title: Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

city: Copenhagen

first: Malte

last: Thodberg

address: Blegdamsvej 3B, Building 7 (Maersk Tower)

department: CBMR

institute: University of Copenhagen

summary: Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent of accurate annotation of genes and in particular Transcription Start Sites (TSSs) and thereby core promoters. However, comprehensive genome-wide maps of TSS and their usage across commonly applied laboratorial conditions and treatments for S. pombe are lacking. To this end, we have applied Cap Analysis of Gene Expression (CAGE) to profile TSSs activity in S. pombe cultures exposed to heat shock, nitrogen starvation, peroxide and two commonly applied media, YES and EMM. CAGE allows for nucleotide resolution detection of TSS, which we show is substantially more accurate than existing PomBase annotation. On gene expression levels, we recapitulate known S. pombe stress response patterns, but our data also allowed us to detect many alternative TSSs within gene bodies that are changing their activity between conditions. Some of these have the potential to change the functions of encoded proteins due to coding sequence exclusion. We show that the immediate region around TSSs is almost as conserved as coding sequence across S. pombe strains, but the upstream promoter which houses transcription factor binding sites linked to stress response show high diversity. Our data constitute a central resource for S. pombe transcriptional regulation research.

overall_design: 5'-Cap Analysis of Gene Expression (CAGE) of wt S. pombe subjected to stress and media changes.

first: Axel

last: Thieffry

first: Jette

last: Bornholdt

first: Mette

last: Boyd

first: Christan

last: Holmberhg

first: Adjuna

last: Azad

first: Yun

last: Chen

first: Karl

last: Ekwall

first: Olaf

last: Nielsen

first: Albin

last: Sandelin


title: Different neuronal activity patterns induce different gene expression programs [ChIP-seq]

status: Public on Mar 16 2018

city: Boston

first: Kelsey

last: Tyssowski

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A vast number of different neuronal activity patterns could each induce a different set of activity-regulated genes. Mapping this coupling between activity pattern and gene induction would allow inference of a neuron's activity-pattern history from its gene expression and deepen our mechanistic understanding of activity pattern-dependent synaptic plasticity. In genome-scale experiments comparing brief and sustained activity patterns, we reveal that activity-pattern history can indeed be inferred from gene expression state. We find that brief activity selectively induces a small subset of the activity-regulated gene program that corresponds to the first of three temporal waves of genes induced by sustained activity. These first-wave genes are mechanistically distinct from genes in the later waves because their induction requires MAPK/ERK signaling but does not require de novo translation. Thus, the same mechanisms that establish the multi-wave temporal structure of gene induction also enable different gene sets to be induced by different activity patterns.

overall_design: ChIP-seq data from neurons in the presence/absense of MEK inhibition and neuronal activity.

middle: M

first: Nicholas

middle: R

last: DeStefino


title: Transcriptome-wide HITS-CLIP of Quaking (QKI) in TGF-Beta-treated HMLE (Mesenchymal-like) cells

status: Public on Mar 15 2018

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

type: Expression profiling by high throughput sequencing

summary: Members of the miR-200 family are critical gatekeepers of the epithelial state, restraining expression of pro-mesenchymal genes that drive epithelial-mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR-200c and another epithelial-enriched miRNA, miR-375, exert widespread control of alternative splicing in cancer cells. This is achieved by their strong suppression of the RNA binding protein Quaking (QKI), which is required to mediate the splicing changes regulated by these miRNAs. During EMT, QKI-5 directly binds to and regulates hundreds of alternative splicing events and exerts pleiotropic effects, such as increasing cell migration and invasion and restraining tumour growth, without appreciably affecting mRNA levels. QKI-5 is both necessary and sufficient to direct EMT alternative splicing changes, and this splicing signature is broadly conserved across many epithelial-derived cancer types. Importantly, several actin cytoskeleton-associated genes are directly targeted both by QKI and miR-200c, revealing coordinated control of alternative splicing and mRNA abundance during EMT. These findings demonstrate the existence of a miR-200/miR-375/QKI axis that impacts cancer-associated epithelial cell plasticity through widespread control of alternative splicing.  The purpose of the CLIP experiment was to determine direct targets of QKI.

overall_design: 9 samples: 7 technical replicates of QKI immunoprecipitation, 2 technical replicates of size-matched input samples (controls)

middle: A

first: John

last: Toubia

first: B

middle: K

last: Dredge

first: Andrew

middle: G

last: Bert

first: Phillip

last: Gregory

first: Gregory

middle: J

last: Goodall


title: A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal

status: Public on Mar 14 2018

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

country: China

institute: Institutes of Biomedical Sciences Fudan University

summary: N6-methyladenosine (m6A) is an abundant modification in eukaryotic mRNA, regulating mRNA dynamics by influencing mRNA stability, splicing, export and translation. Recent studies discovered m6A methyltransferases (?writer?), demethylases (?eraser?) and binding proteins (?reader?), which modulate m6A methylation. However, the precise m6A regulating machinery still remains incompletely understood. Here we demonstrate that ZC3H13, a zinc finger protein, plays an essential role in modulating m6A methylation on polyadenylated RNA in the nucleus. ZC3H13 exists in an evolutionary-conserved macromolecular complex containing WTAP, Virilizer and Hakai. We confirm the interaction among those proteins and demonstrate that knockdown of Zc3h13 in mouse embryonic stem cell (mESC) significantly decreases global m6A level on mRNA, mainly at 3? untranslated regions (3? UTR). Interestingly, fractionation assays show that upon Zc3h13 knockdown a great majority of WTAP, Virilizer and Hakai translocate to the cytoplasm and the nuclear presence of the methyltransferase Mettl3 and Mettl14 also decrease significantly. In contrast, knockdown of WTAP, Virilizer or Hakai does not change the nuclear localization of Zc3h13. This suggests that Zc3h13 is required for nuclear localization of the Zc3h13-WTAP-Virilizer-Hakai complex, which is important for RNA m6A methylation. Finally, Zc3h13 depletion, as does WTAP, Virilizer or Hakai, impairs self-renewal and triggers mESC differentiation. Taken together, our findings demonstrate that Zc3h13 plays an essential role in anchoring WTAP, Virilizer and Hakai in the nucleus to facilitate m6A methylation and to regulate mESC self-renewal.

overall_design:
We examined N6-methyladenosine and mRNA profiles in scr and shZc3H13 mouse embryonic stem cells.
MeRIP-seq were performed to examine N6-methyladenosine (m6A) on the transcrits in the cytoplasmic and nuclear fractions of control and Zc3h13 kd mESCs.
RNA-seq were conducted to examine the gene expression profiles of Zc3h13 kd and control mESCs. 3, RIP-seq were carried out to identify Zc3h13  protein binding RNAs in mESCs.

first: Lv

last: Ruitu

first: Diao

last: Jianbo

first: Wen

last: Jing

first: Shi

last: Yang


title: Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer [ChIP-seq]

status: Public on Mar 13 2018

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Steroid hormone receptors are simultaneously active in many tissues and capable of altering each other's function. Estrogen receptor ɑ (ER) and glucocorticoid receptor (GR) are expressed in the uterus and their ligands have opposing effects on uterine growth. In endometrial tumors expressing high levels of ER, we surprisingly found that expression of GR is associated with poor prognosis. Dexamethasone reduced normal uterine growth in vivo; however, this growth inhibition was abolished in estrogen-induced endometrial hyperplasia. We observed low genomic binding site overlap when ER and GR are induced with their respective ligands; however, upon simultaneous induction they co-occupy more sites. GR binding is significantly altered by estradiol with GR recruited to ER bound loci that become more accessible upon estradiol induction. Gene expression responses to co-treatment were more similar to estradiol, but with novel regulated genes. Our results suggest phenotypic and molecular interplay between ER and GR in endometrial cancer.

overall_design: ChIP-seq, ATAC-seq, and RNA-seq data collected from endometrial cancer cell lines induced with dexamethasone, estradiol, or the combination

first: Jay

first: Jeffery

last: Vahrenkamp


title: Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer [ATAC-seq]


title: Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin

city: Beijing

first: Chenhuan

last: Xu

address: 1 Beichen West Road

institute: Beijing Institute of Genomics

type: Methylation profiling by high throughput sequencing

summary: The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Victor

last: Corces


title: RING-finger protein 6 amplification activates JAK/STAT3 pathway by modifying SHP-1 ubiquitylation and associates with poor outcome in colorectal cancer

status: Public on Mar 12 2018

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To elucidate whether  RNF6 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  RNF6 siRNA and control siRNA transfectants.

overall_design: RNA-seq was performed in HT29  colorectal cancer cells after RNF6 knock down

first: Jie

last: Hong


title: Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells

city: Basel

first: Monica

last: Golumbeanu

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle towards HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression. We further validated our results using primary CD4+ T cells isolated from HIV+ individuals.

overall_design: Human primary CD4+ T-cells were infected, cultured, and maintained in a resting, latent phenotype in order to generate a primary model of HIV latency. Latently infected cells were either left untreated, or exposed to SAHA or TCR stimulation, followed by single-cell isolation and single-cell RNA-seq (scRNA-Seq) analysis. Bulk RNA-Seq experiments were also performed as control. To validate the observed cellular heterogeneity in the primary model of HIV latency, we used primary CD4+ T cells isolated from HIV+ individuals. As for the primary HIV latency model, resting cells from HIV+ individuals were either not treated or TCR-treated before single cell isolation and single-cell RNA-Seq.

first: Sara

last: Cristinelli

first: Sylvie

last: Rato

first: Miguel

last: Munoz

first: Matthias

last: Cavassini

first: Niko

last: Beerenwinkel

first: Angela

last: Ciuffi


title: LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies in acute myeloid leukemia (ChIP-Seq)

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Genome-wide binding/occupancy profiling by high throughput sequencing

overall_design: Genome-wide analysis of H3K27ac modification and MEF2C binding in AML with gene knockout or inhibitor treatment

first: Christopher

last: Vakoc


title: Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Analysis of Th17 gene signature in the presence of CD28 costimulation in human CD4 naïve T cells

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

summary: We determined differentially regulated gene expression profile in CD4 naïve T cells cultured in presence or absence of Th17 inducing cytokines (IL23+IL1β) and anti-CD28. We reported that CD28 costimulation induced Th17-suppressive gene signature.

overall_design: Human CD4 naive T cells were cultured as 4 different conditions (Th0, Th0CD28, Th17 and Th17CD28) to examine differentially expressed genes among conditions.

first: Shankar

last: Revu

first: Mandy

last: McGeachy

first: Natalie

last: Rittenhouse


title: Fas promotes T helper-17 cell differentiation and inhibits development of T helper-1 cells by binding and sequestering the STAT1 transcription factor

status: Public on Mar 10 2018

city: Cambridge

first: Aviv

last: Regev

address: 415 Main Street

institute: Broad Institute

summary: The death receptor Fas removes activated lymphocytes through apoptosis. Previous  transcriptional profiling predicted that Fas positively regulates interleukin (IL)-17-producing T helper (Th17) cells. We here demonstrate that Fas promoted the generation and stability of Th17 cells and prevented their differentiation into Th1 cells. Mice with T cell- and Th17 cell-specific deletion of Fas were protected from induced autoimmunity and Th17 cell differentiation and stability was impaired. Fas deficient Th17 cells instead developed a Th1 cell-like transcriptional profile, which we predicted by a new algorithm to depend on STAT1. Experimentally, Fas indeed bound and sequestered STAT1 and Fas deficiency enhanced IL-6 induced STAT1 activation and nuclear translocation, whereas Fas-STAT1 double-deficiency reversed the transcriptional changes induced by Fas deficiency. Thus, our computational and experimental approach identified Fas as a regulator of the Th17-to-Th1 cell balance by controlling the availability of the opposing STAT1 and STAT3 proteins with direct impact on autoimmunity.

overall_design: comparative RNA-seq study comparing the expression of C57BL/6 wildtype vs. Fas-deficient (lpr) sorted naive CD4+ T cells differentiated without cytokines (Th0 cells) or with TGF-β1 with IL-6 (Th17 cells)

first: Gerd

last: Meyer zu Horste

first: Dariusz

last: Przybylski

first: Vijay

last: Kuchroo


title: Epigenetic Rescue of Autism-like Social Deficits in Shank3-Deficient Mouse Models

city: Buffalo

first: Zhen

last: Yan

address: 124 Sherman Hall

department: Physiology and Biophysics

institute: University at Buffalo

summary: To determine whether histone deacetylase (HDAC) inhibition has genome-wide effects on gene expression, we used RNA sequencing to analyze the mRNA profile in prefrontal cortex (PFC) of wild-type (WT) and Shank3-deficient (Shank3+/ΔC) mice treated with romidespin or saline control. We mapped the sequences to 24,420 mouse genes. Compared to WT, 365 genes in saline-treated Shank3+/ΔC mice showed a change in expression values of at least 1.2 fold and p ≤ 0.01 (213 downregulated, 152 upregulated). In romidepsin-treated Shank3+/ΔC mice, ~88% of the downregulated genes (n=187 genes) were normalized to control values. Further analysis of the romidepsin-restored genes revealed enrichment in actin cytoskeleton-mediated transport, signal transduction pathways, and developmental processes.

overall_design:
Comparison of gene expression in prefrontal cortex of wild-type mice, saline-treated Shank3-deficient mice and romidepsin-treated mice
Heterozygous Shank3+/ΔC mice (5-8 weeks old, male) expressing C-terminal (exon 21) deleted Shank3 (Jackson Labs), which exhibited the significant loss of full-length Shank3 expression, and age-matched wild-type littermates (male), were used in the experiments.

first: Luye

last: Qin

first: Kaijie

last: Ma

first: Zi-Jun

last: Wang

first: Zihua

last: Hu


title: Single cell-RNA-seq for airway epithelial cells

status: Public on Mar 09 2018

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

summary: Outputs from single-cell RNA-seq sequenced reads from isolated mouse epithelial cells from homeostatic submucosal glands and Naphthalene-injured surface epithelium of adult mouse airway (P70)

overall_design: Isolated single cells were processed and sequenced using 10X genomics Chromium single-cell RNA-seq protocol and Illumina NextSeq 500

first: Aleksandra

last: Tata

first: Ryan

last: Chow

first: Purushothama


title: Modulation of dietary methionine intake elicits potent, but distinct, anticancer effects on primary vs metastatic tumors

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

summary: Methionine concentration in diet influences the growth rate of metastatic cells in vivo

overall_design: Eight-week-old male C57BL/6J mice were injected with 1x10^5 B16-F10.1 cells via the tail vein. Mice were allowed 21 days to develop pulmonary metastases and then were fed a methionine adequate, methionine deficient or methionine restricted (25% of normal) diet for 2 weeks. Metastatic tissue was then collected and RNA extracted for sequencing.

first: Isabelle

last: Miousse

first: Julia

last: Tobacyk

first: Charles

last: Quick

first: Azemat

last: Jamshidi-Parsian

last: Skinner

first: Rajshekhar

last: Kore

first: Oleksandra

last: Pavliv

first: Stepan

middle: B

last: Melnyk

first: Kristy

last: Kutanzi

first: Fen

last: Xia

first: Robert

last: Griffin

first: Igor

last: Koturbash


title: DNA methylation profile of adipocytes treated with DNMT inhibitor, guadecitabine (100nM, 3X daily).

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

summary: Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion and proximal and direct co-culture of adipocytes . Treatment of adipocytes with hypomethylating agent guadecitabine decreased migration and invasion of OC cells towards adipocytes.

overall_design: Due to this result, we performed methyl-capture-seq of adipocytes treated with DNMT1 inhibitor to analyze differential gene expression changes that occur in the adipocyte that may explain the above observation that hypomethylating agent treatment of adipocytes decrease migration and invasion. In duplicate, subcutaneous, human, primary adipocytes (ATCC) were treated with DMSO control or guadecitabine (100nM, 3X daily) and on day 4, DNA was extracted with AllPrep kit (Qiagen #80204) from adipocytes, sonicated (180-200bp), and used as input for methylated DNA capture kit (Diagenode) according to manufacturer’s protocol. Mecap-seq libraries were prepared with NEXTflex Methyl-Seq1 kit (Bioo Scientific) according to manufacturer’s protocol. Libraries were verified using Qubit and Bioanalyzer, prior to sequencing on Illumina NextSeq.

first: Jessica

last: Tang

first: Doug

last: Rusch

first: Aaron

last: Buechlein


title: The LINC01138 Drives Malignancies via Activating Arginine Methyltransferase 5 in Hepatocellular Carcinoma

status: Public on Mar 11 2018

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Our study have demonstrated LINC01138 acts as an oncogenic driver that promotes cell proliferation, tumourigenicity, tumour invasion and metastasis through physically interacting with Arginine Methyltransferase 5 (PRMT5) in HCC cells. In order to investigate the related signaling pathways regulated by LINC01138 or PRMT5, we performed the unbiased transcriptome profiling using high-throughput RNA sequencing in SMMC-7721 cells transfected with si-LINC01138 or si-PRMT5. Here we showed the LINC01138/PRMT5 axis is an ideal therapeutic target for HCC treatment.

overall_design: Illuminate the related signaling pathways and biological processes regulated by LINC01138 or PRMT5 in human liver cancer SMMC-7721 cells through high-throughput sequencing data.

first: Shenglin

last: Huang

first: Xianghuo

last: He


title: Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

summary: To understand how mutations in Matrin 3 (MATR3) cause amyotrophic lateral sclerosis (ALS) and distal myopathy, we used transcriptome and interactome analysis, coupled with microscopy. Over-expression of wild-type (WT) or F115C mutant MATR3 had little impact on gene expression in neuroglia cells. Only 23 genes, expressed at levels of >100 transcripts showed ≥1.6-fold changes in expression by transfection with WT or mutant MATR3:YFP vectors. We identified ~123 proteins that bound MATR3, with proteins associated with stress granules and RNA processing/splicing being prominent. The interactome of myopathic S85C and ALS-variant F115C MATR3 were virtually identical to WT protein. Deletion of RNA recognition motif (RRM1) or Zn finger motifs (ZnF1 or ZnF2) diminished the binding of a subset of MATR3 interacting proteins. Remarkably, deletion of the RRM2 motif caused enhanced binding of >100 hundred proteins. In live cells, MATR3 lacking RRM2 (ΔRRM2) formed intranuclear spherical structures that fused over time into large structures. Our findings in the cell models used here suggest that MATR3 with disease-causing mutations is not dramatically different from WT protein in modulating gene regulation or in binding to normal interacting partners. The intra-nuclear localization and interaction network of MATR3 is strongly modulated by its RRM2 domain.

overall_design: RNA-seq of untransfected cells or cells with overexpression of YFP, WT MATR3, or ALS mutation MATR3

middle: D


title: RNA sequencing data from triple-negative breast cancer patient-derived xenografts (PDX)

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: RNAseq was performed on WHIM2 and WHIM30 PDX mammary tumors, brain metastases, and single cell suspensions over time.

overall_design: Comparison of gene expression profiles between two PDX models of triple-negative breast cancer, and between primary tumors, cell suspensions, and brain metastases within the PDX lines.

first: Tia

middle: H

last: Turner

first: Mohammad

last: Alzubi

first: Sahib

middle: S

last: Sohal

first: Amy

middle: L

last: Olex

first: Mikhail

last: Dozmorov

first: J

middle: C

last: Harrell


title: Methionine supplementation and radiation in mouse jejunum

first: Kyle

last: Navel

summary: Methionine supplementation exarcerbates radiation injury in the mouse jejunum

overall_design: Eight week old CBA/J male mice received 0 or  8.5 Gy of gamma radiation on a methionine adequate or supplemented (300%) diet for 6 days

first: Isabelle

last: Miousse

first: Charles

last: Skinner

first: Rupak

last: Pathak

first: Sarita

last: Garg

first: Stepan

last: Melnyk

first: Martin

last: Hauer-Jensen


title: Etv5 ChIP-seq in AT2 cells

status: Public on Mar 08 2018

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

summary: Alveolar type II (AT2) cell dysfunction contributes to a number of  significant human pathologies including respiratory distress syndrome,  lung adenocarcinoma, and debilitating fibrotic diseases,  but the critical transcription factors that maintain AT2 cell identity  are unknown. Here we show that the E26 transformation-specific  (ETS) family transcription factor Etv5 is essential tomaintain AT2 cell  identity. Deletion of Etv5 from AT2 cells produced gene and protein  signatures characteristic of differentiated alveolar type I (AT1) cells.  Consistent with a defect in the AT2 stem cell population, Etv5 deficiency  markedly reduced recovery following bleomycin-induced  lung injury. Lung tumorigenesis driven by mutant KrasG12D was  also compromised by Etv5 deficiency. ERK activation downstream  of Ras was found to stabilize Etv5 through inactivation of the cullin-  RING ubiquitin ligase CRL4COP1/DET1 that targets Etv5 for proteasomal  degradation. These findings identify Etv5 as a critical output of  Ras signaling in AT2 cells, contributing to both lung homeostasis and tumor initiation.

overall_design: AT2 cells (2 X 10^7) were isolated from 10- to 12-wk-old  C57BL/6 mice. Active Motif Epigenetic Services performed  ChIP assays.

first: Z

last: Zhang

first: S

last: Kummerfeld


title: Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

summary: Tumor microenvironment plays a pivotal role in cancer progression; however, little is known regarding how differences in the microenvironment affect characteristics of cancer cells. Here, we investigated the effects of tumor microenvironment on cancer cells by using mouse tumor models. After 3 cycles of inoculation and extraction of human pancreatic cancer cells, including SUIT-2 and Panc-1 cells, from tumors, distinct cancer cell lines were established; 3P cells from the pancreas obtained using the orthotopic tumor model, and 3sc cells from subcutaneous tissue obtained using the subcutaneous tumor model. On cell re-inoculation of these cells, the 3sc cells and, more prominently, the 3P cells, exhibited higher tumorigenic activity than the parental cells. The 3P cells specifically exhibited low E-cadherin expression and high invasiveness, suggesting that they were endowed with the highest malignant characteristics. RNA-sequence analysis demonstrated that distinct signaling pathways were activated in each cell line and that the 3P cells acquired a cancer stem cell-like phenotype. Among cancer stem cell-related genes, those specifically expressed in the 3P cells, including NES, may be potential new targets for cancer therapy. The mechanisms underlying the development of highly malignant cancer cell lines were investigated. Individual clones within the parental cells varied in tumor-forming ability, indicating the presence of cellular heterogeneity. Moreover, the gene expression profile of each clone changed after orthotopic inoculation. The present study thus suggests that both selection and education processes are involved in the development of highly malignant cancer cells.

overall_design: Expression of mRNA in the highly malignant sublines of SUIT-2 and Panc-1 cells xenografted into mice.

first: Kei

last: Takahashi

first: Shogo

last: Ehata

first: Yasuyuki

last: Morishita

first: Manabu

last: Soda

first: Hiroyuki

last: Mano

first: Kohei

last: Miyazono


title: Soft Hydrogels Support Differentiation of Induced Pluripotent Stem Cells toward Mesenchymal Stromal Cells [methylation]

first: Wolfgang

last: Wagner

summary: Induced pluripotent stem cells (iPSCs) can be differentiated toward mesenchymal stromal cells (MSCs), but at least on epigenetic level this transition remains incomplete with the current culture conditions. Hydrogels provide a more physiologic three-dimensional environment for in vitro cell culture than conventional tissue culture plastic (TCP). In this study, we followed the hypothesis that growth and differentiation of primary MSCs and of iPSC-derived MSCs (iMSCs) can be enhanced on hydrogels. To this end, we used a hydrogel made of human platelet lysate (hPL). MSCs were effectively cultured on and inside hPL-gel and demonstrated more structured deposition of extracellular matrix (ECM) components than TCP. Furthermore, hPL-gel supported differentiation of iPSCs toward MSCs. Unexpectedly, the differentiation process seemed to be hardly affected by the substrate: iMSCs generated either on TCP or hPL-gel did not reveal differences in morphology, immunophenotype, or differentiation potential. Moreover, global gene expression and DNA-methylation profiles were almost identical in iMSCs generated on TCP or hPL-gel. Our results indicate that matrix elasticity is less crucial for directed lineage-specific differentiation toward MSCs than expected.

overall_design: iPSC were differentiated toward MSC either on human platelet lysate (hPL) gel or on tissue culture plastic (TCP) to compare impact on DNA methylation profiles with Illumina Infinium 450k Human Methylation BeadChip.

first: Roman

last: Goetzke

first: Julia

last: Franzen

first: Alina

last: Ostrowska

first: Michael

last: Vogt

first: Gerd

last: Klein

first: Björn

last: Rath

last: Zenke


title: RNA-seq data of adipocytes co-cocultured with OVCAR5 in Boyden chamber (4d)

first: Kenneth

last: Nephew

summary: We indirectly cocultured OVCAR5-RFP cells using a 0.45 micron Boyden chamber with or without adipocytes for 4 days, collected the RNA from adipocytes, and performed RNA-seq

overall_design: To identify potential changes in methylation and gene expression due to the 2-way communication between adipocytes and OC cells. In triplicate, SGBS adipocytes were indirectly cocultured with or without OVCAR5-RFP cells using a 0.45 micron Boyden chamber for 4 days. Then RNA-seq was performed on adipocytes.

first: Jessica

last: Tang

first: Doug

last: Rusch

first: Aaron

last: Buechlein


title: BET bromodomain proteins regulate enhancer function during adipogenesis

status: Public on Mar 07 2018

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Developmental transitions are guided by master regulatory transcription factors. During adipogenesis, a transcriptional cascade culminates in expression of PPARg and C/EBPa, which orchestrate activation of the adipocyte gene expression program. However, the coactivators controlling PPARg and C/EBPa expression are less well characterized.  Here we show the bromodomain-containing protein, BRD4, regulates transcription of PPARg and C/EBPa.  Analysis of BRD4 chromatin occupancy reveals that induction of adipogenesis in 3T3L1 fibroblasts provokes dynamic redistribution of BRD4 to de novo super enhancers proximal to genes controlling adipocyte differentiation. BET bromodomain inhibition impedes BRD4 occupancy at these de novo enhancers and disrupts transcription of Pparg and Cebpa, thereby blocking adipogenesis. Furthermore, silencing of these BRD4-occupied distal regulatory elements at the Pparg locus by CRISPRi demonstrates a critical role for these enhancers in the control of Pparg gene expression and adipogenesis in 3T3L1s. Together, these data establish BET bromodomain proteins as time- and context-dependent coactivators of the adipocyte cell state transition.

overall_design: BRD4 and RNA Pol2 ChIP-Seq and corresponsing whole cell extract controls in 3T3L1 fibroblasts undergoing adipogenic differentiation in the presence of JQ1

first: Jonathan

last: Brown

middle: E


title: EZH2 and H3K27me3 ChIP-seq in E14 mouse embryonic stem cells harboring wildtype or mutant EZH2.

status: Public on Mar 06 2018

city: Washington

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th Pl Nw

institute: FBRI at Virginia Tech Carilion

summary: We report the occupancy and catalysis of wildtype and allosteric activation-decifient mutants of EZH2 in E14 mESC by ChIP-seq.

overall_design: Examination of EZH2 and H3K27me3 deposition on chromatin in E14 mESC with different EZH2 genotypes.

first: Danny

last: Reinberg


title: High fat diet-induced modifications in membrane lipid and mitochondrial-membrane protein signatures precede the development of hepatic insulin resistance in mice

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

institute: Hemholtz Center Munich

summary:
In this survey we effectively combined transcriptomics, proteomics and targeted-metabolomics to analyse the temporal relationship of alterations in liver preceding and accompanying the development of HFD-mediated hepatic insulin resistance. To assess HFD-mediated alterations in physiological parameters, insulin sensitivity, and molecular adaptations in liver male C3HeB/FeJ mice treated with a high-fat diet (HFD) for 7, 14, or 21 days and compared to age- matched controls fed low-fat diet (LFD).
Data indicate early systemic increases in pro-inflammatory signals, in hepatic DAG but not hepatic TAG concentrations prior to development of hepatic insulin resistance. We propose a hypothesis via which a HFD-mediated increase in the hepatic long-chain acyl-carnitine moiety in liver alters mitochondrial membrane physiology and beta-oxidation rates, thereby contributing to oxidative stress and the development of insulin resistance in liver. Alterations in the enrichment of respiratory chain complex proteins, substrate transporters, VDACs, and long-chain carnitines in mitochondrial membranes likely affect mitochondrial membrane topology, membrane dynamics (fission and fusion) and bioenergetics as well as the cross-talk between the mitochondria and other cellular compartments. In conclusion, we emphasize a tight association between HFD-induced early modifications in the organisation of mitochondrial membranes paving the road for hepatic insulin resistance.

overall_design: We performed gene expression microarray analysis on liver from C3HeB/FeJ (C3H) males during 7, 14 or 21 days HFD challenge.

first: Melanie

last: Kahle

first: Alexander

last: Schaefer

first: Anett

last: Seelig

first: Jürgen

last: Schultheiß

first: Moya

last: Wu

first: Michaela

last: Aichler

first: Jörn

last: Leonhardt

first: Birgit

last: Rathkolb

first: Jan

last: Rozman

first: Hakan

last: Sarioglu

first: Stefanie

last: Hauck

first: Marius

last: Ueffing

first: Eckhard

last: Wolf

first: Gabi

last: Kastenmueller

first: Jerzy

last: Adamski

first: Axel

last: Walch

first: Martin

last: Hrabe de Angelis

first: Susanne

last: Neschen


title: DNA methylation in airway and parenchymal fibroblasts from individuals with and wthout COPD

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

country: United Kingdom

institute: University of Nottingham

summary:
Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease of the lungs that is currently the fourth leading cause of death worldwide. Genetic factors account for only a small amount of COPD risk, but epigenetic mechanisms including DNA methylation, have the potential to mediate the interactions between an individual?s genetics and environmental exposure. DNA methylation is highly cell type specific and individual cell type studies of DNA methylation in COPD are sparse. Fibroblasts are present within the airway and parenchyma of the lung and contribute to the aberrant deposition of extracellular matrix in COPD. No assessment or comparison of genome-wide DNA methylation profiles in airway and parenchymal fibroblasts from individuals with and without COPD has been undertaken. These data provide valuable insight into the molecular mechanisms contributing to COPD and the differing pathologies of small airways disease and emphysema in COPD.
Methods: Genome-wide DNA methylation was evaluated at over 485,000 CpG sites using the Illumina Infinium HumanMethylation450 BeadChip array in airway (non-COPD n=8, COPD n=7) and parenchymal fibroblasts (non-COPD n=18, COPD n=28) isolated from individuals with and without COPD. Targeted gene expression was assessed by qPCR in matched RNA samples.
Results: Differentially methylated DNA regions were identified between cells isolated from individuals with and without COPD in both airway and parenchymal fibroblasts. Only in parenchymal fibroblasts was differential DNA methylation associated with differential gene expression. A second analysis of differential DNA methylation variability identified 359 individual differentially variable CpG sites in parenchymal fibroblasts. No differentially variable CpG sites were identified in airway fibroblasts. Five differentially variable methylated CpG sites, associated with three genes were subsequently assessed for gene expression differences. Two genes (OAT and GRIK2) displayed significantly increased gene expression in cells isolated from individuals with COPD.
Conclusions: Differential and variable DNA methylation was associated with COPD status in parenchymal fibroblasts but not airway fibroblasts. Aberrant DNA methylation was associated with altered gene expression imparting biological function to DNA methylation changes. Changes in DNA methylation are therefore implicated in the molecular mechanisms underlying COPD pathogenesis and may represent novel therapeutic targets.


title: Mycobacterium tuberculosis tRNA induces IL-12p70 via synergistic activation of pattern recognition receptors within a cell network.

city: Los Angeles

first: Caroline

last: Keegan

address: 615 Charles E. Young Drive South 246 OHRC

institute: UCLA

summary: Analysis of gene expression profiles identified a mycobacterial tRNA-induced innate immune network resulting in the robust production of IL-12p70, a cytokine required to instruct an adaptive Th1 response for host defense against intracellular bacteria.

overall_design: Gene expression profiles induced by microbial ligands in human PBMC (three independent donors), at three timepoints.

first: Stephan

last: Krutzik

first: Mirjam

last: Schenk

first: Phillip

middle: O

last: Scumpia

first: Jing

last: Lu

first: Yan

last: Pang

first: Brandon

last: Russell

first: Kok

last: Lim

first: Scarlet

last: Shell

first: Erin

last: Prestwich

first: Dan

last: Su

first: David

last: Elashoff

first: Robert

middle: M

last: Hershberg

first: Barry

last: Bloom

first: John

middle: T

last: Belisle

first: Sarah

last: Fortune

first: Peter

last: Dedon

first: Matteo

last: Pellegrini

last: Modlin


title: RNA-seq of SCLC PDX models treated with EP

first: Benjamin

middle: Jacob

last: Drapkin

state: MASSACHUSETTS

address: 149 13th Street, room 7330-M

department: Cancer Center

institute: Massachusetts General Hospital

summary: We report the correlation of transcript abundance with response to EP in 19 PDX models of SCLC

overall_design: Single-end RNA-seq was performend on fresh-frozen samples of 19 patient-derived xenografts, and transcript abundance was then correlated with sensitivity to EP in vivo.

first: Camilla

last: Christensen

first: Ruben

last: Dries


title: Fine Resolution Mapping of TF binding and Chromatin  Interactions

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Monitoring the location of transcription factors (TFs) binding to DNA is key to understanding  transcriptional regulation. The main tool for mapping TF binding is ChIP-seq and its variants.  However, current ChIP-based methods are hampered by at least one of the following limitations:  large input requirements, low spatial resolution, and limited compatibility with high-throughput  automation. Here, we describe SLIM-ChIP (Short fragment enriched, Low input, Indexed,  MNase ChIP), which overcomes these challenges by combining enzymatic fragmentation of  chromatin and on-bead indexing of immobilized TF-DNA complexes. We show that SLIM-ChIP  reproduces high resolution binding map of yeast Reb1 similarly to the high-resolution TF  mapping methods ChIP-exo and ORGANIC. Yet, SLIM-ChIP requires substantially less input  material, and is fully compatible with high-throughput procedures. We further demonstrate the  robustness and flexibility of SLIM-ChIP by probing Abf1 and Rap1 in yeast and CTCF in mouse  embryonic stem cells. Finally, we show that the unique combination of high resolution and  preservation of DNA protection patterns by SLIM-ChIP provide an additional layer of information  on the chromatin landscape surrounding the bound TF. We used this information to identify a  class of Reb1 sites in which the proximal -1 nucleosome tightly interacts with Reb1 and unlike  in most Reb1 sites is refractory to remodeling by the RSC complex. Importantly, the interaction  of Reb1 with the -1 nucleosome prevents transcription initiation and can serve as a more  general mechanism for maintaining unidirectional transcription. Altogether, SLIM-ChIP is an  attractive solution for mapping DNA binding proteins in a more informative context regarding  their surrounding chromatin occupancy landscape at a single cell level.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: The dataset includes several ChIP-Seq experiments of yeast and mouse ESCs transcription factors.  Reb1 (yeast) ChIP was performed in several Mnase levels and different numbers of input cells (five samples overall). Mouse CTCF ChIP was performed in several Mnase levels (five samples overall). Abf1 and Rap1 (yeast) were mapped using a mix of different Mnase levels (one sample each).


title: Gene expression analysis of human cancer associated fibroblasts (CAFs) stimulated with Platelet-Derived Growth Factor (PDGF)-CC

city: Lund

first: Kristian

last: Pietras

address: Medicon Village, Building 404:A3

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary:
This study is part of a larger effort set to determine the factors requried for the crosstalk between tumor cells and fibroblasts in breast cancer.
Specifically, the primary aim of this microarray analysis is to detail the soluble factors secreted by cancer-asociated fibroblasts following stmulation with PDGF-CC.

overall_design: CAF2 cells were either left untreated (control) or stimulated with human recombinant PDGF-C for 6 or 48 hours. Three (3) biological replicates for each of the three conditions were used for the analysis, for a total of 12 samples

first: Eliane

last: Cortez


title: Gene Expression in Human Rhabdomyosarcoma

first: Sowmya

last: Iyer

summary: Gene expression analysis identified unique transcriptional changes in rhabdomyosarcoma when compared with normal muscle.  Our studies focused on a gene called VANGL2 that regulated growth and self-renewal in embryonal rhabdomyosarcoma.

overall_design:
RNA-seq data for 106 samples are included - 5 normal muscle  and 101 Rhabdomyosarcoma (SRA accession SRP048220,  dbGaP accession phs000720.v2.p1, Bioproject accession PRJNA238612)
---------------------
Authors state that the following "Data for the 22 patient samples are not in dbGaP yet, but will be made available soon":
RMS202.1
RMS2021
RMS2022
RMS2026
RMS2033
RMS205.1
RMS2059
RMS206.1
RMS2060
RMS209.1
RMS2096
RMS2103
RMS2119
RMS222.1
NCI0003
NCI0075
NCI0082
NS127muscle
NS128muscle
NS129muscle
NS132muscle
NS134muscle

first: Javed

last: Khan

first: Jack

last: Shern

last: Langenau


title: Expression data from murine colorectal tumours of control and IL-6Ralpha-deficient mice fed a high fat diet

city: Cologne

first: thomas

last: wunderlich

state: NRW

address: Gleueler Str. 50

institute: MPI for Metabolism Research

summary: Obesity increases colorectal cancer despite other disturbances. We have used the AOM/DSS protocol to induce colitis-associated cancer in control and IL-6Ra deficient animals. Tumours were microdissected and globalgene expression was analysed using microarray.

overall_design: Upon weaning control and IL-6Ralpha-deficient animals were fed a High fat diet (HFD) for 14 weeks. Azoxymethane (AOM) (10mg/kg) was injected at week 8 and 4 days later 1.5% dextrane sodium sulphate (DSS) was supplied in the drinking water for 5 days. Mice were sacrificed 62 days after AOM injection and colorectal tumours were microdissected and processed for RNA isolation.

first: F

last: Wunderlich

first: Claudia


title: Ultra-parallel ChIP-seq by barcoding of intact nuclei

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples.
Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources.
Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design:
RELACS ChIP-seq has been firstly validated using HepG2 cells and compared with traditional sonication-based protocol. For this purpose, ChIP against six histone modifications and two transcription factors has been performed. 20 parallel technical replicates were investigated for RELACS within the same ChIP.
A sensitivity test for RELACS has been also performed. For this, seven technical replicates containing 10,000, 1,000 and 100 cells each have been barcoded and merged to be processed in three separated ChIPs (containing 7x10,000, 7x1,000, 7x100 cells respectively). ChIP sensitivity has been investigated for H3K4me3, H3K27me3 and CTCF.
To demonstrate ChIP parallelization we applicated RELACS for barcoding 8 separate organs extracted from two mice and processed within the same ChIP. For mouse experiments H3K27ac, H3K36me3, H3K27me3 ChIPs (and input controls) have been performed.
https://github.com/dpryan79/Misc/blob/master/InternalBarcodes/demultiplex_relacs.py

first: Laura

last: Arrigoni

first: Hoor

last: Al-Hasani

first: Fidel

last: Ramirez

first: Ilaria

last: Panzeri

first: Devon

middle: P

last: Ryan

first: Diana

last: Santacruz

first: Nadia

last: Kress

first: Andrew

last: Pospisilik

first: Ulrike

last: Boenisch


title: H3K27me3 ChIP-seq of naïve CD4 T cells

city: New York

first: Marc-Werner

last: Dobenecker

state: New York

address: 1230 York Ave, Box 301

institute: The Rockefeller University

summary: Differentiation and activation of T cells require the activity of numerous histone lysine methyltransferases (HMT) that control the transcriptional T cell output. One of the most potent regulators of T cell differentiation is the HMT Ezh2. Ezh2 is a key enzymatic component of the Polycomb repressive complex 2 (PRC2) that silences gene expression by histone H3 di/tri-methylation at lysine 27.  Surprisingly, in many cell types, including T cells, Ezh2 is localized in both the nucleus and the cytosol. Here we show the presence of a nuclear-like PRC2 complex in T cell cytosol and demonstrate a role of cytosolic PRC2 in T cell antigen receptor mediated signaling. We show that short-term suppression of PRC2 precludes TCR driven T cell activation in vitro. We also demonstrate that pharmacological inhibition of PRC2 in vivo greatly attenuates the severe T cell driven autoimmunity caused by Treg depletion. Our data reveal cytoplasmic PRC2 is one of the most potent regulators of T cell activation and points towards the therapeutic potential of PRC2 inhibitors for the treatment of T cell driven autoimmune diseases.

overall_design: We analyzed 4 different samples. WT naïve CD4+ T cells, Ezh1 -/- naïve CD4+ T cells, Ezh2 fl/fl CD4-cre naïve CD4+ T cells, and Ezh1 -/- Ezh2 fl/fl CD4-cre naïve CD4+ T cells

first: Jonas

last: Marcello

first: Uwe

last: Schaefer

first: Alexander

last: Tarakhovsky


title: Profiling of transcription and chromatin accessibility of leukemic stem cells

status: Public on Mar 05 2018

city: Dallas

first: Lawrence

last: Lum

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Genome-wide study of methylation profile of human cytotoxic CD4 T cells

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: The methylation profile of human cytotoxic CD4 T cells was compared to their naive counterpart, to central memory Th1 cells,  and to naive and cytotoxic CD8 T cells in order to elucidate the epigenetic basis of cytotoxic differentiation in CD4 T cells.

overall_design: Total genomic DNA obtained from ex-vivo isolated blood lymphocytes of 5 CMV-seropositive healthy adults. For each subject, five populations were sorted: naive CD4, naive CD8, central memory CD4 Th1 cells, cytotoxic CD28- CD4 T cells and cytotoxic CD27- CD8 T cells.


title: Expression data of hPSCs differentiated into Paraxial mesoderm

first: Jerome

last: Chal

address: 77 ave Louis Pasteur

institute: Brigham and Women's Hospital

summary: Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide, we establish conditions for the differentiation of monolayer cultures of human pluripotent stem (hPSC) cells into PSM-like cells without the introduction of transgenes or cell sorting. We differentiated human PSCs in serum-free medium supplemented with Chir99021 only (C medium) or with also the Bmp inhibitor LDN193189 (CL medium). In vivo, the PSM cells are first expressing MSGN1 (posterior PSM marker) and then mature to express Pax3 (anterior PSM marker). After 4-5 days of differentiation of hPSCs, MSGN1-positive cells were FACS-sorted and their transcriptome analyzed.

overall_design: Human PSCs differentiated for 0, 4-5 days in serum-free medium containing a Chir (C medium) or Chir and Ldn (CL medium) to study paraxial mesoderm in vitro

first: Ziad

middle: A

last: Tanoury

first: Olivier

last: Tassy


title: GSF1243: RNA-seq data of adipocytes treated with DNMT1 inhibitor, guadecitabine (100nM), for 3 days

status: Public on Mar 02 2018

city: Bloomington

first: Kenneth

last: Nephew

institute: Indiana University

summary: Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion and proximal and direct co-culture of adipocytes .increased OC proliferation alone or after treatment with carboplatin. Treatment of adipocytes with hypomethylating agent guadecitabine decreased migration and invasion of OC cells towards adipocytes. Due to this result, we performed RNA-seq of adipocytes treated with DNMT1 inhibitor to analyze differential gene expression changes that occur in the adipocyte that may explain the above observation that hypomethylating agent treatment of adipocytes decrease migration and invasion.

overall_design: In duplicate, subcutaneous, human, primary adipocytes (ATCC) were treated with DMSO control or guadecitabine (100nM, 3X daily) and on day 4, RNA was harvested from the adipocytes using the RNAEasy kit (Qiagen). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.

first: Jessica

last: Tang

first: Doug

last: Rusch

first: Aaron

last: Buechlein


title: Drosophila esc mutants show Hox-derepression along the AP axis in CNS

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

institute: The University of Queensland

summary: Mutating esc (extra sex-combs), maternal and zygotic, leads to loss of H3K27me3 and affects Hox-patterning along the AP-axis in neurogenesis

overall_design: Control (OregonR) flies are compared to esc-maternal zygotic mutants at stage 14 and 15 in pooled bulk RNAseq, with over 200 embryos per group.

first: Behzad

middle: Y

last: Salmani


title: DNA methylation data from ESCs derived by polar body transfer reconstructed embryos (PBTESCs)

status: Public on Mar 04 2018

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

summary:
Here we report the derivation of human ESCs from the polar body thansfer reconstructed embryos. We choose three cell lines from all the cell lines and compare the DNA methylation state.
We use human methylation chip to compare genomic DNA methylation level among three PB1 transfer human ES cell lines and three PB2 transfer human ES cell lines.

overall_design: We collected fresh ESCs samples of 3 cell lines from PB1 transfer and 3 cell lines from PB2 transfer each at around 10^6 cells in similar passage. DNA methylation profile of these cell lines were performed on Infinium Human Methylation450 BeadArray

first: Zhi-Jiang

last: Chen

first: Jinsong

last: Li


title: Minoxidil alters extracellular matrix gene expression, improving vascular compliance and organ perfusion in a model of chronic vascular stiffness

city: Bethesda

first: Beth

last: Kozel

state: MD

address: 10 Center Dr

department: Translational vascular medicine branch

institute: NHLBI/NIH

summary: Elastin insufficiency causes globally reduced caliber blood vessels and arterial stiffnesss that contribute to reduction of blood flow to end organs such as the brain.  Treatment with minoxidil increases vessel caliber and blood flow.

overall_design: Samples were collected from 3 groups: untreated mice (n=4),    mice on minoxidil for 2 weeks (n=4) and those on drug for 2 weeks and off-drug for 1 week (n=4).

first: Delong

last: Liu


title: Combination Treatment of Acute Myeloid Leukemia Cells with DNMT and HDAC Inhibitors: Predominant Synergistic Gene Downregulation Associated with Gene Body Demethylation

city: Heidelberg

first: Kersten

middle: Henrik

last: Breuer

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center (DKFZ)

summary: DNA-hypomethylating agents approved for older AML patients, are clinically tested in combination with histone deacetylase inhibitors (HDACi).The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2'deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi. Transcriptome analyses revealed that a combined treatment with DAC and HDACi panobinostat or valproic acid effected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative analysis of the methylome and transcriptome showed that a massive downregulation of genes, including oncogenes (e.g.c-MYC) and epigenetic modifiers (e.g. KDM2B and SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation, and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatment, and for a better understanding of responses in trials where this approach is clinically tested.

overall_design: Examination of H3K9 acetylation and H3K27 acetylation in U937 cells after decitabine +- panobinostat/entinostat treatment

first: Nadja

last: Blagitko-Dorfs

first: Pascal

last: Schlosser

first: Gabriele

last: Greve

first: Dietmar

last: Pfeifer

first: Ruth

last: Meier

first: Annika

last: Baude

first: David

last: Brocks

first: Christoph

last: Plass

first: Michael

last: Lübbert


title: Small RNA Sequencing of Colorectal Adenoma Patient Plasma

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: In our study, we generated and sequenced small RNA libraries from blood plasma samples.  These samples were obtained from patients undergoing colonoscopy and are balanced for age, sex, and self-identified ancestry.  From the sequencing data, we derived small-RNA feature counts and performed an analysis for differential expression between patients with and without colorectal adenoma.  We found numerous significant associations, including hsa-miR-335-5p and a RNA fragment of the theoretical transcript, AK126744.

overall_design: The are 822 fastq files in this submission consisting of sequencing replicates and library generation replicates from 240 patient samples. In this set there are 126 samples from "normal" patients with no findings and 114 from patients for whom a colorectal adenoma was found.  Also included is a count table after read processing.

first: Richard

last: Myers


title: Profiling of chromatin accessibility by ATAC-seq in hematopoietic LSK cells and leukemic stem cells of AML

first: Lawrence

last: Lum

summary: Epigenetic changes in cancerous cells including alterations in histone methylation facilitate the installation of growth-promoting signaling networks by altering DNA accessibility to transcriptional machinery. The oncofusion protein MLL-AF9 promotes deviant histone methylation and induces acute myelogenous leukemia (AML) in animals. Despite observations supporting a role for WNT signaling in AML pathogenesis, we have a limited mechanistic account of how cancerous growth is sustained in this context. Using chemical antagonists of WNT signaling and genetic ablation of the WNT chaperone Wntless (Wls), we identified the homeobox domain gene Sine oculis 1 (Six1) to be an atypical WNT-controlled target gene in MLL-AF9-transformed leukemic stem cells (LSCs). Elimination of Wls or Six1 in MLL-AF9 LSCs, or their exposure to WNT pathway inhibitors results in extended survival in LSC-transplanted recipient mice suggesting that WNT/SIX1 signaling is critical to MLL-AF9 transformation. Profiling of chromatin accessibility changes using ATAC-seq of MLL-AF9 transformed cells reveals chromatin remodeling in Six1 DNA regions that support binding of the transcriptional effector TCF7L2. Our data suggests de novo installation of a WNT/SIX1 signaling axis is critical to the development of some forms of AML and reveals how epigenetic alterations can re-assemble master regulatory pathways controlling cell fate with cancer-promoting consequences.

overall_design: ATAC-seq was performed to determine the chromatin accessibility in hametopoietic LSK cells and leukemic stem cells of AML

first: Lishu

last: Zhang


title: RNA-dependent intergenerational inheritance of enhanced synaptic plasticity after environmental enrichment

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We have analyzed sperm small RNAome by small RNA-sequencing.

overall_design: Examination of sperm small RNAome of wild type adult (3 months old) mice.

first: Cemil

last: Kerimoglu

first: Andre

last: Fischer


title: RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: It has been gradually established that the vast majority of human tumors are extraordinarily heterogeneous at a genetic level. To accurately recapitulate this complexity, it is now evident that in vivo animal models of cancers will require to recreate not just a handful of simple genetic alterations, but possibly dozens and increasingly intricate. Here, we have combined the RCAS/TVA system with the CRISPR/Cas9 genome editing tools for precise modelling of human tumors. We show that somatic deletion in neural stem cells (NSCs) of a variety of known tumor suppressor genes (Trp53, Cdkn2a and Pten), in combination with the expression of an oncogene driver, leads to high-grade glioma formation. Moreover, by simultaneous delivery of pairs of guide RNAs (gRNAs) we generated different gene fusions, either by chromosomal deletion (Bcan-Ntrk1) or by chromosomal translocation (Myb-Qk), and we show that they have transforming potential in vivo and in vitro.

overall_design: Bcan-Ntrk1 tumorspheres, Myb-Qk gRNA transduced NSCs, Ctrl gRNA transduced NSCs, Cdkn2a gRNA PDGFB tumorspheres, Pten gRNA PDGFB tumorspheres, and Trp53 gRNA PDGFB tumorspheres. 2 replicates each.

first: Massimo

last: Squatrito


title: Mouse Embryo Sox1 cre-dependent knockout of EED

status: Public on Mar 01 2018

first: Stefan

last: Thor

summary: Floxed EED homozygote mice are knocked-out by Sox1-driven Cre to remove H3K27me3 during neurogenesis

overall_design: Control mice are compared to EED-cKO mice in bulk RNAseq, in dissected forebrain and spinal cord

first: Jonathan

last: Rakar


title: ChIP-seq with DNA methylation inhibitor in HCT116

status: Public on Mar 28 2018

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Heterochromatin conformation is essential for endogenous retroviruses (ERVs) silencing. However, extensive maps of heterochromatin modifications H3K9me2/3 at ERV regions have not yet been provided in human cancer cells. Our ChIP-seq results showed that ERVs tend to be concentrated in regions of heterocromatin, which are marked by the presence of H3K9me3. We also observed dramatic increases H3K9me2/3 in the ERVs after transient treatment with DNA methylation inhibitor.

overall_design: ChIP-seq using H3K9me2 and H3K9me2 antibodies were performed in the human colon cancer cell line HCT116, following DNA methylation inhibitor treatment.

first: Peter

last: Jones


title: Next-generation sequencing of three memory OT-I cell subsets from mice infected with vesicular stomatitis virus

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

summary:
Purpose: RNA-seq analysis of three memory OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice infected with vesicular stomatitis virus. The hypothesis tested in the present study was that KLRG1+ effector CD8 T lymphocytes differentiate into KLRG1- memory CD8 T lymphocytes and provide long-lasting immunity against infectious diseases and malignancies.
Methods: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 70 days post infection with ovalbumin-expressing vesicular stomatitis virus (VSV-OVA) (experiment 3).
Results: Using RNA-seq technology, we performed genome-wide transcriptional profiling of three memory OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-) and identified 36 genes differentially expressed (> 1.5-fold) between exKLRG1 and KLRG1- Reporter- memory OT-I cells, and 132 differentially expressed genes between exKLRG1 and KLRG1+ Reporter+ memory OT-I cells. We then confirmed the expression of 15 genes/molecules by qRT-PCR and/or flow cytometry.
Conclusions: Our study represents the first fate mapping analysis of KLRG1+ effector OT-I cells, demonstrates that KLRG1+ effector OT-I cells differentiate into all memory T cell lineages thereby promoting protective immunity. RNA-seq also identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells.

overall_design: Total RNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 70 days post infection with ovalbumin-expressing vesicular stomatitis virus (VSV-OVA).


title: ATAC-seq of naive and three effector OT-I cell subsets from mice infected with Listeria monocytogenes

summary:
Purpose: ATAC-seq analysis of naive and three effector OT-I cell subsets (from a Klrg1-Cre fate reporter mouse model) isolated from the spleen of C57BL/6 mice 0 and 8 days post infection with OVA-expressing Listeria monocytogenes. The hypothesis tested in the present study was that chromatin remodeling in KLRG1+ effector CD8 T lymphocytes promotes the differentiation into KLRG1- memory CD8 T lymphocytes that provide long-lasting immunity against infectious diseases and malignancies.
Methods: DNA was obtained from 50,000 FACS-purified OT-I cell subsets isolated from spleen 0 and 8 days post infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA) (experiment 3).
Results: Using ATAC-seq technology, we analyzed the chromatin accessibility landscape of naive and three effector OT-I cells (KLRG1+ Reporter+, KLRG1- Reporter+ (exKLRG1) and KLRG1- Reporter-).
Conclusions: Our study represents the first fate mapping analysis of KLRG1+ effector OT-I cells, demonstrates that KLRG1+ effector OT-I cells differentiate into all memory T cell lineages thereby promoting protective immunity. RNA-seq identified CX3CR1 as a marker of circulating exKLRG1 early memory OT-I cells, and ATAC-seq analysis revealed that chromatin remodeling enabled exKLRG1 memory cells to exhibit both a high cytotoxic and proliferative capacity.

overall_design: Genomic DNA was obtained from FACS-purified OT-I cell subsets isolated from spleen 0 or 8 days post infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA).


title: KLRG1+ Effector CD8+ T Cells Lose KLRG1, Differentiate Into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity


title: Glucagon contributes to liver zonation in mice [Gcg infusion]

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal function. Wnt/beta-catenin signaling controls metabolic zonation by activating genes in the perivenous hepatocytes, while suppressing genes in the periportal counterparts. We now demonstrate that glucagon opposes the actions of Wnt/beta-catenin signaling on gene expression and metabolic zonation pattern. The effects were more pronounced in the periportal hepatocytes where 28% of all genes were activated by glucagon and inhibited by Wnt/beta-catenin. The glucagon and Wnt/beta-catenin receptors and their signaling pathways are uniformly distributed in periportal and perivenous hepatocytes and the expression is not regulated by the opposing signal. Collectively, our results show that glucagon controls gene expression and metabolic zonation in the liver through a counter play with the Wnt/beta-catenin signaling pathway.

overall_design: Gene expression profiling of Gcg-/- and wild type mice in liver with and without glucagon infusion.

first: Xiping

last: Cheng

first: Jesper

last: Gromada


title: Glucagon contributes to liver zonation in mice

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

overall_design: Refer to individual Series


title: Germinal Center B cells RNA-Seq (WT and Cbl-/-Cblb-/-)

city: Montreal

first: Hua

last: Gu

state: QC

address: 110 avenue des pins ouest

country: Canada

institute: IRCM

summary: We report the RNA transcriptome difference between WT and Cbl-/-Cblb-/- GC B cells

overall_design: Exmaine RNA expression in WT and Cbl-/-Cblb-/- GC B cells

first: Xin

last: Li


title: transcriptome studies of BRD4 inhibitor BDF-1253 on renal clear carcinoma 786-O cells

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: As an epigenetic reader, BRD4 is important for the recognition of acetylated lysines and regulation of transcription. As BRD4 regulates the expression of several survival genes, such as c-Myc and Bcl-2, which is vital for the survival of tumor cells, then it is closely involved in various kinds of cancers. Accumulating evidence has proven that BRD4 could serve as a novel anti-cancer pharmaceutical target, and small-molecular BRD4 inhibitors have promising potentials in the treatment of BRD4-related cancers and other diseases. In this study, a novel category of BRD4 inhibitors, which are originated from an approved drug Nitroxoline and its analogues, were synthesized and evaluated by biochemical and cellular assays, as well as the method of crystallography and xenograft mice models. In renal cell carcinoma cell lines, these compounds exhibited efficient inhibition against the expression and protein abundance of BRD4 downstream genes. Moreover, the complex crystal structures of several compounds in this series with the first bromodomain of BRD4 were solved, which revealed the binding mechanism of this novel category of BRD4 inhibitors and facilitated further structural modifications. This series of novel BRD4 inhibitors is promising to become drug candidates for the treatment of renal cell carcinoma after further development and assessments.

overall_design: RNA-Seq in renal clear carcinoma cells in the presence or absence of BRD4 inhibitor BDF-1253

first: Hao

first: Zhifeng

last: Chen


title: Trisomy-TAC-seq

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

summary: TAC-seq experiment to detect in vitro fetal trisomy at different range of fetal fraction. Fetal fraction ranges are 0%, 5%, 10%, 15%, 20%, 25%, 30% and 100%.

overall_design: 16 samples, 8 individuals, 2 replicas per individual.

first: Mariann

last: Koel

first: Kaarel

last: Krjutskov

first: Tatjana

last: Jatsenko


title: targeted allele counting by sequencing (TAC-seq)

state: Tartumaa

address: Teaduspargi tänav 13

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: High-coverage TAC-seq expression

summary: Transcriptomic biomarker detection assay for targeted 57 human uters endometrium receptivity testing

overall_design: 9 individuals, 18 samples, 2 timepoints (LH+2 and LH+8). 2 samples per individual, one from each timepoint. 64 targets (57 biomarkers and 7 ERCC spike-ins).


title: MicroRNA markers of human endometrial receptivity

summary: The goal of the study was to compare the miRNA profile of pre-receptive and receptive endometrium collected from women from the same menstrual cycle.

overall_design: Six pairs of pre-receptive and receptive endometrial tissue samples were analysed with small-RNA sequencing.

first: Agne

last: Velthut-Meikas

first: Andres

last: Salumets


title: Glucagon contributes to liver zonation in mice [Gcg KO]

overall_design: Gene expression profiling of Gcg-/- and wild type mice in liver


title: GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

institute: University of Saskatchewan

summary: Transcriptional control of any biological process occurs through the action of one to many gene regulatory networks (GRNs), but studies analyzing GRN interaction are lacking.  To address this, we tested for the first time in vivo the hypothesis that two independent GRNs, which are active during formation of two discrete skeletal cell types (immature chondrocytes and osteoblasts), interact during differentiation of a third skeletal cell type (mature chondrocytes).  These three cell types were isolated from the mouse embryo specifically using laser capture microdissection, and then RNA was extracted.  Multiple analyses of corresponding RNA-seq data supported the hypothesis.  Gene co-expression network analyses of differentially expressed genes suggested that one GRN containing the chondrogenic transcription factor Sox9 characterizes immature chondrocytes, one GRN containing the osteogenic transcription factor Runx2 characterizes osteoblasts, and both GRNs operate in mature chondrocytes.  Indeed, mature chondrocytes differentially expressed fewer genes than the other cell types, consistent with the idea that overlapping actions of the immature chondrocyte and osteoblast GRNs regulate mature chondrocytes.  Clustering analyses provided molecular insights into potential GRN interactions.  Several genes in mature chondrocytes had expression levels that represented an averaging between levels in the immature chondrocyte and osteoblast.  Interestingly, expression levels of one gene cluster, containing the hallmark mature chondrocyte genes Collagen type 10a1 and Indian hedgehog, suggested a synergistic interaction between immature chondrocyte and osteoblast GRNs.  In addition to identifying novel genes expressed in mature chondrocytes, these results outline a novel in vivo experimental system through which to understand GRN organization and interaction.

overall_design: Skeletal tissue mRNA profiles of C57BL/6J mice were generated by RNA sequencing, in triplicate, using Illumina HiSeq 2500.

first: Amir

last: Ashique

first: Katie

last: Ovens

first: Patsy

last: Gómez-Picos

first: Ian

last: McQuillan


title: Actomyosin-mediated tension orchestrates uncoupled respiration in adipose tissues

city: Berkeley

first: Greg

last: Timblin

state: CA

department: MCB

institute: UC Berkeley

summary: The activation of brown/beige adipose tissue (BAT) metabolism and the induction of uncoupling protein-1 (UCP1) expression are essential for BAT-based strategies to improve metabolic homeostasis. Adrenergic signaling is viewed as a key regulator of thermogenesis and UCP1-expression in BAT, while also operating as a potent contractile stimulator in muscle. The muscle-like gene expression patterns of UCP1+ adipocytes have previously been utilized as tissue specific markers, but have not been attributed with any functional role. Here, we demonstrate that BAT utilizes actomyosin machinery to generate tensional responses following adrenergic stimulation, similar to muscle tissues. We show that activation of actomyosin mechanics are critical for the acute induction of oxidative metabolism and uncoupled respiration in UCP1+ adipocytes. Additionally, actomyosin-mediated elasticity regulates mechanosensitive transcriptional co-activators, YAP/TAZ, that facilitate the thermogenic capacity of adipocytes. These unappreciated signaling and mechanical mechanisms may inform future strategies to promote the expansion and activation of brown/beige adipocytes.

overall_design: RNAseq was used to compare gene expression between BAT and perigonadal WAT from 22 week-old C57BL/6N mice fed a high-fat diet for 14 weeks (4 replicates per tissue). Additonally, RNAseq was used to compare gene expression in a BAT cell line treated with vehicle control or 100µM Blebbistatin for 24 hours (3 replicates per condition). All data was generated using Illumina HiSeq2500.


title: The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [RNA-seq]

city: New York

first: Nicholas

middle: D.

last: Socci

address: 1275 York Ave

department: bioinformatics core

institute: Memorial Sloan Kettering Cancer Center

summary: Gene fusions arising from chromosomal translocations are key oncogenic drivers in soft tissue sarcomas but little is known about how they exert their oncogenic effects. Our study explores the molecular mechanisms by which the SS18-SSX fusion oncoprotein subverts epigenetic mechanisms of gene regulation to drive synovial sarcoma. Using functional genomics, we identify KDM2B – a histone demethylase and core component of a non-canonical Polycomb Repressive Complex 1 (PRC1.1) – as selectively required for sustaining synovial sarcoma cell transformation. SS18-SSX physically interacts with PRC1.1 and co-associates with SWI/SNF and KDM2B complexes on unmethylated CpG islands genome-wide. Via KDM2B, SS18-SSX binds and aberrantly activates expression of a series of developmentally regulated transcription factors that would otherwise be targets of polycomb-mediated repression, which is restored upon KDM2B depletion leading to irreversible mesenchymal differentiation. Thus, SS18-SSX de-regulates developmental programs to drive transformation by hijacking a transcriptional repressive complex to aberrantly activate gene expression.

overall_design: RNA-Seq of  human synovial sarcoma cells (HS-SY-II) in control cells (Ren.173) and upon knockdown of SS18-SSX1 (SS18.273 and SSX.1274) or of KDM2B (KDM2B. 4395 and KDM2B.4835) in duplicates.

first: Ana

last: Banito

first: Scott

middle: W

last: Lowe


title: AMPK promotes survival of c-Myc positive melanoma cells by suppressing oxidative stress

city: Lausanne

first: Freddy

last: Radtke

state: VAUD

address: Station 19

department: ISREC

institute: Ecole Polytechnique Fédérale de Lausanne

summary: Although c-Myc is essential for melanocyte development, its role in cutaneous melanoma, the most aggressive skin cancer, is only partly understood. Here we used the NrasQ61KINK4a-/- mouse melanoma model to show that c-Myc is essential for tumor initiation, maintenance and metastasis. c-Myc expressing melanoma cells were preferentially found at metastatic sites, correlated with increased tumor aggressiveness and high tumor initiation potential. Abrogation of c-Myc caused apoptosis in primary murine and human melanoma cells. Mechanistically, c-Myc positive melanoma cells activated and became dependent on the metabolic energy sensor AMP-activated protein kinase (AMPK), a metabolic checkpoint kinase that plays an important role in energy and redox homeostasis under stress conditions.  AMPK pathway inhibition caused apoptosis of c-Myc expressing melanoma cells, while AMPK activation protected against cell death of c-Myc depleted melanoma cells through suppression of oxidative stress. Furthermore, TCGA database analysis of early stage human melanoma samples revealed an inverse correlation between c-Myc and patient survival, suggesting that c-Myc expression levels could serve as a prognostic marker for early stage disease.

overall_design: RNA-seq on primary versus metastatic c-Myc high melanoma cells

first: Alain

last: Kfoury

first: Marion

last: Leleu


title: The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma


title: Targeted microRNA-sequencing for precise biomarker molecule counting

summary: This study introduced a novel targeted allele counting by sequencing (TAC-seq) method to quantify miRNA molecules.

overall_design: 12 endometrial samples were sequenced, four samples in duplicate.

first: Kadri

last: Rekker

first: Priit

last: Paluoja


title: The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [ATAC-seq]

overall_design: ATAC-Seq of  human synovial sarcoma cells (HS-SY-II) in control cells (Ren.173) and upon knockdown of SS18-SSX1 (SSX.1274) or of KDM2B (KDM2B. 4395)


title: The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [ChIP-seq]

overall_design: Chromatin occupancy by ChIP-Seq of endogenously tagged SS18-SSX (HA-tag), KDM2B, BRG1 and examination of H3K27me3 mark in human synovial sarcoma cells (HS-SY-II) in control cells (Ren.173) and upon knockdown of SS18-SSX1 (SSX.1274) or of KDM2B (KDM2B. 4395)


title: Comprehensive molecular profiling of children with recurrent cancer II

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

summary:
to explore possible treatment targets and reasons for agressive children cacners by comprehensive molecular profiling on several platforms
to explore copy number aberrations related to cancers

overall_design: diagnostics of children meeting the oncologist with recurrent or agressive cancers where treatment options have been exhausted

first: Olga

last: Østrup

first: Karsten

last: Nysom

first: David

last: Scheie

first: Ane

last: Schmidt

first: Rene

last: Mathiasen

first: Lisa

last: Hjalgrim

first: Tina

last: Olsen

first: Jane

last: Skjøth-Rasmussen

first: Birthe

last: Henriksen

first: Finn

last: Nielsen

first: Peder

last: Wehner

first: Henrik

last: Schrøder

first: Astrid

last: Sehested

first: Catherine

last: Rechnitzer

first: Maria

last: Rossing


title: Comprehensive molecular profiling of children with recurrent cancer

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: Gene expression of attached and suspended Bim-/- Bmf-/- murine kidney epithelial cells

status: Public on Feb 28 2018

city: Worcester

first: Roger

middle: J

last: Davis

state: MA

address: 373 Plantation St Suite 309

institute: University of Massachusetts Medical School

summary: Suspension-induced cell death, or anoikis, is implicated in different stages of breast development as well as tumor progression and metastasis. The pro-apoptotic BH3-only proteins BIM and BMF are known positive regulators of anoikis. We examined the gene expression changes that occur in BIM-/- BMF-/- cells during attachment and suspension.  This study is supplemental to our work establishing  a role for JNK in anoikis (Girnius N, Davis RJ. 2017. JNK promotes epithelial cell anoikis by transcriptional and post-translational regulation of BH3-only proteins. (2017) Cell Reports 21: 1910-1921; doi: 10.1016/j.celrep.2017.10.067)

overall_design: Bim-/- Bmf-/- murine kidney epithelial cells were cultured in attached or suspended conditions and gene expression was analyzed.  Three independent libraries were analyzed per condition.

first: Nomeda

last: Girnius


title: Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma [patient]

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

summary: Our study identifies TACSTD2 as a novel regulator of two major HCV entry factors, CLDN1 and OCLN, which is strongly downregulated in malignant hepatocytes. These results provide new insights into the complex process of HCV entry into hepatocytes and may assist in the development of more efficient cellular systems for HCV propagation in vitro.

overall_design: Samples of tumorous and non-tumorous liver tissue were obtained from 8 patients with HCV-associated hepatocellular carcinoma (HCC)

first: Vandana

last: Sekhar

first: Teresa

last: Pollicino

first: Ronald

last: Engle

first: Farah

last: Alayli

first: Marta

last: Melis

first: Juraj

last: Kabat

first: Ashley

last: Tice

first: Anna

last: Pomerenke

first: Nihal

last: Altan-Bonnet

first: Fausto

last: Zamboni

first: Paolo

last: Lusso

first: Suzanne

middle: U

last: Emerson

first: Patrizia

last: Farci


title: Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity

city: Boston

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary: Beige and brown adipocytes generate heat in response to reductions in ambient temperature. When warmed, both beige and brown adipocytes exhibit morphological ‘whitening’, but it is unknown whether or to what extent this represents a true shift in cellular identity. Using cell type-specific profiling in vivo, we uncover a unique paradigm of temperature-dependent epigenomic plasticity of beige, but not brown, adipocytes, with conversion from a brown to a white chromatin state. Despite this profound shift in cellular identity, warm whitened beige adipocytes retain an epigenomic memory of prior cold exposure defined by an array of poised enhancers that prime thermogenic genes for rapid response during a second bout of cold exposure. We further show that a transcriptional cascade involving the glucocorticoid receptor and Zfp423 can drive warm-induced whitening of beige adipocytes. These studies identify the epigenomic and transcriptional bases of an extraordinary example of cellular plasticity in response to environmental signals.

overall_design: Ucp1-NuTRAP and Adipoq-NuTRAP mice exposed to different temperatures were used for brown, beige or white adipocyte-specific transcriptomic and epigenomic analysis.

first: Hyun

last: Roh


title: Genome-Wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: The emergence of influenza A viruses (IAV) from zoonotic reservoirs poses a great threat to human health. As seasonal vaccines are ineffective against zoonotic strains, and newly transmitted viruses can quickly acquire drug resistance, there remains a need for host- directed therapeutics against IAV. Here, we performed a genome-scale CRISPR/Cas9 knockout screen in human lung epithelial cells with a human isolate of an avian H5N1 strain. Several genes involved in sialic acid biosynthesis and related glycosylation pathways were highly enriched post-H5N1 selection, including SLC35A1, a sialic acid transporter essential for IAV receptor expression and thus viral entry. Importantly, we have identified capicua (CIC) as a negative regulator of cell intrinsic immunity, as loss of CIC resulted in heightened antiviral responses and restricted replication of multiple viruses. Therefore, our study demonstrates that the CRISPR/Cas9 system can be utilized for the discovery of host factors critical for the replication of intracellular pathogens.

overall_design: A pooled library of A549 cells lacking individual genes was generated using CRISPR/Cas9 gene deletion technique (A549-GeCKO library; genome-wide CRISPR knockout library). The single guide RNA (sgRNA) representation in the A549-GeCKO library was sequenced. The A549-GeCKO library was subjected to 5 consecutive rounds of infection with a human isolate of low pathogenic H5N1 influenza virus and the sgRNA enriched in the resistant population were sequenced (Prelim Rd 5). In addition, a sequential screen was performed in biological duplicates and the sgRNA eriched after each round of infection were sequenced (Rd 1-5, Rep1-2 )

first: Julianna

last: Han

first: Jasmine

last: Perez

first: Cindy

last: Chen

first: Asiel

last: Benitez

first: Matheswaran

last: Kandasamy

first: Yoontae

last: Lee

first: Jorge

last: Andrade

first: Benjamin

last: tenOever

first: Balaji

last: Manicassamy


title: Expression of mutant Asxl1 perturbs hematopoiesis and promotes susceptibility to leukemic transformation

first: Omar

last: Abdel-Wahab

department: HOPP

institute: MSKCC

summary: Additional Sex Combs Like 1 (ASXL1) is frequently mutated in myeloid malignancies and clonal hematopoiesis of indeterminate potential (CHIP). Although loss of ASXL1 promotes hematopoietic transformation, there is growing evidence that ASXL1 mutations might confer an alteration of function. Here we identify that physiological expression of a C-terminal truncated Asxl1 mutant in vivo using conditional knock-in (KI) results in myeloid skewing, age-dependent anemia, thrombocytosis, and morphologic dysplasia. Although expression of mutant Asxl1 altered the functions of hematopoietic stem cells (HSCs), it maintained their survival in competitive transplantation assays and increased susceptibility to leukemic transformation by co-occurring RUNX1 mutation or viral insertional mutagenesis. KI mice displayed substantial reductions in H3K4me3 and H2AK119Ub without significant reductions in H3K27me3, distinct from the effects of Asxl1 loss. ChIP-seq analysis demonstrated opposing effects of wildtype and mutant Asxl1 on H3K4me3. These findings reveal that ASXL1 mutations confer HSCs with an altered epigenome and increase susceptibility for leukemic transformation, presenting a novel model for CHIP.

overall_design: Asxl1 mutant knock-in mouse model mimicking CHIP

first: Reina

last: Nagase

first: Daichi

last: Inoue

first: Alessandro

last: Pastore

first: Takeshi

last: Fujino

first: Hsin-An

last: Hou

first: Norimasa

last: Yamasaki

first: Susumu

last: Goyama

first: Makoto

last: Saika

first: Akinori

last: Kanai

first: Yasuyuki

last: Sera

first: Sayuri

last: Horikawa

first: Yasunori

last: Ota

first: Shuhei

last: Asada

first: Yasutaka

last: Hayashi

first: Kimihito

last: Kawabata

last: Takeda

first: Hwei-Fang

last: Tien

first: Hiroaki

last: Honda

first: Toshio

last: Kitamura


title: Comparison of primary vs immortalized HUVEC

city: Braunschweig

first: Tobias

last: May

address: Inhoffenstrasse 7

institute: InSCREENeX GmbH

summary:
Fundamental research and drug development for personalized medicine necessitates cell cultures from defined genetic backgrounds. However, providing sufficient numbers of authentic cells from individuals poses a challenge. Here, we present a new strategy for rapid cell expansion that overcomes current limitations. Using a small gene library, we expanded primary cells from different tissues, donors and species. Cell type specific regimens that allow the reproducible creation of cell lines were identified. In depth characterization of a series of endothelial and hepatocytic cell lines confirmed phenotypic stability and functionality. Applying this technology enables rapid, efficient and reliable production of unlimited numbers of personalized cells. As such, these cell systems support mechanistic studies, epidemiological research and tailored drug development.
In these experiments primary HUVEC were compared to immortalized HUVEC with respect to their global gene expression pattern.

overall_design: The global gene expression profile of primary and immortalized HUVEC was analyzed. In addition primary human fibroblasts (4 samples; from three different donors) as control cells were included in this experiment. The immortalized HUVEC lines are derived from the same donor as the primary cells and were treated with the following gene combinations (MYC, ID1, ID2 - e-hUVEC-2); (MYC, ID1, FOS - e-hUVEC-8); (MYC, ID2, FOS - e-hUVEC-9). Each HUVEC sample (primary or immortalized) was run in duplicate.

first: Franziska

last: Klein


title: Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma [cell line]

first: Giacomo

last: Diaz

overall_design: Microarrays were performed on Huh7.5 and HepG2 cell lines maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% FBS and 2mM L-glutamine.

first: Vandana

last: Sekhar

first: Teresa

last: Pollicino

first: Ronald

last: Engle

first: Farah

last: Alayli

first: Marta

last: Melis

first: Jurai

last: Kabat

first: Ashley

last: Tice

first: Anna

last: Pomerenke

first: Nihal

last: Altan-Bonnet

first: Fausto

last: Zamboni

first: Paolo

last: Lusso

first: Suzanne

last: Emerson

first: Patrizia

last: Farci


title: Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma

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

overall_design: Refer to individual Series


title: Epigenetic activation during Th17 cell differentiation is impaired after TRIM28 deletion

city: Beijing

first: Yu

last: Jiang

address: Zhongguancun North Ave

institute: Tsinghua University

summary: Cell fate decision is mediated by epigenetic mechanisms. We have analyzed naive T cell differentiation into Th17 cells, which is regulated by environmental cytokines and their downstream transcription factors. RORγt is a lineage-specific master transcription factor for Th17 cells. Although epigenetic mechanisms have been implicated in Th17 cell differentiation, how transcription factors interact to activate epigenetic program is unclear. Here we show that tripartite motif containing 28 (TRIM28) expression in Th17 cells is required for cytokine production and autoimmune diseases. Genome-wide occupancy analysis reveals that TRIM28 bound regions contain many super-enhancers, which are impaired after TRIM28 or STAT3 but not RORγt deletion. Importantly, TRIM28 exists in a complex with STAT3 and RORγt; TRIM28 recruitment to the Il17 gene requires STAT3, and further promotes RORγt recruitment. TRIM28 thus is a key player in the epigenetic activation during T cell differentiation.

overall_design: Examination of the H3K27Ac modifications in 2 WT and 2 TRIM28KO cells

first: Ying

last: Liu

first: Huiping

last: Lu

first: Shao-cong

last: Sun

first: Wei

last: Jin

first: Xiaohu

last: Wang

first: Chen

last: Dong