title: p62 sustains a protumorigenic gene signature in melanoma opposing mRNA-dependent decay

city: Madrid

first: Karras

last: Panagiotis

state: Madrid

address: Calle Melchor Fdez Almagro

department: Molecular Oncology

institute: CNIO

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

overall_design: Refer to individual Series


title: BAP1 links epigenetic regulation of ferroptosis to tumor suppression

status: Public on Jul 05 2018

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

country: USA

institute: University of California Irvine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Compared to the well-established roles of apoptosis in tumor suppression, the roles and regulatory mechanisms of ferroptosis, a non-apoptotic form of cell death, in tumor biology remain much less understood. BRCA1-associated protein 1 (BAP1) encodes a nuclear de-ubiquitinating (DUB) enzyme to reduce histone 2A ubiquitination (H2Aub) on chromatin, and is a tumor suppressor in several human cancers. Here, integrated transcriptomic, epigenomic, and cancer genomic analyses link BAP1 to metabolism-related biological processes, including oxidative stress response, and identify cystine transporter SLC7A11 as a BAP1-repressed target gene with high relevance to BAP1-mediated tumor suppression in human cancers. Functional studies reveal that BAP1, in a DUB-dependent manner, decreases H2Aub occupancy on the SLC7A11 promoter and represses SLC7A11 expression, and that BAP1 inhibits cystine uptake and promotes ferroptosis through repressing SLC7A11 expression. Finally, we show that BAP1 inhibits tumor development partly through SLC7A11, and that cancer-associated BAP1 mutants lose their abilities to repress SLC7A11 and to promote ferroptosis. Together, the results of our study show that BAP1 executes its tumor suppression function at least partly through its regulation of SLC7A11 and ferroptosis, and uncover a previously unappreciated mechanism coupling ferroptosis to tumor suppression.

overall_design: ChIP-seq of H2AK119ub was applied in UMRC6 EV, BAP1 WT and C91A cells

first: Yilei

last: Zhang

first: Boyi

last: Gan


title: p62 sustains a protumorigenic gene signature in melanoma opposing mRNA-dependent decay [UACC62_6days]

country: Spain

summary: Metastasis is a common cancer hallmark which however, may be acquired by tumor-type specific mechanisms. Here we identify p62/SQSTM1 as a modulator of metastatic genes selectively enriched in melanoma. Loss- and gain-of-function analyses of p62 effectors revealed FERMT2 as an indicator of poor patient prognosis. Analyses in tumor cells, clinical biopsies and genetically-engineered mice (to compare p62 vs. ATG5) demonstrated that known p62 roles in autophagy and stress responses were not essential in melanomas. Instead, a genome-wide transcriptomic/proteomic/interactomic approach demonstrated that p62 controls FERMT2 and yet additional pro-metastatic genes by modulating transcript stability. This function of p62 was exerted by recruiting RNA-binding proteins, here exemplified by IGF2BP1. These data illustrate how genetically altered cancers can coordinately fuel pro-metastatic signatures.

overall_design: Two-condition experiment: shp62 vs. shControl. Biological replicates: 3 control replicates, 3 transfected replicates. 2 cell lines: SK-Mel-103, UACC62. 2 exposure times: 3 days, 6 days. This dataset includes cell line UACC62 at day 6.

first: Panagiotis

last: Karras

first: Estela

last: Cañon

first: Tonantzin

middle: G

last: Calvo

first: Metehan

last: Cifdaloz

first: Raul

last: Martinez

first: Cristina

last: Tejedo

first: Eva

last: Perez-Guijarro

first: Gonzalo

last: Gómez-López

first: Pilar

last: Ximenez-Embun

first: Javier

last: Muñoz

first: Diego

last: Megias

first: Pablo

middle: L

last: Ortiz-Romero

first: Jose

last: Rodríguez-Peralto

first: Erica

last: Riverio-Falkenbach

first: María

middle: S

last: Soengas


title: Genome-wide hydroxymethylcytosine pattern changes in basal-like breast cancer patients

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

type: Methylation profiling by high throughput sequencing

summary: Ten eleven translocation enzymes (TET1-3) convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), inducing DNA demethylation and gene regulation. They are often downregulated in cancer, yet the upstream cause of this event remains largely unknown. Here, we show increased TET1 expression in basal-like breast cancer (BLBC), specifically in tumors with low expression of immune markers and low infiltration by immune cells. Furthermore, we identify an anti-correlation between TET1 expression and NF-κB, a major immune regulatory family, in BLBC tissues. In vitro and in vivo, TET1 is downregulated in breast cells upon activation of NF-κB, through binding of p65 to its consensus sequence in the TET1 promoter. Moreover, we uncover genome-wide 5hmC changes related to TET1 regulation in BLBC. Finally, these findings are extended to other cancer types, including melanoma, lung and thyroid cancers. Collectively, our data suggest a novel mode of regulation for TET1, linking TETs and immunity, two major features of cancer.

overall_design: Genome-wide profiling of DNA hydroxymethylation in 4 pairs of matched tumor and normal breast

first: Evelyne

last: Collignon

first: Annalisa

last: Canale

first: Clémence

last: Al Wardi

first: Emilie

last: Calonne

first: Dedeurwaerder

last: Sarah

first: Whitney

last: Barham

first: Soizic

last: Garaud

first: Céline

last: Naveaux

first: Sophie

last: Bouchat

first: Carine

last: Van Lint

first: Karen

last: Willard-Gallo

first: Christos

last: Sotiriou

first: Agnès

last: Noel

first: François

last: Fuks


title: p62 sustains a protumorigenic gene signature in melanoma opposing mRNA-dependent decay [UACC62_3days]

first: Karras

last: Panagiotis

overall_design: Two-condition experiment: shp62 vs. shControl. Biological replicates: 3 control replicates, 3 transfected replicates. 2 cell lines: SK-Mel-103, UACC62. 2 exposure times: 3 days, 6 days. This dataset includes cell line UACC62 at day 3.

first: Panagiotis

last: Karras

first: Estela

last: Cañon

first: Tonantzin

last: Calvo

first: Metehan

last: Cifdaloz

first: Raul

last: Martinez

first: Cristina

last: Tejedo

first: Eva

last: Perez-Guijarro

first: Gonzalo

last: Gómez-López

first: Pilar

last: Ximenez-Embun

first: Javier

last: Muñoz

first: Diego

last: Megias

first: Pablo

last: Ortiz-Romero

first: Jose

last: Rodríguez-Peralto

first: Erica

last: Riverio-Falkenbach


title: Genome-wide methylation and hydroxymethylcytosine pattern changes in basal-like breast cancer patients

first: Martin

last: Bizet


title: p62 sustains a protumorigenic gene signature in melanoma opposing mRNA-dependent decay [SKMEL_6days]

overall_design: Two-condition experiment: shp62 vs. shControl. Biological replicates: 3 control replicates, 3 transfected replicates. 2 cell lines: SK-Mel-103, UACC62. 2 exposure times: 3 days, 6 days. This dataset includes cell line SK-Mel-103 at day 6.

first: María

last: Soengas


title: p62 sustains a protumorigenic gene signature in melanoma opposing mRNA-dependent decay [SKMEL_3days]

first: Karras

last: Panagiotis

overall_design: Two-condition experiment: shp62 vs. shControl. Biological replicates: 3 control replicates, 3 transfected replicates. 2 cell lines: SK-Mel-103, UACC62. 2 exposure times: 3 days, 6 days. This dataset includes cell line SK-Mel-103 at day 3.


title: Anti-Tumor Activity of Entrectinib, a Pan-TRK, ROS1 and ALK Inhibitor, in ETV6-NTRK3-Positive Acute Myeloid Leukemia

city: San Diego

first: Ian

middle: M

last: Silverman

state: California

address: 4545 Towne Centre Court

department: Computational Biology

institute: Ignyta Inc.

type: Expression profiling by high throughput sequencing

summary: Activation of TRK family tyrosine kinases by chromosomal rearrangement has been shown to drive a wide range of solid tumors and hematologic malignancies. TRK fusions are actionable targets as evidenced by recent clinical trial results in solid tumors. Entrectinib (RXDX-101) is an investigational, orally available, CNS-active, highly potent and selective kinase inhibitor with low nanomolar potency against TRKA/B/C, ROS1 and ALK kinase activities. Here, we demonstrate that TRK kinase inhibition by entrectinib selectively targets preclinical models of TRK fusion-driven hematologic malignancies. In acute myeloid leukemia (AML) cell lines with endogenous expression of the ETV6-NTRK3 fusion gene, entrectinib treatment blocked cell proliferation and induced apoptotic cell death in vitro with sub-nanomolar IC50 values. Phosphorylation of the ETV6-TRKC fusion protein, as well as phosphorylation of known TRKC downstream signaling effectors, was inhibited by entrectinib treatment in a dose-dependent manner. Sensitivity to entrectinib was dependent on expression of the ETV6-TRKC fusion protein. In xenograft models, entrectinib treatment at clinically relevant doses resulted in tumor regression, which was accompanied by elimination of residual cancer cells from the bone marrow. Our preclinical data demonstrate the potential of entrectinib as an effective treatment for patients with TRK fusion-driven AML and provide rationale for the clinical development of entrectinib in molecularly defined hematologic malignancies.

overall_design: Analysis of exon-level rna expression and putative fusions in two cell lines

first: Robert

last: Shoemaker

first: Kristen

last: Smith


title: LiCl treated KG1a cells, irradiated at 4Gy and 8Gy, incubated for 48hr

status: Public on Jul 02 2018

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

country: India

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

summary: Gene expression following ionizing radiation exposure to LiCl treated cells

overall_design: LiCl pre-treated KG1a cells irradiated at 4Gy and 8Gy in triplicate

first: Yogesh

middle: K

last: Verma

middle: U


title: Roles of AtR8 lncRNA in defense responses in Arabidopsis thaliana

status: Public on Jul 04 2018

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

department: Department of Plant Molecular Biology

institute: University of Delhi, South Campus

summary: AtR8 is a long non-coding RNA transcribed by RNA polymerase III in Arabidopsis which is responsive to hypoxic stress and salicylic acid. To understand the role of AtR8 lncRNA, microarray was carried out in the mutant seedlings of AtR8 and compared with wild type seedlings.

overall_design: Three biological replicates of atr8 mutant lines and A. thaliana (L.) Heynh. Accession WS (control) plants were used for microarray study

first: Shuang

last: Li

first: Saraswati

last: Nayar

first: Juan

last: Wu

first: Yasushi

last: Yukawa


title: Expression data from LNCaP clonal isolates over-expressing HIST1H1A or Vector Control.

city: Bethesda

first: Kendra

last: Williams

state: MD

address: 50 South Dr, Bldg 50

department: NHGRI

institute: NIH

summary:
HIST1H1A is a member of the linker histone family that is involved in correct folding and compaction of chromatin.
We used lentival transduction to stably express HIST1H1A in human prostate cancer LNCaP cells and examined the changes in gene expression.

overall_design: A total of 8 samples were analyzed, in pairwise comparison using Partek. Genes with Benjamini-Hochberg corrected p-value <0.05 were selected.

middle: A

first: Minnkyong

last: Lee

first: Jean

last: Winter

first: Derek

last: Gildea

first: Carla

last: Calagua

first: Natasha

last: Curry

first: Jens

last: Lichtenberg

first: Huihui

last: Ye

first: Nigel

middle: P

last: Crawford


title: Establishment of adult epidermal organoid cultures from canine hair follicles and interfollicular epidermis

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The epidermis and associated appendages ensure a number of critical functions necessary for survival and social interactions. Perturbations of epidermal stem cell homeostasis lead to a variety of skin diseases affecting humans and dogs. Therefore, the establishment of an in vitro system to investigate canine epidermal stem cells, representing a model for human diseases, is essential. Here we report the establishment and characterization of organoids derived from microdissected canine hair follicles (HFs) and interfollicular epidermal (IFE). Gene and protein expression analysis revealed high mRNA and protein levels of keratin 5 and 14, IFE differentiation markers and intercellular molecules (e.g., keratin 10 and desmoglein), indicating a strong basal cell signature as well as differentiation towards mature epidermis. Key markers of HF stem cells were lacking. This suggests that, independently of the tissue of origin, both organoid lines develop into the same cell type (basal IFE-like keratinocytes). Signaling pathways members important for regulation of HF growth and cycling (such as Wnt, Hh, BMP and Notch) were present in both HF and IFE organoids at low levels. Withdrawal of growth factors (Noggin, R-spondin and FGFs) resulted in upregulation of markers such as KRT16, IVL, KRT17 and SOX9, showing the potential of the organoids to develop towards more differentiated tissue. However, for induction of HF signatures or hair growth, addition of different growth factors or dermal papilla co-culture might be required. Taken together, our in vitro culture system can provide the basis to address hair growth and explore epidermal function/regeneration, allowing us to further investigate pathomechanisms of cutaneous disorders in dogs and potentially human patients.

overall_design: We establish an organoid culture system for long-term expansion of mouse epidermal stem cells. Using histological methods as well as low-coverage multiplexed RNA sequencing, we show that cultured organoids resembled interfollicular epidermis. We analyzed a total of 23 samples, including 6 controls that are isolated from the skin of dog. None-passaged as well as cultured organoids were compared with replicates. Differences growth factors and small molecules that allow expansion of organoids were compared with replicates.

first: Dominique

middle: J

last: Wiener

last: Basak

first: Priyanca

last: Asra

first: Kim

last: Boonekamp

first: Kai

last: Kretzschmar

first: Angelos

last: Papaspyropoulos

first: Hans

last: Clevers


title: Single-Cell Transcriptome Analysis of Lineage Diversity and Microenvironment in High-Grade Glioma

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

summary: Despite extensive molecular characterization, we lack a comprehensive picture of lineage identity, differentiation, and microenvironmental composition in high-grade gliomas (HGGs). We sampled the cellular milieu of HGGs with massively-parallel single-cell RNA-Seq. While HGG cells can resemble glia or even immature neurons and form branched lineage structures, mesenchymal transformation results in unstructured populations. Glioma cells in a subset of mesenchymal tumors lose their neural lineage identity, express inflammatory genes, and co-exist with marked myeloid infiltration, implying a molecular interaction between glioma and immune cells. Finally, we found that myeloid cells can resemble microglia, macrophages, or a hybrid state, and enrichment of these cells is predictive of poor survival.

overall_design: Performed single cell RNA-seq on tens of thousands of dissociated high-grade glioma tissue cells from 8 human patients.

first: Jinzhou

last: Yuan

first: Hanna

last: Levitin


title: A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage

status: Public on Jul 01 2018

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka a duplicate of dmrt1, acting as master sex-determining gene, has a tightly timely and locally patterned gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3’ UTR (D3U-box) was shown to mediate transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka two RNA-binding proteins with antagonizing properties competitively target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. Such evolutionary conservation of the D3U-box motif within the dmrt1 genes and among genomes of metazoans together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells, suggest this new mechanism for controlling RNA stability is not restricted to fishes, but might also apply to other vertebrates.

overall_design: Transgenic fish were generated using the CRISPR/Cas 9 technology targeting intron #2 and exon #5 of the ol-bsf gene,resulting in truncated non-functional OL-BSF protein. Total RNAs were extracted from adult medaka testes.

first: Manfred

last: Schartl

first: Cornelia

last: Schmidt

first: Susanne

last: Kneitz

first: Clara

last: Gobe

first: Martina

last: Regensburger

first: Aurélie

last: Le Cam

first: Mateus

middle: C

last: Adolfi

first: Christina

last: Lillesaar

first: Dagmar

last: Wilhelm

first: Michael

last: Kraeussling

first: Qiaowei

last: Pan

first: Brigitte

last: Mourot

first: Béatrice

last: Porcon

first: Maëlle

last: Pannetier

first: Eric

last: Pailhoux

first: Laurence

last: Ettwiller

first: Dirk

last: Dolle

first: Yann

last: Guiguen

first: Amaury

last: Herpin


title: In vivo metabolic disorders induced by a pesticide cocktail at the Acceptable Daily Intake level

city: Toulouse

first: laurence

last: Gamet-Payrastre

address: 180 chemin de Tournefeuille

department: Human alimentation

institute: INRA ToxAlim

summary: Consumers are exposed through food intake to a cocktail of pesticides at low doses. Epidemiological evidence suggested a link between pesticide exposure and the development of the metabolic syndrome. We used a mouse model to mimic consumer exposure and assessed the metabolic consequences of a chronic dietary exposure to a cocktail of 6 commonly used pesticides (boscalid, captan, chlorpyrifos, thiofanate, thiacloprid and ziram) at non-toxic doses (acceptable daily intake ADI). One year of exposure induced body weight and adiposity gain, hepatic steatosis and glucose intolerance in males. Females did not display significant changes in body weight but displayed fasted hyperglycemia and perturbations of gut-microbiota related urinary metabolites. Exposure of mice invalidated for the constitutive androstane receptor (CAR) demonstrated that this nuclear receptor was involved in the observed sexual dimorphic response to pesticide exposure. These results demonstrate for the first time that chronic dietary exposure to a pesticide cocktail at the ADI levels induces metabolic perturbations favouring obesity and diabetic state and raise the questions of the relevance of the ADI levels of individual pesticides when present in mixture.

overall_design: Thirty-six males and 36 females were housed in the laboratory animal room (23 ± 2 ºC) and segregated into 2 groups, each including 18 females and 18 males, fed the pesticides-enriched or the control diet for 52 weeks. Body weight, glucose tolerance were serially measured. At death, blood, liver, epididymal adipose tissue (WAT) were collected and serum biochemical parameters were measured. Liver were analyzed for fatty acid content, histology. Hepatic gene expression studies were performed by microarray ..Gene expression profiles were performed on 6 liver samples per group at the GeT‐TRiX facility (GénoToul, Génopole Toulouse Midi-Pyrénées) using Agilent Sureprint G3 Mouse GE v2 microarrays (8x60K, design 074809) following the manufacturer's instructions. For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium). 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions. Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software and fluorescence signal extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters. Microarray data were analyzed using R (www.r-project.org, R v. 3.1.2), using Bioconductor packages (www.bioconductor.org, v 3.0, as described in GEO accession GSE. Raw data (median signal intensity) were filtered, log2 transformed and normalized using quantile method3 .  A model was fitted using the limma lmFit function4. Pair-wise comparisons between biological conditions were applied using specific contrasts. A correction for multiple testing was applied using Benjamini-Hochberg procedure 5for False Discovery Rate (FDR).   Hierarchical clustering was applied to the samples and the differentially expressed probes using 1-Pearson correlation coefficient as distance and Ward’s criterion for agglomeration. The clustering results are illustrated as a heatmap of expression signals.   Functional annotation clustering of GO Biological Process were performed using “Search Tool for the Retrieval of Interacting Genes” (String V10)6 and DAVID Bioinformatics Resources 6.7

first: Céline

last: Lukowicz

first: Claire

last: Naylies

first: Frédéric

last: Lassere

first: Arnaud

last: Polizzi

first: Yannick

last: Lippi


title: Dietary intake of antioxidant curcumin reduces eIF2 phosphorylation and diacylglycerol and glycerolipid contents in white adipose tissue of obese mice

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

country: Japan

institute: Food Research Institute, National Agriculture and Food Research Organization

summary: To elucidate the bioactive property of the dietary antioxidant curcumin, we examined tissue distribution and the gene expression- and lipidomic-profiles in epididymal white adipose tissue (eWAT) of the diet-induced obese mice. Dietary intake of curcumin (0.1% W/W) didn’t affect the eWAT weight and the plasma lipid levels but reduced the levels of lipid peroxidation marker in eWAT. Curcumin was a slightly accumulated in eWAT and altered the gene expression associated with eukaryotic translation initiation factor 2 (EIF2) signaling. Curcumin suppressed the endoplasmic reticulum (ER) stress-related eIF2 phospholyration, the accumulation of macrophages and the expression of oxidative stress-sensitive transcription factor NF-κB p65 and leptin, whereas anti-inflammatory effect wasn’t enough to reduce the TNF-α and IFN-γ levels. Lipidomic- and gene expression analysis suggests that curcumin reduced the contents of some diacylglyverols (DAGs) and DAG derived glycerophospholipids by suppressing the expressions of lipogenesis-related glycerol-3-phosphate acyltransferase 1 and lipolysis-related adipose triglyceride lipase.

overall_design: 6-week-old C57BL/6J male mice were fed AIN93G diet or Wesern diet [39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose] or Western diet containing 0.1% curcumin for 16 weeks.

first: M


title: Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development.

first: Robin H.

last: van der Weide

state: Utrecht


title: LncRNA NMR knockdown and overexpression in esophageal squamous cell carcinoma cell lines

city: Beijing

first: Yuan

last: Li

address: Panjiayuannanli No.17

country: China

institute: National cancer center/cancer hospital

summary: Long noncoding RNAs (lncRNAs) are emerging as key regulators in cancer and play complicate and critical roles in regulating various key biological processes including chromatin modification, transcription and post-transcriptional processing. We identified a novel transcript, lncRNA NMR, which was upregulated in esophageal squamous cell carcinoma (ESCC) and significantly associated with overall survival of ESCC patients and and is identical to ENST00000432429.1 in GENCODE v13 or ENST00000432429.5 in Ensembl release 83. Here, we sought to determine the alterations of trancriptome after shRNA-mediated knockdown and transient overexpression of lncRNA NMR in ESCC KYSE70 and KYSE450 cell lines．

overall_design: Knockdown and overexpression of LncRNA NMR were performed in ESCC KYSE70 and KYSE450 cell lines with controls, respcectively. A total of 8 samples (2 knockdown with 2 controls and 2 overexpression with 2 controls) were used for RNA sequencing analysis.

first: Jie

last: He


title: Systemic gain and loss of chromatin architecture throughout zebrafish development [4C]

summary: Chromosomes are three-dimensional structures in the nucleus that are organized at multiple levels. Studies in mammals have shown that chromosomes segregate in active and inactive compartments (A and B, resp.). A compartments have high transcription activity, high GC-content and replicate early in S-phase. B compartments on the other hand are transcriptionally inactive, have low CG content are often found at the nuclear periphery. Every compartment is further divided into megabase-sized Topologically Associated Domains (TADs), the functional units of gene regulation. Regions within such a domain preferentially interact with each other. TAD positions are conserved between mouse and human genomes. However, it is unclear if non-mammalian vertebrates also show these organizational features and how these change throughout development. We have generated Hi-C maps for zebrafish embryos and show that the structural features of mammalian genomes (A/B-compartments and TADs) are also found in this species. We find that the genes within TADs show spatial co-expression. Moreover, the order of genes within a TAD is conserved to other vertebrate species. One of the key features of development is the switch from maternally loaded mRNAs to the transcriptional activation of the zygotic genome, known as Zygotic Genome Activation (ZGA). Prior to ZGA we see both TADs and compartments. Paradoxically, after the initiation of transcription, TADs and compartments completely disappear. These features are progressively re-established in the following developmental stages. Our results show that chromosome conformation can be formed independent of transcription. Analysis of active enhancer and promoter marks after ZGA showed that promoters and enhancers are enriched at future TAD-boundaries. Later in time, when TADs are present, the enrichment of active enhancers at the TAD-boundaries is lost. These data suggest that proximal enhancer-promoter interactions are needed for gene regulation when TADs are not in place. The loss of both TADs and compartments represent an interesting avenue for the further study of factors involved in the formation of the structural features of vertebrate chromosomes.

overall_design: Embryos of 4, and 24 hours after fertilisation were processed for 4C

first: Robin

middle: H

first: Elzo

last: de Wit


title: Gene expression profiles of Fir1 (RNAi) animals

city: Shanghai

first: Qing

last: Jing

state: Shanghai

address: 320 Yue Yang Road

department: Institute of Health Sciences

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The goal of this study was to identify Fir1 downstream genes that were required for local proliferation. Fir1(RNAi) animals displayed reduced local proliferation near the wound,while the proliferation far from the wound was  not decreased after Fir1 RNAi. The regenerating pieces following Fir1 RNAi were expected to only show decreased levels of the genes near the wound relative to control RNAi animals.

overall_design: Animals were administrated by Fir1 dsRNA for 8 days, amputated after pharynx. 48 hours later, RNA from the region adjacent to the wound(part1) and the region far from the wound(part2) in Fir1(RNAi) tail pieces was harvested with Trizol. Two biological replicates were used. Then the RNA was hybridized on a microarray with RNA from control RNAi animals.

first: Xiaoshuai

last: Han


title: Toxic metal tolerance of Arabidopsis arenosa inoculated with fungal endophyte Mucor sp. Gene expression study

city: Kraków

first: Piotr

last: Rozpądek

address: Gronostajowa 7a

department: Małopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

summary: To determine the mechanisms of improved toxic metal tolerance of A. arenosa inoculated with Mucor sp.  whole gemone microarray profiling was employed. Metal toxicity altered the expression of 5169 probe sets; 2861 genes were up-regulated and 2308 down-regulated. Inoculation with the fungi induced changes in the expression of 899 probes from the above presented data set; 492 genes were up-regulated and 314 were down-regulated. The expression of 93 genes (63 and 30, up and down-regulated respectively) was affected by both treatments (Fig. 5A-B). Genes differentially expressed in E+ plants vs E- from mine dump substrate were subject to GO analysis (gene ontology) to identify enriched terms with a cut-off rate of 0.01. The majority of the genes upregulated belonged to ROS metabolism, response to biotic and abiotic stimuli, response to ion starvation and ET biosynthesis and signaling functional categories. Among down-regulated transcripts GO analysis revealed a significant enrichment in the regulation of anthocyanin biosynthesis term.

overall_design: Gene expression profiles of roots of A. arenosa inoculated at 2 leaf seedling stage (10 days after germination), grown in substrate from the “Bolesław”(Poland, (50°16'58"N   19°32'9"E) mine dump, polluted with Zn, Cd, Fe and Pb, not inoculated grown in the same substrate and plants not inoculated grown in commercially available soil were compared. In order to distinguish between the effect of fungi colonization and toxic metal stress on the plants transcriptome, we compared global gene expression of E- plants cultivated in control substrate (commercially available soil mixed with sand in a 2:1 v:v ratio) with E- A. arenosa grown in substrate from the mine dump. Subsequently, the obtained data set was compared to the gene expression profile of Mucor sp. inoculated plants grown in the toxic metal enriched environment (mine dump substrate).

first: Rafał

last: Ważny

first: Agnieszka

last: Domka


title: Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition and tumorigenesis of non-small cell lung cancer

first: Jiejun

last: Shi

summary: Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues, and by providing binding platforms for “reader” proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Recently, we identified the YEATS domain of AF9 as a novel acetyllysine-binding module, and showed that the ENL YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. The human genome encodes four YEATS domain proteins, including GAS41; however, the importance of the GAS41 YEATS domain, in human cancer remains largely unknown. Here we report that GAS41 is frequently amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell proliferation, survival, and transformation. Biochemical and crystal structural studies demonstrate that GAS41 binds to histone H3 acetylated on H3K27 and H3K14, a specificity that is distinct from that of AF9 or ENL. ChIP-seq analyses in lung cancer cells reveal that GAS41 colocalizes with H3K27ac and H3K14ac on the promoters of actively transcribed genes. Depletion of GAS41 or disruption of the interaction between its YEATS domain and acetylated histones impairs the association of histone variant H2A.Z with chromatin, and consequently, suppresses cancer cell growth and survival both in vitro and in vivo. Overall, our study identifies GAS41 as a histone acetylation reader that controls a transcriptional program essential for NSCLC tumorigenesis by modulating histone H2A.Z deposition.

overall_design: ChIP-seq of GAS41, H2AZ, H3K27Ac, H3K14Ac, and H3K4me3 were applied in H1299 cells; mRNA-seq of shNT and shGAS41 in H1299 cells.

first: Chih-Chao

last: Hsu

first: Xiaobing


title: Triple Negative Breast tumors: SPARC Positive Tumors vs SPARC Negative Tumors

city: São Paulo

first: Ana Carolina

last: Pavanelli

state: SP

address: Dr. Arnaldo 251

department: Radiologia e Oncologia

country: Brazil

institute: ICESP

summary:
The aim of this study was evaluate the transcriptome changes in the comparison between triple negative tumors with increased SPARC expression and triple negative tumors with decreased SPARC expression according to Nagai et al., 2011 (Breast Cancer Res Treat (2011) 126:1–14)
The results generated could be of particular interest to better define the prognostic impact of SPARC expression in triple negative breast tumors

overall_design: Two-condition experiment,Triple negative Tumors with SPARC Positive  expression vs Triple negative Tumors with SPARC Negative expression. Biological replicates: 2 ,Triple negative Tumors with  SPARC Negative expression and 2 Triple negative Tumors with  SPARC Positive expression

first: Ana

first: Paulo

middle: R

last: de Alcantara Filho

first: Maria

last: Nagai


title: Identification and validation of single sample breast cancer radiosensitivity gene expression predictors [Illumina HT12 v4 data]

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

country: Sweden

institute: Lund University

summary:
Purpose
To develop a radiosensitivity gene expression assay to predict the response to adjuvant radiotherapy (RT) after breast conserving surgery (BCS) in breast cancer.
Patients and methods
Fresh frozen primary tumors from 336 patients operated with BCS with or without RT were collected. Patients were split in a discovery cohort (N=172) and a validation cohort (N=164). Genes predicting ipsilateral breast tumor recurrence (IBTR) in an Illumina HT12 v4 whole transcriptome analysis were combined with genes from the literature (248 genes in total) to develop a targeted radiosensitivity assay on the Nanostring nCounter platform. Single sample predictors (SSPs) for IBTR based on a k-top scoring pairs algorithm were trained stratified for estrogen receptor (ER) status and RT. Two previously published profiles (radiosensitivity index, RSI, and radiosensitivity score, RSS) were also tested in our data
Results
The SSPs were prognostic for IBTR in ER+RT- patients (AUC 0.67, p=0.005), ER+RT- patients (AUC=0.89, p=0.015) and ER-RT+ patients (AUC=0.78, p<0.001). Among ER+ patients, radiosensitive tumors had an excellent effect of RT (p<0.001), while radioresistant tumors had no effect of RT (p=0.4) and a high risk of IBTR (55% at 10 years). Our SSPs developed in ER+ tumors and the RSS correlated with proliferation, while SSPs developed in ER- tumors correlated with immune response. RSI negatively correlated with both proliferation and immune response.
Conclusions
Our targeted SSPs were prognostic for IBTR and has the potential to stratify patients for RT. The biology behind models may explain the different performance in subgroups of breast cancer.

overall_design:
Total RNA was extracted from fresh frozen breast cancer tissue and analyzed with Illumina HT12 v4 according to standard procedures.
Please note that the ilmn_data_final_processed (SUPPLEMENTAL DATA).csv file contains the finally batch effect corrected and probe filterd data.


title: Mesothelioma cells: Control vs CD26 knockdown

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: CD26 is a prognostic factor in many cancers and implicated as therapeutic target. Knockdown of CD26 on mesothelioma cells H226 and JMN inhibit tumor progression. In order to elucidate CD26-mediated pathway for tumor progression, CD26 was knocked down on H226 and JMN cells, and RNAs from these cells were subjected to Microarray analysis.

overall_design: By analyzing microarray data of CD26 knockdown, select candidate molecules, and validate its expression on control and CD26 knocked down cells by qRT-PCR. Then, protein expression will be studied.

first: Toshihiro

last: Okamoto

first: Chikao

last: Morimoto


title: Expression data from lung tissue in mild-moderate COPD

city: BARCELONA

first: Guillaume

last: Noell

address: C/Casanova 143

institute: CIBER Enfermedades Respiratorias, Grupo 10, IDIBAPS-Fundació Privada Clínic de Barcelona

summary:
Rationale: Chronic Obstructive Pulmonary Disease (COPD) is associated with a complex pulmonary and systemic immune response.
Objective: To characterize and relate the lung tissue and circulating blood network immune response in COPD.
Methods: Lung tissue and circulating blood samples were simultaneously obtained from COPD patients (current smokers n=28 and former smokers n=16) and controls (current smokers n=9 and non-smokers n=12) undergoing thoracic surgery. We used flow cytometry to assess the immune cell composition, Affymetrix arrays to determine whole lung mRNA expression, and Weighted Gene Co-expression Network Analysis (WGCNA) to characterize and compare the pulmonary and systemic immune responses in patients and controls.
Results: In lung tissue of current smokers with COPD (vs. non-smokers and former smokers with COPD) we observed a significant increase in the proportion of intermediated phenotype macrophages (Mphage) expressing both M1 and M2 markers, whereas that of M1 Mphage (pro-inflammatory) and CD4+ and CD8+ T-lymphocytes were decreased. These changes were not mirrored in circulating blood but WGCNA identified three modules of co-expressed genes that related, respectively to: (1) the total proportion of lung Mphage (extracellular matrix and angiogenesis genes) ; (2) active smoking (T cell and apoptosis related genes); and, (3) severity of airflow limitation (cilium organization genes).
Conclusions: In mild/moderate COPD, the main pulmonary immune cell alterations relate to current smoking, involve changes in the proportion of Mphage and T cells and are associated with changes in whole lung tissue transcriptome. These cellular pulmonary changes are not mirrored in the systemic circulation.

overall_design: Fresh lung tissue was preserved in RNAlater® (Life Technologies, US). From 53 individuals, total RNA was isolated with PureLink RNA-MiniKit (Life Technologies, US), quantified by Nanodrop (Thermo Scientific, Germany). RNA samples with integrity numbers (RIN) ≥ 7 (Agilent technologies, Germany), where analyzed with the Affymetrix GeneChip® Human Genome U219 Array Plate at the IDIBAPS genomics platform. Microarray results were RMA normalized and probes in the lowest quartile of variability were removed. Remaining probes were then collapsed to gene Symbols and a weighted gene co-expression network (WGNCA) was built with soft thresholding power of 9, on a total of 53 individuals. The analysis produced 24 modules, each containing a set of unique genes. Module eigengenes were correlated with variables of interest (FEV1, Smoking status, Lung Monocytes, Lung T Lymphocytes, macrophages and BMI).

first: Tamara

last: Cruz

first: Alejandra

last: López-Giraldo

first: Sandra

last: Casas-Recasens

last: Garcia

first: Laureano

last: Molins

first: Manel

last: Juan

first: Marco

last: Fernandez

first: Alvar

last: Agustí

first: Rosa

last: Faner


title: Effect of Rosmarinic acid in Pseudomonas aeruginosa PAO1 at expression level

city: Granada

first: Matilde

last: Fernández

address: Profesor Albareda 1

department: Estación Experimental del Zaidín

institute: Consejo Superior de Investigaciones Científicas

summary: We report a next-generation sequencing of total RNA from Pseudomonas aeruginosa PAO1 grown in presence of rosmarinic acid (RA) 100mM. Data analysis in comparison with cells grown in absence of RA revealed that the plant compound RA induces a broad transcriptional response in this bacterium, quite similar to the quorum sensing response.

overall_design: RNAseq of three samples of Pseudomonas aeruginosa PAO grown with rosmarinic acid 100 uM and three samples of the same bacterium grown without rosmarinic acid (control). As rosmarinic acid was dissolved in DMSO, the same amount of DMSO was added to the control cultures.

first: Andrés

last: Corral-Lugo

first: Tino

last: Krell


title: Bisulfite methylome sequencing of msh1 memory line in tomato

status: Public on Jun 30 2018

city: State College

first: Sally

last: Mackenzie

state: PA

address: 362 North Frear

department: Biology

institute: Penn State University

summary: MSH1 depletion caused whole genome wide Methylome changes in Arabidopsis, to conduct comparative genomic analysis, here we generate methylome for MSH1-RNAi line and transgene segregated out msh1 memory line in tomato

overall_design: 3 wildtype plants, and 3 msh1 memory plants been sequenced

first: Xiaodong

last: Yang


title: The Nonstop decay and the RNA silencing systems operate cooperatively in plants

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

summary: Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which can be produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. The cleavage products are degraded by general decay systems or subjected to silencing amplification. The balance between decay and silencing amplification might be finely regulated by unknown mechanisms. Here we show that NSD is required for the elimination of 5’cleavage product when mi- or siRNA-guided silencing complex cleaves in the coding region. Thus NSD might regulate the frequency of silencing amplification.

sample_organism:
Arabidopsis thaliana
Nicotiana benthamiana

overall_design: To verify if NSD is also involved in the degradation of 5’ cleavage products of endogenous miRNA targets, RNA-seq libraries (in triplicates) were prepared with random primers from ribo-depleted RNA samples, which were isolated from Pelota- and Control silenced N. benthamiana leaves (RNA-seq1 and RNA-seq2 experiments) and from wild type (Columbia) and pelota1 and hbs1 T-DNA mutant Arabidopsis thaliana leaves (Arabidopsis RNA-seq). N. benthamiana sequencing was repeated twice.

first: István

last: Szádeczky-Kardoss

first: Tibor

last: Csorba

first: Andor

last: Auber

first: Anita

last: Schamberger

first: Tünde

last: Nyikó

first: János

last: Taller

first: Tamás

middle: I

last: Orbán

first: József

last: Burgyán

first: Dániel


title: Identification and validation of single sample breast cancer radiosensitivity gene expression predictors

first: Martin

last: Sjöström

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

overall_design: Refer to individual Series


title: RNA-Seq gives insights into genetic regulation of the drought-stress response in the cassava leaves

city: Nanning

first: Yan

middle: mei

last: zhu

address: XiXiangTang District University Road No. 100

institute: Guangxi University

summary: Cassava is a drought–resistant food crop in tropical and subtropical regions. Although cassava is a relatively drought-tolerant species, the development and yields are greatly affected by the adverse drought conditions. Information about molecular breeding will obtain by studying genetic regulatory mechanism. In this study, we demonstrate the drought-tolerant mechanisms in leaves of both cassava varieties(Xinxuan048 and KU50) by using RNA-Seq technique. 1,880 and 2,066 differentially expressed genes(DEGs) were induced by drought stress in leaves of KU50 and Xinxuan048, respectively. DEGs in the response to drought stress involve in many regulated pathways. ROS- and ABA-associated signaling pathways and photosynthesis-associated regulation are mainly elucidated. In addition, alternative splicing and ingle nucleotide polymorphism also involve in drought-stress responses in both cassava varieties, showing their important roles in response to drought stress in leaves. This study not only increases the understanding of physiological and molecular mechanisms to the drought response in cassava, but also lays a solid foundation on the breeding of drought-resistant varieties using molecular methods.

overall_design: plants were treated under normal condition and drought stress.RNA-Seq was performed on leaf of the species under different treatment .

first: Yanmei

last: Zhu

first: Xinglu

last: Luo

first: Tangwei

last: Huang


title: Transcriptome analysis of early submergence-responsive genes in deepwater rice

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary:
The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp).
In this research, we have searched for genes responsible for submergence escape from a deepwater rice cultivar Pin Gaew 56 (PG56).

overall_design: A total of 20 chips were used for microarray. Total RNAs were extracted from intercalary meristem of PG56

first: Soong-Taek

last: Hwang

first: Dongsu

last: Choi


title: Chromatin landscape of human visceral and subcutaneous adipocytes

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

summary: Obesity is characterized by the excess of body fat leading to impaired health. Abdominal fat is particularly harmful and is associated with cardiovascular and metabolic diseases and cancer. In contrast, subcutaneous fat is generally considered less detrimental. The mechanisms that establish the cellular characteristics of these distinct fat types in humans are not fully understood. Here, we explored whether differences of their gene regulatory mechanisms can be investigated in vitro. For this purpose, we in vitro differentiated human visceral and subcutaneous pre-adipocytes into mature adipocytes and obtained their gene expression profiles and genome-wide H3K4me3, H3K9me3 and H3K27ac patterns. Subsequently, we compared those data with public gene expression data from visceral and subcutaneous fat tissues. We found that the in vitro differentiated adipocytes show significant differences in their transcriptional landscapes, which correlate with biological pathways that are characteristic for visceral and subcutaneous fat tissues, respectively. Unexpectedly, visceral adipocyte enhancers are rich on motifs for transcription factors involved in the Hippo-YAP pathway, cell growth and inflammation, which are not typically associated with adipocyte function. In contrast, enhancers of subcutaneous adipocytes show enrichment of motifs for common adipogenic transcription factors, such as C/EBP, NFI and PPARgamma, implicating substantially disparate gene regulatory networks in visceral and subcutaneous adipocytes. Consistent with the role in obesity, predominantly the histone modification pattern of visceral adipocytes is linked to obesity-associated diseases. Thus, this work suggests that the properties of visceral and subcutaneous fat tissues can be studied in vitro and provides preliminary insights into their gene regulatory processes.

overall_design:
ChIP-Seq for H3K4me3, H3K9me3 and H3K27ac of in vitro differentiated human visceral and subcutaneous adipocytes. Two biological replicates were performed.
RNA-Seq of visceral and subcutaneous pre-adipocytes (1x) and mature adipocytes (2x).

first: Kristin

last: Bokelmann

first: B

last: Ghadimi

first: Sebastian

last: Dango


title: DNA methylation profiling of promoter DNA associated to the T2D.

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

type: Methylation profiling by genome tiling array

summary: The Mouse Promoter Array is designed for chromatin immunoprecipitation (ChIP) experiments. Sequences used in the design of the Mouse Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker.

overall_design: In total 12 samples, 6 T2D mice and 6 control mice were selected for Mouse promoter methylation status was tested.

first: Fuu-Jen

last: Tsai


title: Gas41 links histone acetylation to H2A.Z deposition and stem cell identity maintenance

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: The histone variant H2A.Z is essential for maintaining the identity of embryonic stem cell (ESC) by keeping bivalent developmental genes at a poised state. However, how H2A.Z is deposited into the bivalent domains remains unknown. In mammals, two chromatin-remodeling complexes, Tip60/p400 and SRCAP, exchange the canonical histone H2A for H2A.Z in the chromatin. Here we show that Glioma Amplified Sequence 41 (Gas41), a shared subunit of the two H2A.Z-depositing complexes, functions as a reader of histone acetylation and recruits Tip60/p400 and SRCAP to deposit H2A.Z into specific chromatin regions including bivalent domains. The YEATS domain of Gas41 bound to acetylation on histone H3K27 and H3K14 both in vitro and in cells. Crystal structure of the Gas41 YEATS domain in complex with the H3K27ac peptide revealed that, similar to the AF9 and ENL YEATS domains, Gas41 YEATS forms a serine-lined aromatic cage for Kac recognition; mutations of either the aromatic residues of YEATS domain or the nearby residue of H3K27 abrogated the interaction. In mESCs, knockdown of Gas41 led to cell differentiation as the result of derepression of differentiation genes. Importantly, the differentiated morphology was rescued by expressing wild type Gas41, but not the YEATS domain mutated counterparts that do not recognize histone acetylation. Mechanically, we found that Gas41 depletion led to reduction of H2A.Z levels and a concomitant reduction of H3K27me3 levels at the promoters of a subset of bivalent genes. Together, our study identifies the Gas41 YEATS domain as a reader of histone acetylation and establishes a link between histone acetylation and H2A.Z deposition in the maintenance of ESC identity.

overall_design: ChIP-seq of H2AZ, H3K27Ac, H3K27me3,  H3K4me3, H3K14ac,  were applied in J1 mouse ES cells; mRNA-seq of shNT and shGas41 in J1 mouse ES cells.

first: Chih-Chao

last: Hsu

first: Xiaobing


title: Paternal cold exposure enhances brown adipose tissue sensitivity in offspring and ameliorates diet induced obesity

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Research in recent years has focused on environmental effects that control tissue functionality and systemic metabolism. We show here in a retrospective analysis that presence of brown adipocytes and date of birth are correlated and linked to BMI. In a mouse model system, we demonstrate that pre-conception cold exposure leads to improved systemic metabolism and protects from diet induced obesity, through the sperm via the paternal lineage. Using a brown fat ablation model, we show that this effect is mediated by brown adipose tissue. Furthermore, through RNAseq and DNA methylation analysis we identify Adrb3 as a putative signaling mechanism which could mediate the effects of pre-conception cold exposure and could account for the heterogeneity of brown adipose tissue responsiveness. Taken together, our results identify paternal cold exposure as a stimulus which induces a hyper-active state in brown adipose tissue leading to improved adaptation to overnutrition and hypothermia in the offspring.

overall_design: WGBS-seq of sperm from control and cold stimulated mice

first: Ferdinand

last: von Meyenn

first: Wolf

last: Reik

first: Sun

last: Wenfei

first: Dong

last: Hua

first: Wolfrum

last: Christian


title: The functions of KDM5A in regulation of p53

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary: We reveal that the histone demethylase KDM5A suppresses p53 activity by inhibiting its translation initiation.

overall_design: Biological duplicate samples were treated with siRNA for 72 hours.

first: Jun

last: Yang


title: Genome-wide analysis of galectin-4 mediated gene signature in PCa

city: Taipei

first: Chin-Hsien

state: Others

address: Nan-Kang

department: ABRC

institute: Academia Sinica

summary: Prostate cancer (PCa) causes significant mortality among men worldwide. Galectin-4 plays an important roles in regulatiog cancer metastasis and high level of galectin-4 correlated with poor survival in subpopulation of PCa patients.  To further understand the galectin-4-mediated signature and develop effective treatment, we froced expressed galectin-4 in 22Rv1 and LNCaP  cells, and downregulated galectin-4 in 22Rv1-M4 cells. Next,  cDNA microarray were applyed to study galectin-4-mediated gene expression and cancer progression.

overall_design: To further study galectin-4 effect, galectin-4 gene was forced expressed in 22Rv1 and LNCaP, and downregulated in 22Rv1-M4. Total RNA expression were analyzed in cDNA microarray.

first: Sheue-Fen

last: Tzeng

first: Mong-Hsun

first: Pei-Wen

last: Hsiao


title: KMT2C medaites the estrogen dependence of breast cancer through regulation of ERα enhancer function

city: New York

first: Kinisha

last: Gala

address: 417 E. 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: KMT2C is a key regulator of ERα activity whose loss allows for hormone independent proliferation in MCF7 cells

overall_design: Examination of RNA seq and ChIP seq in cells with KMT2C knockdown as well as cells with KMT2C knockdown that have gorwn out in hormone-deprived media

first: Sarat

last: Chandarlapaty


title: Translation elongation mediated quality control of integral membrane protein synthesis

city: Berkeley

first: Ligia

last: Acosta-Sampson

address: 2151 Berkeley Way, Room 320, MC 5230

department: MCB/EBI

institute: UC Berkeley

summary: Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. cerevisiae relative to the transporter with Neurospora-derived coding sequence (hereafter NC for the mRNA). We performed ribosome profiling and RNA deep sequencing of cells expressing NC and OPT grown at mid-exponential phases, respectively. Differences in ribosome occupancy on NC and OPT transcripts suggested increased rates of translation elongation of the N-terminal sequence of OPT in contrast to NC, which may be responsible for the slow-growth phenotype of cells expressing OPT.

overall_design: Examine ribosome footprints and mRNA abundance in biological replicates of S. cerevisiae strains expressing a cellodextrin transporter gene (cdt-1) and the codon-optimized version of cdt-1, respecitively

first: Kristina

last: Döring

first: Yuping

last: Lin

first: Vivian

middle: Y

last: Yu

first: Bernd

last: Bukau

first: Günter

last: Kramer

first: Jamie

middle: D

last: Cate


title: H.pylori infections induces a transcriptional signature in gastric eosinophils, as determined by RNA sequencing

status: Public on Jun 29 2018

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Eosinophils are highly abundant throughout the gastrointestinal tract. However, their function in bacterially-induced gastrointestinal inflammatory disorders is poorly understood. In this study, we have examined the function and regulation of gastric eosinophils in the steady state and during infection with Helicobacter pylori. We find that eosinophils are recruited to sites of infection, make direct contact with live bacteria, and activate a signature transcriptional program.

overall_design: SiglecF+ CD11b+ MHCII- gastric eosinophils were sorted by flow cytometry from the gastric lamina propria of individual H. pylori-infected  B6 mice or uninfected controls and compared for their gene expression profile.

first: Isabelle

last: Arnold

first: Anne

last: Muller


title: Transcription profiling of tomato leaves treated with harpin, chitosan nanoparticles and harpin loaded chitosan nanoparticles against untreated controls

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: We studied the transcriptome changes in tomato against treatment with harpinPss, chitosan nanoparticles (CSNPs), and harpin loaded chitosan nanoparticles (H-CSNPs). We measured and compared the difference in transcript accumulation  between treated- and control tomato leaves. Two independent experiments were performed at each time (24 h, 48 h and 72 h).

overall_design: Organism : Lycopersicon esculentum, Agilent's Tomato Gene Expression  4x44k Array (AMADID: 022270).

first: Appa

last: Podile

first: Sravana

last: Nadendla


title: Transcriptome changes of whole kidney from conditional Vhl gene knockout in sub-populations of mouse kidney tubule cells

status: Public on Jun 28 2018

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

institute: China Medical University

summary: We are studying a tumor suppressor gene, von Hippel-Lindau (VHL). In humans, VHL mutations cause renal cell carcinoma of the clear cell type (ccRCC). We have generated a knockout mouse strain in which mouse Vhl is conditionally deleted in the kidney epithelium (that is, a subset of tubules including collecting ducts and ascending loop of Henle). Instead of ccRCC, these mice developed severe inflammation and fibrosis, accompanied by hyperplasia and the appearance of transformed clear cells. These phenotypes therefore support the notion that inflammation is the tissue precondition of cancer. Our hypothesis is that VHL loss-of-function-induced inflammation contribute to the initiation of carcinogenesis, through a mechanism that we want to determine. The aim of the microarray is to identify genes involved in the overgrowth of the epithelium, as well as in inflammation and fibrosis that may be important for ccRCC initiation.

overall_design: This study is comprised of 6 Mouse Gene 2.0 ST arrays profiling whole kidney lysate from wild-type (VhlloxP/loxP) mice or from mice in which the Vhl gene has been conditionally knocked out in kidney tubules (Hoxb7-Cre+, Vhlflox/flox) (n=3 per genotype). The latter is an animal model of clear cell renal cell carcinoma (ccRCC).

first: Hannah

last: Bader


title: Differential gene expression in hair follicle-derived germline stem cells (HFGSCs) and germline stem cells (GSCs) compared with hair follicle (HF) cells.

city: Anseong

first: Buom-Yong

last: Ryu

state: Gyeonggi-Do

address: Seodong-daero

department: Animal Science and Technology

institute: Chung-Ang University

summary: Comparison of different cell lines between HFGSCs, GSCs, and HF cells at gene expression level. Results provide important information of genes expressed in the HFGSCs.

overall_design: Total RNA obtained from isolated HFGSCs and GSCs compared to HF cells.

first: Yong-Hee

last: Kim


title: DNA methylation reprogramming after spinal nerve injury

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

summary: Purpose: Nerve injury-induced hyperactivity of primary sensory neurons in the dorsal root ganglion (DRG) contributes critically to chronic pain development, but its underlying mechanisms remain incompletely understood. Chronic neuropathic pain has a clear epigenetic component, however, most studies so far have focused on histone modifications. We determined changes of DNA methylation in the rat DRG, spinal cord, and prefrontal cortex after spinal nerve ligation (SNL).

overall_design: We used a rat model of neuropathic pain induced by spinal nerve ligation (SNL). We analyzed DNA methylation in neural tissues at tens of thousands of CCCGGG target sites by the DREAM method (digital restriction enzyme analysis of methylation) based on sequential SmaI and XmaI digests and resolution of methylation signatures  by high througput Illumina sequencing.

first: Judit

last: Garriga

first: Geoffroy

last: Laumet

first: Shao-Rui

last: Chen

first: Yuhao

last: Zhang

first: Jozef

last: Madzo

first: Jean-Pierre

last: Issa

first: Hui-Lin

last: Pan


title: Spi-C expression in intestinal or bone marrow macrophages

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.


title: DNA methylatioin analysis of breast cancer cell lines with TET1 knockout


title: Transcriptome analysis of Htn1 mediated resistance against E .turcium

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

institute: University of Zürich

summary: Wall associated kinases (WAKs) have recently been identified as major components of fungal and bacterial disease resistance in several cereal crop species. However, the molecular mechanisms of WAK-mediated resistance remain largely unknown. Here, we applied the RNAseq approach to investigate the function of the maize gene ZmWAK-RLK1 (Htn1) that confers quantitative resistance to northern corn leaf blight (NCLB) caused by the hemibiotrophic fungal pathogen Exserohilum turcicum. A transcriptome analysis of near-isogenic lines (NILs) differing for ZmWAK-RLK1 revealed that several genes involved in the biosynthesis of the secondary metabolites benzoxazinoids (BXDs) were differentially expressed in the presence of ZmWAK-RLK1.

overall_design: Two maize genotypes (w22, B37) containing or not the gene Htn1, were infected or not with E .turcium. Three biological replicates of each interaction were collected. Infected samples were taken at four different time points (0h, 9h, 3d and 10d after inocluation). In total 48 samples

first: Ping

last: Yang

first: Simon

middle: G

last: Krattinger

first: Beat

last: Keller


title: DREAM of MDA-MB-231 cells with TET1 knockout

summary: DNA hypermethylation is known to contribute to the formation of cancer.  However, DNA hypomethylation has received far less attention and the factors controlling the balance between hypo and hypermethylation and its impact on tumorigenesis remains unclear.  Triple negative breast cancer (TNBC), a subtype of breast cancer that does not overexpress the hormone receptors or HER2/NEU, is one of the most hypomethylated cancers observed.  Importantly, TNBCs are often a therapeutic challenge because of advanced presentation and lack of targeted therapies. TET1 is a DNA demethylase that regulates DNA methylation, hydroxymethylation and gene expression.  We found that TET1 is specifically overexpressed in TNBC, where it is associated with hypomethylation and a worse overall survival.  Further, we uncover an intricate network connecting TET1 expression to maintaining activation of cancer specific pathways, including PI3K, EGFR and PDGF.  In TET1 KO cells, we observed reduced phospho-4EBP1 and decreased expression of genes in the PI3K pathway, suggesting loss of PI3K-mTOR activity is concomitant with loss of TET1.  Additionally, TET1 KO cells have reduced cellular proliferation and migration.  Our work establishes TET1 as an oncogene that contributes to the aberrant hypomethylation observed in cancer and suggests TET1 could serve as a novel druggable target for therapeutic intervention.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of MDA_MB_231 cells with TET1 knockout (single clones), including empty vector control pooled cells and empty vector single clones.  Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

first: Charly

last: Good

first: Shoghag

last: Panjarian

first: Andrew

last: Kelly

first: Bela

last: Patel


title: Loss of Trem2 in microglia leads to widespread disruption of cell coexpression networks in mouse brain

city: London

first: Guillermo

last: Carbajosa

address: Guy’s Hospital, St Thomas Street

department: Medical and Molecular Genetics

institute: King's College London

summary:
Rare heterozygous coding variants in the triggering receptor expressed in myeloid cells 2 (TREM2) gene, conferring increased risk of developing late-onset Alzheimer's disease, have been identified. We examined the transcriptional consequences of the loss of Trem2 in mouse brain to better understand its role in disease using differential expression and coexpression network analysis of Trem2 knockout and wild-type mice. We generated RNA-Seq data from cortex and hippocampus sampled at 4 and 8 months. Using brain cell-type markers and ontology enrichment, we found subnetworks with cell type and/or functional identity. We primarily discovered changes in an endothelial gene-enriched subnetwork at 4 months, including a shift toward a more central role for the amyloid precursor protein gene, coupled with widespread disruption of other cell-type subnetworks, including a subnetwork with neuronal identity. We reveal an unexpected potential role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signaling hub, suggesting an underlying link between immune response and vascular disease in dementia.

Methods: We performed differential expression and co-expression network analysis on a RNA-Seq profiled Trem2 knockout (KO) mouse using two brain areas sampled at 4- and 8-months to obtain a systems level view of the effects of the absence of Trem2.
Results: The absence of Trem2 has a stronger effect at an earlier age with the number of differential expressed (DE) genes being 17-fold greater at 4 months than at 8 months in cortex. By integrating DE genes and network analysis, we discovered gene clusters associated with the disruption of blood vessel formation at 4 months of age and protein targeting primarily affecting the hippocampus at 8 months. Further integration of cell type and ontology information revealed a large disruption of a gene module enriched for endothelial cell markers coinciding with the module enriched for neuron cell markers having weaker connections to modules with oligodendrocyte and astrocyte identities. The module with neuronal identity has decreased expression only in the KO where it has closer association with a new module enriched for phagocytic functions.
Conclusions: Combining gene co-expression and differential expression analysis on a newly generated RNA-Seq profiled Trem2 KO mouse demonstrate that the absence of Trem2 produces a disruption which mainly affects endothelialon related processes at 4 months of age. It results in a ripple effect that disrupts the cross-talk of other cell types at 8 months, including reduced expression of a gene module enriched in neuron related functions and a shift towards a more central role for App. This study reveals an unexpected role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signaling hub suggesting new paths for investigation at the intersection between Trem2, Alzheimer’s disease and vascular dementia.

overall_design: Hippocampus and cortex were selected because they represent tissues affected in AD at early and late stages, respectively (Matarin 2015, Mastrangelo 2008). Brain tissue samples were obtained from male Trem2 knockout (KO) and wild type (WT) control mice at two time points: 4 months and 8 months. These time points span the onset and late disease stages in well established AD mouse models (Matarin 2015). RNA-Seq was used to profile the transcriptomes for each sample. Two technical replicates were obtained for each sample.

first: Karim

last: Malki

first: Nathan

last: Lawless

first: Hong

last: Wang

first: John

middle: W

last: Ryder

first: Eva

last: Wozniak

first: Kristie

last: Wood

first: Charles

last: Mein

first: Richard

last: Dobson

first: Davi

last: Collier

first: Michael

last: O'Neill

first: Angela

last: Hodges

first: Stephen

last: Newhouse


title: Expression of Spi-C in intestinal CX3CR1high macrophages

status: Public on Jun 27 2018

first: Daisuke

last: Okuzaki

summary:
In murine large intestinal lamina propria, CX3CR1high resident Mfs possess anti-inflammatory properties and thereby support intestinal homeostasis. Unlike other tissue-resident MΦs, transcription factors that regulate differentiation and function of CX3CR1high MΦs in the large intestine are poorly understood. Thus, to identify transcription factors specifically expressed in CX3CR1high MΦs among large intestinal lamina propria innate myeloid cells, we comprehensively analyzed the genes expression profiles in CX3CR1high MΦs, CX3CR1- CD11b+ CD11c+ cells, CD11b- CD11chigh DCs, and CD11b+CD11c- cells.
CD11b- CD11chigh DCs, expressing CD103, in the colon highly expressed transcription factors Batf3, Irf8, and Zbtb46, which have been reported to be required for development of CD103+ DCs. Among four subsets, CX3CR1high macrophages showed the highest expression level of Spic. Transcription factor Spi-C has been reported to be crucial for development of splenic RPMΦs and a fraction of BMMΦs, and thereby contributes to iron recycling.

overall_design: CD11chigh CD11b- DCs, CD11c- CD11b+ cells, CD11c+ CD11b+ CX3CR1high Mϕs, and CD11c+ CD11b+ CX3CR1- cells were collected from large intestinal lamina propria, then perfomed microarray experiments.

first: Hisako

last: Kayama

first: Kiyoshi

last: Takeda


title: Decreased expression of a subset of TLR-dependent genes by heme-inducible Spi-C

summary: To determine the functions of Spi-C in innate immune responses, we investigated the overall gene expression patterns in M-CSF-BMDMΦs prepared from Spicflox/flox and Lyz2-cre; Spicflox/flox mice. M-CSF-BMDMΦs were stimulated with or without LPS following heme treatment and used for RNA-seq analysis.

overall_design: Control and Spic–/– BMDMΦ pretreated with 40 μM hemin for 18 h were stimulated with (designated ‘CNT_4’ and ‘cKO_4’, respectively) or without (designated ‘CNT_0’ and ‘cKO_0’, respectively) 100 ng/ml LPS for 4 h.


title: Evaluation of copy number variation detection between high-resolution array CGH and low-coverage short-insert and mate-pair whole-genome sequencing

status: Public on Jun 26 2018

city: Palo Alto

first: Bo

last: Zhou

state: CA

address: 3165 Porter Drive, Rm 2260

department: Psychiatry

institute: Stanford University

summary: In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons.  With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading.  However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed.  Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878.  CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project.  Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation.  Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays.  Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.

overall_design: To detection of Cri-du-chat deletion and other CNVs from NA16595 DNA (obtained from Coriell) using Illumina MEGA array

first: Xianglong

last: Zhang


title: poly-A RNA profiling of Drosophila neural stem cells (type I NBs) and GMCs of different ages reveal genes involved in cell fate stabilization

city: Vienna

first: Sebastian

last: Wissel

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology (IMBA)

summary: Drosophila melanogaster neural stem cells (neuroblasts [NBs]) divide asymmetrically by differentially segregating protein determinants into their daughter cells. Although the machinery for asymmetric protein segregation is well understood, the events that reprogram one of the two daughter cells toward terminal differentiation are less clear. In this study, we use time-resolved transcriptional profiling to identify the earliest transcriptional differences between the daughter cells on their way toward distinct fates. By screening for coregulated protein complexes, we identify vacuolar-type H+–ATPase (v-ATPase) among the first and most significantly down-regulated complexes in differentiating daughter cells. We show that v-ATPase is essential for NB growth and persistent activity of the Notch signaling pathway. Our data suggest that v-ATPase and Notch form a regulatory loop that acts in multiple stem cell lineages both during nervous system development and in the adult gut. We provide a unique resource for investigating neural stem cell biology and demonstrate that cell fate changes can be induced by transcriptional regulation of basic, cell-essential pathways.

overall_design: Comparison of transcriptomes of wild-type type I NBs and GMCs of different ages (1.5h, 3h or 5h old) isolated by FACS from Drosophila melanogaster larval brains.

first: Heike

last: Harzer

first: Thomas

last: Burkard

first: Juergen

last: Knoblich


title: Gene expression analysis of OX40+ Tregs from human liver tissues

city: Milano

first: valeria

last: ranzani

address: via Francesco Sforza 35

country: Italy

institute: INGM

summary:
Analysis of the gene signature of OX40+ Tregs, in comparison to OX40- Tregs and Tconvs, freshly isolated from liver cirrhosis and tumor of chronic HCV patients.
Results provide insights into the metabolic mechanisms of Treg proliferation in premalignant/malignant contexts.

overall_design: Total RNA extracted from OX40+ or OX40- Tregs or Tconvs, obtained from peripheral blood or from fragments of cirrhotic and tumor (hepatocellular carcinoma) liver tissue. Samples from 5 chronic HCV patients (4M+1F, aged 53-80 years) were pooled.

first: Silvia

last: Piconese

first: Valeria

last: Ranzani


title: Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells [methylation]

city: Los Angeles

first: Gangning

last: Liang

address: 925 W 34th St

institute: University of Southern California

summary: For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).

overall_design: Bisulphite converted DNA from the 34 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Minmin

last: Liu


title: LHP1 interacts with ATRX through plant-specific domains at specific loci targeted by PRC2

first: haifeng

last: WANG

institute: Gregor Mendel Institute of Molecular Plant Biology

summary: Heterochromatin Protein 1 (HP1) is a major regulator of chromatin structure and function. In animals, the network of proteins interacting with HP1 is mainly associated with constitutive heterochromatin marked by H3K9me3. HP1 physically interacts with the putative orthologue of the SNF2 chromatin remodeler ATRX, which controls deposition of the histone variant H3.3 in mammals. In Arabidopsis thaliana, we show that the orthologue of ATRX participates in H3.3 deposition and characterize the function of conserved domains of plant ATRX. We show that the plant Like HP1 (LHP1) interacts with ATRX through domains that evolved specifically in land plants ancestors. Interaction between ATRX and LHP1 affects the expression of a limited subset of genes controlled by the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), including the flowering time regulator FLC. In the context of flowering time, ATRX function requires the novel LHP1-interacting domain and the ATPase of the ATRX SNF2 helicase. We conclude that distinct evolutionary pathways led to interaction between ATRX and HP1 in mammals or its counterpart LHP1 in plants, resulting in distinct modes of transcriptional regulation.

overall_design: 1 sample (mutant) + 1 reference sample (control)

first: Haifeng

last: Wang

first: Danhua

last: Jiang

first: Elin

last: Axelsson

first: Sean

last: Montgomery

first: Sarah

last: Holec

first: Bas

last: Pieters

first: Abbas

last: AI Temimi

first: Jasmin

last: Mecinović

first: Frédéric

last: Berger

first: Zdravko

last: Lorković


title: Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells [gene expression]

summary: There is an urgent need for developing more effective therapies for aggressive hepatocellular carcinoma (HCC). Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi) currently in clinical trials for HCC and shows greater stability and performance over first generation DNMTis. The aim of this study is to identify potential therapeutic targets of SGI-110 for clinical trials.

overall_design: HCC cell lines (SNU398, HepG2 and SNU475) were used to evaluate effects of SGI-110 by an integrative analysis of DNA methylation, nucleosome accessibility and gene expression profiles following the transient SGI-110 treatment and its clinical relevance by comparing to HCC clinical data from TCGA.


title: The primary transcriptome of Acinetobacter baumannii ATCC 17978

status: Public on Jun 25 2018

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

summary: Transcriptomics by RNA-seq provides unparalleled insight into bacterial gene expression networks, enabling a deeper understanding of the regulation of pathogenicity, mechanisms of antimicrobial resistance, metabolism, and other cellular processes. Here we present the transcriptome architecture of Acinetobacter baumannii ATCC 17978, a species emerging as a leading cause of antimicrobial resistant nosocomial infections. Differential RNA-seq (dRNA-seq) examination of model strain ATCC 17978 in 16 laboratory conditions identified 3731 transcriptional start sites (TSS), and 110 small RNAs, including the first identification of 22 sRNA encoded at the 3′ end of mRNA.

overall_design:
Transcriptome analysis of Acinetobacter baumannii ATCC 17978 from Early Stationary Phase (ESP) in L-broth and from a pool of 16 different environmental conditions using RNA-seq.

Please note that one half of the RNA pooled sample [RNA_pool] was digested with Terminator Exonuclease (TEX) to enrich for 5'-PPP RNA species [i.e. TEX_RNA_pool].

last: Kröger

first: Andrew

last: Cameron


title: LSD1 inhibition exerts its anti-leukemic effect by recommissioning PU.1- and C/EBPα-dependent enhancers in AML

first: Richard

last: Koche

state: New York

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: LSD1 inhibition exerts its anti-leukemic effect by recommissioning PU.1- and C/EBPα-dependent enhancers in AML [ChIP-seq]

summary: Epigenetic regulators are recurrently mutated and aberrantly expressed in acute myeloid leukemia (AML). Targeted therapies designed to inhibit these chromatin-modifying enzymes, such as the histone demethylase lysine specific demethylase 1 (LSD1) and the histone methyltransferase DOT1L, have been developed as novel treatment modalities for these often refractory diseases. A common feature of many of these targeted agents is their ability to induce myeloid differentiation, suggesting that multiple paths toward a myeloid gene expression program can be engaged to relieve the differentiation blockade that is uniformly seen in AML. We performed a comparative assessment of chromatin dynamics during the treatment of MLL-AF9-driven murine leukemias and MLL-rearranged patient-derived xenografts using two distinct but effective differentiation-inducing targeted epigenetic therapies, the LSD1 inhibitor GSK-LSD1 and the DOT1L inhibitor EPZ4777. Intriguingly, GSK-LSD1 treatment caused global gains in chromatin accessibility, whereas treatment with EPZ4777 caused global losses in accessibility. We captured PU.1 and C/EBPα motif signatures at LSD1 inhibitor-induced dynamic sites and ChIP-seq revealed co-occupancy of these myeloid transcription factors at these sites. Functionally, we confirmed that diminished expression of PU.1 or genetic deletion of C/EBPα in MLL-AF9 cells generates resistance of these leukemias to LSD1 inhibition. These findings reveal that pharmacologic inhibition of LSD1 represents a unique path to overcome the differentiation block in AML for therapeutic benefit.

overall_design: ChIP-sequencing

first: Monica

last: Cusan

first: Sheng

middle: F

last: Cai

first: Scott

last: Armstrong


title: Cooperation between TLX1 and the NUP214-ABL1/STAT5 signaling in T-cell acute lymphoblastic leukemia

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associated with overexpression of the TLX1 or TLX3 transcription factors in T-cell acute lymphoblastic (T-ALL). Here we show that NUP214-ABL1 kinase cooperates with TLX1 in driving T-ALL development using a transgenic mouse model. Using ChIP-seq and ATAC-seq, we show that TLX1 and STAT5, the downstream effector of NUP214-ABL1, selectively increase the accessibility of enhancer regions, and cooperatively activate the expression of key proto-oncogenes such as MYC and BCL2. Moreover, MYC is also part of the TLX1/STAT5 complex and inhibition of both MYC and STAT5 leads to reduction of target gene expression.

overall_design:
RNA-sequencing of different conditions: wild type, NUP214-ABL1 +, TLX1 +, NUP214-ABL1+TLX1 +, NUP214-ABL1+TLX3 +. Transgenic mouse samples and ALL-SIL cell line. Xenografts of patient samples.  Before and after treatment with Imatinib.
ChIPmentation sequencing with different antibodies: STAT5, TLX1, H3K4me3, H3K27ac, p300 and BRD4. Transgenic mouse with NUP214-ABL1+TLX1 +.
ATAC-sequencing for different conditions in mouse: wild type, NUP214-ABL1 +, TLX1 +, NUP214-ABL1+TLX1 +.

first: Marlies

last: Vanden Bempt

first: Charles

last: De Bock

first: Jan

last: Cools


title: Total and AGO1 immunoprecipitated small RNA from Arabidopsis thaliana wild-type and ago1-57 mutant

status: Public on Jun 22 2018

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

type: Non-coding RNA profiling by high throughput sequencing

summary: In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role[AQ1] in microRNA (miRNA) and small interfering RNA (siRNA)- mediated silencing and is a key component in antiviral responses. The polerovirus F-box P0 protein triggers AGO1 degradation as a viral counterdefense. Here, we identified a motif in AGO1 that is required for its interaction with the S phase kinase-associated protein1-cullin 1-F-box protein (SCF) P0 (SCFP0) complex and subsequent degradation. The AGO1 P0 degron is conserved and confers P0-mediated degradation to other AGO[AQ2] proteins. Interestingly, the degron motif is localized in the DUF1785 domain of AGO1, in which a single point mutation (ago1-57, obtained by forward genetic screening) compromises recognition by SCFP0. Recapitulating formation of the RNA-induced silencing complex in a cell-free system revealed that this mutation impairs RNA unwinding, leading to stalled forms of AGO1 still bound to double-stranded RNAs. In vivo, the DUF1785 is required for unwinding perfectly matched siRNA duplexes, but is mostly dispensable for unwinding imperfectly matched miRNA duplexes. Consequently, its mutation nearly abolishes phased siRNA production and sense transgene posttranscriptional gene silencing. Overall, our work sheds new light on the mode of AGO1 recognition by P0 and the in vivo function of DUF1785 in RNA silencing.

overall_design: 4 samples examined: Arabidopsis thaliana total and AGO1 immunoprecipitated small RNA from Col0 WT plants and ago1-57 mutant (2 biological replicates for each). To reduce technical variability, each sample was split and sequenced in 2 independent lanes.

first: Benoît

last: Derrien

first: Marion

last: Clavel

first: Nicolas

last: Baumberger

first: Taichiro

last: Iki

first: Thibaut

last: Hacquard

first: María

last: Ponce

first: Olivier

last: Voinnet

first: Véronique

last: Ziegler-Graff

first: Hervé

last: Vaucheret

first: José

middle: L

last: Micol

first: Pascal

last: Genschik


title: Infectious laryngotracheitis virus induces paracrine apoptosis in uninfected cells through repression of p53 signalling

status: Public on Jun 21 2018

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: We sequenced mRNA from LMH cells infected with ILTV, uninfected apoptotic cells and apoptotic cells cultured in conditioned medium.

overall_design: Examination of mRNA levels in individual condition were compared

first: Shengwang

last: Liu


title: MicroRNA profiles of murine macrophages infected with different strains of Leptospira spp

status: Public on Jun 23 2018

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

institute: FMVA-UNESP

summary: Leptospirosis is a neglected zoonotic disease of global importance. Despite its prevalence, pathogenesis is still poorly understood. Recent discoveries have placed miRNAs in the regulation of the infection process of several bacterial diseases. Here, we suggest that post-transcriptional regulation, mediated by miRNAs, may play a role in host response to infection in leptospirosis in a species and virulence-specific manner.

overall_design: Four treatments were performed in triplicates in J774A.1 macrophages in vitro, as follows: non-infected control cells and cells infected with virulent, attenuated and saprophyte strains of Leptospira. Following 8h of infection, total RNA was extracted and 250 ng of total RNA (RIN 10) was used to evaluate the miRNA profile using the microarray Affymetrix® miRNA 4.1 Array strip. Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm. Next, statistical analysis was performed in the TAC software (Affymetrix) by ANOVA (fold change ± 1.5, p <0.01).

first: Leandro

middle: E

last: Garcia

first: Erivelto

last: Júnior

first: Larissa

middle: M

last: Melo

first: Jaqueline

last: Bragato

first: Valéria

last: Lima

first: Juliana

last: Peiró

first: Daniel

last: Arnold

first: Márcia

last: Marinho


title: LSD1 inhibition exerts its anti-leukemic effect by recommissioning PU.1- and C/EBPα-dependent enhancers in AML [ATAC-seq]

city: New York

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

overall_design: ATAC-sequencing

first: Monica

last: Cusan

first: Sheng

last: Cai

middle: P

first: Scott

middle: A

last: Armstrong


title: Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells

first: Gangning

last: Liang

type:
Expression profiling by array
Methylation profiling by array


title: Gene expression of native Jurkat human leukemia cell line following 8h Brd4 inhibition by MMQO

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

summary: Basal Jurkat cell gene expression and MMQO treated Jurkat cell gene expression

overall_design: Jurkat cancer cells were grown in rich media, treated with MMQO for 8 hours or left untreated. Total RNA was extracted to monitor basal gene expression

first: Jordan

last: Albert

first: Abner

last: Erik


title: Ogye body map RRBS data

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

summary: The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).

overall_design:
Preparation of reduced representation bisulfite sequencing (RRBS) libraries were followed by the Illumina’s RRBS protocol. 5ug of genomic DNA is digested by restriction enzyme MspI, purified with the QIAquick PCR purification kit (QIAGEN), was used for library preparation using TruSeq Nano DNA Library Prep Kit. Eluted DNA fragments are end-repaired, extended to the 3′ end with an ‘A’, and is ligated with Truseq adapters. Once ligation had been assessed, the product ranging from 175 to 225bp (insert DNA of 55–105 plus adaptors of 120 bp) were excised from a 2%(w/v) Low Range Ultra Agarose and purified using the QIAquick gel extraction protocol. The purified DNA was converted with the EpiTect Bisulfite Kit (Qiagen, 59104). The bisulfite-converted DNA libraries is amplified by PCR (four cycles) using PfuTurbo Cx DNA polymerase (Agilent, 600410). The final product is then quantified using qPCR and qualified using the Agilent Technologies 2200 TapeStation. The final product is sequenced using the HiSeq™ 2500 platform.

The affiliations for each contributor:
HS Hong 1, HH Chai 3,4, KW Nam 1, DJ Lim 3, KT Lee 3, YJ Do 3, CY Cho 5, JW Nam 1,2
1   Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Republic of Korea; yohae25@gmail.com (H.H.); nkw0228@gmail.com (K.N.); jwnam@hanyang.ac.kr (J.N.)
2   Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Republic of Korea; jwnam@hanyang.ac.kr (J.N.)
3   Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea; hanha@korea.kr (H.C.); lim.dj@korea.kr (D.L.); leekt@korea.kr (K.L.); clonea@korea.kr (Y.D.);
4   College of Pharmacy, Chonnam National University, Kwangju 61186, Republic of Korea
5   Animal Genetic Resource Research Center of National Institute of Animal Science, RDA, Namwon 55717, Republic of Korea; bloodtype@korea.kr (C.C.);

first: J

first: H

middle: S

last: Hong

first: K

first: D

middle: J

last: Lim

middle: T

last: Lee

first: Y

last: DO

first: C

last: Cho

last: Chai


title: CPD-seq map of UV damage formation in human fibroblasts

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: UV light is an initiating factor in the etiology of human melanoma due to its production of mutagenic DNA photoproducts, primarily cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. UV-induced mutations are heterogeneously distributed across melanoma genomes, being enriched, for example, in regions of compact heterochromatin and at active transcription factor binding sites (TFBS). Differential ability of nucleotide excision repair (NER) to remove UV-induced DNA lesions in these regions has been proposed as the primary factor establishing the observed regional differences in melanoma mutation density. However, it is not fully understood to what extent the binding of transcription factors and chromatin structure affect UV damage formation, nor how variations in initial damage levels contribute to mutagenesis. Here, we directly mapped sites of CPD formation across the genome in human cells, and show that variations in UV damage formation, due to primary chromatin structure and transcription factor binding, are strongly correlated with local differences in melanoma mutation density. Analysis of individual transcription factors revealed that the E26 transformation-specific (ETS) family is the major contributor to increased somatic mutation density at TFBS in melanoma, primarily because DNA binding by ETS family transcription factors stimulates the formation of CPD lesions, generating UV damage 'hotspots'. Moreover, many ETS binding sites, including those associated with known cancer genes, are recurrently mutated in human melanomas. These findings establish variable lesion formation as a key contributor to mutation heterogeneity in cancer.

overall_design: UV-induced cyclobutane pyrimidine dimers (CPDs) were mapped across the genome of NHF1 cells immediately following UV irradiation (0 hr time point) with doses of 100 J/m2 or 20 J/m2 of UVC light. As a control, isolated NHF1 genomic DNA (i.e., naked DNA) was irradiated in vitro with UV dose of 80 J/m2 of UVC light.

first: Peng

last: Mao