title: Dynamics of genomic, epigenomic, and transcriptomic aberrations during stepwise hepatocarcinogenesis

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

summary: Hepatocellular carcinoma (HCC) undergoes a stepwise progression from liver cirrhosis (LC) to low-grade dysplastic nodule (LGDN), high-grade dysplastic nodule (HGDN), early HCC (eHCC), and progressed HCC (pHCC). Here, we profiled multi-layered genomic, epigenomic, and transcriptomic aberrations in the stepwise hepatocarcinogenesis. Initial DNA methylation was observed in eHCC (e.g., DKK3, SALL3, and SOX1) while more extensive methylation was observed in pHCC. In addition, eHCCs showed an initial loss of DNA copy numbers of tumor suppressor genes in the 4q and 13q regions, thereby conferring survival benefits to cancer cells. Transcriptome analysis revealed that HGDNs expressed endoplasmic reticulum (ER) stress-related genes, while eHCC started to express oncogenes. Furthermore, integrative analysis indicated that expression of the serine peptidase inhibitor, Kazal type 1 (SPINK1), played a pivotal role in eHCC development. Significant demethylation of SPINK1 was observed in eHCC compared to HGDN. The study also demonstrated that ER stress may induce SPINK1 demethylation and expression in liver cancer cells. In conclusion, these results reveal the dynamics of multiomic aberrations during malignant conversion of liver cancer, thus providing novel pathobiological insights into hepatocarcinogenesis.

overall_design: Differential methylation profiling from liver cirrhosis (n=6), dysplastic nodules (n=11), early HCC (n=9), and progressed HCC (n=6).


title: Transcriptional analyses of two mutants of Podospora anserina impaired for sexual development

status: Public on Sep 16 2019

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

summary: A whole genome microarray approach has been engaged in the heterothallic euascomycete Podospora anserina to identify genes that are differentially expressed beetwen a wild type kinetics of sexual reproduction and two mutant strains ∆RID and ∆SMR1.

overall_design: With GPL10116 : reference design with a WT strain. Three independant  biological replicates for three times of the kinetic (T12, T24 and T30) and four biological replicates for the ∆RID mutant and the ∆SMR1 mutant strains, the common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5,

first: Véronique

last: Berteaux

first: Fabienne

last: Malagnac

first: Robert

last: Debuchy

first: Jinane

last: Ait benkhali


title: mTOR coordinates transcriptional programs and mitochondrial metabolism of activated Treg subsets to protect tissue homeostasis

status: Public on Sep 12 2019

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

summary: Regulatory T (Treg) cells derived from the thymus (tTreg) and periphery (pTreg) play central and distinct roles in immunosuppression, but mechanisms governing the generation and activation of Treg subsets in vivo remain uncertain. Here, we report that mechanistic target of rapamycin (mTOR) unexpectedly supports the homeostasis and functional activation of tTreg and pTreg cells. Further, mTOR signaling is crucial for programming activated Treg cell effector function to protect immune tolerance and tissue homeostasis. Treg-specific deletion of mTOR drives spontaneous TH2 responses and altered barrier tissue homeostasis, associated with reductions in both thymic derived effector Treg (eTreg) and pTreg cells. Mechanistically, mTOR acts downstream of antigenic signals to drive IRF4 expression and mitochondrial metabolism, and accordingly, disruption of mitochondrial metabolism severely impairs Treg cell suppressive function and their homeostasis in tissues. Collectively, our results demonstrate that mTOR coordinates transcriptional and metabolic programs in activated Treg subsets to mediate tissue homeostasis

overall_design: We used microarrays to explore global gene expression profiles in unstimulated cTreg cells or cTreg cells activated in the presence or absence of mTOR inhibitors Torin 1 and PP242. YFP+CD4+CD62L+iCD44- cTreg cells from Foxp3-YFP+ transgenic mice were sort-purified from peripheral lymphoid tissues and cultured in vitro. cTreg cells were activated using anti-CD3 and anti-CD28 antibodies in the presence of recombinant IL-2 for 20h and simultaneously treated with vehicle (DMSO), Torin 1 (50 nM) or PP242 (500 nM) before extraction of total RNA for microarray analysis. Biological triplicates of each treatment group were analyzed.

first: Nicole

last: Chapman

first: Hu

last: Zeng

first: Thanh-Long

last: Nguyen

first: Yanyan

last: Wang

first: Yogesh

last: Dhungana

first: Hongbo

last: Chi


title: ALDH high activity  or low activity cell in 4T1 bearing mice

status: Public on Sep 06 2019

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

summary: The gene expression in ALDH high or low activty cell in 4T1 bearing mice was measured.

overall_design: 4T1 cells from 4T1 bearing mice sorted to the ALDH high activty or low activty cells using ALDEFLUOR kit. Total RNA was isolated from each cells.

first: Naoya

last: Matsunaga

first: Atsushi

last: Doi

first: Kaori

last: Yasuda


title: Effect of TIC10/ONC201 on glioma cells

status: Public on Sep 18 2019

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

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

overall_design: U87 cells were treated with 10 µM of ONC201 or 0.1% DMSO as the negative control. After 72 hours treatment, total RNA was isolated and analyzed.

first: Chiaki

last: Ishida

first: Markus

last: Siegelin


title: Gene expression profile (GEP) of miR-382-5p-overexpressing CD34+ cells

status: Public on Sep 04 2019

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary: Primary Myelofibrosis (PMF) is a Philadelphia negative chronic myeloproliferative neoplasm characterized by bone marrow fibrosis, enhanced oxidative stress and high levels of serum pro-inflammatory cytokines. To identify genes and miRNAs potentially involved in PMF pathogenesis, we have previously carried out an integrative analysis of gene and microRNA expression profiles of PMF hematopoietic stem cells (HSPCs), which allowed us to identify miR-382-5p as up-regulated miRNA (Norfo R. et al, Blood 2014). Overexpression experiments in normal CD34+ cells have already demonstrated its central role in HSPC fate decision toward granulocyte lineage (Zini R. et al, Stem Cell Dev 2016). In this study, to further characterized the role of miR-382-5p in PMF pathogenesis, we performed a gene expression profile analysis in normal CD34+ HSPCs overexpressing miR-382-5p. Among the down-regulated genes upon miR-382-5p upregulation, we selected the anti-oxidant superoxide dismutase 2 (SOD2), depicted as the most favorable predicted target by TatgetScan 7.0. Firstly, luciferase reporter assay confirmed SOD2 as a real target of miR-382-5p. Furthermore, we showed that enforced miR-382-5p expression in CD34+ cells reduced SOD2 expression and activity, induced ROS accumulation, and oxidative DNA damages, as well as enhanced CD34+ cell proliferation. Afterwards, to confirm miR-382-5p as a key player in PMF pathogenesis, we performed inhibition experiments in PMF CD34+ cells revealing that miR-382-5p silencing restored SOD2 expression and activity, induced ROS disposal, decreased DNA oxidation and impaired cell proliferation.

overall_design: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments at 24 hours after the last nucleofection of mirVana mimic miR-382-5p in CD34+ hematopoietic stem/progenitor cells (HSPCs).

first: Chiara

last: Rossi

first: Roberta

last: Zini

first: Sebastiano

last: Rontauroli

first: Samantha

last: Ruberti

first: Zelia

last: Prudente

first: Greta

last: Barbieri

first: Elisa

last: Bianchi

first: Simona

last: Salati

first: Elena

last: Genovese


title: Reactivation of super-enhancers by KLF4 in human Head and Neck Squamous Cell Carcinoma

city: Buffalo

first: Michael

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Head and Neck Squamous Cell Carcinoma (HNSCC) is a disease of significant morbidity and mortality ranked as the sixth leading cause of cancer worldwide rarely diagnosed in early stages. Despite extensive genetic research, development of therapeutics and diagnostic markers has been limited due to the extensive heterogeneity and complexity of the disease. Herein, we generated a comprehensive understanding of the transcriptional regulatory aberrations in HNSCC based on the epigenomic and transcriptomic study of the mesenchymal cell line SCC25. Our findings support a fundamental role for the transcription factor Krüppel-like Factor 4 (KLF4) in HNSCC, through its binding to differential active regulatory elements, the majority of which are super-enhancers, and the transcriptional upregulation of key HNSCC cancer genes. Upregulation of these targets often realizes with the concurrent action of TP63 or ERG. Approximately 70% of the activated targets bear a simultaneous loss of the H3K27me3 histone repressive mark and are confirmed EZH2 targets in healthy states, corroborating the tumor suppressor role of the Polycomb Repressive Complex 2 in head and neck cancers. Our current results lead us to propose a model where the upregulation and binding of KLF4 activates the HNSCC state, by re-activating repressed chromatin domains at key genes via super-enhancers.

overall_design: Comparison of the epigenomic and transcriptome landscape for the head and neck sequamous cell carcinoma cell line SCC25 with the normal cell line HGEP.

first: Maria

last: Tsompana

middle: J


title: Notch signaling is required for induction of an innate T cell development program in human thymus

status: Public on Sep 05 2019

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: CD4 CD8 double positive (DP) thymocytes progressively shut down Notch signaling after β-selection allowing progression of the DP program and positive selection of conventional CD4 and CD8 single positive T cells. In contrast, innate CD8+ T cells are selected from DP precursors shortly after β-selection. Here, we investigated whether notch signaling is required for the initiation of the innate T cell developmental program upon TCR engagement. We show that, after β-selection, Notch activation limits progression to late DP cells and favors the development of TCRαβ/CD3 expressing CD8dim early DP progenitors. TCR engagement in these Notch dependent  TCRαβ+ early DP precursors does not induce prominent apoptosis, but rather induces T-bet expression by an mTOR-dependent mechanism. Our findings indicate that Notch signaling drives the launch of an innate effector program in response to TCR agonist selection in the thymus.

overall_design: Three samples are analyzed. The first sample comes from native thymus tissue. CD34+ postnatal thymocytes were transduced to express either TCRalpha (second sample) or TCRbeta (third sample). Subsequently, the transduced thymocytes were cultured on OP9-DL1 cells. When the cells were double positive, the cells were harvested sorted for immature CD3+ DP cells transgenic for the TCR.

first: Greet

last: Verstichel

first: Bart

last: Vandekerckhove


title: Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells

status: Public on Sep 24 2019

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

type: Expression profiling by high throughput sequencing

summary: To follow the changes in the transcriptional programs accompanying the specification of the embryonic Lgr5+ cells we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E13.5 and E15.5). EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Lgr5+ progenitors were purified on the basis of GFP fluorescence from Lgr5GFP-Cre-ERT mice (Barker et al. 2007). Double positive embryonic progenitors were isolated by FACS based on GFP and tdTomato fluorescence.

overall_design: Intestinal epithelial cells from two embryonic stages (E13.5 and E15.5) were used. For embryonic stages biological triplicates were analysed.

first: Natalia

last: Soshnikova


title: Archaic and modern bone DNA methylation maps from the Neanderthal, Denisovan, modern human and chimpanzee

city: Jerusalem

first: David

last: Gokhman

address: Givat Ram, Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

type: Methylation profiling by high throughput sequencing

summary: Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
DNA methylation maps were reconstructed from several human groups, including two Neanderthals, one Denisovan and five anatomically modern humans (Ust Ishim, Stuttgart, Loschbour, I1583 and La Braña 1). Additionally, present-day DNA methylation maps were produced from two present-day human bones (WGBS) and two chimpanzee bones (WGBS and RRBS).

The metadata for the following samples are included in the supplementary file 'GSE96833_metadata_reanalysis_samples.xls':
- Altai Neanderthal Reconstructed Methylome
- Denisovan Reconstructed Methylome
- Modern Human (Ust Ishim) Reconstructed Methylome
- Modern Human (Stuttgart) Reconstructed Methylome
- Modern Human (Loschbour) Reconstructed Methylome
- Vindija Neanderthal Reconstructed Methylome

first: Liran

last: Carmel

first: Tomas

last: Marques-Bonet

first: Alexander

last: Meissner

first: Carles

last: Lalueza-Fox

last: Reich

first: Eran

last: Meshorer

first: Ron

last: Pinhasi

first: Julio

middle: M

last: Vidal

first: María

middle: E

last: Prada

first: Meir

last: Liebergall

first: Leonid

last: Kandel

first: Deus

last: Mjungu

first: Anne

middle: C

last: Stone

first: Ellen

last: Quillen

first: Ronald

last: Bontrop

first: Ivanela

last: Kondova

first: Iddi

last: Lipende

first: Pere

last: Gelabert

first: Manuel

last: Ferrando-Bernal

first: Hongcang

last: Gu

first: Mario

last: Novak

first: Songül

last: Alpaslan-Roodenberg

first: Nadin

last: Rohland

first: Heng

last: Li

middle: A

last: Nieves-Colón

first: Swapan

last: Mallick

first: Malka

last: Nissim-Rafinia

first: Raquel

last: García-Pérez

first: Genevieve

last: Housman

first: Lily

last: Agranat-Tamir


title: Macrophages mediate systemic tissue health after remote injury

status: Public on Aug 31 2019

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Functions of tissue-resident macrophages in the steady state and after direct injury to the vital organs they inhabit are currently emerging. Yet, whether macrophages react to injury systemically and remotely, for instance how lung, liver or renal macrophages respond to myocardial infarction and stroke, remains obscure. Here we report that after myocardial infarction, stroke and peritonitis, macrophage populations expand in most distant organs through local cell proliferation and recruitment. Transcriptome profiling reveals a profound, system-wide response of macrophages to remote injury in all organs. This response is determined by the host organ rather than by injury type.

overall_design: We analyzed flow-sorted macrophages from lung, kidney, heart, liver and brain in the steady state, and after myocardial infarction, stroke and peritonitis induced by cecal ligation and puncture. At least three replicates were analyzed per organ and disease condition, for a total of 56 samples.

first: Friedrich

middle: F

last: Hoyer

first: Matthias

last: Nahrendorf


title: Genome-wide maps of histone acetylation status in renal fibroblasts.

status: Public on Sep 01 2019

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary: In numerous forms of organ injury, interstitial fibrosis is a final common pathway. Despite recent epidemiological studies, therapies to focus on fibrosis and to delay progressive renal failure are limited. Previously our group showed that sphingosine kinase 2 deficient-mice (SphK2-/-) develop less fibrosis in folic acid-induced or unilateral ischemia-reperfusion injury (IRI)-induced kidney fibrosis models. Sphingosine 1-phosphate (S1P) is produced by two sphingosine kinase isoforms (SphK1 and SphK2). S1P is involved in diverse functions, but the role of S1P produced by SphK2 is gathering attention as treatments focused on epigenetics have been developed. SphK2 is primarily located in the nucleus and S1P produced by SphK2 inhibits histone deacetylase (HDAC) and changes in histone acetylation status, which can lead to an altered target gene expression. We identified that bone marrow stromal cell antigen-1 (Bst1/CD157) is a gene related with kidney fibrosis based on the combination of genome-wide analysis and in vivo screening. SphK2 regulates Bst1 expression and Bst1-/- mice develop less fibrosis after unilateral IRI and are protected against renal bilateral IRI. Bone marrow chimera experiments further revealed the importance of Bst1 expression on hematopoietic cells. Furthermore we identified the role of Bst1 expression in neutrophils for inducing renal ischemia-reperfusion injury and fibrosis.

overall_design: Examination of 2 different histone modifications in 3 cell types.

first: Tsuyoshi

last: Inoue

first: Youichiro

last: Wada

first: Mark

middle: D

last: Okusa


title: c-Met activation leads to the establishment of a TGFb regulatory network required for bladder cancer invasion

status: Public on Aug 23 2019

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Aberrant c-Met activation and upregulation of its cognate ligand HGF are frequently observed in bladder cancer and have been shown to regulate downstream pathways involved in proliferation, motility, and invasion. The precise mechanism underlying HGF/c-MET mediated invasion in bladder cancer is partly addressed by this microarray dataset. HGF activates the canonical TGFb signaling pathway to enhance epithelial mesenchymal transition and bladder carcinoma invasion.

overall_design: NBTII cell line were treated with HGF at timepoint 0 hr, 2 hr, 4 hr, 6 hr, 9 hr, 24 hr and 48 hr.

first: Sim

middle: W

last: Jing

first: Jean

middle: P

last: Thiery

first: Tan

middle: T

last: Zea


title: Effects of Src on gallid alpha herpesvirus 1 intercellular spread

status: Public on Aug 22 2019

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

country: China

institute: Xi'an Jiaotong University

summary: We sequenced mRNA from ILTV uninfected or infected LMH cells with or without Src inhibition.

overall_design: Examination of mRNA levels in individual condition were compared. Four independent experiments were performed.

first: Shengwang

last: Liu


title: PAX1-SET1B Interaction Drives Multiple Phosphatases and Inhibits Oncogenic Cascades

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

summary: Functional studies of PAX1 were tested in cervical cancer cell lines in vitro and in vivo.

overall_design: The 1st batch cells were collected after treating EGF for a week and provied as control samples. The 2nd batch cells were collected after treating EGF for two weeks and induced PAX1 expression at the last week, and the 3rd batch cells were collected after treating EGF for three weeks and induced PAX1 expression at the last two weeks.

first: Po-Hsuan

last: Su

first: Rui-Lan

last: Huang


title: Expression data in Ucp2+/+ (WT) and Ucp2-/- (KO) colon tumors from AOM/DSS-treated mice

status: Public on Aug 27 2019

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
The objective of the study was to evalute the changes in gene expression associated to UCP2 invalidation in colon tumors from AOM/DSS-treated mice
We used microarrays (Mouse Gene 2.0) to investigate gene expression in Ucp2+/+ and Ucp2-/- colon tumors

overall_design: Mice were sacrificed at week 15 after starting AOM/DSS protocol and colon tumors from Ucp2+/+ and Ucp2-/- mice were collected

first: Marie-Clotilde

last: Alves Guerra

first: Esther

last: Aguilar Fadó


title: Transcriptional profiling of Setd5 mutant cortical neural progenitors

status: Public on Sep 15 2019

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Setd5 inactivation in neural stem cells, zebrafish and mouse leads to a significant H3K36 hypo-methylation mostly detectable along the gene bodies. Consequently, this chromatin alteration perturbs RNA processing during elongation, compromising the transcriptional output. This gene dysregulation affects proliferative dynamics of NSCs and synaptic wiring in the neuronal derivatives, ultimately resulting in behavioral deficits in adult mice.

overall_design: 3 wt clones and 3 Setd5 het clones of NSC edited in Setd5 locus with CRISPR/Cas9

first: Alessandro

last: Sessa

first: Vania

last: Broccoli


title: Subpopulations of activated hepatic stellate cells defined and inhibited by WT1 expression

status: Public on Aug 21 2019

city: Edinburgh

first: Timothy

middle: James

last: Kendall

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

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

overall_design: Refer to individual Series


title: Transformation of NIH3T3 cells by the forced expression of wild-type YAP or its stabilized form

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: YAP is known as a proto-oncogene with which the aberrant expression causes numerous types of cancer. To elucidate the molecular mechanisms underlying the acquisition of cancerous traits of normal cells by YAP overexpression, the wild-type YAP or its stabilized form was overexpressed in NIH3T3 cells. We found that the forced expression of either wild-type YAP or its derivative alone was sufficient for transforming NIH3T3 cells and we then analyzed the global expression profiles of the control NIH3T3 cells or those overexpressing wild-type or stabilized YAP.

overall_design: The wild-type mouse Yap or the degradation resistant Yap in which serine at 112 was mutated by alanine was expressed in NIH3T3 cells.

first: Masazumi

last: Nishimoto

first: Masataka

last: Hirasaki

first: Yosuke

last: Mizuno


title: Whole genome expression analysis of subpopulations of activated hepatic stellate cells defined by WT1 expression

summary: Transciptional heterogeneity of scar-orchestrating cells in liver fibrosis, defined by WT1 expression, after chronic tetrachloride injury in vivo (WT1-high and WT1-low) or activation in vitro (WT1-negative).

overall_design: Total RNA isolated from WT1-high and WT1-low activated stellate cells isolated by FACS after density centrifugation from livers of WT1GFP/+ mice chronically injured with carbon tetrachloride, and from WT1-negative cells from in vitro activated day 7 hepatic stellate cells.


title: Identifications of a novel group of intra-genic interactive putative enhancers reveals a distinctive enhancer architectures in plants

status: Public on Aug 20 2019

city: Atlanta

first: Hsiao-Lin

middle: V.

last: Wang

state: GA

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

summary:
ABSTRACT: Enhancers are important regulators of gene expression in eukaryotes; however, only a few enhancers have been identified in plants, and the genome-wide identifications are lacking.
To investigate enhancers in Arabidopsis thaliana, we analyzed the chromatin landscape, RNA Pol II occupancy, and the polyadenylated and non-polyadenylated Arabidopsis transcriptomes, using exosome-deficient lines to capture stable and unstable transcripts.
Here we identified the set of unique >1900 regions, termed Putative Enhancers (PEs), carrying canonical chromatin signatures of metazoan transcriptional enhancers.
Almost of PEs are intra-genic and transcriptionally active. Unexpectedly, most of the PE carrying these signatures are associated with the 3′ ends of protein-coding genes, enriched in transcription factor binding, with binding motifs resembling polyadenylation signals, thus linking links two hubs of very different, functionally and mechanistically distinct processes – cleavage/polyadenylation and transcription termination of protein-coding genes with transcriptional activation/regulation of different genes. And may present a novel DNA elements with regulatory potential.
Additionally, according to high resolution Arabidopsis Hi-C data 24% of identified PEs interact with other protein-coding genes intrachromosomally, through binding by the same set of transcription factors, supporting the notion of co-regulation of expression between PEs and their targets. We also confirmed that PEs are highly conserved in the recently sequenced 1035 different Arabidopsis accessions.

overall_design: Identifications and characterization of a novel putative intragenic enhancers (PEs) in Arabidopsis. To determine if the identified PEs are actively transcribed we profiled the RNA expression in WT and the exosome deficient Arabidopsis seedlings. Since eRNAs (transcripts arising at enhancer locus) varied by their polyadenylation status, we collected both the polyadenylated RNAs (polyA(+)) and the pool of ribo-minus RNA depleted of rRNAs to increase our detection for non-polyadenylated RNA, and subjected to high throughout sequencing. The bioinformatics protocols used for processing RNA-seq datasets, transcriptome assembly, and profiling transcriptional activity are described in further details in the associated publication.

middle: V

first: Julia

last: Chekanova


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in O sativa

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: The sRNA population (sequence identity and distribution of abundances) in O sativa was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from O sativa leafs were created using HD and standard Illumina adapters, the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu


title: ALDH high or low cell in 4T1 cell

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: The gene expression in ALDH high or low activty cell in 4T1 cell was measured.

overall_design: 4T1 culture cell sorted to the ALDH high activty or low activty cells using ALDEFLUOR kit. Total RNA was isolated from each cells.

first: Naoya

last: Matsunaga

first: Atsushi

last: Doi

first: Kaori

last: Yasuda


title: Primary muscle cells from in-utero undernourished mice

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: ICR mice, age 6-8 weeks.(Harlan, Indianapolis, IN, USA). Housed individually with controlled temperature, humidity, and light-dark cycle (0600h – 1800h). Pregnant mice were housed individually with ad libitum access to standard rodent chow (T.2018, Harlan Teklad, Indianapolis, IN, USA). On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. After delivery, mothers were given ad libitum access to chow and 24 hours after birth, litters were equalized to eight. We studied mice from 2 groups: in utero undernourished offpring (U) and control offspring (C). Primary muscle cells were isolated from the quadriceps of U and C at 3 weeks old. Isolated primary muscle cells were grown on Matrigel coated flasks in low glucose (5.5 mmol/L) Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 20% FBS, 1X antibiotic-antimycotic, 2.5μg/ml gentamycin and 2.5ng/ml basic fibroblast growth factor.  When cells reached approximately 90% confluency, they were differentiated in low glucose DMEM supplemented with 2% FBS, 1X antibiotic-antimycotic, and 2.5μg/ml gentamycin. Other cells were cultured overnight in substrate limited medium (glucose and glutamine free DMEM supplemented with 0.5mM glucose, 1mM glutamine, 0.5mM carnitine and 1% (v/v) FBS; pH 7.4).

overall_design: RNA expression analysis of primary muscle cells from in-utero undernourished mice, cultured in substrate limited medium and standard medium.

first: Georges

middle: N

last: Kanaan

first: Brittany

last: Beauchamp

first: Olivier

last: Charette

first: Kijoo

last: Kim

first: Mary-Elizabeth

last: Patti

first: Alexandre

last: Blais

first: Mary-Ellen

last: Harper


title: Temporal analysis of mRNA from panicle tissue from field grown rice under high nighttime temperatures

status: Public on Aug 15 2019

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

institute: NCSU

summary: A IR64 variety of rice was grown in a field plot at the International Rice Research Institute (IRRI) in the Philippines. The data gained from the experiment provides information of the daily transcriptional changes occur in panicle tissue during an important developmental period under control and warm night temperatures.

overall_design: When the plants reached 50% flowering, panicle tissue was harvest at ~3 hour intervals for 24 hours. There are 8 timepoints with 4 replicates at each timepoint with two conditions (Control and WNT) for a total of 64 samples. Additionally there is a gradient set with consists of 2 timepoints with 4 replicates and 4 conditions (24C, 26C, 28C, and 30C).

first: Lovely

last: Lawas

first: Ashlee

last: Valente

first: Adam

middle: R

last: Leman

first: Dmitry

middle: O

last: Grinevich

first: S

last: Jagadish

first: Colleen

last: Doherty


title: Gene expression profiling of 126 colorectal cancer tissue samples

status: Public on Nov 11 2019

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

type:
Expression profiling by array
Third-party reanalysis

summary: We have compared gene expression profiling by RNA sequencing and exon-resolution microarrays to determine the impact of analysis platform on clinically relevant transcriptomic subtyping frameworks. These samples represent a subset of the total series analyzed.

overall_design: This series consists of 3 new colorectal cancer tissue samples analyzed on Affymetrix Human Transcriptome 2.0 Arrays and reanalysis of 123 GSMs from GSE24550, GSE29638, GSE69182 and GSE96528 performed on HTA_2.0 or  HuEx-1_0-st Affymetrix arrays and analyzed with the platform-specific BrainArray version 22 GENECODEG custom CDF.

first: Ina

last: Eilertsen

first: Ragnhild

last: Lothe


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum without TAP treatment

first: Tamas

last: Dalmay

summary: The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from S Lycopersicum leafs were created using HD and standard Illumina adapters, without a TAP treatment; the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu


title: Deep sequencing of olive (Olea europaea l.) Short RNAs identifies microRNAs targeting involved in drupe ripening

status: Public on Aug 11 2019

city: Rende

first: Fabrizio

last: Carbone

state: CS

address: C.da Li Rocchi Vermicelli

department: Research Centre for Olive, Citrus and Tree Fruit

institute: Council for Agricultural Research and Economics (CREA)

summary: The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations making them particularly attractive to animals and humans. Usually, there is a progressive chromatic change characterized by a final red-brown color of both epidermis and mesocarp. This event has an exception in the ‘Leucocarpa’ cultivar, in which we observed the destabilization in the equilibrium between the metabolism on chlorophyll and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white coloration of the fruits.   Recently, transcription profiling of ripening olives from ‘Leucocarpa’ and ‘Cassanese’ cultivars, through an Illumina RNA-seq approach, has provided some information about genes involved in fruit maturation as flavonid and anthocyanin transcripts.   To study the possible gene differences involved in flavonoids and anthocyanins biosynthetic pathways during ripening possibly caused by small nuclear RNA (snRNA) in olive drupes, the snRNA libraries of fruit ripening from ‘Leucocarpa’ and ‘Cassanese’ were constructed with RNAs from drupes at 100 and 130 DAF (Days After Flowering) and sequenced by Illumina approach. Comparing sequence information, 130 conserved microRNAs (miRNA) in the Viridiplantae were detected belonging 14 miRNA families. For the remaining read not-matched with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 miRNAs were considered as putative novel. To increase insights into the functions of known and putative novel miRNA in olive, putative target genes were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 32 and 186 transcripts were predicted as targets of 130 known and 492 putative novel miRNA, respectively. The identified target genes are involved in a broad range of biological processes.   Interestingly, some genes involved in negative regulation of anthocyanin metabolic process, were identified as target of miR168 suggesting that this miRNA family is likely operative during color transition in olive.

overall_design: Olive drupes, of Olea europaea L. Cassanese (a) and Leucocarpa. for each cultivar, drupes(n = 30) were randomly collected at 100 and 130DAF.

first: Leonardo

last: Bruno

first: Gaetano

last: Perrotta

first: Maria

middle: B

last: Bitonti

first: Innocenzo

last: Muzzalupo

first: Adriana

last: Chiappetta


title: Combined Treatment with L-Carnitine and Nicotinamide Riboside Improves Hepatic Metabolism and Attenuates Obesity and Liver Steatosis

city: Leiden

first: Martine

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Abstract: Obesity characterized by adiposity and ectopic fat accumulation is associated with the development of non-alcoholic fatty liver disease (NAFLD). Treatments that stimulate lipid utilization may prevent the development of obesity and comorbidities. This study evaluated the potential anti-obesogenic hepatoprotective effects of combined treatment with L-carnitine and nicotinamide riboside, i.e., components that can enhance fatty acid transfer across the inner mitochondrial membrane and increase nicotinamide adenine nucleotide (NAD+) levels, which are necessary for β-oxidation and the TCA cycle, respectively. Ldlr −/−.Leiden mice were treated with high-fat diet (HFD) supplemented with L-carnitine (LC; 0.4% w/w), nicotinamide riboside (NR; 0.3% w/w) or both (COMBI) for 21 weeks. L-carnitine plasma levels were reduced by HFD and normalized by LC. NR supplementation raised its plasma metabolite levels demonstrating effective delivery. Although food intake and ambulatory activity were comparable in all groups, COMBI treatment significantly attenuated HFD-induced body weight gain, fat mass gain (−17%) and hepatic steatosis (−22%). Also, NR and COMBI reduced hepatic 4-hydroxynonenal adducts. Upstream-regulator gene analysis demonstrated that COMBI reversed detrimental effects of HFD on liver metabolism pathways and associated regulators, e.g., ACOX, SCAP, SREBF, PPARGC1B, and INSR. Combination treatment with LC and NR exerts protective effects on metabolic pathways and constitutes a new approach to attenuate HFD-induced obesity and NAFLD.

overall_design: Experimental design  The mice were supplied with food and tap water ad libitum and mice were fed standard lab chow (Ssniff R/M diet V1530, Uden, The Netherlands) until they were 12–15 weeks old. Subsequently, 74 mice were divided into five experimental groups. The healthy reference group continued to receive a chow diet (n = 13) and the high-fat diet control group (HFD) received a NAFLD inducing diet (45 kcal% fat from lard, 35 kcal% from carbohydrates, primarily sucrose and 20% kcal from protein; D12451, Research Diets, New Brunswick, NJ, USA) as described previously [17] (n = 16). L-carnitine (0.4% w/w, Sigma-Aldrich, Zwijndrecht, The Netherlands; LC group; n = 15), nicotinamide riboside (0.3% w/w, NovAlix, Cedex, France; NR group; n = 15) and the combination of both (COMBI group, n = 15) were mixed through the HFD and the respective groups were treated with these diets for 21 weeks.   Gene Expression and Pathway Analysis: Total-RNA isolation kit (Bio-connect, Huissen, The Netherlands) was used to extract RNA from snap-frozen livers. The RNA concentration was measured spectrophotometrically using a NanoDrop 1000 (Isogen Life Science, De Meern, The Netherlands). To assess the quality of the isolated RNA, the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands) was used. Next, messenger RNA (mRNA) library was produced for next generation sequencing following the manufacturer′s protocol NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The quality and yield of the PCR products were consistent with the expected size distribution (300–800 base pairs). Clustering and DNA sequencing were performed by GenomeScan BV (Leiden, The Netherlands) using a NextSeq 500 sequencer (Illumina, San Diego, CA, USA). The sequences were directly aligned with the mouse reference genome (GRCm38p4) using the Start 2.5 algorithm with default settings.

first: Kanita

last: Salic

first: Eveline

last: Gart

first: Florine

last: Seidel

first: Lars

last: Verschuren

first: Martien

last: Caspers

first: Wim

last: van Duyvenvoorde

first: Kari

last: Wong

first: Jaap

last: Keijer

first: Ivana

last: Bobeldijk-Pastorova

first: Peter

middle: Y

last: Wielinga

first: Robert

last: Kleemann


title: Colonizing and infecting subclones diverge during Staphylococcus aureus infection

status: Public on Aug 14 2019

city: New York

first: Kieran

middle: Ifan

last: Chacko

address: One Gustave L. Levy Place

department: Genetic & Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Therapy of Staphylococcus aureus bacteremia is often ineffective, even under optimal conditions, and adapted subclones with attenuated agr-mediated virulence activation are associated with persistent infection and mortality. To understand how apparent loss of virulence leads to increased mortality, we sequenced complete genomes from clone pairs from colonizing and infected sites of patients in whom S. aureus demonstrated a within-host downshift in agr function in the infecting isolate.  Clone pairs with a downshift in agr function showed substantial genetic divergence compared to wild-type pairs from controls. Complementation studies further identified an agr-defective bacteremic strain that was highly virulent in vivo, which we linked to a mutation that restored expression of the agr-regulated ess/Type-VII secretion system; a known virulence factor. Our results suggest that selection pressure during invasive infection is strong enough to mutationally bypass agr-deficiency associated loss of virulence, and that efforts to suppress agr function may need to be reconsidered.

overall_design: Clonal S. aureus isolates from colonizing (nares) and infecting sites (blood) were obtained from a single patient. Whole-genome comparisons of single colonies from both isolates revealed 361 genetic variants between strain genomes, including a loss of agr functionality in the blood strain. To assess the impact of non-agr mutations engineered an agr knockout of the wild-type nares strain and complemented the naturally occurring agr mutant blood strain.  Wild-type agr genes were transduced in single copy to the naturally occurring agr-defective variant using the staphylococcal pathogenicity island (SaPI)-1 attC locus as the insertion site. The four different strains were then grown to late log (OD600 of ~0.8) and profiled by directional RNA-Seq, in duplicate.

first: Deena

last: Altman

first: Mitchell

middle: J

last: Sullivan

middle: I

first: Divya

last: Balasubramanian

first: Theodore

last: Pak

first: William

last: Sause

first: Krishan

last: Kumar

last: Sebra

first: Gintaras

last: Deikus

first: Oliver

last: Attie

first: Hannah

last: Rose

first: Martha

last: Lewis

first: Yi

last: Fulmer

first: Ali

last: Bashir

first: Andrew

last: Kasarskis

first: Eric

last: Schadt

first: Anthony

last: Richardson

first: Victor

last: Torres

first: Bo

last: Shopsin

first: Harm

last: van Bakel


title: Global RNA expression of fibromodulin reprogrammed human BJ fibroblasts

status: Public on Aug 10 2019

city: Los Angeles

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

summary: RNA-seq analysis of fibromodulin reprogrammed human BJ fibroblasts to obtain the global transcripton of the yield fibromodulin reprogrammed (FReP) cells.

overall_design: RNA-seq is done in two seperated batches of FReP cells. TopHat followed by Cufflinks will be used to analyze the gene expression levels.


status: Public on Aug 25 2019

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

institute: Keio University School of Medicine

summary: Single cell RNA sequencing for mesenteric CD31+ cells derived from control and endothelial-specific Folliculin (Flcn) knockout mice at postnatal day 8

overall_design: mRNA profiles of 8-day old contorol and endothelial-specific Flcn knckout mice. One experiment for each genotype.

first: Yutaka

last: Suzuki


title: Global gene expression analysis in TAE sensitive and resistant Kelly cells.

status: Public on Aug 07 2019

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary: We performed gene expression profiling by Affymetrix primeview array in both TAE sensitive, resistant and JQ1-treated resistant Kelly cells.

overall_design: Expression profiles of TAE sensitive, resistant and JQ1-treated resistant Kelly cells using GeneChip® PrimeView™ Human Gene Expression Array, in duplicate,for a total of 6 individual samples.

first: David

last: Debruyne

first: Rani

last: George


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in M truncatula, with TAP treatment

first: Tamas

last: Dalmay

summary: The sRNA population (sequence identity and distribution of abundances) in M truncatula was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from M truncatula leafs were created using HD and standard Illumina adapters, with  a TAP treatment; the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu

first: Archana

last: Singh


title: Genome wide SMC1-mediated chromatin looping changes in TAE sensitive and resistant Kelly cells

summary: We performed SMC1-mediated ChIA-PET analysis in both TAE sensitive and resistant Kelly cells.

overall_design: SMC1 ChIA-PET data from TAE sensitive and resistant Kelly cells were generated by deep sequencing using Illumina HiSeq 2000.

first: Daniel

last: Day


title: Analysis of the Effect of Fibulin-1 on Fibroblast Growth Factor 8 Signaling

status: Public on Aug 16 2019

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: We have previously shown that human fibulin-1 (FBLN1) is a binding partner of fibroblast growth factor 8 (FGF8) and affects its expression and signaling. Herein, we investigate the mechanisms by which FBLN1 affects FGF8 signaling. Fibulin-1 (Fbln1) -deficiency in mouse embryo fibroblasts (MEF) caused downregulation of Fgf8 as well as fibroblast growth factor receptors (Fgfr) 1 and 3 and several downstream genes in the Fgf8 pathway, including Six1, Eya1 and Barx1. The Fgf8-regulated putative DiGeorge syndrome gene, Tbx1, was also significantly downregulated. Fbln1-deficiency in MEFs caused upregulation of Sonic hedgehog (Shh), an established upstream regulator of Fgf8. Surprisingly, this was accompanied by downregulation of several Shh signaling pathway targets, including patched1, smoothened, Gli1 and Gli3. Analysis of Fbln1-null embryonic hindbrain and arch regions showed that Shh was upregulated in the 2nd arch but downregulated in arches 1, 3 and 4. A broader transcriptomic analysis of mouse hindbrain and arches confirmed that Fbln1 deficiency caused changes in the mitogen activated protein kinase (Mapk) and Wnt signaling pathways. Biochemical tests showed that Fbln1 binds to Shh and that its absence blocks secretion of Shh by MEFs. Based on these results, Fbln1 affects Fgf8 signaling by influencing expression of Shh and its downstream targets, including Mapk and Wnt signaling pathways. This affect may involve direct interaction of Fbln1 with Shh in a manner facilitating the production of secreted Shh.

overall_design: Tissue containing hindbrain and pharyngeal arches 1-4 was isolated from Fbln 1 null (n=5) and wildtype (n=5) E10.5 mouse embryos for microarray comparison.

first: Waleed

last: Twal

middle: L


title: Gene expression profile of primary epidermal keratinocytes (HEKs) stimulated with lawsone

status: Public on Aug 06 2019

city: Berlin

first: Teresa

last: Domaszewska

state: Berlin

address: Chariteplatz 1

department: Immunology

institute: Max Planck Institute for Infection Biology

summary: The study aimed to interrogate whether the 1,4-naphtoquinone derivative lawsone activates the aryl hydrocarbon receptor (AhR) downstream transcriptional program in keratinocytes and is capable of modulating skin homeostasis. The study has been performed on human primary epidermal keratinocytes (HEKs), which represent the first line of defense against exogenous molecules. HEK cells were treated with the vehicle control DMSO (control), stimulated with lawsone or with the TLR2 ligand Pam2CSK4. Transcriptional profiles of HEK cells were studied to investigate the regulation of AhR -related genes, Nrf2-related genes and epidermal differentiation and keratin genes. We demonstrated that lawsone was sensed by keratinocytes and activated AhR. In particular, lawsone efficiently activated the transcriptional program of AhR and promoted keratinocyte differentiation.

overall_design: Three-condition experiment: HEK cells treated with the vehicle control DMSO (control) vs. HEK cells stimulated with lawsone (10 µM) (Law). As negative control we used HEK cells stimulated with the TLR2 ligand Pam2CSK4 (300 ng/mL) (TLR2). One biological replicate. control= ctrl; lawsone= Law; Pam2CSK4=TLR2.

first: January

last: Weiner 3rd

first: Hans

last: Mollenkopf

first: Laura

last: Lozza


title: Identification and Characterization of House Dust Mites-associated Immunogenic RNA

status: Public on Aug 01 2019

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

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

sample_organism:
Dermatophagoides pteronyssinus
Mus musculus

overall_design: Refer to individual Series


title: TAE sensitive and resistant Kelly cells


title: Transcriptional changes in mouse lungs induced by house dust mite

summary: We examined the transcriptional changes in mouse lungs induced by house dust mite (HDM), D.f. extract and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that HDM  strongly triggered an inflammatory response.

overall_design: Total RNA was isolated from the lung of  wild type or TLR3MAVS double knockout mice  that were treated with PBS or  HDM (D.f.) extract for  14-16 hours. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 . Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Yi

last: Zou

first: Xiao-Dong

last: Li


title: Expression data of miRNA from parental B16F0 cells and B16F0 exosomes [miRNA]

city: Morgantown

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

summary:
As a type of secreted membrane vesicle, exosomes are emerging as an important mode of cell-to-cell communication. The objective of this study was to compare the abundance of mRNA and miRNA present in the parental B16F0 cell to mRNA and miRNA present in exosomes isolated from B16F0 conditioned media.
Identifying local mechanisms of immunosuppression is a key barrier for expanding the clinical benefit of cancer immunotherapy. While exosomes are emerging as a new mode of intercellular communication, their role in establishing a malignant tissue niche remains unclear. Similar to the sculpting of tumor antigens during oncogenesis, a related hypothesis is that proteins secreted by malignant cells are shaped by somatic evolution. To test this hypothesis, we characterized the biological influence of tumor-derived exosomes on immune cell function.

overall_design: 8 Total samples were analyzed. The abundance of miRNAs was estimated based on the average expression of all core probesets for a miRNA measured by Affymetrix microarray. The probability of a gene being expressed above background by random chance was estimated using the negative control probesets and a Welch's t-test, where the degrees of freedom were calculated using the Welch-Satterthwaite equation. A p-value of less than 0.01 was used for estimating the distribution of miRNA expression between cells and exosomes while a p-value of less than 1e-9 was used for qRT-PCR validation and pathway enrichment analysis.  The lower p-value incorporates a Bonferroni correction for multiple hypothesis testing.


title: SUN protein regulates transcription-associated epigenetic modification

status: Public on Aug 04 2019

city: Shanghai

first: jingmin

last: Guan

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biolog

institute: Shanghai Institutes for Biological Sciences

summary: We report the difference of genome-wide chromatin profiling of histone modifications in mammalian cells after PBS or LPS treatment. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse peritoneal macrophages. We find that lysine 4 and lysine 9 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential.Trimethylation of lysine 9 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of mammalian cells after LPS treatment.

overall_design: Examination of 2 different histone modifications in mouse peritoneal macrophages after LPS treatment.

first: Shi

last: Jiao

first: Chuanchuan


title: Expression profiling of lncRNA and mRNA in Hepatocellular carcinoma

first: Ji-Min

last: Zhu

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital of Fudan University

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

summary: To explore critical roles of lncRNA and mRNA playing in the pathogenesis of hepatocellular carcinoma, the Agilent microarray was used to simultaneously profile lncRNA and mRNA expression in 7 pairs of HCC and matched adjacent tumor-free tissues.

overall_design: In total, seven pairs of HCC and matched adjacent tumor-free tissues were collected during the surgery from HCC patients admitted to Zhongshan Hospital of Fudan University between 2008 and 2009.

first: Hai-Rong

first: Xiang-Nan

last: Yu

first: Guang-Cong

last: Zhang

first: Xuan

last: Shi

first: Enkhnaran

last: Bilegsaikhan

first: Hong-Ying

last: Guo

first: Tao-Tao

last: Liu

first: Ling

last: Dong

first: Shu-Qiang

last: Weng

first: Xi-Zhong

last: Shen


title: Amphiregulin Mediates the Hormonal Regulation on R-spondin1 Expression in the Mammary Gland

first: Ajun

last: Geng

state: Shanghai

address: 320 Yue-Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: We have used RNA-seq to examine RNA differential expression between Sca1+ and Sca1- luminal cells in mouse mammary gland.We have used RNA-seq to examine RNA differential expression between E2Pg treatment and control cultured luminal cells.

overall_design: Examine RNA differential expression among subsets of freshly sorted mouse mammary gland epithelial cells. And examine RNA differential expression between E2Pg treatment and control cultured luminal cells

first: Cheguo

last: Cai

middle: A

last: Zeng


title: H3K36me3 protects the mouse epigenome from single nucleotide variations [CGH]

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

type: Genome variation profiling by genome tiling array

summary: Copy numbers of mouse cells (ESCs and NIH3T3) carrying a series of single-site histone mutants or shRNAs comparing with control empty cells. Genomic DNA from candidate cells and control cells were respectively labeled by Cy5 or Cy3 and analyzed by array-based comparative genomic hybridization (aCGH).

overall_design: multipule stable cell lines carrying histone mutants and shRNA against Suv39h1 or h2 were analyzed.

first: FangLin

last: Kang

first: Jianfeng

last: Chang


title: Human Papillomavirus (HPV) genomic integration, expression and E6/E7 splicing patterns in cervical cancer associated with HPV16 or HPV18 infection

city: Rio de Janeiro

first: Ayslan

middle: Castro

last: Brant

state: Rio de Janeiro

address: Andre Cavalvanti 37

department: Genetics

country: Brazil

institute: National Institute of Cancer

summary: Human papillomavirus (HPV) genome integration into the host genome, blocking E2 expression and leading to overexpression of E6 and E7 viral oncogenes, is considered a major step in cervical cancer development. In high-risk HPVs, E6 and E7 oncogenes are expressed as a bicistronic pre-mRNA, with alternative splicing producing the ultimate mRNAs required for E6 and E7 translation. Given the number of alternative donor and acceptor splicing sites, ten E6/E7 different alternative transcripts might be formed for HPV16 and three for HPV18, although only six isoforms have been previously reported for HPV16. In the present work, we employ high-throughput sequencing of invasive cervical cancer transcriptome (RNA-Seq) to characterize the expression of the HPV genome in 24 invasive cervical cancers associated with HPV16 and HPV18 single infections. Based on high-resolution transcriptional maps, we herein report three viral gene expression patterns which might be associated with the presence of the viral genome in episomal and/or integrated stages. Alternative mRNAs splicing isoforms coding for E6 and E7 oncoproteins were characterized and quantified, and two novel isoforms were identified. Three major isoforms (E6*I, E6*II, and E6+E7) were detected for HPV16 and two for HPV18 (E6*I and E6+E7). Minor transcript isoforms, including the novel ones, were very rare in some tumor samples or were not detected. Our data suggested that minor transcript isoforms of E6/E7 do not play a relevant role in cervical cancer.

sample_organism:
Homo sapiens
Human papillomavirus 16
human papillomavirus 18

overall_design: RNA-Seq analysis of 24 uterine cervix tumors and CaSki cell line.

middle: C

first: Miguel

middle: M

last: Moreira


title: Homo sapiens whole blood.

status: Public on Jul 31 2019

city: Jena

first: Philipp

last: Kämmer

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

summary: RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

overall_design: Examination of three biological replicates.

first: Sylvie

last: McNamara

first: Sascha

last: Brunke

first: Jörg

last: Linde


title: Homo sapiens whole blood infected with Candida spp. (here: Candida tropicalis)

summary: Homo sapiens fresh whole blood was infected with Candida tropicalis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Candida tropicalis gene expression.

sample_organism:
Candida tropicalis
Homo sapiens

platform_organism:
Candida tropicalis
Homo sapiens

overall_design: Examination of three biological replicates for each of the 6 time points.


title: Transcriptome profiling of human pluripotent stem cell-derived mesenchymal stem cells (hPSC-MSCs), hPSCs, and tissue-derived hMSCs

city: Zhunan, Miaoli County

first: Li-Tzu

last: Wang

address: 35 Keyan Road

department: Institute of Cellular and System Medicine

institute: National Health Research Institutes (NHRI)

summary: Transcriptome profiling analysis of human embryonic stem cell-derived MSCs (hESC-MSCs), induced pluripotent stem cell-derived MSCs (hiPSC-MSCs), hESCs, hiPSCs, bone marrow-derived MSCs (hBM-MSCs), and placenta-derived MSCs (hP-MSCs).

overall_design: MSC RNA samples were derived from one hESC-MSCs, one hiPSC-MSCs, one parental hESCs of hESC-MSCs, one parental hiPSCs of hiPSC-MSCs, two hBM-MSCs,  and two hP-MSCs.

first: Wei

last: Lee

first: Shih

middle: S

last: Jiang

first: B

last: Yen


title: The expression profiles of lncRNAs during C2C12 myoblasts differentiation

city: Wuhan

first: lvwei

middle: jian

last: jun

state: Hubei

address: shizishan street, NO.1

department: College of Animal science and technology

institute: huazhong agriculture university

summary: To systematically identify lncRNAs involved in muscle cell differentiation, the lncRNA microarrays was used to identify differentially expressed lncRNAs during C2C12 cells differentiation (Proliferation myoblast and 2, 5, 8 days after differentiation, represented by D0, D2, D5 and D8. respectively)

overall_design: The expression profile of lncRNAs in C2C12 cells was measured at proliferation and 2, 5, 8 days after cells differentiation, Three independent experiments were performed at each stage.

first: Zuo

last: Bo

first: Lv

last: Wei

first: Xia

last: Pan

first: Xu

last: Yan

first: Zheng

last: Dai

first: Wang

last: Jing

last: Shan

first: Zeng

last: Rui

first: Liu

last: Lei

first: Li

last: Liang


title: lncRNA SYISL contributes to the genome-wide expression during myogenic differentiation

summary: In order to screen the target genes regulated by SYISL,we  transfected the siRNA to knock down SYISL gene (si-SYISL) and negative control siRNA (si-NC), induced cells to differentiate for 2 days. The results suggest that SYISL knockdown broadly inhibits cell cycle genes expression, and promotes myogenic differentiation-associated genes expression.

overall_design: We further transfected the siRNA to knock down SYISL gene (si-SYISL) and induced cells to differentiate for 2 days. Then, we used microarray to analyze genome-wide gene changes after SYISL knockdown in C2C12 cells differentiated for 2 days.

first: Jin

last: Jun


title: Comparison of DNMT1 inhibitors by methylome profiling identifies unique signature of 5-aza-2'deoxycytidine [methylation]

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

institute: Ulster University

summary:
Dacogen (DAC/ 5-aza-2’deoxycitidine/Aza) is currently used to treat myeloid dysplastic syndrome (MDS) and is in trials for Acute Myeloid Leukaemia (AML) and some solid cancers. As a hypomethylating agent it is thought to act by inhibiting the enzymes which add methyl groups to DNA, chief among them DNMT1. Improved targeting has been hindered by a lack of understanding of the off-target effects following treatment.
Both Dacogen and DNMT1 siRNA caused overall hypomethylation in the treated cells, with the latter proving more efficient at demethylation at gene bodies in particular.  Amongst the targets experiencing demethylation, some hypomethylated promoters were unique to Dacogen treatment and therefore off-target with respect to the reduction in DNMT1. An unexpected phenomenon almost exclusively caused by DAC treatment was gain in methylation. Our results suggest Dacogen is also having an important effect on methylation unrelated to the inhibition of DNMT1, suggesting further avenues for therapeutic improvements.

overall_design: We performed a comparative treatment of the same normosomic, non-transformed fibroblast cell line hTERT1604 over three days with either the pharmacological 5-Aza-2’deoxycitidine (Aza) or with SMARTpool siRNA directly targeting DNMT1. DNA was collected for analysis of methylation levels using Illumina Human Methylation 450k BeadChip methylation arrays. Data was analysed in R using the tailored RnBeads pipeline and in-house scripts.

first: Sarah-Jayne

last: Mackin

first: Karla

last: O’Neill

middle: P


title: Comparison of DNMT1 inhibitors by methylome profiling identifies unique signature of 5-aza-2'deoxycytidine (expression)


title: Comparison of DNMT1 inhibitors by methylome profiling identifies unique signature of DAC

type:
Expression profiling by array
Methylation profiling by array


title: Gene expression profile of hepatocellular carcinoma patients in Taiwan

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary: SUMMARY: Hepatocellular carcinoma(HCC) is one of the most malignant tumors in the world. In this study, we used microarray analysis to develop gene expression profile of HCC patients in Taiwan.We showed the gene expression signature between tumor and normal samples.

overall_design: Overall design: 8 normal tissue and 24 hepatocellular carcinoma patients with stage T1,T3a,T3b were selected for RNA extraction and showed the gene expression profile.

first: Hsieh

last: Sen-Yung


title: Sequence-specific binding of small RNAs to antithrombin with functional effects

city: Cartagena

first: Ginés

last: Luengo-Gil

address: C/ Mezquita s/n. 1ª planta

department: Department of Pathology

country: Spain

institute: UCAM

overall_design: Identification of RNA bound to antithrombin

first: Irene

last: Martínez-Martínez

first: Javier

last: Corral


title: Gene expression profiles proton-induced in brest cell lines

status: Public on Jul 29 2019

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

summary: Literature data report the helpful role of specific molecularly based signatures to predict response to treatment in cancer, including breast cancer (BC) disease. As known, BC is a heterogeneous disease presenting distinct subtypes with different clinical outcomes. Thus, the choice of a unique treatment plan for all BC patients, including radiation therapy (RT), may be not the best option. Technological advances in RT are evolving with the use of proton beams, which reduce the dose administered to the heart compared to conventional RT. However, limitate data regarding proton-induced molecular changes are currently available. The aim of this study was therefore to study gene expression profiles induced by proton irradiation with 0.5, 2 and 9 Gy of Ionizing radiation (IR) doses in breast cells. The great amount of data here collected, represent an useful tool to better understand the molecular mechanisms elicited by proton irradiation, thereby filling the existing lack of data in the literature.

overall_design:
Proton-induced gene expression changes in non- tumorigenic (MCF10A) and in tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. New Samples were named as follow: MCF10A_0,5Gy_proton; MCF10A_2Gy_proton; MCF7_0,5Gy_proton; MCF7_2Gy_proton; MDA-MB-231_0,5Gy_proton; MDA-MB-231_2Gy_proton.
In addition, we have re-used the previous samples in GSE103472 (18 samples out of 37 as included in the current records).


title: Imidazole-4-carboxamide (ICA) effect on Oryza sativa

status: Public on Jul 26 2019

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

institute: Shizuoka University

summary: Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the “fairy”, ICAproduced by the fairy ring-forming fungus and the mechanism of its growth-inhibiting activity using DNA microarray. We invetigate expression profiling of rice seedlings treated with ICA for the mechanism of its growth-inhibiting activity.

overall_design: Two-condition experiment, control vs. ICA-treated rice (2 and 10 uM)

first: Jae-Hoon

last: Choi

first: Hirokazu

last: Kawagishi


title: Analysis of miRNA expression profiles of porcine granulosa cells overexpressing RBP4

status: Public on Jul 24 2019

city: Changchun

first: Yun

last: Zhao

state: Jilin

address: Xi'an Road

department: College of Animal Sciences

institute: Jilin University

summary: To illustrate molecular pathways associated with the effects of RBP4 on GCs, we used high-throughput sequencing to detect differential gene expression in GCs overexpressing RBP4.

overall_design: mRNA profiles of porcine granulosa cells were generated by deep sequencing, in triplicate,

first: Chunjin

last: Li


title: Effect of photoperiod on gene expressions in guard cells.

status: Public on Jul 22 2019

city: Chikusa-ku

first: Toshinori

last: Kinoshita

state: Nagoya

address: Furo-cho

department: Graduate School of Science

institute: Nagoya university

summary: To clarify the molecular mechanism in photoperiod-dependent regulation of stomatal movements, we performed RNA sequences in isolated guard cell protoplasts from Arabidopsis thaliana.

overall_design: Gene expression in guard cell protoplast was measured from SS (short day 5 weeks) or SL (short day 3 weeks and long day 2 weeks) condition plants.  Three independent experiments were performed using independent plant batch for each experiment.


title: Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana

city: St. Louis

first: Lucia

last: Strader

state: MO

address: One Brookings Drive, CB-1137

department: Biology

institute: Washington University in St. Louis

summary: The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The AUXIN RESPONSE FACTOR (ARF) family of transcription factors regulates auxin-responsive gene expression and exhibit nuclear localization in regions of high auxin responsiveness. Here we show that activating ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. The intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, thus providing a mechanism for cellular competence for auxin signaling.

overall_design: RNA-seq analysis of Col-0 (Wt), Col-0 carrying UBQ10:YFP-ARF19, and Col-0 carrying UBQ10:YFP-ARF19K962A in the absence and presence of auxin treatment.


title: H3K36me3 protects the mouse epigenome from single nucleotide variations [mRNA-Seq]

first: Jin

last: Sun

summary: The goals of this project are to study the transcriptome profiling (RNA-seq) of mouse embryonic stem cells by histone mutants incorporation (H3.1K3M, H3.1K36M vs H3.1wt) or shRNA-mediated knockdown of methyl-transferase Suv39h1/h2 (shSuv39h1, shSuv39h2 vs shNC)

overall_design: mRNA profiles of mES stable cell lines with overexpression of H3.1WT, H3.1K9M, H3.1K36M and shNC, shSuv39h1, shSuv39h2 were generated by deep sequencing, in double, using Illumina next-generation sequencing.

first: FangLin

first: Xuan

last: Kang

first: Jianfeng

last: Chang


title: Identification and Characterization of HDM D.p. immunogenic RNA

first: Yidong

last: Chen

institute: UT Health Science Center at San Antonio

summary: We examined the sequence information of the gel-extracted and purified RNA bands #1,#2 and #3 derived from  House Dust Mite (HDM) D.p. immunogenic RNA. The individula RNA band was utilized for RNA-seq analysis.

overall_design: The gel-extracted RNA bands #1,#2 and #3 derived from  House Dust Mite (HDM) D.p. immunogenic RNA. 100ng RNA from each band was used for RNA-Seq library preparation by following the KAPA total RNA-Seq Kit with RiboErase (HMR) sample preparation guide with some modifications. Samples were run on an Illumina HiSeq 3000 platform.

first: Yi

last: Zou

first: Xiao-Dong


title: H3K36me3 protects the mouse epigenome from single nucleotide variations

summary: We adopt histone H3 mutants competitive incorporation system to screen the effects of them on genetic fidelity. We find incorporation of H3K36M, an oncogenic histone mutant, produce a cancer or ageing-like genetic landscape by punctuating the H3K36me3/H3K9me3 dependent DNA repair mechanism. This work firstly get a direct relationship between epigenetic inheritance and genomic stability

overall_design: In order to study the relationship between epigenetic dysregulation and genetic stability, we overexpress several histone H3 single-substitution mutants in mouse embryonic stem cells and get stable cell lines respectively carrying H3K36M or H3K9M. After a certain round culture, we analyze the genetic signature of these cells by high-throughput sequencing of exome-sequencing, ChIP-seq and aCGH. Comparing with the cells carrying wide-type H3 after identical culture condition, we summarize the genetic signature of histone mutation. Based on the surprising cross-talk between H3K36me3 and H3K9me3, we further find the mechanism of Suv39h modifier on the genetic stability.


title: The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression

status: Public on Jul 18 2019

city: New York

first: Wenjing

last: Su

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: The mechanisms that enable immune evasion at metastatic sites are poorly understood. We show that the Polycomb Repressor Complex 1 (PRC1) drives colonization of the bones and visceral organs in double-negative prostate cancer (DNPC). In vivo genetic screening identifies CCL2 as the top prometastatic gene induced by PRC1. CCL2 governs self-renewal and induces the recruitment of M2-like tumor-associated macrophages and regulatory T cells, thus coordinating metastasis initiation with immune suppression and neoangiogenesis. A catalytic inhibitor of PRC1 cooperates with immune checkpoint therapy to reverse these processes and suppress metastasis in genetically engineered mouse transplantation models of DNPC. These results reveal that PRC1 coordinates stemness with immune evasion and neoangiogenesis and point to the potential clinical utility of targeting PRC1 in DNPC.

overall_design: PC3 prostate cancer cells stably expressing RNF2 shRNA or Scramble shRNA, or treated with PRT4165 or GW-516.

first: Hyun Ho

last: Han

first: Yan

last: Wang

first: Boyu

last: Zhang

first: Bing

last: Zhou

first: Yuanming

last: Cheng

first: Alekya

last: Rumandla

first: Goutam

last: Chakraborty

first: Jie

first: Guangli

last: Yang

first: Guocan

first: Neal

last: Rosen

first: Howard

last: Scher

first: Ouathek

last: Ouerfelli

first: Filippo

middle: G

last: Giancotti


title: Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction

status: Public on Jul 15 2019

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Long non-coding RNAs (lncRNAs) function in a wide range of processes by diverse mechanisms, though their roles in regulation of oncogenes and/or tumor suppressors remain rather elusive. We performed a global search for lncRNAs affecting MYC activity using a systems biology-based approach with a K supercomputer and the GIMLET algorism based on local distance correlations. Consequently, MYMLR was identified and experimentally shown to maintain MYC transcriptional activity and cell cycle progression despite the low levels of expression. A proteomic search for MYMLR-binding proteins identified PCBP2, while it was also found that MYMLR places a 557-kb upstream enhancer region in the proximity of the MYC promoter in cooperation with PCBP2. These findings implicate a crucial role for MYMLR in regulation of the archetypical oncogene MYC and warrant future studies regarding the involvement of low copy number lncRNAs in regulation of other crucial oncogenes and tumor suppressor genes.

overall_design: Microarray analysis using a SurePrint G3 Human GE 8 x 60K v2 Microarray G4851B (Agilent) was conducted

first: Taisuke

last: Kajino

first: Teppei

last: Shimamura

first: Shuyi

last: Gong

first: Kiyoshi

last: Yanagisawa

first: Lisa

last: Ida

first: Masahiro

last: Nakatochi

first: Sebastian

last: Griesing

first: Yukako

last: Shimada

first: Keiko

last: Kano

first: Motoshi

last: Suzuki

first: Satoru

last: Miyano


title: 1,25(OH)D3 effect on colonic organoids from wt and VDR KO mice

status: Public on Jul 21 2019

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

institute: IIB

summary: VitaminD deficiency has been related to a higher incidence of colorectal cancer. In order to further study the effect of VDR and its ligand as genome modulators we established stem cell enriched cultures of wt and VDR KO mice, treated with the active metabolite of Vitamin D and analyzed the changes in total RNA expression.

overall_design: Organoid 3D stem cell enriched culture was established from colon crypts from 3 wt mice and 3 VDR KO mice. The cultures were treated for 72 houres with either vehicle (EtOH) or VDR ligand 1,25(OH)2D3, the active form of VitaminD. Gene expression was analyzed with an Agilent microarray design ID 028005, P/N G4852A.

first: A

last: Barbáchano

last: Fernández-Barral

last: Costales-Carrera

first: G

last: Ferrer-Mayorga

first: M

last: Larriba

last: Muñoz


title: Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

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: Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic–Uremic Syndrome

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: A dynamic network approach was conducted to investigate the differential Caco-2 response to two STEC isolates - EH41, isolated from a HUS patient in Australia, and Ec472/01, isolated from bovine feces in Brazil - along in vitro enterocyte-bacteria interaction. The genomic analysis was based on temporal gene co-expression analysis (GCN) data in order to gain a better understanding on the molecular mechanisms underlying the capacity to cause HUS. The GCN topological analyses for Caco-2/EH41 group revealed loss of the scale-free status after one hour of interaction, persistence of this condition along the second hour and establishment of a new gene hierarchy thereafter. These events resemble the gene network mechanism of health-disease transition. The new established network represents an adaptive cell response to the pathogen and not the return to a “normal” state. Conversely, the networks for Caco-2/Ec472 group showed a slow and progressive loss of the scale-free status without its restoration at the end of the time interval here studied. These results contribute for a better understanding of the molecular mechanism involved in STEC pathogenicity associated to HUS.

overall_design: The transcriptomic profiles of Caco-2 cells during interaction with STEC strain Ec472/01 were obtained. The time-series adopted equal intervals of 7.5 minutes along 3 hours. We performed a sliding-window analysis to investigate temporal gene co-expression network (GCN) variation along 3 hours of enterocyte-bactria interaction.

first: Priscila

last: Iamashita

first: Silvia

last: Bando

first: Filipi

middle: N

last: Silva

first: Luciano

last: da F Costa

first: Cecilia

last: Abe

first: Fernanda

last: Bertonha

first: Beatriz

middle: E

last: Guth

first: Andre

last: Fujita


overall_design: The transcriptomic profiles of Caco-2 cells during interaction with STEC strain EH41 were obtained. The time-series adopted equal intervals of 7.5 minutes along 3 hours. We performed a sliding-window analysis to investigate temporal gene co-expression network (GCN) variation along 3 hours of enterocyte-bactria interaction.

middle: Y

middle: B


title: Gene expression analysis of wild type and Hedgehog pathway-activated embryonic mouse stomach

status: Public on Jul 09 2019

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary:
The Hedgehog signaling pathway plays important roles in gut development and homeostasis. In this study, we use Affymatrix Miroarray to analyze the gene expression profiles of wild type stomach and SmoM2-expressing stomach at E13.5. The goal of this study is to understand the transcription program regulated by Hedgehog in the developing gut.
SmoM2 is a constitutively active form of Smo, whick leads to Hedgehog ligand independent cell-autonomous pathway activation.

overall_design: Total RNA obtained from freshly isolated E13.5 stomach tissue from wild type and NKX3.2Cre;R26-SmoM2 animals

first: Jennifer

last: Cotton

first: Junhao

last: Mao


title: Expression patterns of key miRNAs in end-stage ADPKD kidneys

status: Public on Jul 30 2019

city: Seoul

first: Sumin

last: Oh

address: Cheongpa-ro 47-gil 100, Yongsan-gu

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

summary: To investigate altered expression patterns of key miRNAs in end-stage ADPKD kidneys, a miRNA microarray analysis was performed using non-ADPKD and ADPKD kidney tissue samples. As a result, total 19 miRNAs were significantly changed in the ADPKD samples compared with non-ADPKD samples. Among these miRNAs, the expression level of the miR-192 family including miR-192 and miR-194 were significantly downregulated in ADPKD.

overall_design: Renal cyst tissue samples were obtained from patients with ADPKD undergoing nephrectomy. As a control, non-ADPKD renal tissue samples were obtained from patients undergoing surgery for clear cell renal cell carcinoma, where malignant cell infiltration was excluded by histology.

first: JongHoon

last: Park

first: YuMi

last: Woo

first: SunYoung

last: Lee

first: DoYeon

last: Kim


title: High malignant potential of betel quid-associated oral verrucous hyperplasia

status: Public on Jul 01 2019

city: Taoyuan

first: Ji-Dung

last: Luo

address: No. 259, Wen-Hua 1st road

department: Graduate Institute of Biomedical Sciences

institute: Chang Gung University

summary: Objectives. Oral verrucous hyperplasia (OVH) is commonly observed in the oral cavity of betel quid chewers that histologically display epithelial hyperplasia with or without dysplasia. Because of the high frequency of synchronous OVH adjacent to oral carcinomas, OVH is considered a potential malignant disorder, and studies of prognostic factors and genetic alterations are required.   Materials and Methods. We conducted a follow-up study of 269 OVH patients at Chi-Mei Medical Center. A Kaplan-Meier analysis and Cox's proportional-hazards regression model were used to calculate the survival rate and prognostic factors of disease recurrence and transformation. Copy number variations (CNVs) were analyzed using a single-nucleotide polymorphism (SNP) array.  Results. The 5-year disease-free and cancer-free survival rates of patients with OVH were 52% and 77%, respectively. Heavy betel quid (BQ) chewing (>20 nuts/day), the severity of oral submucosal fibrosis (OSF), and non-buccal and non-tongue lesions were high risk factors for malignant transformation, while dysplasia did not affect outcomes. A genetic analysis showed that OVH already possessed many CNVs present in oral squamous cell carcinoma (OSCC), and a bioinformatics analysis of CNV-associated genes revealed that the upregulation of CTTN, FOLR3, ORAOV1, PPFIA1, and RNF121 could help identify high-risk OVH patients.  Conclusions. BQ-associated OVH has a high malignant potential, and more attention must be paid to OVH patients who have a heavy BQ chewing habit and advanced OSF, and whose tumor is located at non-buccal and non-tongue regions. The five CNV-associated genes can be used for early diagnosis and for predicting the prognosis.

overall_design: Peripheral blood, VH and oral cancer tissues were obtained from two distinct Taiwanese oral cancer patients. The copy number variations in the three different stage of lesion were identified. Comparing CNVs in serial pre-cancer (VH) and cancer samples could shed the light on tumor formation and progression.

first: Ming-Heng

last: Wu


title: 3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: Epstein-Barr Virus (EBV) encoded Nuclear Antigens (EBNAs) and virus activated NF-B subunits mostly bind to enhancers in EBV transformed lymphoblastoid cells lines (LCLs). Using LCL 3D genome organization map that links EBV enhancers to promoters, we built the most comprehensive virus regulome. EBV regulome contained 1992 genes and enhancers directly linked to them. ~30% of genes essential for LCL growth were linked to EBV enhancers. CRISPR knock out of EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets including MCL1, IRF4, and EBF were identified. MYC ESEs looping to MYC TSS was dependent on EBNAs. CRISPR deletions of MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study defines the most comprehensive host-pathogen interactions on the spatial organiz   ation of chromatin during infection and cancer.

overall_design: Discarded human peripheral blood mononuclear cell from healthy anonymous platelet donors were obtained from Dana Farber Cancer Institute blood bank. Viable peripheral blood mononuclear cells were isolated using LymphoprepTM density gradient centrifugation. Resting B cells were isolated by two step immunomagnetic negative selection using EasySep B Cell Isolation Kit and RosetteSep B Cell isolation Kit (StemCell). Total RNAs were prepared and RNAs depleted for ribosomal RNA were sequenced with Illumina HiSeq 2000.

first: Sizun

last: Jiang

first: Jun

last: Liang

first: Catherine

last: Gerdt

first: Chong

last: Wang

first: Liangru

last: Ke

first: Stefanie

last: Schmidt

first: Yohei

last: Narita

first: Yijie

last: Ma

first: Shuangqi

first: Tyler

last: Colson

first: Benjamin

last: Gewurz

first: Guoliang

last: Li

first: Elliott

last: Kieff

first: Bo

last: Zhao


title: Peritoneal fluid from subjects with endometriosis regulates gene expression in cultured endometrial cells

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Purpose: This study was undertaken to evaluate the effect of peritoneal fluid from subjects with differing stages of endometriosis on gene expression in endometrial stromal cells.   Methods: Peritoneal fluid from subjects with minimal, moderate, and severe stages of endometriosis or without endometriosis (controls) was collected, filtered and separated from peritoneal cells. Telomerase – immortalized human endometrial stromal cells (T-HESC) were treated with the peritoneal fluid samples for 48 hours. RNA was isolated from treated cells and processed for DNA microarray.   Results: 162 genes were found to be differentially expressed in T-HESC cells treated with peritoneal fluid from subjects with differing stages of endometriosis. Three of the differentially expressed genes were chosen for confirmatory studies using quantitative RT-PCR; these were interleukin 8, corin and matrix metalloproteinase 3. The primary gene ontologies identified by microarray highlight functions expected to be involved in the establishment of endometriosis, such as proteases, signal transduction, defense and immune system, cell adhesion, cell cycle and cell death, cytoskeleton, transcriptional regulation and translation, extracellular matrix, and enzymes and metabolism.    Conclusions: This study demonstrated that the severity of endometriosis affected the factors present in peritoneal fluid which, in turn, affected gene expression in endometrial stromal cells.

overall_design: Peritoneal fluid from 12 individual subjects was used to treat T-HESC cells. Subjects were grouped by absence (controls, n=3) or presence of endometriosis.  Subjects with endometriosis were divided into 3 groups: minimal, moderate, or severe endometriosis.  Experimental number was 3 per group.  The 12 samples were analyzed on individual microarrays.

first: Abha

last: Chalpe

first: Jennifer

last: Gubbels

first: Keith

last: Hansen


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma

status: Public on Jul 05 2019

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

institute: IDIBAPS

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


title: Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

institute: Keio University School of Medicine

summary: PIWI-interacting RNAs (piRNAs) are germline-specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRISC complexes) to preserve genomic integrity by repressing transposable elements (TEs). Among PIWI-clade proteins in Drosophila, Piwi transcriptionally silences its targets via heterochromatin formation characterised by H3K9me3 marks and the linker histone H1. Recent studies have shown that Panoramix (Panx) interacts with Piwi–piRISC complexes to induce transcriptional repression of targets mediated by the recruitment of H3K9me3 marks. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms a complex with Panx and Piwi. Nxf2 further associates with p15 (Nxt1), a co-adaptor for nuclear RNA export. However, unlike Nxf1 that plays a major role in mRNA export, Nxf2–p15 instead transcriptionally regulates TEs in the Piwi–piRNA pathway. Panx–Nxf2–p15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. The amino-terminal domain of Nxf2 harbouring RNA binding activity is essential for recruitment of the Piwi–piRISC complex to target TEs. Indeed, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Nxf2–Panx–p15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway. Our results provide an unexpected connection between an NXF variant and small RNA-mediated co-transcriptional silencing.

overall_design: mRNA levels, H3K9me3 occupancy, Nxf2 or Piwi associated RNA, and Piwi associated smRNA in ovarian somatic cells (OSC).

first: Kensaku

last: Murano

middle: W

first: Haruhiko

last: Siomi


title: Differential gene expression in TREM1 -/- vs +/+ myeloid cells 48h after MCAo-RP

status: Public on Jul 02 2019

city: Stanford

first: Katrin

middle: I

last: Andreasson

state: California

address: 1201 Welch Rd, MSLS P250

department: Neurology and neurological sciences

institute: Stanford University

summary:
Stroke is a multiphasic progress characterized by neuron damage due to hypoxia followed by secondary damage from the subsequent inflammatory immune response.  Infiltrating myeloid cells induce cerebral damage through pro-inflammatory cytokines, chemokines, proteases and generation of reactive oxygen species (ROS).
Triggering receptor expressed on myeloid cells 1 (TREM1) is exclusively expressed on myeloid cells and acts as an amplifier of pro-inflammatory innate immune responses. Using microarray analysis, we aim to identify the expression differences and functional change of these myeloid cells after TREM1 knockout in mice post stroke.

overall_design: TREM1-/- vs +/+ C57B6/J male mice underwent transient cerebral ischemia (MCAo-RP). At 48 hours after MCAo-RP, myeloid cells in ischemic hemisphere were isolated, stained with biomarkers (CD45, CD11b, and Ly6g) and sorted immediately by Fluorescence-activated cell sorting (FACS). Affimetrix Clariom microarray was used to examine differential gene expression on microglia, macrophages, and neutrophils from ischemic hemisphere.

first: Qingkun

last: Liu


title: Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

city: Cardiff

first: Natalia

last: Sevane

address: Museum Avenue

department: Biosciences

institute: Cardiff University

summary: Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus’ arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. Reduced representation bisulfite sequencing (RRBS) was used to assess differences in methylation in Creole and Spanish samples and revealed 334 differentially methylated regions (DMRs) using high stringency parameters (p-value < 0.01,  4 CpGs within a distance of 200 bp, mean methylation difference > 25%), annotated to 263 unique features. Gene ontology analysis revealed candidates involved in tropical adaptation processes, including genes differentially hyper- or hypomethylated above 80% in Creole samples displaying biological functions related to immune response (IRF6, PRGDR, FAM19A5, PRLYRP1), nervous system (GBX2, NKX2-8, RPGR), energy management (BTD), heat resistance (CYB561) and skin and coat attributes (LGR6). Our results entail that major environmental changes imposed on Creole cattle has had an impact on their methylomes measurable today, which affects genes implicated in important pathways for adaptation. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models.

overall_design: Three Creole (Costeño con Cuernos n = 2, San Martinero n = 1) and three Spanish (Retinta n = 1, Asturiana de los Valles n = 1, Lidia n = 1) samples belonging to five cattle breeds were analysed using reduced representation bisulfite sequencing (RRBS).

first: Michael

last: Bruford


title: SETD5 is a H3K36 methyltransferase which preserves transcriptional fidelity during brain development and neuronal wiring

status: Public on Jul 10 2019

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento