI2/ZEB1/TWIST1 is significantly associated with patients overall survival after chemo-radiotherapy treatment. All these results, associated with our previous conduced ones with differentiated cells, clearly established that FGFR1-FOXM1 dependent GSC radioresistance pathway is a central actor of GBM treatment resistance and a key target to inhibit in the aim to increase the sensitivity of GBM to the radiotherapy.

overall_design: Cells were transfected with different small interfering RNAs (siRNA): an aleatory sequence, SiScramble siRNA and siRNAs specific for FGFR1 (QIAGEN, SI02224677, Courtaboeuf, France). Total RNAs were isolated either from Neurospheres 48h post-transfection and hybridized on Affymetrix microarrays.

first: V

last: Gouaze-Andersson

first: C

last: Toulas


title: Expression data from normal human osteoclast transdifferentiated from immature dendritics in vitro or treated with gamma delta t cell

city: fuzhou

first: xiaolin

last: zhu

address: chazhong road

country: China

institute: fujian medical university

summary: We used microarrays to detail the global gene expression in osteoclast transdifferrent from immature dendritics in vitro, or treated with gamma delta t cell

overall_design: Osteoclasts transdifferent from immature dendritcs from two normal human, or treated with gamma delta t cell were for RNA extraction and hybridization on Affymetrix

first: Xiaolin

last: Zhu


title: Expression data of iPSC-derived motor neurons from healthy donor, FALS, SALS, and drug-treated them

city: Sinjuku-ku, Tokyo

first: Koki

last: Fujimori

address: 35 Shinanomachi

department: Physiology

institute: Keio University

summary:
We established several iPSCs from healthy donors, familial ALS (FALS) patients, and sporadic ALS (SALS) patients. Using our differentiation protocol originally developed, we differentiated these iPSCs toward spinal motor neurons (MNs) and reproduced ALS pathology in a dish.
In addition, we screened a drug candidate which suppressed the detected ALS-related phenotypes of these ALS models.
For clarifying the molecular mechanisms of the ALS pathologies and the screened drug, we used microarrays to detail the global program of gene expression reflecting the MN pathology of FALS/SALS, and carefully compared with healthy donors and/or drug-treated ALS models based on their expression profiles.

overall_design: We isolated RNA from iPSC-derived MNs (healthy donor: 4 samples, untreated FALS: 6 samples, untreated SALS: 4 samples, drug-treated FALS: 6 samples, drug-treated SALS: 4 samples. Total 24 samples) for the gene expression microarray analysis. All of the iPSC lines we used were low passage number (less than 15).

first: Hideyuki

last: Okano


title: Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity

city: San Diego

first: Chi-Yeh

last: Chung

state: CA

address: 10770 Science Center Drive

institute: Pfizer Inc.


title: Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [RNA-seq]

summary: We performed RNA-seq on normal mammary cell populations and mouse mammary tumor cell populations

overall_design: The transcriptomes of mouse normal mammary populations and mouse mammary tumors were profiled. Two biological replicates for the normal and PY230 cells. Four or five biological replicates for the C3-1-TAg cells.

first: Geoffrey

last: Wahl

first: Christopher

last: Dravis


title: Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ChIP-seq]

summary: We performed H3K27ac ChIP-seq on normal mammary cell populations and SOX10 ChIP-seq on PY230 tumors

overall_design: ChIPmentation method (Schmidl et al., 2015) was perfromed on dissociated, FACS isolated normal mammary cell populations and bulk PY230 tumors


title: Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer

city: Columbus

first: Carlo

middle: M.

last: Croce

address: 460 West 12th Avenue

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

summary:
We analyzed small-RNA sequencing data from plasma-derived exosome (PEV) from a cohort of NSCLC patients at different stages.
We identified two ED miRNAs in circulation able to distinguish between normal and tumor sample subtypes.

overall_design: A total of 26 frozen plasma samples received as generous gift from the NYU plasma bank (courtesy of H.I. Pass MD, IRB approved protocol) and grouped into the following three categories: 7 control smokers, 11 early stage NSCLC, and 8 late stage NSCLC.

first: M

last: Acunzo

first: P

last: Nana-Sinkam


title: Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia (CHINFAM Data Set)

city: Utrecht

middle: P

last: Boks

address: Heidelberglaan 100

department: Psychiatry

country: Netherlands

institute: UMC Utrecht

type: Methylation profiling by genome tiling array

summary: Epigenetic changes may account for the doubled risk to develop schizophrenia in individuals exposed to famine in utero. We therefore investigated DNA methylation in a unique sample of patients and healthy individuals conceived during the great famine in China. Subsequently we examined two case-control samples without famine exposure in whole blood and brain tissue. To shed light on the causality of the relation between famine exposure and DNA methylation we exposed human fibroblasts to nutritional deprivation. In the famine exposed schizophrenia patients we found significant hypermethylation of the dual specificity phosphatase 22 (DUSP22) gene promoter (Chr6:291687-293285) (N=153, p=0.01). In this sample DUSP22 methylation was also significantly higher in patients independent of famine exposure (p=0.025), suggesting that hypermethylation of DUSP22 is also more generally involved in schizophrenia risk. Similarly, DUSP22 methylation was also higher in two separate case-control sample not exposed to famine using DNA from whole blood (N=64, p=0.03) and postmortem brains (N=214, p=0.007). DUSP22 methylation showed strong genetic regulation across chromosomes by a region on chromosome 16 which was consistent with new 3D genome interaction data. The presence of a direct link between famine and DUSP22 transcription was supported by data from cultured human fibroblasts that showed increased methylation (p=0.048) and expression (p=0.019) in response to nutritional deprivation (N=10). These results highlight a first epigenetic locus that is genetically regulated across chromosomes and that is involved in the response to early life exposure to famine and that is relevant for a major psychiatric disorder.

overall_design: Bisulphite converted DNA from whole blood of 54 non-famine exposed healthy controls (CTR_Non_famine), 51 non-famine schizophrenia patients (SCZ_Non_famine), 25 famine exposed healthy controls (CTR_Famine) and 50 famine exposed schizophrenia patients (SCZ_Famine) was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Marco


title: Next Generation Sequencing  of LdlrKO  LXRα-phosphorylation disrupted macrophage transcriptomes

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

department: Medicine

institute: University College London

summary: Liver X Receptors (LXRα and β) are ligand-activated transcription factors that play a key role in the control of lipid homeostasis, as well as modulation of immunity and inflammation. Besides ligand binding, LXR activity can be regulated by posttranslational modifications, such as phosphorylation. This study aims to assess changes in bone marrow derived macrophage transcriptional profiles of mice that carry LysMcre directed phosphorylation deficient-version of LXRα compared (S196A) to wild-type (WT).

overall_design: BMDM mRNA profiles of either LdlrKO or M-LXRα-S196A-LdlrKO male mice after being fed a Western diet for 12 weeks. 12 samples, 4 groups, in triplicate: (1) LdlrKO basal, (2) LdlrKO+ ligand, (3) M-LXRα-S196A-LdlrKO basal, (4) M-LXRα-S196A-LdlrKO+ligand

first: Matthew

middle: C

last: Gage


title: Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

institute: King's College London

platform_organism:
Homo sapiens
synthetic construct


title: Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia (DUTCHSCZ Data Set)

overall_design: Bisulphite converted DNA from whole blood of 49 healthy controls (CTR) and 15 schizophrenia patients (SCZ) was hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [RNA-seq]

summary: Keloids represent a common form of exaggerated wound scarring that cause considerable morbidity. Moreover, there are limited data on molecular mechanisms underlying keloids and effective therapies are lacking. To gain new insight in the transcriptomic alterations of wound healing in keloid-prone individuals, we followed an integrative approach of RNA-Seq and miRNA expression data analysis in serial skin biopsies of the same site (baseline and six weeks after wounding) in keloid-prone (n=8) and healthy matched control individuals (n=6). Bioinformatic analysis identified 37 miRNAs and 1449 genes that are differentially expressed specifically in keloid-prone individuals during wound healing. Pathway enrichment analysis was undertaken in the RNA-Seq data and identified NOTCH signaling, MAPK signaling, and Toll-like receptor pathways to be altered in keloid-prone individuals after wounding. In addition, dysregulation of DNA repair, p53 signalling and metabolic pathways (RNA, protein, fructose, mannose and glycerophospholipid metabolism) was highlighted during keloid formation. Gene association network analysis demonstrated divergent average expression profiles of cytokine signaling genes, as well as lipid metabolism genes between keloid-prone and healthy individuals during wound healing. In summary, our study provides a comprehensive and integrative analysis of the keloid transcriptome and miRNAome and highlights biological pathways that feature during keloid formation.

overall_design: RNA-seq of keloid or healthy control skin.

first: Alexandros

last: Onoufriadis

first: Chao

middle: K

last: Hsu

first: Chrysanthi

last: Ainali

first: Chuin

middle: Y

last: Ung

first: Ellie

last: Rashidghamat

first: Hsing-San

last: Yang

first: Hsin-Yu

last: Huang

first: Umar

last: Niazi

first: Jui-Chu

first: Rosamond

last: Nuamah

first: Alka

last: Saxena

first: Emanuele

last: de Rinaldis


title: Endothelial Cell CD36 Optimizes Tissue Fatty Acid Uptake

status: Public on Jun 28 2018

city: Manhattan

first: Tenzin

last: Lhakhang

address: 550 First Avenue

summary: Movement of circulating fatty acids (FAs) to parenchymal cells requires their transfer across the endothelial cell (EC) barrier. The multi-ligand receptor cluster of differentiation 36 (CD36) facilitates tissue FA uptake and is expressed in ECs and parenchymal cells such as myocytes and adipocytes. Whether tissue uptake of FAs is dependent on EC or parenchymal cell CD36, or both, is unknown. Using a cell-specific deletion approach, we show that CD36-mediated FA transport across ECs rate-limits tissue FA uptake, and its loss leads to metabolic effects in parenchymal cells.

overall_design: We created Cd36 loxp mice and crossed Cd36 loxp mice with Tie2-cre and MHC-cre mice to generate endothelial cell and cardiomyocyte Cd36 knockout mice. Use these animal models to study the effect of endothelial cell Cd36 on the lipids and glucose metabolism.


title: ATAC-Seq chromatin profiling of Suz12-deleted or wild-type organoids derived from basal or luminal mouse mammary epithelial cells

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Fixed DNA was isolated from organoids grown from single sorted luminal or basal populations from the mammary glands of Rosa26-creERT2 Suz12 flox female mice. Cultures were treated with 4-hydroxytamoxifen to induce deletion of Suz12.

overall_design: Three biological replicates were prepared for both the basal-derived and luminal-derived organoids. Wild-type and Suz12-deleted samples were prepared from both basal and luminal organoids. ATAC-seq was carried out on an Illumina Nextseq 500 to produce 40-70 million 75 bp paired-end reads per sample.

first: Michael

last: Milevskiy


title: The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (RNA-Seq)

city: New York

first: Yuheng

last: Lu

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3’UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and  deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3’UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems.

overall_design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS. Each condition has 3 sequencing replicates.

first: Alexander

last: Rudensky


title: A role for p53 in the adaptation to glutamine starvation through the expression of Slc1a3

city: Glasgow

first: Neil

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary: Numerous mechanisms to support cells under conditions of transient nutrient starvation have been described. The tumor suppressor protein p53 can contribute to the adaptation of cells to metabolic stress through various mechanisms that may help cancer cell survival in nutrient limiting conditions. We show here that p53 helps cancer cells to survive glutamine starvation by promoting the expression of SLC1A3, an aspartate/glutamate transporter that allows the utilization of aspartate to support cells in the absence of extracellular glutamine. Under glutamine deprivation, SLC1A3 expression maintains electron transport chain and tricarboxylic acid cycle activity, promoting de novo glutamate, glutamine and nucleotide synthesis to rescue cell viability. Tumor cells with high levels of SLC1A3 expression are resistant to glutamine starvation and SLC1A3 depletion retards the growth of these cells in vitro and in vivo, suggesting a therapeutic potential for SLC1A3 inhibition.

overall_design: We quantify transcription via high throughput RNA sequencing in HCT116 cells (WT1 and WT2 clones) grown in complete medium (CM) or in glutamine-free medium (GD) for 48 hours.

first: Mylene

last: Tajan

first: Andreas

last: Hock

first: Julianna

last: Blagih

first: Christiaan

middle: F

last: Labuschagne

first: Flore

last: Kruiswijk

first: Timothy

last: Humpton

first: Peter

last: Adams

first: Karen

middle: H

last: Vousden


title: Genetic vulnerability to DUSP22 promotor hypermethylation is involved in the relation between in utero famine exposure and schizophrenia

first: M

last: Boks

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

overall_design: Refer to individual Series


title: Mutant p53 regulates enhancer-associated H3K4 monomethylation through interactions with the methyltransferase MLL4

first: Shannon

last: Lauberth

state: California

address: 9500 Gilman Drive #0322, Bonner Hall 3202

institute: UCSD

summary: In this study, we establish a mechanism in which mutant p53 cooperates with MLL4 to regulate aberrant enhancer activity and tumor promoting gene expression in response to chronic TNF-a signaling.

overall_design: Examination of MLL4 binding in SW480 colon cancer cells as well as mutant p53 binding and H3K4me1 accumulation in control (LacZ) or p53 depleted SW480 cells following treatment with TNF-a for 16 hr.

first: Homa

last: Rahnamoun

first: Juyeong

last: Hong

first: Zhengxi

last: Sun

first: Jihoon

last: Lee

first: Hanbin


title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

first: Ambrose

middle: J

last: Carr

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI


title: DNA methylation analysis of breast cancer Hs578T cells with TET1 knockout

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: Both gains and losses of DNA methylation are common in cancer but the factors controlling this methylation balance remain unclear. Triple negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU is one of the most hypomethylated cancers observed. In search for an explanation for this, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. Through bioinformatic analyses in both breast and ovarian cancer cell line panels, we uncovered an intricate network connecting TET1 to hypomethylation and activation of cancer specific oncogenic pathways including PI3K, EGFR and PDGF. TET1 expression correlated with sensitivity to drugs targeting the PI3K-mTOR pathway. CRISPR mediated deletion of TET1 in two independent TNBC cell lines resulted in reduced expression of PI3K pathway genes, upregulation of immune response genes and substantially reduced cellular proliferation, suggesting dependence of oncogenic pathways on TET1 overexpression. Our work establishes TET1 as a potential oncogene that contributes to aberrant hypomethylation in cancer and suggests that TET1 could serve as a novel druggable target for therapeutic intervention.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of Hs578T cells with TET1 knockout by CRISPR (single clones) and empty vector control single clones.  Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

first: Charly

middle: R

last: Good

first: Shoghag

last: Panjarian

first: Andrew

last: Kelly

first: Jozef

last: Madzo

first: Bela

last: Patel

first: Jean-Pierre

last: Issa


title: Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13

status: Public on Jun 27 2018

city: Auburndale

first: Mei

last: Zeng

address: 360 Longwood Avenue

department: cancer biology

institute: Dana Farber Cancer Institute

summary: High-grade serous ovarian cancer is characterized by extensive copy number alterations, among which the amplification of MYC oncogene occurs in nearly half of tumors. We demonstrate that ovarian cancer cells highly depend on MYC for maintaining their oncogenic growth, indicating MYC as a therapeutic target for this difficult-to-treat malignancy.  However, targeting MYC directly has proven difficult. We screen small molecules targeting transcriptional and epigenetic regulation, and find that THZ1 –a chemical inhibiting CDK7, CDK12, and CDK13–markedly downregulates MYC. Notably, abolishing MYC expression cannot be achieved by targeting CDK7 alone, but require the combined inhibition of CDK7, CDK12, and CDK13. In all 11 independent patient derived xenografts models derived from heavily pre-treated ovarian cancer patients, administration of THZ1 induces significant tumor growth inhibition with concurrent abrogation of MYC expression. Our study indicates that targeting these transcriptional CDKs with agents such as THZ1 may be an effective approach for MYC-dependent ovarian malignancies.

overall_design: We performed ERCC spike-in normalized RNA-sequencing experiments to quantify transcriptional changes upon THZ1 treatment. We profiled two of the human ovarian cancer cell lines, KURAMOCHI and COV362. Cells were treated with DMSO, THZ1 50nM, or THZ1 250nM for six hours. All samples were prepared in biological duplicate.

first: Mousheng

last: Xu

first: Nathanael

last: Gray


title: GENERATION OF HEPATIC STELLATE CELLS BY DIRECTED DIFFERENTIATION OF HUMAN PLURIPOTENT STEM CELLS

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Hepatic stellate cells (HSC) are the main stromal cell component of the liver. In healthy liver, quiescent HSC participate in the homeostasis of extracellular matrix (ECM) and store vitamin A. Liver injury causes HSC activation, where they participate in the wound-healing response, by producing ECM components as well as cytokines involved in liver regeneration and inflammation. Moreover, HSC are the main cell type responsible for fibrosis progression. The lack of homogeneous cultures and renewable sources of human HSC has limited the studies of the role of HSC in liver injury, repair anf fibrosis. Here we report a procedure to direct the differentiation of human pluripotent stem cells (PSC) to HSC. The HSC–like population (iPS-HSC) was enriched in PDGFRβ positive cells that expressed key HSC markers. Whole genome transcriptomic analysis revealed that iPS-HSC displayed features intermediate to quiescent and activated HSC. Functional analysis demonstrated that iPS-HSC accumulated retinyl esters into lipid droplets and responded to injury mediators. Moreover, when cultured with HepaRG hepatocytes as aggregates, iPS-HSC support long-term hepatocyte metabolic function and respond to hepatocyte toxicity by activating and promoting organoid fibrogenesis.

overall_design: The genome wide transcriptome of 3 freshly isolated iPS-HSC cells (iHSC), 3 iPS-HSC cells at passage 1 iHSC_p1), 3 iPSC samples harvested from the differentiation plate on day 0, (IPSC) and finally, 3 parental BJ1 fibroblast (hfibro) samples were assessed using Affymetrix HG-U219 genechips (Affymetrix)

first: M

last: Coll

first: L

last: Perea

first: J

first: P

last: Sancho


title: Global analysis of gene expression changes following LINE1 inhibition [III]

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

institute: MRC Laboratory of Medical Sciences

summary: Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28  to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.

overall_design: 3 replicates each of mouse embryos at early 2C or 4C stage, after zygote microinjection with 0.75mM RC control or LINE1 ASOs used for RNA extraction and library generation (12 samples total)

first: Chih-Jen

last: Lin

first: Miguel

last: Ramalho-Santos


title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing

first: Ambrose

last: Carr

summary: Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer, with important implications for characterizing tumor-infiltrating immune cells.

overall_design: Single-cell RNA sequencing was performed on eight donors using the InDrop v2 protocol. For each donor populations of CD45+ immune cells were assayed for trancriptome-wide RNA-sequence. At least one replicate was taken for each donor.

first: Elham

last: Azizi

first: George

last: Plitas

middle: E

last: Cornish

first: Catherine

last: Konopacki

first: Sandhya

last: Prabhakaran

first: Juozas

last: Nainys

first: Kenmin

last: Wu

first: Vaidotas

last: Kiseliovas

first: Manu

last: Setty

first: Kristy

last: Choi

first: Rachel

last: Fromme

first: Phuong

last: Dao

first: Peter

middle: T

last: McKenney

first: Ruby

last: Wasti

first: Krishna

last: Kadaveru

first: Linas

last: Mazutis

first: Alexander

last: Rudensky

first: Dana

last: Pe’er


title: SCNT embryos are defective for H3K27me3 imprinting [ChIP-seq]

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), yet the success rate is very low. Recent studies have revealed H3K9me3 in donor cells and abnormal Xist activation as epigenetic barriers that impede SCNT reprogramming. Here we overcome both barriers by using Xist knockout donor cells combined with overexpressing Kdm4d and achieved the highest cloning efficiency in mice. However, post-implantation developmental defects and abnormal placenta were still observed, indicating presence of additional epigenetic barriers impedes SCNT cloning. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified many abnormally methylated regions in SCNT embryos, despite successful global methylome reprogramming. Strikingly, allelic transcriptome and ChIP-seq analyses of preimplantation SCNT embryos revealed a complete loss of H3K27me3 imprinting, which likely accounts for postimplantation developmental defects of SCNT embryos. This study not only provides an efficient method for mouse cloning, but also paves the way for further improving SCNT cloning efficiency.

overall_design: ChIP-seq comparing H3K27me3 between mouse morula-stage embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT)


title: RNA-SEQ of epididymal white adipose tissue of mice on different Mg and fat diets

city: Nijmegen

first: Steef

last: Kurstjens

address: Geert Grooteplein Zuid 30

institute: Radboudumc

summary: C57Bl/6J mice were put on a low fat diet (10 kcal% palm oil) or high fat diet (60 kcal% palm oil), combined with a low dietary Mg2+ (0.03 w/w% or 0.21 w/w%) for a period of 17 weeks. White adipose tissue was harvested and total RNA isolated using TRIzol, of which 5 samples per group were sent to BGI-China for RNA-Sequencing.

overall_design: RNA-SEQ of eWAT of WT mice on 17 week low or high fat & low or normal Mg2+ diets

first: Jeroen

last: De Baaij


title: SCNT embryos are defective for H3K27me3 imprinting


title: SCNT embryos are defective for H3K27me3 imprinting [Bisulfite-seq]

summary: Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), yet the success rate remains very low. Recent studies have revealed two epigenetic barriers, H3K9me3 in donor cells and abnormal Xist activation, that impede SCNT reprogramming. Here we overcome both barriers by combining the use of Xist knockout donor cells and overexpressing Kdm4d, which allowed us to achieve the highest mouse cloning efficiency. However, SCNT-associated developmental defects and abnormal placenta were still observed, suggesting the existence of additional epigenetic defects in these SCNT embryos. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified many abnormally methylated regions in SCNT embryos, despite successful global methylome reprogramming. Strikingly, allelic transcriptome analyses of SCNT blastocysts revealed a complete loss-of-imprinting at the H3K27me3-dependent imprinted genes, which may account for postimplantation developmental defects of SCNT embryos. This study thus not only provides the most efficient method for mouse cloning but also points the way for further improve SCNT cloning.

overall_design: WGBS comparing the methylation characteristics between mouse blastocyst-stage embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT).

first: Shogo

last: Matoba

first: Huihan

last: Wang

first: Falong

last: Lu

first: Kumiko

middle: A

last: Iwabuchi

first: Lin

last: Yang

first: William

last: Press

first: Jeannie

last: Lee

first: Atsuo

last: Ogura

first: Yi

last: Zhang


title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing

first: Ambrose

last: Carr

overall_design: Single-cell RNA sequencing was performed on three patients using the 10x genomics TCR profiling kits. For each patient, populations of T-cells were assayed for both TCR sequence and trancriptome-wide RNA-sequence. Two donors have a replicate experiment.

first: Elham

last: Azizi

first: George

last: Plitas

first: Andrew

last: Cornish

first: Catherine

last: Konopacki

first: Sandhya

last: Prabhakaran

first: Juozas

last: Nainys

first: Kenmin

last: Wu

first: Vaidotas

last: Kiseliovas

first: Manu

last: Setty

first: Kristy

last: Choi

first: Rachel

middle: M

last: Fromme

first: Phuong

last: Dao

first: Peter

last: McKenney

first: Ruby

last: Wasti


title: SCNT embryos are defective for H3K27me3 imprinting [RNA-seq]

first: Li

last: Shen

overall_design: RNA-seq comparing mouse blastocyst-stage embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer

first: Shogo

last: Matoba

first: Huihan

last: Wang

first: Falong

last: Lu

first: Kumiko

last: Iwabuchi

first: Lin

last: Yang

first: William

last: Press

first: Jeannie

last: Lee

first: Atsuo

last: Ogura


title: Unique features and clinical importance of acute alloreactive immune responses

city: Birmingham

first: Archana

last: Sharma-Oates

address: Haworth Building

department: Centre for Computational Biology

institute: University of Birmingham

summary: By 2 weeks after stem cell transplantation, there was differentiated changes in T cell phenotype between autograft and allograft. RNA-seq was used to reveal the different transcription profiles of these T cells at week 2 after SCT.

overall_design: Compare the transcription profile of the T cells in allograft and autograft transplantation patients.

first: Charlotte

last: Inman

first: Suzy

last: Eldershaw


title: Regulation of brown fat homeostasis by H19 lincRNA

status: Public on Jun 26 2018

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

state: NRW

address: Gleueler Strasse 50

country: Germany

institute: Max-Planck-Institute for Metabolism Research


title: Regulation of brown fat homeostasis by H19 lincRNA [I]

summary: Increases in organismal energy expenditure, as during cold exposure or exercise training, can improve metabolic health. This process is dependent also on brown adipose tissue (BAT) thermogenesis in mice and humans. Understanding and harnessing the molecular circuits activating BAT function is thus of great interest to devise novel approaches to counteract obesity and type 2 diabetes (T2D). In contrast to protein-coding genes, the role of long noncoding RNAs (lncRNAs) during BAT differentiation and function remains poorly understood. To address this, we performed RNA-Seq and identified the maternal allele-specific (imprinted) lncRNA H19 increased upon cold-mediated BAT activation and decreased upon chronic diet-induced obesity (DIO) BAT dysfunction. An inverse correlation of H19 expression with body-mass indices (BMI) was observed in a cohort of >160 lean and obese humans. H19 silencing impaired adipogenesis and oxidative metabolism in brown but not white adipocytes, while H19 gain-of-function increased nutrient oxidation and mitochondrial respiration, thus supporting a BAT-regulatory role for H19. In vivo H19 overexpression protected against DIO, improved insulin sensitivity and rescued DIO-mediated defects in energy expenditure in conjunction with improved mitochondrial biogenesis. In contrast, BAT-selective H19 loss decreased energy dissipation and sensitized towards high fat diet-induced body weight gains. When investigating other parent-of-origin specific, monoallelically expressed genes, we strikingly observed that paternally expressed genes (PEGs) were largely absent from BAT and coordinately downregulated during brown adipogenesis, whilst the same gene set was robustly expressed in white fat stores, a phenomenon not observed for maternally expressed genes (MEGs). Using H19 loss- and gain-of-function in primary adipocytes, we demonstrate that H19 acts as ‘PEG gatekeeper’ in brown, not white adipocytes, potentially due to recruitment of PEG-inactivating H19-MBD1 complexes in mature brown adipocytes. The exclusive PEG expression in white adipose tissuer could underly the observed susceptibility of mice exhibiting high PEG abundances towards DIO-evoked weight gain. Collectively, we here define novel roles for the imprinted lncRNA H19 in brown adipocyte differentiation and function in vitro, control of energy expenditure in vivo and repression of paternal allele-specific gene expression in BAT. This has far-reaching implications for our understanding of how monoallelical gene expression affects metabolic eustasis in both rodent models and, potentially, human patients.

overall_design: Analyze which lncRNAs correlate with brown adipose tissue function.

first: Elena

last: Schmidt


title: Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary:
Background: Ageing is characterised by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of ageing on B cell development, we have profiled gene expression and chromatin features, including histone modifications and chromosome conformation focused on promoter interactions, globally in murine bone marrow pro-B and pre-B cells.

Results: Our analysis revealed that the expression levels of most genes are generally preserved in B cell precursors isolated from aged as compared to young mice. Nonetheless, age-specific expression changes are observed at numerous genes and are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions and nuclear compartmentalisation. We identified transcriptional downregulation of components of the insulin-like growth factor signalling pathway, in particular downregulation of Irs1 and upregulation of miR/Let-7 expression, as a signature of the aged phenotype. Remarkably, these expression changes are associated with specific alterations in H3K27me3, suggesting that Polycomb-mediated repression plays a role in precursor B cell ageing.

Conclusions: Components of the insulin-like growth factor signalling pathways are key targets of epigenetic regulation in ageing in bone marrow B cell precursors.

overall_design: 12 total RNA-seq samples (rRNA-depleted; 3 replicates from pro-B and pre-B cells sorted from young and aged mice); 4 nuclear RNA-seq samples (2 replicates from pro-B cells sorted from young and aged mice); 16 microRNA-seq samples (4 replicates from pro-B and pre-B cells sorted from young and aged mice); 16 ATAC-seq samples (4 replicates from pro-B and pre-B cells sorted from young and aged mice); 4 CTCF ChIP-seq samples (2 replicates from pre-B cells sorted from young and aged mice); 8 H3K4me3 ChIP-seq samples (2 replicates from pro-B and pre-B cells sorted from young and aged mice); 8 H3K27me3 ChIP-seq samples (2 replicates from pro-B and pre-B cells sorted from young and aged mice); 4 H3K27ac ChIP-seq samples (1 sample from pro-B and pre-B cells sorted from young and aged mice); 4 Hi-C samples (2 replicates from pre-B cells sorted from young and aged mice); 4 Promoter Capture Hi-C samples (2 replicates from pre-B cells sorted from young and aged mice)

first: Daniel

last: Bolland

first: Claudia

last: Stellato

first: Stefan

last: Schoenfelder

first: Hashem

last: Koohy

first: Louise

middle: S

last: Matheson

first: Mikhail

last: Spivakov

last: Fraser

first: Anne

last: Corcoran

first: Patrick

last: Varga-Weisz


title: Epigenetic and transcriptomic profiling of mammary gland development and tumor models disclose regulators of cell state plasticity [ATAC-seq]

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

summary: We performed ATAC-seq on normal mammary cell populations and mouse mammary tumor cell populations

overall_design: ATAC-seq was performed on freshly sorted cell nuclei as detailed in the Methods section of the manuscript

first: Geoffrey

last: Wahl

first: Christopher

last: Dravis


title: The transcription factor Rfx7 limits metabolism of NK cells promoting their maintenance and immunity

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: Regulatory factor X 7 (Rfx7) is an uncharacterized member of a family of transcription factors playing essential functions in ciliogenesis and immunity. Given the prominent expression of Rfx7 in lymphoid organs, we generated mice with Rfx7-deletion in the hematopoietic compartment. We assessed the function of Rfx7 in natural killer cells, which are innate lymphoid cells that protect from viral infections and cancer. By comparing the transcriptome of Rfx7-deficient and control NK cells isolated from bone marrow and spleen, we identified negative regulators of cell metabolism among the genes regulated by this transcription factor.

overall_design: There are 12 NK cells samples profiles for transcriptomics by RNA sequencing. NK cells come either from spleen or bone marrow, and are either RFX7 wild-type (from Vavicre Rfx7wt/wt mice) or knock-out (from Vavicre Rfx7fl/fl mice) (in triplicate for each condition).

first: Greta

last: Guarda


title: Von Hippel-Lindau protein is required for optimal alveolar macrophage terminal differentiation, self-renewal and function.

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: The rapid transit from hypoxia to normoxia in the lung that follows the first breath in newborn mice coincides with alveolar macrophage (AM) differentiation. However, whether sensing of oxygen affects AM maturation and function has not been previously explored. We have generated mice whose AMs show a deficient ability to sense oxygen after birth by deleting Vhl, a negative regulator of HIF transcription factors, in the CD11c compartment (CD11c∆Vhl mice). VHL-deficient AMs show an immature-like phenotype and an impaired self-renewal capacity in vivo that persists upon culture ex vivo. VHL-deficient phenotype is intrinsic in AMs derived from monocyte precursors in mixed bone marrow chimeras. Moreover, unlike control Vhlfl/fl, AMs from CD11c∆Vhl mice do not revert pulmonary alveolar proteinosis when transplanted into Csf2rb-/- mice, demonstrating that VHL contributes to AM-mediated surfactant clearance. Thus, our results suggest that optimal AM terminal differentiation, self-renewal, and homeostatic function requires their oxygen sensing capacity.

overall_design: BAL AMs were pooled from 5-7 age and sex-matched mice per genotype and further purified by positive selection with anti-CD11c-microbeads (Miltenyi Biotec), following manufacturer’s instructions. Cell lysis was performed with buffer RLT (Qiagen), containing 10µ/ml β-mercaptoethanol and RNA was isolated with RNeasy Plus Mini Kit (Qiagen). RNA concentration and integrity were determined with an Agilent 2100 Bioanalyzer (Caliper Life Science). Samples with RNA integrity values > 8 were further processed. A total of 3 pools per genotype were used for RNA Seq.

first: Helena

last: Izquierdo

first: Paola

last: Brandi

last: Gómez

first: Ruth

last: Conde-Garrosa

last: Priego

first: Michel

last: Enamorado

first: Sarai

last: Martínez-Cano

first: Iria

last: Sánchez

first: Laura

last: Conejero

last: Jiménez-Carretero

first: Silvia

last: Martín-Puig

first: Martin

last: Guilliams

last: Sancho


title: Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq_2]

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

summary: Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. We scanned the mammalian genome for targets eligible for TDMD and found a dominant miRNA:target pair, consisting of a target (SerpinE1) extraordinarily induced upon serum stimulation and two matched miRNAs (miR-30b/c) quickly downregulated. We verified directly the occurrence of TDMD by interfering specifically with the miR-:target interaction, keeping target and miRNA expression at endogenous levels, using CRISPR/cas9 mediated deletion of the miR-30 responsive element (MRE) of SerpinE1. In MRE-KO cells, we observed the stabilization of the predicted miRNAs, with no evidence of alterations in precursors or unrelated miRNAs, suggesting that TDMD is occurring and has been disrupted by a single MRE deletion. At molecular level miRNA degradation occurs within physiological ranges of target expression (upon 1000 copies per cells) and is accompanied by modification on 3’ends (tailing, mostly through adenylation). TDMD suppression was sufficient to shift the activity of miR-30b/c towards other shared targets, modulate significantly gene expression and, thus, influence cellular functions, including cell proliferation, apoptosis, and adhesion. In conclusion, these data strongly support the existence of a novel and sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets in mammalian cells.

overall_design: mRNA regulation in wild type and MRE_KO cells (where the miR-30 microRNA responsive element within Serpine1 3'UTR was deleted by CRISPR/Cas9 genome editing) in quiescence and upon serum-stimulation.

last: Ghini

first: Matteo

last: Marzi


title: RNA-Seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature

first: Mike

last: Chapman

address: Long Road

department: Haematology

institute: University of Cambridge

summary:
Improving outcomes in multiple myeloma will not only involve development of new therapies, but better use of existing treatments. We performed RNA sequencing (RNA-Seq) on samples from newly diagnosed patients enrolled into the phase II PADIMAC study. Using an empirical Bayes approach and synthetic annealing, we developed and trained a seven-gene signature to predict treatment outcome. We tested the signature on independent cohorts treated with bortezomib- and lenalidomide-based therapies. The signature was capable of distinguishing which patients would respond better to which regimen. In the CoMMpass dataset, patients who were treated correctly according to the signature had a better progression-free and overall survival than those who were not. Indeed, the outcome for these correctly treated patients was non-inferior to those treated with combined bortezomib, lenalidomide, and dexamethasone (VRD).
PADIMAC: Bortezomib, Adriamycin and Dexamethasone (PAD) therapy for previously untreated patients with multiple myeloma: Impact of minimal residual disease (MRD) in patients with deferred ASCT (autologous stem cell transplant)

overall_design: RNA-Seq data from 44 patients enrolled into the PADIMAC study who provided RNA with an RNA Integrity score of 6 or greater. Thirteen out of forty-four patients had at least a very good partial remission sustained for at least a year without progression and were labelled as "bortezomib-good".


title: Ribosome profiling experiment in control or Elp3 depleted B16 melanoma cells

city: Liegge

first: pierre

last: close

address: Avenue de l'hopital

department: GIGA-Institute

country: Belgium

institute: University of Liege

summary: We report the application of ribosome profiling using high-throughput sequencing and total mRNA used for normalisation upon depletion of ELP3 protein in B16 melanoma cells.

overall_design: Examination of Ribosome distribution across mRNAs in control or Elp3 depleted B16 melanoma cells

first: Benoit

last: Charloteaux

first: Francesca

last: Rapino

first: Pierre

last: Close


title: Tumor suppressor functions of DAXX through histone H3.3 deposition pathway in pancreatic neuroendocrine tumor

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary:
Purpose: Pancreatic neuroendocrine tumors (PanNETs) have considerable malignant potential. Frequent somatic mutations and loss of DAXX protein expression have been frequently found in PanNETs. DAXX is known as a transcriptional repressor, however, molecular functions underlying loss of DAXX remain unclear in PanNETs.
Experimental Design: We evaluated DAXX-knockdown (KD) and -knockout (KO) PanNET cells were analyzed for in vitro and vivo. The target genes were screened by microarray and chromatin immunoprecipitation (ChIP) assays for DAXX, histone H3.3 and H3K9me3 complex.
Results: Microarray and ChIP analyses of DAXX-KD/KO identified 13 genes as the direct targets of DAXX transcriptional repressor. Among them, 5 genes were suppressed by DAXX/H3.3/H3K9me3 pathway. DAXX-KD/KO increased sphere forming activity, but it was suppressed by knockdown of the target gene. In xenograft models, tumorigenicity was significantly increased in DAXX-KO cells with high expression of the target. Clinically, higher recurrence was recognized in PanNETs with low expression of DAXX and high expression of the target than others.
Conclusions: DAXX plays as a tumor suppressor and DAXX/H3.3 complex suppresses target genes by promoting H3K9me3 in PanNETs. DAXX and its target molecule might be effective biomarkers and therapeutic candidates.

overall_design: Two human NET cell lines QGP1 (PanNET) and NCI-H727 (bronchial NET) were obtained from the Health Science Research Resources Bank (Osaka, Japan) and the American Type Culture Collection (Manassas, VA), respectively. Microarray analysis was performed to compare gene expression patterns between DAXX-KD and DAXX-NC QGP1 cells. After uncharacterized genes were excluded, 81 and 96 genes were up- and down-regulated at >2-fold changes in DAXX-KD QGP1 cells.

first: Hiroki

last: Ueda

first: Yoshimitsu

last: Akiyama

first: Shu

last: Shimada

first: Satoshi

last: Matsumura

first: Yusuke

last: Mitsunori

first: Arihiro

last: Aihara

first: Daisuke

last: Ban

first: Takanori

last: Ochiai

first: Atsushi

last: Kudo

first: Minoru

last: Tanabe

first: Shinji

last: Tanaka


title: DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [scRNA-Seq, scBS-Seq]

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation.

overall_design: 267 cells collected from 3 stages of mouse embryonic development (E4.5, E5.5 and E6.5)

first: Steffen

last: Rulands

first: Heather

last: Lee

first: Stephen

last: Clark

first: Christof

last: Angermueller

first: Sebastien

last: Smallwood

first: Gavin

last: Kelsey

first: Oliver

last: Stegle

first: Benjamin

middle: D

last: Simons

first: Wolf

last: Reik


title: Systems genetics of sleep regulation

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

institute: University of Lausanne

summary: We used a systems genetics approach in the BXD genetic reference population of mice and assembled a comprehensive experimental knowledge base comprising a deep ‘sleep-wake’ phenome, central and peripheral transcriptomes, and plasma metabolome data, collected under undisturbed baseline conditions and after sleep deprivation.

overall_design:
We subjected mice from 33 BXD/RwwJ lines, 4 BXD/TyJ, the two parental strains (B6 and D2), as well as F1 individuals from reciprocal crosses between the parental lines, to a deep behavioral and molecular phenotyping with steady-state RNA levels in brain and liver under control and sleep deprivation.
Sleep deprivation was performed during 6h (ZT0-6), animals were sleep deprived in their home cage by “gentle handling” . Half of the animals were sleep deprived (SD), the other half was left undisturbed in another room (i.e., control or Ctr). Both SD and Ctr mice were sacrificed at ZT6, i.e., immediately after the end of the SD, for sampling of liver and cerebral cortex tissue.
The mice initially sacrificed for tissue collection yielded to 277 cortex and 277 liver samples of good quality. Equal amounts of RNA from biological replicates (same strain/line and experimental condition) were pooled.
In addition, to assess the stability of outcome variables over time, parental lines were sampled twice; i.e., at the start (labelled B61 and DB1) and end (labelled B62 and DB2) of the breeding and data-collecting phase which spanned 2 years (March 2012- December 2013).
In summary we generated 172 RNA-seq data sets.

first: Shanaz

last: Diessler

first: Yann

last: Emmenegger

first: Ioannis

last: Xenarios

first: Paul

last: Franken


title: Modulating Immune Cells to Prevent Breast Cancer Lung Metastasis

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

summary: Current lack of insight into mechanisms governing breast cancer metastasis has precluded development of curative therapies. Metastasis-initiating cells (MICs) are cancer cells uniquely equipped to establish metastatic outgrowths and are thought to cause recurrence and therapeutic resistance. Using various models of early metastatic disease, we have uncovered mechanisms by which certain primary tumors can prevent MICs from generating secondary tumors. In such cases, the primary tumor elicits a systemic immune response involving IL-1β expressing innate inflammatory cells that infiltrate the distant MIC microenvironment. Elevated IL-1β levels at the metastatic site prevent MICs from generating their highly proliferative E-cadherin-positive epithelial progeny. Thus, when the inherent plasticity of MICs is impeded, robustly growing tumors cannot be established. Ablation of the pro-inflammatory response or IL-1R inhibition relieves the block in differentiation and results in MIC colonization. Our data reveal complex and potentially life-prolonging interactions that occur between primary tumors and disseminated MICs that could be exploited to improve survival of patients at risk for metastatic disease.

overall_design: To examine the effect of the presence of a distal mammary tumor on gene expression in murine lungs . At least three replicates from each sample class were used, with adjustment for preparation batch and analyzed.

first: Zafira

last: Castano

first: Sandra

last: McAllister


title: RNA-seq of Hs578T cells with TET1 knockout

first: Jozef

last: Madzo

address: 403 Haddon Avenue

institute: Coriell Institute

summary: Both gains and losses of DNA methylation are common in cancer but the factors controlling this methylation balance remain unclear. Triple negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU is one of the most hypomethylated cancers observed. In search for an explanation for this, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. Through bioinformatic analyses in both breast and ovarian cancer cell line panels, we uncovered an intricate network connecting TET1 to hypomethylation and activation of cancer specific oncogenic pathways including PI3K, EGFR and PDGF. TET1 expression correlated with sensitivity to drugs targeting the PI3K-mTOR pathway. CRISPR mediated deletion of TET1 in two independent TNBC cell lines resulted in reduced expression of PI3K pathway genes, upregulation of immune response genes and substantially reduced cellular proliferation, suggesting dependence of oncogenic pathways on TET1 overexpression. Our work establishes TET1 as a potential oncogene that contributes to aberrant hypomethylation in cancer and suggests that TET1 could serve as a novel druggable target for therapeutic intervention.

overall_design: Three biological replicates of empty vector single clones and TET1 KO single clone (in triplicate) were used to make RNA-seq libraries.  Fold change of each gene was calculated by comparing changes in expression in KO compared to the empty vector control samples

first: Charly

last: Good

first: Shoghag

last: Panjarian

first: Andrew

last: Kelly

first: Bela

last: Patel

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa


title: The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [human DNase-Hypersensitivity]

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

summary: We mapped and systematically annotated the cis-regulatory elements in moue human primordial germ cells (PGCs).

overall_design:
We profiled DNase I hypersensitive sites (DHSs) in 20 mouse and 13 human PGC samples, 4 mouse and 10 human gonad somatic samples, 4 mouse embryonic stem cell (ESC) samples and 2 mouse epiblast like cell (EpiLC) samples.
Please note that processed data was generated from both rep1 and rep2 samples together and is linked to the correspoding 'rep1' sample records.

first: Jingyi

last: Li


title: Nasal DNA methylation is associated with childhood asthma

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

summary: Genomewide DNA methylation profiling of nasal DNA from control and asthmatic children. Methylation profiles were generated by the Illumina Infinium HumanMethylation450 beadchips.

overall_design: Bisulfite converted DNA were hybridized to the Illumina Infinium HumanMethylation450 beadchips

first: Xue

last: Zhang


title: Knockdown of TSPAN8 gene expression in the SH-SY5Y neuroblastoma cell line

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary:
Bipolar disorder (BD) has an estimated heritability of about 80%. Different pathways and candidate genes may contribute to the pathogenesis of BD, but definite mechanisms are yet unresolved. In a previous study, we identified the single nucleotide polymorphism (SNP) rs4500567, located in the upstream region of Tetraspanin 8 (TSPAN8), to be associated with bipolar disorder (BD).
The SNP´s minor allele results in a predicted binding site for the transcription factor Nuclear Factor Interleukin 3, regulated (NFIL3); luciferase assays confirmed allele-specific TSPAN8 expression levels.

overall_design: To define the global effect of altered TSPAN8 gene expression, we performed a knockdown of TSPAN8 in SH-SY5Y cells followed by microarray analysis.

first: Christoph

last: Schartner

first: Heike

last: Weber

first: Florian

last: Freudenberg

first: Antonia

last: Post

first: Lena

last: Weißflog

first: Andreas

last: Reif


title: PARCLIP analysis of NONO and SFPQ from U2OS and Hela cells

city: Nedlands

first: Archa

last: Fox

address: 35 Stirling Highway

institute: University of Western Australia

summary: To identify the RNA targets of the RNA binding proteins NONO and SFPQ in two different cell types, PARCLIP was carried out (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using a monoclonal antibody that recognises a NONO/SFPQ heterodimer. In this analysis, only the target gene NEAT1 was analysed, to show the binding sites for NONO and SFPQ in this transcript in the two cell lines.

overall_design: HeLa and U2OS cells were cultured and crosslinked according to the PARCLIP protocol. An antibody that pulls down the NONO/SFPQ heterodimer was used to purify these specific complexes. One replicate sample in each case was sequenced and analysed. Analysis of Neat1_2 regions that bind the paraspeckle proteins NONO and SFPQ was performed

first: Simon

last: Kobelke

first: Tomohiro

last: Yamazaki


title: The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [mouse ChIP-seq]

overall_design: We mapped the H3K4me3 modifications of 2 E14.5 female PGC samples. We also profiled the H3K27me3 modifications of 2 E14.5 female and 2 E14.5 male PGC samples.We also profiled the H3K27ac modifications of 1 E16.5 male PGC sample.


title: The landscape of accessible chromatin in mouse and human primordial germ cells (PGC) [mouse DNase-Hypersensitivity]


title: The landscape of accessible chromatin in mouse and human primordial germ cells (PGC)

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

status: Public on Jun 25 2018

city: Oklahoma City

first: Patrick

last: Gaffney

state: OK

address: 825 NE 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary: To fully comprehend how genetic variants influence phenotypes, we must understand the functions of the epigenome. To   assess the degree to which genetic variants influence epigenome activity, we integrate epigenetic and genotypic data from lupus patient lymphoblastoid cell lines to identify variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs). We demonstrate that enhancer hQTLs are enriched on autoimmune disease risk haplotypes and disproportionately influence gene expression variability compared with non-hQTL variants in strong linkage disequilibrium.  We show that the epigenome regulates HLA class II genes differently in individuals who carry HLA-DR3 or HLA-DR15 haplotypes, resulting in differential 3D chromatin conformation and gene expression. Finally, we identify significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.

overall_design: H3K27ac ChIP-seq, H3K4me1 ChIP-seq, H3K27ac HiChIP-seq, CTCF HiChIP-seq, and RNA-seq data are generated from 25 lymphoblastoid cell lines (LCLs) from European-American patients with systemic lupus erythematosus

first: Richard

middle: C

last: Pelikan

first: Jennifer

last: Kelly

first: Stuart

last: Glenn


title: RNAseq of CD31-/CD45- pneumocytes after 4 weeks of KRasG12V activation by tamoxifen and 2 weeks of chase

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

institute: IMDEA ALIMENTACION

summary: We report the RNAseq data obtained from 50.000-100.000 CD31-/CD45- pneumocytes isolated by FACS from mice harboring a normal dose or one extra copy of the Sirt1 gene, and a tamoxifen-inducible oncogenic KI alelle of KRasG12V after 4 weeks of tamoxifen treatment plus 2 weeks without tamoxifen. Pneumocytes with the activated form of the inducible KRasG12V oncogene sere selected making use of the fluorescent reporter gene Katushka (located at an independent locus), by detecting Katushka fluorescence.

overall_design: Four replicates of each genetic group (Sirt1-WT and Sirt1-Tg) pneumocytes were used for this study. Sirt1-WT were used as reference controls.

first: Pablo

last: Fernandez-Marcos

first: Roberto

last: Martin-Hernández

first: Luis

last: Costa-Machado


title: UGA Folic acid supplementation in pregnant women

city: Atlanta

first: Anna

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

summary: DNA samples were derived from maternal blood collected during a baseline prenatal visit and at delivery.

overall_design: 47 Samples

first: Lynn

middle: B

last: Bailey

first: Hea

last: Park

first: Alicia

last: Smith

first: Dorothy

last: Hausman

last: Fleming

first: Gisselle

last: Rosa

first: Marie

last: Caudill

first: Victoria

middle: L

last: Bland

first: Olga

last: Malysheva

first: Gail

middle: P

last: Kauwell

first: Andrew

last: Sokolow

first: Susan

last: Fisher


title: Differential gene expression of tissue-resident memory and effector memory T cells in breast cancer

status: Public on Jun 24 2018

city: Parkville

first: Chengzhong

last: Ye

state: Victoria

address: Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade

department: Bioinformatics Division

summary: Two infiltrating T cell populations (CD8+CD69+CD103+ and CD8+CD69+CD103-) were isolated from 3 breast cancer tumors by FACS for gene expression profiliing.

overall_design:
Unstranded RNA-seq were completed for 2 T cell populations from 3 tumors, comparing profiles within and across tumors.
Raw data requires controlled access and is deposited at EGAS00001002845.

first: Peter

last: Savas

first: Sherene

last: Loi


title: Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation

first: Carolyn

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: Plasmacytoid dendritic cells (pDCs) play a critical role in bridging the innate and adaptive immune systems. pDCs are specialized type I interferon (IFN) producers, which has implicated them as initiators of autoimmune pathogenesis. However, little is known about the down-stream effectors of type I IFN signaling that amplify autoimmune responses. Here we have used a chemokine reporter mouse to determine the CXCR3 ligand responses in DCs subsets. Following TLR7 stimulation conventional type 1 and type 2 DCs (cDC1 and cDC2 respectively) uniformly upregulate CXCL10. By contrast, the proportion of chemokine positive pDCs was significantly less, and stable CXCL10+ and CXCL10 - populations could be distinguished. CXCL9 expression was induced in all cDC1s, in half of the cDC2 but not by pDCs. In all DC subsets, type I IFNs were the main inducer of CXCR3 chemokines, as IFNAR receptor blocking or deficiency completely abrogated reporter expression. Chemoki ne producing potential was not concordant with the previously identified markers of pDC heterogeneity. Finally, we show that CXCL10+ and CXCL10 - populations are transcriptionally distinct, expressing unique transcriptional regulators, IFN signaling molecules, chemokines, cytokines and cell surface markers. This work highlights CXCL10 as a downstream effector of type I IFN signaling and suggests a division of labor in pDCs subtypes that likely impacts their function as effectors of viral responses and as drivers of inflammation.

overall_design: Comparison of gene expression in different haematopoietic cell types

first: Wei

last: Shi

first: Yang

last: Liao

first: Tracey

last: Baldwin

first: Joanna

last: Groom


title: Single-cell RNA-seq of six thousand purified CD3+ T cells from human primary TNBCs

institute: Walter and Eliza Hall Institute of Medical Research

summary: CD3+ T cells were isolated by FACS from primary tumour tissues of two triple-negative breast cancer patients. Sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation were done according to the protocol supplied by the manufacturer. Libraries were sequenced on an Illumina HiSeq 2500 High Output Mode using V4 clustering and sequencing chemistry to achieve 100 bp paired-end reads.

overall_design: Transcriptional profiling was completed for 5,174 CD3+ T cells from the first patient and 1,137 CD3+ T cells from the second patient.

first: Agus

last: Salim

first: Terence

last: Speed


title: Chemical Screen Identifies a Geroprotective Role of Quercetin in Premature and Physiological Aging

status: Public on Jun 23 2018

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: Aging increases the vulnerability to various diseases. The main goal of aging research is to find therapies that attenuate aging and alleviate aging-related diseases. In this study, we screened a nature product library for geroprotective compounds using Werner syndrome (WS) human mesenchymal stem cells (hMSCs), a premature aging model that we recently established. Ten candidate targets were identified and quercetin was further investigated due to its leading effects. Mechanistic studies revealed that in WS hMSCs, quercetin alleviated senescence via the enhancement of cell proliferation and the restoration and differentiation of heterochromatin architecture. RNA-seq analysis uncovered that quercetin and Vitamin C exerted geroprotective effects through different mechanisms. Besides WS hMSCs, quercetin also attenuated cellular senescence in Hutchinson-Gilford progeria syndrome (HGPS), physiological-aging and replicative-senescent hMSCs. More importantly, quercetin significantly improved the exercise endurance of old C57Bl/6 mice. Taken together, our study identifies quercetin as a geroprotective agent against premature and physiological aging, providing a novel therapeutic intervention for treating premature aging and promoting healthy aging.

overall_design: Transcriptome analysis of Werner syndrome (WS) human mesenchymal stem cells under basal or quercetin treated condition.

first: Guanghui


title: The cis-regulatory function of long mononucleotide A-T repeats in maintaining high transcription activity in cancer

city: Bangkok

first: Piyapat

last: Pin-on

address: ChalongKrung

country: Thailand

institute: KMITL

summary: To explore gene expression profiles in A549 lung cancer cell line after transfection CPP-AGO1-polyUs that shown potential reduce cell proliferation and cell growth.

overall_design: Gene expression profiles in A549 were explored at 48 hours after transfection 600 ng of CPP-AGO1 protein and 200 nM of U21 in conjugation buffer and incubated at 37 oC water-bath for 30 minutes. Two groups of A549 transfected CPP-AGO1-U21 and scramble consisting of 3 samples in each group were studied.

first: Apiwat

last: Mutirangura


title: Widespread intronic polyadenylation inactivates tumor suppressor genes in leukemia

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

summary: DNA mutations are known cancer drivers.  Here, we investigated if mRNA events that are upregulated in cancer can functionally mimic the outcome of genetic alterations.  3′-seq or RNA-seq were applied to normal and malignant B cells from chronic lymphocytic leukemia (CLL; N = 59).  We discovered widespread upregulation of truncated mRNAs and proteins in primary CLL cells that were not generated by genetic alterations but occurred through intronic polyadenylation (IPA).  IPA-generated truncated mRNAs were often recurrent (N = 330) and predominantly affected genes with tumor-suppressive functions.  The IPA-generated truncated proteins often lack the tumor-suppressive functions of the corresponding full-length proteins (DICER, FOXN3), and several even acted in an oncogenic manner (CARD11, MGA, CHST11).  In CLL, inactivation of tumor-suppressor genes (TSGs) through aberrant mRNA processing is substantially more prevalent than loss of TSGs through genetic events.  We further identified novel TSG candidates that are inactivated by IPA in leukemia and by truncating DNA mutations in solid tumors.  These genes are understudied in cancer as their overall mutation rates are lower than those of well-known TSGs.  Our findings show the need to go beyond genomic analyses in cancer diagnostics, as mRNA events that are silent at the DNA level are widespread contributors to cancer pathogenesis through inactivation of TSGs.

overall_design:
Examination of IpA isoforms in chronic lymphocytic leukemia (CLL) patients.
13 3'-seq samples from current study.
15 RNA-seq samples from current study, of which 8 were used only for validation of IpA events.
14 3'-seq samples from GSE111310 (GSM3028273-GSM3028286).
18 RNA-seq samples from GSE111310 (GSM3028302-GSM3028319).
17 samples from SRP029953.

first: Shih

last: Lee

first: Christina

last: Leslie

first: Christine

last: Mayr


title: Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming

first: Yifang

address: Haidian District

institute: Peking University

summary: We profile 36,199 single-cell transcriptomes at multiple timepoints throughout a highly efficient chemical reprogramming system using RNA-sequencing and reconstruct their progression trajectories. Through identifying sequential molecular events, we reveal that the dynamic early embryonic-like programs account for successful reprogramming from XEN-like state to pluripotency, including the transcriptomic signature of concomitant two-cell (2C) embryonic-like and early pluripotency program and the epigenetic signature of notable genome-wide DNA demethylation.

overall_design: Single cell RNA-Seq, bulk RNA-Seq and whole-genome bisulfite sequencing (WGBS) analyse the molecular mechanism of highly efficient chemical reprogramming system.

first: Ting

last: Zhao

first: Yao

last: Fu

first: Jialiang

last: Zhu

first: Qian

last: Zhang

first: Hongkui

last: Deng


title: Precardiac Organoids Form Two Heart Fields via Bmp/Wnt Signaling

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

summary: The discovery of the first heart field (FHF) and the second heart field (SHF) led us to understand how cardiac lineages and structures arise during development. However, it remains unknown how they are specified. Here, we generate precardiac spheroids with pluripotent stem cells (PSCs) harboring GFP/RFP reporters under the control of FHF/SHF markers, respectively. GFP+ cells and RFP+ cells appear from two distinct areas and develop in a complementary fashion. Transcriptome analysis shows a high degree of similarities with embryonic FHF/SHF cells. Bmp and Wnt are among the most differentially regulated pathways, and gain- and loss-of-function studies reveal that Bmp specifies GFP+ cells and RFP+ cells via the Bmp/Smad pathway and Wnt signaling, respectively. FHF/SHF cells can be isolated without reporters by the surface protein Cxcr4. This study provides novel insights into understanding the specification of two cardiac origins, which can be leveraged for PSC-based modeling of heart field/chamber-specific disease.

overall_design: We sought to determine the cellular identities of PSC-derived GFP+ and RFP+ cells. To do this, GFP+ and RFP+ CPCs were FACS-isolated from the spheroids at day 5.5 or from Hcn4GFP; Tbx1Cre; Ai9 mouse embryos at E7.75 and subjected to RNA-sequencing.

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