title: Inflammatory Gene Changes in Spleens from WT and Rescued GR-C3 Knockin Mice Treated with LPS

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Glucocorticoids are primary stress hormones and their synthetic derivatives are widely used clinically. The therapeutic efficacy of these steroids is limited by severe side effects and glucocorticoid resistance. Multiple glucocorticoid receptor (GR) isoforms are produced by alternative translation initiation; however, the role individual isoforms play in controlling tissue-specific responses to glucocorticoids in vivo is unknown. We have generated knockin mice that exclusively express the most active receptor isoform, GR-C3. The GR-C3 knockin mice die at birth due to respiratory distress but can be completely rescued by antenatal glucocorticoid administration. Rescued GR-C3 mice exhibited alterations in circadian rhythm in a sexually dimorphic manner and in sensitivity to lipopolysaccharide (LPS)-induced endotoxemia. To evaluate the ability of glucocorticoids to protect against LPS-induced inflammation, we measured gene expression in spleens from WT and rescued GR-C3 knockin mice that had been treated with vehicle or LPS for 3 and 24 hours. The GR-C3 isoform was found to be deficient in its ability to repress a large cohort of immune and inflammatory genes.

overall_design: GR-C3 knockin mice were generated by standard gene targeting procedures.  In brief, ES cells were generated in which exon 2 of the NR3C1 gene was replaced by a neomycin cassette. An exchange vector was generated containing a hygromycin cassette and a mutant NR3C1 exon 2 in which the ATG start codon for GR-C3 was left intact but mutated to ATC for each of the other seven translational isoforms. The exchange vector and Cre-recombinase were transfected into the targeted ES cells by electroporation, and positive ES cells were selected using G418 (sensitive) and hygromycin (resistant). A GR-C3 positive ES cell clone was injected into C57Bl/6 blastocysts to create chimeric mice. Chimeric males were bred with C57Bl/6 females for germline transmission, and the hygromycin cassette was deleted using Flp-deleter mice. The resulting mice were maintained on a C57Bl/6 background and intercrossed to produce WT, heterozygous GR-C3 knockin, and homozygous GR-C3 knockin mice.  Homozygous GR-C3 knockin mice die at birth due to respiratory distress but can be completely rescued by antenatal glucocorticoid treatment. Adult male WT and rescued homozygous GR-C3 knockin mice were injected intraperitoneally with PBS or LPS (10μg/g body weight).  Mice were sacrificed 3 hours and 24 hours after LPS administration and the spleen was removed. Total RNA was isolated from the spleens (n=4 per treatment group) using TRIzol reagent according to the manufacturer's instructions.

first: Sivapriya

last: Ramamoorthy

first: Robert

middle: H

last: Oakley

first: John

last: Cidlowski


title: Atrial Molecular Asymmetry Precedes the Emergence of Cardiac Septation

status: Public on May 09 2018

city: Bad Nauheim

first: Almary

middle: Victoria

last: Guerra Rodríguez

state: Hessen

address: Ludwigstrasse 43

department: Dept. III Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Defensive effect of microRNA-200b/c against amyloid-beta peptide-induced toxicity in Alzheimer’s disease models

status: Public on May 08 2018

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

country: Japan

institute: National Center for Geriatrics and Gerotology

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

summary: MiRNA molecules are important post-transcriptional regulators of gene expression in the brain function. Altered miRNA profiles could represent a defensive response against the pathogenesis of neurodegenerative disorders, such as Alzheimer's disease (AD). Endogenous miRNAs have lower toxic effects than other gene silencing methods, thus enhancing the expression of defensive miRNA could be an effective therapy. However, little is known about the potential of targeting miRNAs for the treatment of AD. Here, we examined the function of the miR-200 family (miR-200a, -141, -429, -200b, -200c), identified using miRNA microarray analysis of cortical tissue from Tg2576 transgenic mice. In murine primary neurons, we found that upregulation of miR-200b or -200c was induced by the addition of amyloid beta (Aβ). Neurons transfected with miR-200b or -200c reduced secretion of Aβ in conditioned medium. Moreover, mice infused with miR-200b/c into the brain were relieved of memory impairments induced by intracerebroventricular injection of oligomeric Aβ, and demonstrated proper spatial learning in the Barnes maze. To gain further understanding of the relationship between miR-200b/c and Aβ, we identified target mRNAs via an RNA-binding protein immunoprecipitation-microarray assay. Western blot analysis showed that expression of ribosomal protein S6 kinase B1 (S6K1), a candidate target, was inhibited by miR-200c. S6K1, a downstream effector of mammalian target of rapamycin (mTOR), serves as a negative feedback mediator that phosphorylates insulin receptor substrate 1 at serine residues (IRS-1pSer). S6K1-dependent IRS-1pSer suppresses insulin signaling leading to insulin resistance, which is frequently observed in AD brains. Notably, miR-200b/c transfection of SH-SY5Y cells reduced the levels of IRS-1pSer. This finding indicates that miR-200b/c has the potential to alleviate insulin resistance via modulation of S6K1. Taken together, miR-200b/c may contribute to reduce Aβ secretion and Aβ-induced cognitive impairment by promoting insulin signaling.

overall_design: Wild-type C57BL/6J mice (Wt) and Tg2576 mice (Tg) at the age of 10 month; early phase of Aβ accumulation (Wt; n=3, Tg; n=3) or 17 month; plateau phase of Aβ accumulation (Wt; n=3, Tg; n=3) were used for dissection of the cortex or the whole brain tissue.   Total RNA including both large and small RNA was extracted, and performed miRNA array and gene expression array.

first: Sayuri

last: Higaki

first: Masashi

last: Muramatsu

first: Akio

last: Matsuda

first: Kenji

last: Matsumoto

first: Jun-ichi

last: Sato

first: Makoto

last: Michikawa

first: Shumpei

last: Niida


title: The fission yeast Schizosaccharomyces pombe: H3K9me2 and Fep1-GFP ChIP-chip

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip analyses of H3K9me2 (in WT 30°C, WT 18°C, ccr4∆ 18°C, ccr4∆fep1 18°C, ago1∆ 18°C, WT + 2,2′-bipyridyl 18°C), Fep1-GFP (in WT), Ssn6-MYC ChIP in WT and Fep1∆.

overall_design: H3K9me2: WT 30°C vs WT 18°C, WT 18°C vs ccr4∆ 18°C vs ccr4∆fep1 18°C, WT 18°C vs WT + 2,2′-bipyridyl 18°C, WT 18°C vs ago1∆ 18°C. Ssn6 ChIP: WT vs feb1∆.

first: Pamela

middle: S

last: Gallagher

first: David

last: Wheeler

first: Gobi

last: Thillainadesan

first: Jothy

last: Dhakshnamoorthy

first: Vanivilasini

last: Balachandran

first: Christopher

last: Wellman

middle: I


title: The fission yeast Schizosaccharomyces pombe


title: Identification of long noncoding RNAs in T-ALL cell lines

status: Public on May 07 2018

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-seq of T-ALL cell lines

overall_design: RNA-seq of T-ALL cell lines (Jurkat, RPMI-8402, CCRF-CEM, MOLT-4, HPB-ALL, TALL-1, DND-41, Loucy).

first: Shi

last: Tan

first: Takaomi

last: Sanda


title: ERF deletion rescues RAS deficiency in mouse embryonic stem cells [expression profiling]

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

country: Spain

institute: CNIO

summary: RAS proteins are key regulators of growth factor signaling. Here we show that deletion of all RAS genes in mouse embryonic stem cells (mES) leads to an overall reduction in protein translation, limits their long-term proliferative capacity and incapacitates them to differentiate. Deletion of ERF, a transcriptional repressor of the ETS family, rescues proliferation and differentiation of RAS-deficient mES cells and allows the development of teratomas lacking RAS genes. Upon RAS deletion, ERF translocates to the nucleus where it binds to multiple enhancers of key RAS targets suppressing their expression. We also reveal recurrent losses of ERF in cancer and show that ERF deficiency increases the resistance of cancer cells to pharmacological inhibition of the RAS pathway. In summary, we here reveal a central role for ERF in coordinating RAS signaling in pluripotent cells, and identify a synthetic viable interaction that bypasses the requirement for RAS proteins in mammalian cells.

overall_design:
We performed differential expression analysis in untreated and OHT-treated H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert ES cells. In the untreated condition ERF remains out of the nuclei by ERK-dependent phosphorylation, whereas ERF goes to the nuclei and binds its targets in the OHT-treated cells due to the absence of MAPK pathway signaling. We performed the same analysis in ERF-ko H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert ES cells.
genotype: ERF-WT (H-Ras−/−;N-Ras−/−;K-Raslox/lox;RERTert/ert ES cells): Sample A1, Sample B1, Sample A1-OHT, Sample B1-OHT
genotype: ERF-KO (H-Ras−/−;N-Ras−/−;K-Raslox/lox;RERTert/ert ES cells): Sample A2, Sample B2, Sample A2-OHT, Sample B2-OHT
treatment: OHT: Sample A1-OHT, Sample B1-OHT, Sample A2-OHT, Sample B2-OHT
treatment: untreated: Sample A1, Sample A2, Sample B1, Sample B2
biological replicate: Sample A1-OHT, Sample B1-OHT
biological replicate: Sample A2-OHT, Sample B2-OHT
biological replicate: Sample A1 , Sample B1
biological replicate: Sample A2 , Sample B2

first: Cristina

last: Mayor-Ruiz

first: Sergio

last: Ruiz

first: Óscar

last: Fernández-Capetillo


title: ERF deletion rescues RAS deficiency in mouse embryonic stem cells

type: Genome binding/occupancy profiling by high throughput sequencing


title: ERF deletion rescues RAS deficiency in mouse embryonic stem cells [ChIP-seq]

overall_design: We performed ChIP-seq analysis by pulling down ERF-bound genomic sequences in untreated and OHT-treated H-Ras−/−; N-Ras−/−; K-Raslox/lox; RERTert/ert ES cells. In the untreated condition ERF remains out of the nuclei by ERK-dependent phosphorylation, whereas ERF goes to the nuclei and bound its targets in the OHT-treated cells due to the absence of MAPK pathway signaling.

first: Mayor-Ruiz

last: Cristina

first: Ruiz

last: Sergio

first: Fernandez-Capetillo

last: Óscar


title: Analysis of early changes in mouse heart transcriptome after myocardial infarction

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

summary: Alternative splicing of RNA is an underexplored area of transcriptional response. We hypothesized that early changes in alternatively spliced genes may be important for responses to cardiac injury. The goal of this study was to use high throughput sequencing to determine which genes undergo alternative splicing in the initial response to ischemia after myocardial infarction.

overall_design: After ligation of the left anterior descending (LAD) artery in mice, ischemic heart tissue was isolated at 1 day and 3 days post-injury. Tissue was flash frozen and pulverized before RNA extraction. Sham-operated animals (no ligation of artery) were used as controls for each time point. Two mice were used for each condition as biological replicates.

middle: L

first: Vedbar

last: Khadka

first: Ralph

middle: V

last: Shohet


title: RNAseq for Tfam knock under NKX2.5 promoter

status: Public on May 05 2018

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

summary: Tfam inactivation by Nkx2.5Cre caused embryonic lethal myocardial hypoplasia. Tfam inactivation was accompanied by elevated production of reactive oxygen species (ROS) and reduced cardiomyocyte proliferation. Mosaic embryonic Tfam inactivation confirmed that the block to cardiomyocyte proliferation was cell autonomous. Transcriptional profiling by RNA-seq demonstrated activation of the DNA damage pathway.

overall_design: E13.5 TFAM KOx3; E13.5 TFAM CONx3;

first: Donghui

last: Zhang

first: Yifei

last: Li

first: Danielle

last: Heims-Waldron

first: Yuxuan

last: Guo

first: Pingzhu

last: Zhou

first: Qing

last: Ma

first: William

middle: T

last: Pu


title: Transcriptome analysis in endometrioid cell lines with modified Prex2a expression

status: Public on May 04 2018

city: Nagoya

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: We employed gene expression microarray to investigate the influence of Prex2a gene disturbance in gene expression profile of endometrial carcinoma cells.

overall_design: 8 kind of cells with modified Prex2a expression [introduction of  negative control short-haripin (sh) RNA, Prex2a shRNA type 1 or Prex2a shRNA type 2, induction of Prex2a and unmodified] made from 2 cell lines (JHUEM-14, OMC-2). Experiments were performed in duplicates.

first: Yamashita

last: Yoriko

first: Shiomi

last: Kosuke

first: Toyokuni

last: Shinya

first: Akatsuka

first: Takeshita

last: Sho


title: Gene Expression Signatures Prognostic for Relapse in Stage I Testicular Germ Cell Tumors (TGCT)

status: Public on May 21 2018

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary: Design, Setting and Participants  We reviewed patients with SI non-seminoma (NS) and seminoma (S) from an institutional database (2000-2012) managed with active surveillance. NR-NS and NR-S patients were defined as having no evidence of relapse after 2 and 3 years of surveillance respectively. RNA extraction and gene expression analysis was performed on archival primary tumor samples.   Outcome measurements and statistical analysis  Gene-Set-Enrichment-Analysis (GSEA) was conducted in order to identify discriminating biological pathways associated with differentiation of R from NR and S from NS. Hierarchical clustering analysis and Wilcoxon testing were used to evaluate candidate genes and expression patterns that could differentiate NR from R.   Results  57 patients (12 R-NS, 15 RS, 15 NR-NS, 15 NR-S) were identified with median relapse time of 5.6 (2.5-18.1) and 19.3 (4.7-65.3) months in NS and S cohorts respectively. 1039 differential expressed genes were identified that separated R and NR. In R patients, GSEA revealed enrichment in pathways associated with differentiation such as skeletal development (i.e. FGFR1, BMP4, GLI2, SPARC, COL2A1), tissue (i.e. BMP4, SPARC, COL13A1) and bone remodelling (i.e. CARTPT, GLI2, MGP). A discriminative gene expression profile between R and NR cases was discovered when combining NS and S samples using 10 (p=0.03) and 30 (p=0.03) probe signatures. However, this profile was not observed in the S and NS cohorts individually.   Conclusions  A discriminating signature for R and NR was identified for SI TGCT that was not histology specific. Genes associated with active differentiation were enriched in patients with R disease. Further validation is required to determine if this signature provides independent prognostic information to standard pathological risk factors.

first: Aron

middle: R

last: Hansen


title: Bulk and single-cell RNA-seq of mouse blastocyst, blastoid Trophoblast stem cells and  Embryonic stem cells

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We did bulk and single cell RNA sequencing of blastocysts, blastoids, trophoblast stem cells (TSC) and embryonic stem cells (ESC). The goal of these experiment is to describe the transformations of the transcriptome occurring within cells (TSC, ESC) upon formation of a blastoid. E3.25 and E3.5 blastocysts are used as controls. To this end, we first did RNA sequencing of intact structures (E3.25 and E3.5 blastocysts, blastoids, and parental cell lines). In a different series of experiments, we micro-dissected blastocyst, blastoid or trophosphere structures into single cells, and sequenced their mRNAs, to infer cell identity and transcriptome variations.

overall_design: After dissociation of the structures, we harvested single cells, created libraries using the CELSeq protocol, and sequenced their mRNAs.

first: Nicolas

last: Rivron

first: Javier

last: Frias Aldeguer

first: Alexander

last: van Oudenaarden


title: Reduced representation bisulfite sequencing (RRBS) data from cattle monocytes, fibroblasts and sperm cells

status: Public on May 03 2018

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

country: France

institute: INRA

type: Methylation profiling by high throughput sequencing

summary: Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.

overall_design: 6 samples including 3 cell types and two biological replicates per cell type

first: Jean-Philippe

last: Perrier

first: Hélène

first: Maxime

last: Gasselin

first: Luc

last: Jouneau


title: MeDIP-chip from livers, fibroblasts and sperm cells from adult cattle using anti-methylcytosine antibody.

summary: Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the MeDIP-chip technology (methylated DNA immunoprecipitation followed by microarray hybridation).

overall_design: Comparison of MeDIP DNA and input DNA with a dye-swap technical repetition for every sample; 11 samples in total, including 4 liver samples, 3 fibroblast samples and 4 sperm samples.


title: gene expression in Tc1 vs Tc9 cells

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

summary: gene expression in Tc1 vs Tc9 cells

overall_design: compare gene expression difference in Tc1 and Tc9 cells

first: Xingzhe

last: Ma


title: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [ATAC-seq]

status: Public on May 02 2018

city: Worcester

first: Lucio

last: Castilla

address: 364 Plantation Street

department: MCCB

institute: University of Massachusetts

summary: We recently reported the discovery of a small molecule inhibitor, AI-10-49 which can specially inhibit the protein-protein interaction between RUNX1 tumor suppressor and CBFβ-SMMHC oncogene. We also demonstrated that AI-10-49 can re-establish the RUNX1 transcriptional program in inv(16) cells and can extend the survival of inv(16) leukemic mice. To identify the changes in chromatin accessibility associated with AI-10-49, we performed ATAC-seq analysis in ME-1 cells [human inv(16) leukemia cell line] treated with AI-10-49.

overall_design: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours and cells were tagmented using Tn5 transposase. DNA libraries were sequenced using 100bp paired end reads on an Illumina HiSeqTM 2000. Two independent experiments were conducted for DMSO as well as AI-10-49 treatments.

first: John

middle: A

last: Pulikkan

first: Mahesh

last: Hegde

first: A

middle: M

last: Ahmad

first: Houda

last: Belaghzal

first: Anuradha

last: Illendula

first: Jun

last: Yu

first: Kelsey

last: O’Hagan

first: J

last: Ou

first: C

last: Muller-Tidow

first: Scot

last: Wolfe

first: Lihua

middle: J

last: Zhu

first: Job

last: Dekker

last: Bushweller


title: Higher levels of heteroplasmy at OriL control mtDNA copy number, glucose metabolism and lifespan in mice

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Higher levels of the 12A heteroplasmy control mitochondrial function and metabolic pathway, consequently affecting the lifespan in mice.

overall_design: The transcriptomes of liver obtained from C57BL/6J-mtAKR (higher 12A heteroplasmy at OriL) was compared with those from C57BL/6J (lower 12A heteroplasmy at OriL)  by RNAseq.

first: Misa

last: Hirose

first: Saleh

last: Ibrahim

first: Axel

last: Künstner


title: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia

first: Lucio

last: Castilla

last: Pulikkan


title: CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [ChIP-seq]

summary: We recently reported the discovery of a small molecule inhibitor, AI-10-49 which can specially inhibit the protein-protein interaction between RUNX1 tumor suppressor and CBFβ-SMMHC oncogene. We also demonstrated that AI-10-49 can re-establish the RUNX1 transcriptional program in inv(16) cells and can extend the survival of inv(16) leukemic mice. To identify the epigenetic changes as well as RUNX1 binding associated with AI-10-49, we performed genome wide analysis of H3K27ac histone mark as well as RUNX1 bindings in ME-1 cells [human inv(16) leukemia cell line] treated with AI-10-49.

overall_design: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours, crosslinked chromatin was immunoprecipitated with H3K27 acetylation and RUNX1 antibodies. DNA libraries were sequenced using 50bp single end reads on an Illumina HiSeqTM 4000.

first: John

last: Hegde

last: Ahmad


title: Long genes linked to autism harbor intragenic super-enhancer-like chromatin domains

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: Genetic variants associated with autism spectrum disorders (ASDs) are enriched for genes encoding synaptic proteins and chromatin regulators. Although the role of synaptic proteins in ASDs is well studied, the mechanism by which disruptions of chromatin regulators promote the development of ASDs remains unclear. Here we identify 184 neuronal long genes containing super-enhancer-like chromatin modifications across their gene bodies, which we term SE long genes. We show that SE long genes exhibit reduced transcriptional RNA Polymerase II pausing, higher transcription initiation frequency, and higher expression levels. The gene body regions of SE long genes display active epigenomic status and are organized into a highly connected chromatin unit. Notably, SE long genes are enriched in known ASD-associated genes related to the synapse and signaling pathways. These characteristics present a molecular link between chromatin regulators and synaptic function, and suggest a mechanism by which disruptions in these chromatin regulators compromise the synapse. Indeed, we show that the expression of SE long genes is more sensitive to the disruptions of autism-risk chromatin regulators, including Kmt2c, Kdm5c, Kdm6b, and Mecp2, than non-SE long genes. We propose that the transcriptional impairment of SE long genes by dysfunctional chromatin regulators is a general molecular mechanism for ASD pathogenesis.

overall_design: ChIP-seq, ATAC-seq, and DNA methylation in the mouse cortex

first: Deborah

last: Kwon

first: Brian

last: Johnson

first: Maria

last: Fasolino

first: Janine

last: Lamonica

first: Yoon

last: Kim

first: Tae

first: Zhaolan

last: Zhou


title: Analysis of chromatin landscapes in early human development reveals epigenetic transition during ZGA

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

summary: Upon fertilization, drastic chromatin reorganization occurs during human preimplantation development. However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored. Deciphering such process is crucial for understanding both early human development and in vitro fertilization. Here, we investigated genome-wide chromatin accessibility in human preimplantation embryos by employing an improved ATAC-seq that uses as few as 20 cells. We found widespread accessible chromatin in early human embryos that overlaps extensively with putative cis-regulatory sequences and transposable elements. Integrative analyses showed both conservation and divergence in regulatory circuitry between human and mouse early development, and between naïve human pluripotency in vivo and human embryonic stem cells. Surprisingly, we also found widespread open chromatin at the 2-cell stage despite its minimal transcription activities. Such accessible chromatin loci are readily found at CpG-rich promoters. Unexpectedly, many others are located in distal regions enriched for transcription factor binding sites and overlap with partially methylated domains (PMDs) in human oocytes. A large portion of these regions then rapidly become inaccessible upon zygotic genome activation (ZGA). Importantly, such drastic transition of chromatin accessibility during ZGA is well conserved in mouse embryos. Furthermore, it strongly correlates with the reprogramming of non-canonical H3K4me3 (ncH3K4me3), a form of histone mark that is uniquely present in oocytes and pre-ZGA embryos and contributes to genome silencing. Finally, both the reprogramming of chromatin accessibility and ncH3K4me3 during ZGA is completely blocked upon transcription inhibition, indicating a critical role of zygotic transcription in shaping early epigenomes. Together, these data revealed conserved chromatin state transition during ZGA in human and mouse early development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC-seq and RNA-seq were applied on human pre-implantation embryos and mouse transcription blocked embryos to examine the chromatin state as well as their transcriptome

first: Jingyi

last: Wu

first: Bofeng

last: Liu

first: Jiawei

last: Xu

first: Yingpu

last: Sun


title: Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition [ChIP-Seq]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: During normal or pathological epithelial-to-mesenchymal transition, epithelium-specific gene expression is shut down, with the DNA-binding factor ZEB1 acting as a master suppressor of epithelial identity. Here, we show that ZEB1 occupies primate-specific tandem repeats (TRs) harboring dozens of copies of its DNA-binding motif and located within genomic loci relevant for epithelial identity. Deletion of one such repeat in a quasi-mesenchymal human cancer cell line induced the reacquisition of epithelial features and phenocopied the effects of ZEB1 gene deletion. Since ZEB1 binds clustered motifs in a non-cooperative manner, changes in its nuclear concentration enable graded adjustments of TR occupancy, thus fine-tuning repression level. In addition, high motif density in TRs allows ZEB1 binding (and shutdown of epithelial programs) despite differences in chromatin organization and accessibility among epithelial cell types.

overall_design: Chromatin from human pancreatic ductal adenocarcinoma cell line and human colon carcinoma cell line was immunoprecipitated with anti- ZEB1 or anti-CTCF antibodies and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells (MiaPaCa2 and RKO) and genome edited clonal MiaPaCa2 cells (MiaPaCa2.delta-Repeats and the respective control MiaPaCa2.WT).

first: Gioacchino

last: Natoli


title: Expression in equine cartilage stimulated with IL-1β in vitro

city: Uppsala

last: Löfgren

department: Department of Biomedical Sciences and Veterinary Public Health

institute: Swedish University of Agricultural Sciences

summary: The objective was to study the time-course effects of interleukin-1β (IL-1β) on equine articular cartilage, with the aim to identify genes of relevance for cartilage pathology in osteoarthritis. Changes in gene expression related to inflammation, extracellular matrix, and phenotypic alterations was studied.

overall_design: Articular cartilage explants from the distal third metacarpal bone were collected postmortem from 3 horses without evidence of joint disease. The explants were stimulated with IL-1β for 27 days and global gene expression was measured using Affymetrix microarray. Gene expression in IL-1β stimulated explants was compared to expression in unstimulated explants at days 3, 9, 15, 21 and 27.

first: Emilia

last: Svala

first: Anders

last: Lindahl

first: Eva

last: Skiöldebrand

first: Stina

last: Ekman


title: Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition.

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

overall_design: Refer to individual Series


title: Suppression of regulatory T cells by autoreactive CD8+ T effector cells in rheumatoid arthritis

status: Public on May 01 2018

city: Rome

first: domenico

last: raimondo

address: Viale Regina Elena 324

department: Molecular Medicine

institute: Sapienza University of Rome

summary:
Autoreactive CD8+ T effector (eff) cells specific to vimentin, actin cytoplasmic 1, or non-muscle myosin heavy chain 9 epitopes, evade regulatory T (Treg) cells in patients with rheumatoid arthritis undergoing worsening disease and who would become non-responders to tumor necrosis factor (TNF)-α inhibitor therapy, in contrast to autoreactive CD8+ T naïve (N) cells that are efficiently controlled by Treg cells in healthy individuals or patients who would become responders.
Gene expression analysis revealed that the autoreactive CD8+ TN cell subset is comprised of a heterogeneous population of cells at various stages of development in healthy individuals or patients. Mechanistically, the production of TNF-α by CD8+ TN cells and the killing activity by CD8+ Teff cells in response to the relevant self-antigens influence the endorsement or suppression of Treg function, respectively. These data provide evidence of a previously undescribed role of such mechanisms in the progression and therapy of a prototypical human autoimmune disease, such as rheumatoid arthritis.

overall_design: Nanostring gene expression analysis was performed on RNA extracted from Naïve (N) and effector (Eff) CD8+ T lymphocytes, specific for apoptotic epitopes, sorted from patients with rheumatoid arthritis (P) and from healthy donors (HDs), and 26 samples were analysed: 5 N from HDs, 4 Eff from HDs, 9 N from P and 8 Eff from P.

first: Carmela

last: Martire

first: Ilenia

last: Cammarata

first: Alessandra

last: Citro

first: Domenico

last: Raimondo

last: Carone

first: Giovanna

last: Peruzzi

first: Cristina

last: Cerboni

first: Angela

last: Santoni

first: John

last: Sideny

first: Alessandro

last: Sette

first: Marino

last: Paroli

first: Rosalba

last: Caccavale

first: Edoardo

last: Milanetti

first: Mara

last: Riminucci

first: Silvia

last: Piconese

first: Rossana

last: Scrivo

first: Guido

last: Valesini

first: Elisabetta

last: Cariani

first: Vincenzo

last: Barnaba


title: GDV1 triggers sexual conversion and differentiation in malaria parasites by antagonizing HP1-dependent gene silencing

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

institute: Radboud University Nijmegen

summary: Malaria is caused by Plasmodium parasites that proliferate through iterative cycles of intra-erythrocytic replication. During each cycle a small number of parasites differentiate into gametocytes, the only forms able to infect the mosquito vector and transmit malaria. Sexual commitment is triggered by activation of AP2-G, the master transcriptional regulator of gametocytogenesis. Heterochromatin protein 1 (HP1)-dependent silencing of ap2-g prevents sexual conversion and secures proliferation. Here, we identify gametocyte development 1 (GDV1) as the first upstream activator of the sexual differentiation pathway in P. falciparum. Induction of GDV1 expression is sufficient to activate AP2-G expression and sexual differentiation. We found that GDV1 targets heterochromatin and triggers HP1 eviction preferentially at ap2-g and other gametocyte-specific genes. We further demonstrate that GDV1-dependent activation of ap2-g is controlled via a gdv1 antisense RNA. In summary, we identify GDV1 as an unprecedented cell fate decision factor that induces sexual differentiation by antagonizing HP1-dependent gene silencing.

overall_design: ChIP-seq experiments were performed for the gametocyte development protein 1 (PfGDV1, PF3D7_0935400) in the malaria parasite Plasmodium falciparum strain 3D7. An inducible ectopic overexpression 3D7/PfGDV1-GFP-DD transgenic parasite line was created using the FKBP-destabilization domain Shield-1 system on an episomal expression plasmid. The resulting PfGDV1-GFP-DD transgenic parasite line was used in a comparative ChIP-sequencing time-course experiment. 3D7/GDV1-GFP-DDOFF parasites were split at 28-34 hours post-invasion (hpi), cultured in parallel in absence or presence of Shield-1 and paired chromatin samples were harvested two (TP1), six (TP2) and ten (TP3) hours after Shield-1 addition. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001). In parallel the effect of PfGDV1 overexpression on global PfHP1 occupancy was investigated ten  hours (TP3) after Shield-1 addition using anti-rabbit PfHP1 (Brancucci et al. 2014). Additionally, directional RNA-seq was performed for Plasmodium falciparum F12 wildtype parasites and a gdv1-antisense RNA loss-of-function mutant parasite line (F12/gdv1-asKO) generated using CRISPR/Cas9-based genome editing. F12 and F12/gdv1-asKO parasites were synchronized to obtain an eight hour growth window and were harvested at 32-40hpi and 40-48hpi.

first: Michael

last: Filarsky

first: Eilidh

last: Carrington

first: Igor

last: Niederwieser

first: Suzette

last: Moes

first: Paul

last: Jenoe

first: Richárd

last: Bártfai

first: Till

last: Voss


title: Diet-Induced Obesity Leads to Infarct Expansion, increased neuroinflammation, and Worsened Outcomes after Stroke

city: Palo Alto

first: Brian

middle: D

last: Piening

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford

summary: We used RNA-seq to show that high-fat-diet-fed mice have a larger neuroinflammatory response following stroke.  Elucidating these mechanisms may lead to the development of treatments that will benefit people with obesity who suffer from a stroke.

overall_design: 145 C57BL/6J mice were either fed a 60% kCal fat diet or 6% kCal fat diet for 6 or 15 weeks. Focal ischemia was induced and brain tissue was harvested for RNA-seq.

first: Todd

last: Peterson

first: Marion

last: Buckwalter


title: LRH-1/NR5A2 induces M1 to M2 macrophage phenotypic switch

city: Seville

first: Benoit

middle: Raymond

last: Gauthier

state: Seville

address: Americo Vespucio Avenue

department: Stem Cells

institute: Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)

summary: Strategy to repress autoimmunity and promote islet beta cell regeneration

overall_design: 2 groups, 2 conditions and 3 replicates. Pancreatic sorted cells from mouse  treated with or without LRH1 agonist BL001.

first: Nadia

last: Cobo-Vuilleumier


title: Expression profiling from mouse embryonic stem cells (ESCs)

city: Shanghai

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

summary:
Sin3a, a known master scaffold, provides unique contact surfaces for interaction with particular accessory proteins to repress the transcription of specific genes. Surprisingly, our results also suggest that Sin3a has a role in transcriptional activation.
We compared gene expression differences between Sin3a knockdown and control ESCs with mouse gene expression microarrays and identified an approximately equal distribution of up- and down-regulated genes following Sin3a knockdown in mouse ESCs. We propose that Sin3a collaborates with Tet1 to demethylate adjacent genomic regions and, ultimately, facilitates actively transcribed gene expression in mouse ESCs.

overall_design: Control (shCtrl) or Sin3a knockdown (shSin3a-1) mouse ESCs were used.

first: Fugui

first: Jiuhong

last: Kang


title: LRH-1/NR5A2 for the treatment of autoimmune diseases


title: The evolution of single cell-derived colorectal cancer cell lines is dominated by the continued selection of tumor specific genomic imbalances, despite random chromosomal instability

city: Bethesda

first: Darawalee

last: Wangsa

address: 50 South Drive, Bldg 50, Rm 1408

institute: National Cancer Institute

summary: Intratumor heterogeneity is a major challenge in cancer treatment. To decipher patterns of chromosomal heterogeneity, we analyzed six colorectal cancer cell lines by multiplex interphase FISH. The mismatch repair deficient cell lines DLD-1 and HCT116 had the most stable copy numbers, whereas aneuploid cell lines displayed a higher degree of instability. We subsequently assessed the clonal evolution of a single cell in two aneuploid cell lines, SW480 and HT-29, which both have near-triploid karyotypes but different degrees of chromosomal instability. The clonal compositions of the single cell-derived daughter cell lines, as assessed by multiplex FISH, differed for HT-29 and SW480. Daughters of HT-29 were stable, clonal, and had little heterogeneity. Daughters of SW480 were more heterogeneous, with the single cell-derived daughter cell lines separating into two distinct populations with different ploidy (hyper-diploid and near-triploid), morphology, gene expression and tumorigenicity. To better understand the evolutionary trajectory for the two SW480 populations, we constructed phylogenetic trees which showed ongoing instability in the daughter cell lines.. When analyzing the evolutionary development over time, most single cell-derived daughter cell lines maintained their major clonal pattern, with the exception of one daughter of SW480 that showed a switch involving a loss of APC. Our meticulous analysis of the clonal evolution and composition of these colorectal cancer models shows that all chromosomes are subject to segregation errors, however, specific net genomic imbalances are maintained.  Karyotype evolution is driven by the necessity to arrive at and maintain a specific plateau of chromosomal copy numbers as the drivers of carcinogenesis.

overall_design: Single cell clones were generated from SW480 and HT-29 cells to compare their clonal evolution and heterogeneity

first: Rüdiger

last: Meyer

first: Madison

last: Schiefer

first: E

last: Gertz

first: Daniel

last: Bronder

first: Hesed

last: Padilla-Nash

first: Irianna

last: Torres

first: Cynthia

last: Hunn

first: Lidia

last: Warner

first: Floryne

middle: O

last: Buishand

first: Yue

last: Hu

first: Daniela

last: Hirsch

first: Timo

last: Gaiser

first: Jordi

last: Camps

first: Russell

last: Schwartz

first: Alejandro

last: Schäffer

first: Kerstin

last: Heselmeyer-Haddad

first: Thomas

last: Ried


title: RNA-seq of MMTV-Neu AXL KO tumor grafts in FVB

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: AXL is activated by its ligand GAS6 and is expressed in triple-negative breast cancer cells. We report that AXL is also detected in HER2+ breast cancer specimens where its expression correlates with poor patients’ survival. Using murine models of HER2+ breast cancer, AXL, but not Gas6, was found essential for metastasis. We determined that AXL is required for intravasation, extravasation and growth at the metastatic site. AXL is expressed in HER2+ cancers displaying EMT signatures and contributes to sustain EMT in murine tumors. Interfering with AXL in patient-derived xenograft impaired TGF-β-induced cell invasion. Lastly, pharmacological inhibition of AXL decreased the metastatic burden of mice developing HER2+ breast cancer. Our data identify AXL as a potential co-therapeutic target during the treatment of HER2+ breast cancers to limit metastasis.

overall_design: Differential gene expression profile between tumor grafts of AXL-/- and AXL+/+ cells in FVB mice by RNA sequencing (Illumina HiSEq 2000)

first: Jean-François

last: Côté


title: The Receptor Tyrosine Kinase AXL is Required at Multiple Steps of the Metastatic Cascade during HER2-positive Breast Cancer Progression


title: Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

summary:
Background: To reduce costs of rearing replacement heifers, researchers have focused on decreasing age at breeding and first calving, and to increase returns upon initiation of lactation the focus has been on increasing mammary development prior to onset of first lactation. Enhanced plane of nutrition pre-weaning may benefit the entire replacement heifer operation by promoting mammary gland development and greater future production.
Methods: Twelve Holstein heifer calves (<1 wk old) were reared on 1 of 2 dietary treatments (n = 6/group) for 8 wk: a control group fed a restricted milk replacer at 0.45 kg/d (R, 20% crude protein, 20% fat), or an accelerated group fed an enhanced milk replacer at 1.13 kg/d (EH, 28% crude protein, 25% fat). At weaning (8 wk), calves were euthanized and sub-samples of mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested upon removal from the body. Total RNA from both tissues was extracted and sequenced using the Illumina HiSeq2500 platform. The Dynamic Impact Approach (DIA) and Ingenuity Pathway Analysis (IPA) were used for pathway analysis and functions, gene networks, and cross-talk analyses of the two tissues.
Results: When comparing EH vs R 1,561 genes (↑895, and ↓666) and 970 genes (↑506, and ↓464) were found differentially expressed in PAR and MFP, respectively. DIA and IPA results highlight a greater proliferation and differentiation activity in both PAR and MFP, supported by an increased metabolic activity. When calves were fed EH, the PAR displayed transcriptional signs of greater overall organ development, with higher ductal growth and branching, together with a supportive blood vessel and nerve network. These activities were mediated by intracellular cascades, such as AKT, SHH, MAPKs, and Wnt, probably activated by hormones, growth factors, and endogenous molecules. The analysis also revealed strong communication between MFP and PAR, with the first enhancing the development of PAR through secreted growth factors and the recruitment of immune cells.
Conclusion: The transcriptomics and bioinformatics approach highlighted the mechanisms that mediate the mammary gland response to a higher plane of nutrition in the pre-weaning period.

overall_design: Twelve Holstein heifer calves were randomly assigned to two treatments. The control group was fed 0.45 kg/calf of milk replacer (MR) per day containing 20% crude protein (CP) and 20% fat (a restricted MR, R). The accelerated group was fed 1.13 kg of MR per day at 28% CP and 25% fat (an enhanced MR, EH). Starter feed was introduced at the end of week 4 and kept similar between treatments. Milk replacer was reduced in both treatments to 50% at week 8, to induce weaning. All calves were housed individually with ad libitum access to water. At weaning, calves were euthanized and their whole mammary glands were removed, weighed and dissected.

first: M

last: Vailati-Riboni

first: S

last: Zhan

first: A

last: Geiger

first: J

middle: C

last: McCann

first: R

last: Akers

last: Loor


title: RNA-seq of MMTV-Neu AXL KO tumors

overall_design: Differential gene expression profile between MMTV-Neu tumors of AXL-/- and AXL+/+ by RNA sequencing (Illumina HiSEq 2000)


title: The E3 ubiquitin ligase Siah1 regulates adrenal gland organization and hyperaldosteronism

city: Durham

first: Jian-Liang

last: Li

address: 111 TW Alexander Dr

institute: NIEHS

summary: Primary and secondary hypertension are major risk factors for cardiovascular disease. Elevated secretion of aldosterone resulting from primary aldosteronism (PA) is a key driver of secondary hypertension. Here, we identify an unexpected role for the ubiquitin ligase Siah1 in adrenal gland development and PA. Siah1a-/- mice exhibit altered adrenal gland morphology, as reflected by dysregulated zonation of the glomerulosa, increased aldosterone levels and aldosterone target gene expression, and reduced plasma potassium levels. Genes involved in catecholamine biosynthesis and cAMP signaling are upregulated in the adrenal glands of Siah1a-/- mice, while genes related to retinoic acid signaling and cholesterol biosynthesis are downregulated. Loss of Siah1 leads to increased expression of PIAS1, an E3 SUMO-protein ligase implicated in the suppression of LXR. Notably, SIAH1 sequence variants which impaired SIAH1 ubiquitin ligase activity, resulting in elevated PIAS1 expression, were identified in patients with PA. The involvement of Siah1–PIAS1 in adrenal gland organization and function points to a possible new therapeutic target for hyperaldosteronism.

overall_design: 1 adrenal gland from WT male mouse, 1 adrenal gland from WT female mouse, 1 adrenal gland from siah1a KO male mouse, 1 adrenal gland fromsiah1a KO female mouse, 1 adrenal gland from WT male mouse injected IP with 100ug/kg of ACTH for 1 hour, 1 adrenal gland from WT female mouse injected IP with 100ug/kg of ACTH for 1 hour, 1 adrenal gland from siah1a KO male mouse injected IP with 100ug/kg of ACTH for 1 hour, 1 adrenal gland fromsiah1a KO female mouse injected IP with 100ug/kg of ACTH for 1 hour.

first: Marzia

last: Scortegagna

first: Jian

first: Brian

last: James

first: Ze'ev

last: Ronai


title: Expression data from B6 mouse miR-142 KO and WT dendritic cells (DCs)

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

summary:
DCs are critical for regulating immune responses. miRNAs are  small, noncoding RNAs and play a significant role in regulating immune responses. miR-142 is a hematopoietic specific miRNA. To explore the role of miR-142  in regulating DCs’ immune responses, we generated mutant mice bearing a targeted deletion of the miR-142 gene.
We used microarrays to detail the global program of gene expression underlying the profile changes between miR-142 KO and WT DCs and identified distinct classes of up-regulated or down-regulated genes in steady state or LPS stimulation  during this process.

overall_design: miR-142 KO mice and WT littermates (biological triplicates) matched with age and sex were selected. DCs were purified from spleens by positive selection and processed for RNA isolation and hybridization on Affymetrix microarrays.

first: Pavan

last: Reddy

first: Yaping

last: Sun


title: UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

city: Cambridge

last: Huntly

address: Hills Road

department: Department of Haematology

country: United Kingdom

institute: University of Cambridge

summary: The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.

overall_design: ChIP-Seq analysis for histone modification: H3K4Me1 and for PU.1 binding. Effect of Brg1 knockout on chromatine accessibility in Utx+/+ and Utx-/- HSPC cells (ATAC-Seq). ATAC-seq was also performed on Chd4 knockout Utx+/+ HSPC cells.

first: George

last: Vassiliou


title: Divergent Mechanisms of Oncogenic B Cell Receptor Signaling in Lymphoma

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

summary: B cell receptor (BCR) signaling has emerged as a therapeutic target in B cell lymphomas, but the precise deployment of inhibitors to target oncogenic BCR signaling requires detailed knowledge of the signaling cascades that the BCR triggers in individual tumors. Here, we have used CRISPR-Cas9 screens to investigate whether the ABC and GCB molecular subtypes of diffuse large B cell lymphoma (DLBCL) utilize distinct BCR signaling modes to sustain their proliferation and survival. Constitutive germinal center (GC) BCR signaling in GCB DLBCLs requires the BCR, CD19 and SYK engaging PI(3) kinase for survival. In ABC DLBCLs with oncogenic mutations in the BCR and MYD88, a novel BCR-TLR9-MYD88 signaling supercomplex is assembled on endolysosomal membranes that engages NF-kB. Our data explain why this subset of ABC DLBCL tumors respond frequently to ibrutinib, an inhibitor of BCR-dependent NF- kB activation, while GCB DLBCLs are insensitive, and thus provide a roadmap for the rational development of BCR pathway inhibitors in molecular subtypes of DLBCL.

overall_design: Knockdown of TLR9 (C4) was tested in ABC DLBCL cell lines (HBL1 n=2 and TMD8 n=2) for 1 and 2 days. Knockdown of TLR9 (D7) was tested in ABC DLBCL cell lines (HBL1 n=2 and TMD8 n=2) for 1 and 2 days.


title: What the human sperm methylome tells us

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

institute: Sequentia Biotech SL

type: Methylation profiling by genome tiling array

summary:
Aim: To characterize the sperm methylome in semen samples from 19 donors with proven fertility.
Material and Methods: Bisulfite-converted sperm DNA was hybridized on the HumanMethylation450 Infinium BeadChip platform. CpG fluorescence-intensities were extracted and converted to β-values.
Results: The sperm methylome is highly homogeneous and hypomethylated. Genes with hypomethylated promoters are ontologically associated to biological functions related to spermatogenesis and embryogenesis. Sex-chromosomes are the most hypomethylated chromosomes, supporting data that indicated their essential role in spermatogenesis. Ninety-four genes are resistant to demethylation, being strong candidates for transgenerational inheritance.
Conclusion: Spermatozoa carry a homogeneous methylation profile that is a footprint of past events (spermatogenesis), is designed to facilitate future events (embryogenesis), and has a possible influence in the adult life (transgenerational effects).

overall_design: 19 samples from fertile patients.

first: Cristina

last: Camprubi

last: Cigliano

first: Albert

last: Salas-Huetos

first: Nicolas

last: Garrido

first: Joan

last: Blanco


title: Genetic interrogation of STAT6-mediated macrophage polarization to tumorigenesis in a sterile, penetrant, autochthonous cancer model

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Macrophage recruitment into tumors is correlated with poor outcomes in cancer, which correlate with STAT6-dependent M2 macrophage polarization and wound healing-type responses. Using penetrant, genetic models of neuroblastoma, we found macrophage recruitment was protective against tumor formation while disabling STAT6-mediated M2 polarization had no effect on tumorigenesis, progression or expression of key immunosuppressive pathways. Thus while macrophages are drivers of cancer in this model, non-classical M2 STAT6-independent pathways are plausible targets for cancer therapy.

overall_design: ALK TH-MYCN NB tumor model in C57BL\6 x 129Sv/J

first: Lee-Ann

last: Van de Velde

first: Lidijia

last: Barbaric

first: C

last: Neely

first: Peter

last: Murray


title: Glutaminolysis fuels de novo glutathione synthesis, regulates redox homeostasis and directs T cell differentiation

first: JUN

last: YANG

address: 262 Danny Thomas Place

department: Surgery

summary: We reveal that dimethyl fumarate, a FDA approved drug (BG-12/Tecfidera) for multiple sclerosis, suppresses TH17 differentiation by augmenting intracellular ROS

overall_design: Biological duplicate samples were treated with 50uM of DMF for 6 and 12 hours.

first: Jun

last: Yang

first: Ruoning

last: Wang


title: Skin transcriptome of duck

city: Xi'an

first: Jing

address: 620 district of west chang'an avenue

department: College of life sciences

institute: Anas platyrhynchos

summary: Transcriptome profiles of skin and feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the plumulaceous and flight feathers structure. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcritpomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns.

overall_design: A total of twelve libraries were sequenced from skin and feather follicle tissues of six groups (n=2 for each; control samples), including the early growth plumulaceous feathers (EP), middle growth plumulaceous feathers (MP), late growth plumulaceous feathers (LP), early growth flight feathers (EF), middle growth flight feathers (MF) and late growth flight feathers (LF).

first: Fumin

last: Lei


title: Identification of GRF9 early responding genes using an estradiol-inducible overexpression (XVE) system.

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary:
The aim of the experiment was to identify genes rapidly responding at their expression level to enhanced expression of the transcription factor GRF9.
The name of the transgenic plant used is GER 9-13.

overall_design: The goal was to identify genes rapidly (within a few hours) responding to enhanced expression of growth regulating factor 9 (GRF9) in Arabidopsis thaliana. To this end, 2-week-old seedlings (2 samples) and detached mature leaves (from 40-day-old soil grown plants - one sample) were induced by 10 µM estradiol for 3, 4 or 6 h respectively. Expression profilling was performed using Affymetrix ATH1 microarrays. Mock-treated seedlings (0.1% ethanol) were used as controls.

first: Mohammad

last: Omidbakhshfard

first: Bernd

last: Mueller-Roeber


title: Murine ES Cells: wild-type (WT) vs. Mto1 knockout (KO)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Transcriptional profiling of mouse embryonic stem cells comparing wild-type ES cells with Mto1-deficient ES cells.

overall_design: Two-condition experiment, WT ES vs. KO ES cells. Biological replicates: 1 WT, 1 KO, independently grown and harvested. One replicate per array.

first: Fan-Yan

last: Wei

first: Kazuhito

last: Tomizawa


title: Simultaneous Downregulation of MTHFR and COMT in Switchgrass Affects Plant Performance and Induces Lesion-mimic Cell Death

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

summary:
Switchgrass (Panicum virgatum) has been developed into a model lignocellulosic bioenergy crop. Downregulation of caffeic acid O-methyltransferase (COMT), a key enzyme in lignin biosynthesis, led to altered lignification and increased biofuel yield in switchgrass. Methylenetetrahydrofolate reductase (MTHFR) mediated C1 metabolism provides methyl units consumed by COMT. It was predicted that co-silencing of MTHFR and COMT would have a more significant impact on lignification than either of the single genes. However, our results showed that strong downregulation of MTHFR in a COMT-deficient background led to altered plant growth and development, but no significant change in lignin content or composition was found when compared with COMT plants. Another unexpected finding is that the double MTHFR/COMT downregulated plants showed a novel lesion-mimic leaf phenotype.  Molecular analyses revealed that the lesion-mimic phenotype was caused by the synergistic effect of MTHFR and COMT genes, with MTHFR playing a predominant role.
Microarray analysis showed significant induction of genes involved in oxidative and defenserelated processes. The results demonstrated the lack of additive effects of MTHFR and COMT on lignification. Furthermore, this  research revealed an unexpected role of the two genes in the modulation of lesion-mimic cell death as well as their synergetic effects on agronomic performance.

overall_design: High-quality total RNA from duplicate biological replicates of the transgenic lines MT/CO-37 and MT/CO-47 (severe phenotype group), MT/CO-38 and MT/CO-67 (moderate phenotype group) was isolated from young leaves (Leaf 4) at E4 stage using Spectrum157™ Plant Total RNA Kit (Sigma-Aldrich). To eliminate background differences among transgenics, except wild-type plant, MT/CO-60 with no more than 40% decrease of both MTHFR and COMT genes was also selected as a control. Leaf 4 at E4 stage was used because the lesion phenotype at this stage was fully emerged in leaf 2, half developed in leaf 3, but couldn’t be observed in leaf 4. RNA amplification, labelling and hybridization were done as described by Fu et al. (2012).

first: Liang

last: Sun

first: Sijia

last: Liu


title: Effect of in vitro embryo culture and embryo transfer on global expression profiling of the fetal lung tissue in mice

city: Ankara

first: Bengi

last: CINAR KUL

address: İrfan Bastug Caddesi

country: Turkey

institute: Ankara University

summary:
The aim of the present study was to test whether or not redox balance and global gene expression in the lung tissue is altered in fetuses (18 d.p.c.) obtained through the transfer of blastocysts exposed to ambient oxygen levels. The results provide new information demonstrating that embryonic stress imposed at pre-implantation stages of development through ovarian stimulation and/or culture at atmospheric concentrations of oxygen is associated with delayed lung development, increased oxidative stress and dysregulation of several genes involved in various developmental, metabolic and immune regulatory pathways.

Grant Number: TUBITAK-112O259
Grantee Name: Levent Karagenc

overall_design:
Two experimental groups and one control group were included in the study. Fetuses comprising one of the experimental groups were generated through the transfer of in vitro-derived blastocysts to pseudo-pregnant female mice (EGin vitro). Fetuses comprising the second experimental group were generated through the transfer of in vivo-derived blastocysts to pseudo-pregnant female mice (EGin vivo).  In vivo-developed fetuses obtained from naturally ovulating females served as the control group (CG).
In all groups, lung development, redox balance and global gene expression of the lung tissue were determined in fetuses obtained on day18 of gestation.

first: Levent

last: Karagenc

last: Çınar Kul

first: Nedim

last: Karagenç

first: Göksel

last: Doğan

first: Kerem

last: Esmen


title: EZH2 regulates neuroblastoma cell differentiation via NTRK1 promoter epigenetic modifications

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: The polycomb repressor complex 2 molecule EZH2 is now known to play a role in essential cellular processes, namely, cell fate decisions, cell cycle regulation, senescence, cell differentiation, and cancer development/progression. EZH2 inhibitors have recently been developed; however, their effectiveness and underlying molecular mechanisms in many malignancies have not yet been elucidated in detail. Although the functional role of EZH2 in tumorigenesis in neuroblastoma (NB) has been investigated, mutations of EZH2 have not been reported. A Kaplan-Meier analysis on the event free- and overall survival of NB patients indicated that the highexpression of EZH2 correlated with an unfavorable prognosis. In order to elucidate the functional roles of EZH2 in NB tumorigenesis and its aggressiveness, we knocked down EZH2 in NB cell lines using lentivirus systems. The knockdown of EZH2 significantly induced NB cell differentiation, e.g. neurite extension, and the neuronal differentiation markers, NF68 and GAP43. EZH2 inhibitors also induced NB cell differentiation. We performed a comprehensive transcriptome analysis using Human Gene Expression Microarrays and found that NTRK1 (TrkA) is one of the EZH2-related suppression targets. The depletion of NTRK1 canceled EZH2 knockdown-induced NB cell differentiation. Our integrative methylome, transcriptome, and chromatin immunoprecipitation assays using NB cell lines and clinical samples clarified that the NTRK1 P1 and P2 promoter regions were regulated differently by DNA methylation and EZH2-related histone modifications. The NTRK1 transcript variants 1/2, which were regulated by EZH2-related H3K27me3 modifications at the P1 promoter region, were strongly expressed in favorable, but not unfavorable NB. The depletion and inhibition of EZH2 successfully induced NTRK1 transcripts and functional proteins. Collectively, these results indicate that EZH2 plays important roles in preventing the differentiation of NB cells and also that EZH2-related NTRK1 transcriptional regulation may be the key pathway for NB cell differentiation.

overall_design: RNA was extracted at two time points, 8 and 11 days after shEZH2-expressing lentiviral infection, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Zhenghao

last: Li

first: Amallia

middle: N

last: Setyawati

first: Nobuhiro

last: Akita

first: Masayuki

last: Haruta

first: Shunpei

last: Satoh

first: Yoshitaka

last: Shinno

first: Koji

last: Chikaraishi

first: Kyosuke

last: Mukae

first: Jesmin

last: Akter

first: Ryuichi

middle: P

last: Sugino

first: Akira

last: Nakagawara

first: Hiroyuki

last: Aburatani

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: Genetically-defined Diffuse Large B-cell Lymphoma Subsets Arise by Distinct Pathogenetic Mechanisms and Predicts Outcome

first: Björn

last: Chapuy

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

summary: We obtained gene experssion profiles of 52 newly diagnosed diffuse large B-cell lymphoma (DLBCL).

overall_design: From 52 newly diagnosed DLBCL RNA was extracted and subjected to Affynterix U133plus2 gene expression profiling. This newly deposited data was combined with additional 85 previously generated Affymtrix U133plus 2 data from GSE34171.

first: Bjoern

first: Amy

first: Stefano

last: Monti

first: Margaret

last: Shipp


title: TET2 regulates osteoclast differentiation by interacting with RUNX1 and maintaining genomic 5-hydroxymethylcytosine

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show that Tet2 helps regulate the differentiation of macrophages to osteoclases

overall_design: Examination of transcriptome and hydroxymethylome in WT and Tet2 knockout Macrophages

first: Mingjiang

last: Xu

middle: W


title: Next Generation Sequencing Analysis of control and siSRSF1 treated RKO cell Transcriptomes

first: Linlin

last: Chen

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institutes for Biological Sciences

summary: We treated the RKO cells with siSRSF1 or control siRNA for 48 hours. Then we extracted the RNAs and performed the next generation sequencing. By comparing sequcing data from siSRSF1 and contron siRNA treated samples, we profiled the gene expression regulated by siRNA.

overall_design: RKO cells mRNA profiles of Control and siSRSF1 treated samples were generated by deep sequencing, using Illumina HiSeq 2000.


title: Fusion partner directed chromatin occupancy drives the transcriptome heterogeneity of MLL-fusion acute lymphoblastic leukemia

status: Public on Apr 30 2018

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Fusion of the N-terminus of the mixed-lineage-leukemia (MLL) gene with various partner genes drives acute lymphoblastic leukemia (ALL). Despite the fusion proteins sharing some common attributes, transcriptome heterogeneity of MLL-fusion ALL is observed and the underlying mechanism and biological consequences are unknown. We compared the genome-wide occupancy of MLL-Af4 and MLL-AF9 in human ALL cells expressing FLAG-tagged fusion proteins. Although both oncoproteins retain the same MLL N-terminal domains that mediate chromatin binding, the two fusion proteins displayed largely non-overlapping binding profiles, with MLL-AF9 showing preferential binding at repetitive elements. The binding specificity of each fusion protein was associated with differential global gene activation distinguishing the two ALLs. A subset of prednisolone response genes were among the differentially regulated targets, and the resistance related genes were specifically upregulated in MLL-Af4/AF4 cells. These studies provide evidence that distinct chromatin occupancy of different MLL-fusion proteins is one driving force for transcriptome heterogeneity of MLL-fusion ALL, which could potentially result in the disparate therapeutic outcome of the disease.

overall_design: MLL-AF9 ChIP-seq expreiment has been used in this study

first: Shan

last: Lin

first: Anetta

last: Ptasinska

first: Constanze

last: Bonifer

first: James

last: Mulloy


title: PFNF54-Pfs16-GFP-LUC gametocyte time course from commitment to maturity

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary: Plasmodium falciparum gametocytes undergo 14 days of gametocytogenesis to generate mature, transmissible gametocytes. This timecourse delineates the transcriptional profiles of gametocytes from commitment to maturity.

overall_design: P. falciparum NF54-Pfs16-GFP-LUC parasites were induced to produce gametocytes by culturing in glucose-deficient media , before removing asexual parasites from the population by daily 5% D-sorbitol treatments from day 1-4 and thereafter culturing the parasites in glucose positive media and grown under stationary conditions for the entire time course. The timecourse, resulting in a total of 16 samples was hybridized against a Cy3-labeled reference pool of 3D7 mixed stage asexual parasites and NF54-pfs16-GFP-LUC mixed stage gametocytes on a two-color array. Starting at 2 days before induction, samples were Samples were harvested from culture by 0.01%(w/v) saponin addition on days -2 to 7 and via density centrifugation using Nycoprep 1.077 cushions on days 8-13 and stored at -80˚C until RNA isolation using TRIZOL reagent along with on-column extraction using the Qiagen RNeasy kit (Qiagen, Germany).

first: Riëtte

last: van Biljon

first: Roelof

last: van Wyk

first: Lindsey

last: Altenhofen

first: Janette

last: Reader

first: Heather

last: Painter

first: Jandeli

last: Niemand

first: Manuel

last: Llinás

first: Lyn-Marié


title: RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

summary: Translational control is a key determinant of protein abundance, which in turns defines the physiology and pathology of human cells. Initiation of translation is highly regulated in eukaryotes and is considered as the rate-limiting step of protein synthesis. mRNA secondary structures in 5’ untranslated region (UTR) and associated helicases have been characterised as key determinants of translation initiation. Nevertheless the transcriptome-wide contribution of non-canonical secondary structures, such as RNA G-quadruplexes (rG4s), to the translation of human mRNAs remains largely unappreciated. Here we use a ribosome profiling strategy to investigate the translational landscape associated to rG4s-containing mRNAs and the contribution of two rG4s-specialised DExH-box helicases, DHX9 and DHX36, to translation initiation in human cells. We show that rG4-forming sequences in 5’-UTR is associated with decreased translation efficiency which correlate with an increased ribosome density within the 5’-UTRs. We found that rG4s contribute to the translation of upstream open reading frames, and as a consequence, thwart the translation of the associated protein coding sequences (CDS). Depletion of the DHX36 and DHX9 helicases demonstrated that the formation of the rG4 structural motif rather than its nucleotide sequence mediate translation initiation. Our findings unveil a role for non-canonical structures in defining alternative 5’ starts for human mRNAs translation initiation.

overall_design: 11 Ribo-Seq and RNA-Seq matched samples; 1 iCLIP libraries containing two barcoded replicates

first: Pierre

last: Murat

first: Barbara

last: Herdy

first: Avazeh

last: Ghanbarian

first: Guillem

last: Portella

first: Shankar

last: Balasubramanian


title: Examination of tumor samples obtained after laparoscopic supracervical hysterectomy and a derivative leiomyosarcoma

city: Rostock

first: Carsten

last: Holzmann

address: Ernst-Heydemann-Str. 8

department: Institute of Medical Genetics

institute: University Rostock Medical Center

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

summary:
Unexpected malignant tumors are a rare finding after surgery for symptomatic leiomyomas but there is little doubt that morcellation of these lesions is associated with a higher risk of iatrogenic peritoneal spread compared to women having surgery without morcellation. Thus, the FDA has issued a warning against the use of power morcellation in the majority of women undergoing myomectomy or hysterectomy for treatment of fibroids.We pressent a case report of 50year old patient with intervertebral disc degeneration and multiple uterine fibroids decided to have laparoscopic supracervical hysterectomy. 28 months later the patient cystic adnexal massas removed by laparotomy and histologically, classified as leiomyosarcoma. 19 months after this latter surgery MRI revealed a 10 x 8 x 6 cm abdominal mass attached to the liver and numerous other nodules attached to the abdominal wall.
We investigated genomic and expression profiles of four samples obtained from initial surgery and the malignant tumor that appeared 16 month later by molecular inversion probe (MIP) and transcriptome array hybridization. DNA was extracted from FFPE Tissue Samples using Covaris adaptive focused acoutics (AFATM) and truXTRACTM FFPE DNA kit and subjected to array analysis using the Affymetrix OncoScan and human Clariom D platforms according to the manufacturers protocol.

overall_design: Four morcellated specimens of a 50 year old patient with multiple uterine fibroids and a leiomyosarcoma removed 28 later were investigated by molecular inversion probe (MIP) array and transcriptome array analysis. The aim of the study was to investigate if the  leiomyosarcoma had  developed from one of the leiomyomas as a result of secondary genetic alterations and to compare the expression profiles of the tumors.

first: Dirk

last: Koczan

first: Burkhard

last: Helmke

first: Joern

last: Bullerdiek


title: Microbial community and SDIMO analyses of two 1,4-dioxane degrading consortia

city: Houston

first: Ya

last: He

state: Texas

department: Department of Civil and Environmental Engineering

institute: Rice University

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

overall_design: Refer to individual Series


title: Microbial community analyses of two 1,4-dioxane degrading consortia enriched from uncontaminated soils [16s rRNA]

summary:
Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR.  Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites.
DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified.  20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity).  A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.

overall_design: To investigate the microbial community composition of two 1,4-dioxane degrading consortia enriched from uncontaminated soils, 16S rRNA gene sequencing were processed using Illumina Miseq technology. The results show that the main species in these two consortia are Mycobacteria spp.


title: Whole-genome transcriptomic analysis of the cell fate switch induced by Notch activation in mouse mammary cells

city: Paris

first: Silvia

last: Fre

address: 26 rue d’Ulm

department: Genetics and Developmental Biology

institute: Institut Curie

summary: Mice expressing the active form of Notch1(N1ICD) in the basal mammary epithelium (through SMAcreERT mice) were induced to express N1ICD at the onset of puberty (P24). This induces a cell fate switch that results in the acquisition of a luminal identity in the targeted cells. To understand the early signals responsible for this reprogramming of committed basal cells, we analysed by RNAseq the transcriptional changes occurring in the targeted cells after 72h of N1ICD expression. N1ICD-expressing cells express a GFP marker that was used to sort them and GFPpos cells were compared to untargeted basal cells in the same animals (GFPneg).

overall_design: Three replicates from a pool of 2-3 mice each were used for the analysis. GFPpos and GFPneg cells were sorted from the same replicate. A total of 6 samples was sequenced.

first: Steffen

last: Rulands


title: The energetics and physiological impact of cohesin extrusion

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.

overall_design: ChIP-seq, ChIA-PET, insitu Hi-C, 4C, localHiC, ChromRNAseq, and/or RNAseq from mouse stem cells, activated B cells, CH12 cell line, and plasmacytomas

first: Laura

last: Vian

first: Aleksandra

last: Pekowska

first: Suhas

last: Rao

first: Kyong-Rim

last: Kieffer-Kwon

last: Baranello

first: Su-Chen

last: Huang

first: Marei

last: Dose

first: Nathanael

last: Pruett

first: Adrian

last: Sanborn

first: Andres

last: Canela

first: Yakkov

last: Maman

first: Anna

last: Oksanen

first: Wolfgang

last: Resch

first: Xingwang

last: Li

first: Byoungkoo

last: Lee

first: Alexander

last: Kovalchuk

first: Zhonghui

last: Tang

first: Steevenson

last: Nelson

first: Michele

last: Pierro

first: Ryan

last: Cheng

first: Ido

last: Machol

first: Brian

middle: G

last: Hilaire

first: Neva

last: Durand

first: Muhammad

last: Shamim

first: Elena

last: Stamenova

first: Jose

last: Onuchic

first: Yijun

last: Ruan

first: Andre

last: Nussenzweig

first: David

last: Levens

first: Erez

last: Lieberman-Aiden

first: Rafael

last: Casellas


title: Expression data from dosing four different antisense oligonucleotides in mice II

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

summary: We used microarrays to globally profile the gene expression changes observed in liver after 3 days when dosing antisense oligonucleotides in mice

overall_design: Four different antisense oligonucleotides were dosed at 5mg/kg (SPC3833) or 10 mh/kg (all others) on three consecutive days in mice and gene expression changes in in liver relative to saline-treated control mice (n=4) were measured by microarray on day 4


title: Expression data from dosing an antisense oligonucleotide in mice


title: Expression data from dosing an antisense oligonucleotide in mice I

summary: We used microarrays to globally profile the gene expression changes observed in liver after 3 days when dosing an antisense oligonucleotide in mice

overall_design: An antisense oligonucleotides, denoted SPC3833 (n=4) was dosed at 5mg/kg on three consecutive days in mice and gene expression changes in in liver relative to saline-treated control mice (n=4) were measured by microarray on day 4


title: C/EBPα overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1 [RNA-seq]

first: Salam

last: Assi

summary: Acute myeloid leukemia (AML) is a heterogeneous disease caused by recurrent mutations in the transcription regulatory machinery. As a result, malignant myeloid cells display abnormal growth and are blocked in differentiation. One type of recurrent mutations affects RUNX1 which is subject to mutations and translocations, the latter giving rise to fusion proteins with aberrant transcriptional activities. We recently compared the mechanism by which the products of the t(8;21) and the t(3;21) translocation RUNX1-ETO and RUNX1-EVI1 globally reprogram the epigenome. We demonstrated that a main component of the block in differentiation in both types of AML is direct repression of the gene encoding for the crucial myeloid regulator C/EBPα by both fusion proteins. We also showed that CEBPA upregulation is required for the release of the differentiation block after oncogene knock-down. In the study presented here we examined at the global level the response of t(8;21) and t(3;21) cells to C/EBPα overexpression. We show that C/EBPα overexpression does not change oncoprotein expression or globally displace these proteins from their binding sites, but up-regulates a core set of common target genes important for myeloid differentiation and interferes with leukemic growth, highlighting CEBPA regulated pathways as targets for therapeutic intervention.

overall_design: RNA-seq experiments with inducible version of CEBPA (C/EBPα-ER) have been used to study the effect of CEBPA overexpression on the gene expression of t(8;21) and t(3;21) AML

first: Justin

last: Loke

first: Paulynn

middle: S

last: Chin

first: Anna

last: Pickin

last: Keane

first: Anetta

last: Ptasinska

first: Maria

middle: R

last: Imperato

last: Cockerill

first: Constanze

last: Bonifer


title: Expression alterations in vildagliptin treated rats arota

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

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

platform_organism:
Rattus norvegicus
synthetic construct


title: Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx

city: Wuppertal

first: Jan

last: Postberg

state: NRW

address: Heusnerstr. 40

institute: HELIOS University Hospital Wuppertal, Witten/Herdecke University

summary: In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication and acts as host gene trans-regulator. However, functionally relevant spatiotemporal localization and interactions of cccDNA and HBx remain to be understood. This is the first study utilizing circularized chromosome conformation capture (4C) to identify regional virus-host genome interactions. We combined 4C with RNA-seq and ChIP-seq to illuminate the nuclear landscape associated with HBV episomes and HBx. Moreover, we functionally studied HBx-binding to episomal HBV DNA. In human HBV-positive HepaRG hepatocytes, 4C and ChIP revealed specific nuclear localization of HBV episomes and HBx associated with actively transcribed nuclear domains correlating well in size with constrained topological units built up by chromatin fibre loops, which are believed to constitute fundamental cell nuclear architectural units. Interestingly, HBx alone occupied transcribed chromatin domains, and its binding to HBV episomes depended on its C-terminus in vitro. In conclusion, HBx and HBV DNA similarly follow higher-order nuclear assembly patterns, specifically favoring transcriptionally active nuclear compartments. These novel observations may shed light on important unsolved problems: to understand the long-term episomal stability and the facilitation of viral persistence.

overall_design: In different hepatocyte celltypes, the genomic/nuclear association was studied for NLS-HBx-RFP, and several histone H3 PTM and Pol2 (MMH-D3 cells) by ChIP-seq; also cccDNA contacts were studied by 4C-seq, and histone PTM, Pol2 and mRNA were studied by ChIP-seq or mRNA-seq, respectively (HepaRG cell and HepG2.2.15/HepG2 H1.3).

first: Kai

last: Hensel

first: Franziska

last: Cantner

first: Felix

last: Bangert

first: Stefan

last: Wirth


title: C/EBPα overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1 [ChIP-seq]

overall_design: ChIP-seq experiments with inducible version of CEBPA (C/EBPα-ER) have been used to study the effect of CEBPA overexpression on transcription factor binding in  t(8;21) and t(3;21) AML

middle: A


title: Single-cell multi-omics sequencing of human early embryos

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

summary: DNA methylation, chromatin states, and their interrelationships represent critical epigenetic information, but those are largely unknown in human early embryos. Here, we apply scCOOL-seq (Chromatin Overall Omic-scale Landscape Sequencing) to generate a genome-wide map of DNA methylation and chromatin accessibility at single-cell resolution during human preimplantation development. Unlike in mice, the chromatin of paternal genome is already more open than that of maternal genome at the mid-zygote stage in humans, and this state is maintained until the 4-cell stage. After fertilization, genes with high variations in DNA methylation and those with high variations in chromatin accessibility tend to be two different sets. Furthermore, 1,797 (35%) out of 5,155 widely open chromatin regions in promoters closed when transcription activity was inhibited, indicating a feedback mechanism between transcription and open chromatin maintenance. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic reprogramming during human preimplantation development.

overall_design: In total, we analyzed 265 single cells (13 sperm, 9 oocytes, 10 zygotes, 14 2-cell blastomeres, 26 4-cell blastomeres, 48 8-cell blastomeres, 25 morulae blastomeres, 50 ICM, 48 TE and 22 hESCs) as well as 23 alpha-Amanitin treated 8-cell blastomeres.

first: Guo

last: Fan

first: Yun

last: Gao

first: Fuchou

last: Tang


title: Molecular and functional sex differences of noradrenergic neurons in the mouse locus coeruleus [Affymetrix]

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Preclinical work has long focused only on male animals, even though sexual divergence in both baseline behaviors and drug responses clearly impact treatment outcomes in patients.  Psychiatric disorders are notably divergent, with males showing higher prevalence of ADHD and ASD, and females GAD and MDD. This divergence is reflected in quantitative differences in subclincal behaviors. The Noradrenergic neurotransmitter system is targeted by many psychiatric drugs, but is relatively uncharacterized at a molecular level.  We developed a mouse to profile these neurons, defining their both a baseline transcriptome, including druggable receptors, and their molecular  response to stimulation.  We also discovered a remarkable sexual divergence in their gene expression, including functionally increased expression of the EP3 receptor in females – a difference that can be used to modulate stress-induced anxiety in a sex specific manner.  These findings underscore the need to conduct preclinical studies in a manner balanced for sex, and suggest that baseline differences in noradrenergic neurons could underlay sexually divergent behaviors.

overall_design: Replicate pools of 5 mixed sex adult mice from each of two bacTRAP lines (B6;FVB-Tg(Slc6a2-EGFP/Rpl10a)JD1537Jdd/J and B6;FVB-Tg(Slc6a2-EGFP/Rpl10a)JD1538Jdd/J were analyzed.

first: B

last: Mulvey

first: D

middle: L

last: Bhatti

first: S

last: Gyawali

last: Kriaucionis

first: C

last: Ford

first: M

last: Bruchas

first: N

last: Heintz

first: J


title: SDIMO gene analysis of two 1,4-dioxane degrading consortia enriched from uncontaminated soils

first: Ya

last: He

overall_design: To investigate the genes involved in the degradation of dioxane in two consortia enriched from uncontaminated soils, Nested PCR products in the second run were sequenced using Illumina Miseq technology. The results show that the predominance of SDIMOs in these two consortia.


title: Molecular and functional sex differences of noradrenergic neurons in the mouse locus coeruleus [Illumina]

middle: D

summary: Preclinical work has long focused only on male animals, even though sexual divergence in both baseline behaviors and drug responses clearly impact treatment outcomes in patients.  Psychiatric disorders are notably divergent, with males showing higher prevalence of ADHD and ASD, and females GAD and MDD. This divergence is reflected in quantitative differences in subclincal behaviors. The Noradrenergic neurotransmitter system is targeted by many psychiatric drugs, but is relatively uncharacterized at a molecular level.  We developed a mouse to profile these neurons, defining their both a baseline transcriptome, including druggable receptors, and their molecular response to stimulation.  We also discovered a remarkable sexual divergence in their gene expression, including functionally increased expression of the EP3 receptor in females – a difference that can be used to modulate stress-induced anxiety in a sex specific manner.  These findings underscore the need to conduct preclinical studies in a manner balanced for sex, and suggest that baseline differences in noradrenergic neurons could underlay sexually divergent behaviors.

overall_design: Four adult male and four adult female mice from each of two bacTRAP lines (B6;FVB-Tg(Slc6a4-EGFP/Rpl10a)JD60Jdd/J, and B6;FVB-Tg(Slc6a2-EGFP/Rpl10a)JD1538Jdd/J) were injected with LPS or vehicle (sterile PBS) and monitored for lethargy and induction of fever. Samples were handled and hybridized in two batches counterbalanced for mouse line, sex, and LPS exposure.


title: Molecular and functional sex differences of noradrenergic neurons in the mouse locus coeruleus


title: C/EBPα overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1

first: Salam

last: Assi


title: Genes differentially regulated by miR-489

city: Columbia

first: Hexin

last: Chen

state: SC

address: 715 Sumter Street,PSC621

department: Biological sciences

institute: University of South Carolina

summary: To investigate genes regulated by miR-489, gene expression analysis was carried out between control siRNA and miR-489 mimic transfected cells.

overall_design: T47D cells were transfected with miR-489 mimic or control scramble siRNA for 72 hours. RNA was isolated 72 hours post transfection using trizol reagent. Eacsh sample was collected in triplicate.

first: Mithil

last: Soni

first: Yogin

last: Patel


title: Transcriptional coregulator NUPR1 maintains tamoxifen resistance in breast cancer cells

status: Public on Apr 27 2018

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: To support cellular homeostasis and mitigate chemotherapeutic stress, cancer cells must gain a series of adaptive intracellular processes. Here we identify that NUPR1, a tamoxifen (Tam)-induced transcriptional coregulator, is necessary for the maintenance of Tam resistance through physical interaction with ESR1 in breast cancers. Mechanistically, NUPR1 binds to the promoter regions of several genes involved in autophagy process and drug resistance such as BECN1, GREB1, RAB31, PGR, CYP1B1, and regulates their transcription. In Tam-resistant ESR1 breast cancer cells, NUPR1 depletion results in premature senescence in vitro and tumor suppression in vivo. Moreover, enforced-autophagic flux augments cytoplasmic vacuolization in NUPR1-depleted Tam resistant cells, which facilitates the transition from autophagic survival to premature senescence. Collectively, these findings suggest a critical role for NUPR1 as a transcriptional coregulator in enabling endocrine persistence of breast cancers, thus providing a vulnerable diagnostic and/or therapeutic target for endocrine resistance.

overall_design: RNA-seq of MCF-7 cells, tamoxifen resistant MCF-7 cells, tamoxifen resistant NUPR1-depleted MCF-7 cells

first: Lingling

last: Wang

first: Jiashen

last: Sun

first: Yanzhe

last: Li

first: Kai

last: Zhang

first: Yanan

first: Xinzhong

last: Chang

first: Zhenfa

first: Zhe

last: Liu


title: The differential expression of miRNA between murine glioma and PNET

status: Public on Apr 29 2018

city: London

first: Sebastian

last: Brandner

state: State...

address: Queen square house, UCL Institute of Neurology

department: Institute of Neurology

institute: University College London

summary: miRNA expression analysis of mouse glioma and PNET. Glioma was developed from SVZ cells through conditional codeletion of Pten/p53 or Rb/p53; while PNET was developed by codeletion of Rb/p53.

overall_design: Pten/p53 codeleted SVZ cells always developed gliomas, while Rb/p53 cells mainly gave rise to PNET, but a small amout of Rb/p53 mice developed gliomas. Three groups: Pten/p53 glioma, Rb/p53 glioma and Rb/p53 PNET; biological control: each RNA sample was from a mouse tumour, three samples in each group.

first: Ningning


title: Gene expression alternations in vildagliptin treated rats arota

status: Public on Apr 26 2018

first: Qian

summary: Diabetic rats changes gene exprssion in vildagliptin treated rats arota

overall_design: We performed microarray analyses of vildagliptin treated rats arota

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing