title: Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount.  However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification kits applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored.

overall_design: We compared DNA recovery of ten commercial DNA purification reagents from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications.

first: Jian

last: Zhong

first: Jeong

middle: H

last: Lee


title: IRF1 is a transcriptional regulator of ZBP1 promoting NLRP3 inflammasome activation and cell death during influenza virus infection

status: Public on Dec 07 2017

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

summary: Innate immune sensing of influenza A virus (IAV) induces activation of various immune effector mechanisms including the NLRP3 inflammasome and programmed cell death pathways. Although type I IFNs are identified as key mediators of inflammatory and cell death responses during IAV infection, the involvement of various IFN-regulated effectors in facilitating these responses are less studied. Here, we demonstrate the role of interferon regulatory factor 1 (IRF1) in promoting NLRP3 inflammasome activation and cell death during IAV infection. IRF1 functions as a transcriptional regulator of Z-DNA binding protein 1 (ZBP1, also called as DLM1/DAI), a key molecule mediating IAV-induced inflammatory and cell death responses. Therefore, our study identified IRF1 as an upstream regulator of NLRP3 inflammasome and cell death during IAV infection and further highlights the complex and multilayered regulation of key molecules controlling inflammatory response and cell fate decisions during infections.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in influenza-infected bone marrow derived macrophages (BMDM) isolated from Ifnar1-/- , IRF1-/- and wild-type mice.

first: Teneema

last: Kuriakose

first: Min

last: Zheng

first: Thirumala-Devi

last: Kanneganti


title: Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL and PDS5 proteins

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.

overall_design: Analysis of chromatin structure by HiC and ChIP-Seq upon RNAi depletion and auxin-inducible degron (AID) systems.

first: Gordana

last: Wutz


title: Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [scTHS-seq]

status: Public on Dec 11 2017

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California San Diego

summary: Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.

overall_design:
Single DAPI+ nuclei (according to Samples list) were isolated from the visual cortex (BA17), frontal cortex (BA9) and cerebellar hemisphere from 3 separate postmortem adult human brains and processed for single-cell transposome hypersensitive site sequencing (scTHS-seq).

----------------------------
This represents the scTHS-Seq component only

first: Blue

middle: B

last: Lake

first: Song

last: Chen

first: Brandon

middle: C

last: Sos

first: Jean

last: Fan

first: Yun

last: Yung

first: Jerold

last: Chun

first: Peter

middle: V

last: Kharchenko


title: Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming

status: Public on Dec 06 2017

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Somatic cell reprogramming into pluripotent stem cells (iPSC) through the forced expression of defined factors induces changes in genome architecture reflective of the embryonic stem cell state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of what defines cells that successfully reprogram. Here, we characterize the changes that occur across the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of reprogramming intermediates poised to become iPSC. Widespread reconfiguration of chromatin states and transcription factor occupancy occurs early during reprogramming, and cells that fail to reprogram partially retain regulatory elements active in their somatic cell state. A second wave of reconfiguration occurs just prior to cells achieving pluripotency, where a majority of early changes revert to the somatic cell state and many of the changes that define the pluripotent state become established. Our comprehensive characterization of the molecular changes that occur during reprogramming broaden our understanding of the reprogramming process by providing crucial insights into iPSC generation, and shed light on how transcription factors in general access and change the chromatin during cell fate transitions.

overall_design: Profiling of transcription factor occupancy, chromatin accessibility, gene expression and DNA methylation during the reprogramming of MEF cells to iPS cells. Timecourse profiling of MEF cells, FACS sorted reprogramming intermediate cells, and iPS cells with biological replicates.

first: Sam

last: Buckberry

first: Jose

last: Polo

first: Anja

last: Knaupp


title: Gene co-expression networks drive and predict reproductive effects in Daphnia in response to environmental disturbances

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

summary: ncreasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene co-expression networks and generalized additive models to predict effects on reproduction in the aquatic microcrustacean Daphnia. We developed models to predict effects on reproduction upon exposure to different cyanobacteria, different insecticides and binary mixtures of cyanobacteria and insecticides. Models developed specifically for groups of stressors (e.g. either cyanobacteria or insecticides) performed better than general models developed on all data. Furthermore, models developed using in silico generated mixture gene expression profiles from single stressor data were able to better predict effects on reproduction compared to models derived from the mixture exposures themselves. Our results highlight the potential of gene expression data to quantify effects of complex exposures at higher level organismal effects without prior mechanistic knowledge or complex exposure data.

overall_design: Whole transcriptome dual color arrays were used to discover differentially expressed genes following sub-lethal exposure to five cyanobacteria, eight insecticides and their 48 binary mixtures in D. pulex. RNA was isolated from four independent and concurrently replicated exposures of Daphnia to control and all different treatment conditions. RNA was hybridized to microarrays using a full factorial loop design that included dye swaps. Cyanobacteria were Anabaena (ANA), Aphanizomenon (Aph), Cylindrospermopsis (Cyl), Nodularia (Nod) and Oscillatoria (Osl). Insecticides were acetamiprid (ace), carbaryl (carb), chlorpyrifos (chlor), deltamethrin (del), endosulfan (endo), fenoxycarb (fen), tebufenpyrad (teb) and tetradifon (tetra).

first: Michael

middle: E

last: Pfrender

first: Jacqueline

middle: A

last: Lopez

first: Joseph

last: Shaw

first: Karel

last: De Schamphelaere


title: piRNA-mediated regulation of transposon alternative splicing in soma and germline

city: New York

first: Felipe

last: Karam Teixeira

state: New York

address: 540 1st Avenue

department: Skirball Institute

institute: New York University Medical Center

summary: Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. We show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce P-element transposon transcript levels during P-M hybrid dysgenesis, a syndrome that affects germline development in Drosophila. Instead, splicing regulation is mechanistically achieved in concert with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi-piRNA complex proteins Asterix/Gtsf1 and Panoramix/Silencio, as well as Heterochromatin Protein 1a (Su(var)205/HP1a). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster, not only controls the accumulation of Gypsy retrotransposon transcripts but also regulates splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.

overall_design: ChIP-seq: two samples (non-dysgenic and dysgenic F1 progeny) were analyzed in biological replicates. RNA-seq: three comparisons [non-dysgenic vs. dysgenic F1 progeny; aub heterozygous vs. aub mutant (in Harwich background); and piwi heterozygous vs. piwi mutant (in Harwich background)] were analyzed in biological replicates.

middle: K

last: Teixeira

first: Martyna

last: Okuniewska

first: Colin

middle: D

last: Malone

first: Remi-Xavier

last: Coux

first: Donald

last: Rio

first: Ruth

last: Lehmann


title: Next generation sequencing for quantitative analysis of wild type and Y41F transcriptomes

city: Singapore

first: Ee Sin

last: Chen

address: 8 Medical Drive, MD7 level 5

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Next Generation Sequencing (NGS) on total RNA of wild type (WT) and Y41F mutant. The goal of this study is to compare the transcriptome profile of Y41F mutant to WT cells.

overall_design: The transcriptome profile of log phase WT and Y41F cells were generated by RNA-seq, induplicate, using Illumina HiSeq 2000

first: Bingbing

last: Ren

first: Ee

middle: S


title: MicroRNA-7-5p mediates the anti-oncogenic effect of hepatocyte growth factor in the MCF-10A mammary epithelial cell

city: Ilsan

first: Juyeon

last: Ham

address: 32, Dongguk-ro

country: South Korea

institute: Dongguk University

summary: Genome wide expression profiling of breast normal cell line MCF-10A. The Illumina HumanHT-12 v4 Expression BeadChip was used to obtain  expression profiles. This profiling indicates that MicroRNA-7 mediates the activity of HGF to suppress oncogenic proteins, which inhibits cancer progress.

overall_design: Control sample is RNA obtained from  MCF-10A and test sample is RNA obtained from  MCF-10A overexpressing miRNA-7

first: Dawoon

last: Jeong

first: Sunjung

last: Kim


title: The RNA binding protein PTBP1 is necessary for B cell selection in germinal centres

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Antibody affinity maturation occurs in germinal centres (GC) where B cells cycle between the light zone (LZ) and the dark zone. In the LZ GC B cells bearing immunoglobulins with the highest affinity for antigen receive positive selection signals from T helper cells that promotes their rapid proliferation. Here we show that the RNA binding protein PTBP1 is necessary for the progression of GC B cells through late S-phase of the cell cycle and for affinity maturation. PTBP1 is required for the expression of the c-MYC-dependent gene programme induced in GC B cells receiving T cell help and directly regulates the alternative splicing of transcripts increased during positive selection to promote anabolic metabolism and cell proliferation.

overall_design: mRNAseq libraries were generated from light zone and dark zone germinal centre B cells. Light zone and dark zone germinal centre B cells were FACS-sorted from mice immunised with alum precipitated NP-KLH (7 days before cell sorting). Erythrocytes were lysed and GC B cells were enriched before FACS sorting by depleting cells stained with biotinylated anti IgD, CD3e, Gr1 and Ter119 antibodies by MACS. Four biological replicates were carried out per condition. In each biological replicate, GC B cell-enriched splenocytes from 3 to 5 animals of the same genotype and sex were pooled together before FACS sorting. LZ and DZ GC B cells were sorted from the same GC B cell enriched samples. LZ and DZ GC B cells from control CD79a+/+Ptbp1fl/fl and CD79acre/+Ptbp1fl/fl cKO mice were sorted on the same day. Two biological replicates per condition were from females and two from males.

first: Elisa

last: Monzón-Casanova

last: Screen

first: Manuel

last: Díaz-Muñoz

first: Richard

middle: M

last: Coulson

first: Sarah

last: Bell

first: Greta

last: Lamers

first: Michele

last: Solimena

first: Christopher

middle: W

last: Smith

first: Martin

last: Turner


title: Esophageal tissue and serum microRNAs changed in the progression of Barrett’s esophagus in mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Circulating microRNAs (miRNAs) are promising biomarkers for the early detection of cancers. This assay aimed to address potential circulating miRNAs to monitor the progression from Barrett’s esophagus to esophageal adenocarcinoma (EAC).

overall_design: We comprehensively analyzed tissue and serum miRNA expression profiles of BE mice model (L2-IL-1β mice) using microarray analysis. We identified 20 upregulated miRNAs and 44 downregulated miRNAs both in tissues and in sera of 46-week-old mice compared to in 28-week-old mice.

first: Juntaro

last: Matsuzaki

first: Hidekazu

last: Suzuki


title: Genome-wide identification and transcriptomic profiling of auxin concentration and signaling related genes in moso bamboo (Phyllostachys heterocycla)

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

country: China

institute: Fujian Agriculture and Forestry University

summary: Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species.

overall_design: bamboo (Phyllostachys heterocycla) one-month-old seedlings were sprayed with 5μM NAA for 4 hours with 1-hour interval, and the root part were dissected for RNA extraction.

first: Wenjia

last: Wang

first: Shanwen

last: Ye

first: Hangxiao

last: Zhang

first: Changyang

last: Cai

first: Mengqi

last: Xiang

first: Yubang

last: Gao

first: Qiang

last: zhu


title: Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1

city: Stanford

first: Andrew

middle: S.

last: Koh

address: 279 Campus Drive B203

institute: Stanford University

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

overall_design: Refer to individual Series


title: Differential ability of pandemic and seasonal H1N1 influenza 1 A virus to alter function of human neutrophils

status: Public on Dec 05 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Neutrophils are essential cells of host innate immunity. Although the role of neutrophils in defense against bacterial and fungal infections is well characterized, there is relative paucity of information about their role against viral infections. Influenza A virus (IAV) infection can be associated with secondary bacterial co-infection, and it has long been posited that the ability of IAV to alter normal neutrophil function predisposes individuals to secondary bacterial infections. To better understand this phenomenon, we evaluated the interaction of pandemic or seasonal H1N1 IAV with human neutrophils isolated from healthy subjects. These viruses were ingested by human neutrophils and elicited changes in neutrophil gene expression that are consistent with an interferon-mediated immune response. Viability of neutrophils following co-culture with either pandemic and seasonal H1N1 IAV was similar for up to 18 h of culture. Notably, neutrophil exposure to seasonal IAV (but not pandemic IAV) primed these leukocytes for enhanced functions, including production of reactive oxygen species and bactericidal activity. Taken together, our results are at variance with the universal idea that IAV impairs neutrophil function directly to predispose individuals to secondary bacterial infections. Rather, we suggest some strains of IAV prime neutrophils for enhanced bacterial clearance.

overall_design: time course with three treatments, Kawasaki, Mex09 and RPMI

first: Natalia

last: Malachowa

first: Brett

last: Freedman

first: Daniel

first: Scott

last: Kobayashi

first: Vinod

last: Nair

first: Friederike

last: Feldmann

first: Tregei

last: Starr

first: Olivia

last: Steele-Mortimer

first: John

last: Kash

first: Jeffery

last: Taubenberger

first: Heinz

first: Frank

last: DeLeo


title: Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing


title: Foxp2 Overexpression in BACHD mice

first: Myriam

last: Heiman

state: Massachusetts

address: The Picower Institute of Learning & Memory

institute: MIT

summary: Alterations to corticostriatal glutamatergic function are early pathophysiological changes associated with Huntington?s disease (HD). The factors that regulate the maintenance of corticostriatal glutamatergic synapses post-developmentally are not well understood. Recently, the striatum-enriched transcription factor Foxp2 was implicated in the development of these synapses. Here we show that, in mice, overexpression of Foxp2 in the adult striatum of two models of HD leads to rescue of HD-associated behaviors, while knockdown of Foxp2 in wild-type mice leads to development of HD-associated behaviors. We note that Foxp2 encodes the longest polyglutamine repeat protein in the human reference genome, and we show that it can be sequestered into aggregates with polyglutamine-expanded mutant Huntingtin protein (mHTT). Foxp2 overexpression in HD model mice leads to altered expression of several genes associated with synaptic function, genes which present new targets for normalization of corticostriatal dysfunction in HD.

overall_design:
4 mice per group of each: Con+Con, Con+Foxp2, BACHD+Con, BACHD+Foxp2
Foxp2 or Control virus was injected into BACHD and Control mice, mRNA was isolated and sequenced

first: Lea

last: Hachigian

first: Fan


title: Genome-wide maps of chromatin structure in wild-type and nanos mutant primordial germ cells in C. elegans

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

summary: The Nanos family of RNA-binding proteins has been implicated in the specification of primordial germ cells (PGCs) in a wide range of metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of PGCs lacking the nanos homologues nos-1 and nos-2 in C. elegans using cell sorting and RNA-seq. nos-1nos-2 PGCs fail to silence hundreds of genes normally expressed in oocytes and somatic cells, a phenotype reminiscent of PGCs lacking the repressive PRC2 complex. The nos-1nos-2 phenotype depends on LIN-15B, a broadly expressed synMuvB class transcription factor known to antagonize PRC2 activity in somatic cells. LIN-15B is maternally-inherited by all embryonic cells and is down-regulated specifically in PGCs in a nos-1nos-2-dependent manner.  Consistent with LIN-15B being a critical target of Nanos regulation, inactivation of maternal LIN-15B restores fertility to nos-1nos-2 mutants. These studies demonstrate a central role for Nanos in reprogramming the transcriptome of primordial germ cells away from an oocyte/somatic fate by down-regulating an antagonist of PRC2 activity.

overall_design: 4 biological ATAC-seq samples are included in this study. These include two biological samples from wild-type and two biological samples from nos-1 nos-2 mutant PGCs

first: Chih-Yung

last: Lee


title: Epigentic profiling of murine proximal and distal femoral growth plates at E15.5 of mouse gestation

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

summary: GWAS have identified hundreds of loci associated with height.However, determining causal mechanisms is challenging, especially since height-relevant tissues such as the growth plate are difficult to study. To discover mechanisms by which height GWAS variants function, we performed epigenetic profiling of murine femoral growth plates. The profiled open chromatin regions recapitulate known chondrocyte and skeletal biology and are enriched at height GWAS loci, particularly near differentially expressed growth plate genes. These regions are also enriched in binding motifs of transcription factors with known roles in chondrocyte biology. At specific loci, our analyses identified compelling mechanisms for GWAS variants. For example, at the CHYS1 locus, we identified a potentially causal variant overlapping an open chromatin region and predicted to alter binding of HOXD13, important for skeletal development. Thus, integrating biologically relevant epigenetic information (here, from mouse growth plate) with genetic association results can identify biological mechanisms important for human growth.

overall_design: Examination of open chromatin regions in two different growth plates (proximal vs distal femur) at E15.5

first: Evelyn

last: Jagoda

first: Michael

last: Guo

first: Jessica

last: Willen


title: Gene expression data from crypts isolated from WT and Lpcat3 Villin-CreERT2 mice

city: Los Angeles

first: Bo

last: Wang

state: CALIFORNIA

address: 675 Charles E Young Dr. S

department: Pathology and Laboratory Medicine

institute: UCLA

summary:
We used microarray to analyze the global gene expression in crypts isolated from wild-type (Lpcat3F/F) and Lpcat3 tamoxifen inducible intestine-specific knockout (Lpcat3F/F, Villin-CreERT2) crypts.
Phospholipid remodeling is a critical determinant of membrane composition and function. How membrane phospholipid composition affects tissue stem cell function and tumorigenesis is unknown.  Here we demonstrate that Lpcat3-dependent phospholipid remodeling regulates intestinal stem cell (ISC) proliferation and promotes tumorigenesis in intestine.  The objective of generating this dataset was to analyze the effects of Lpcat3 loss of function on gene expression in mouse intestine crypts.

overall_design: Eight- to ten-week old Lpcat3F/F and Lpcat3F/F, Villin-CreERT2 mice were i.p. injected tamoxifen for 5 days (1 mg/mouse/day). Crypts were isolated two weeks post tamoxifen injection.  The RNAs were pooled from 5 mice/group and analyzed using Affymetrix Mouse Genome 430A 2.0 Arrays.

first: Xin

last: Rong

first: Elisa

middle: N

last: Palladino

first: Jiafang

first: Alan

last: Fogelman

first: Martín

middle: G

last: Martín

first: Waddah

last: Alrefai

first: David

last: Ford

first: Peter

last: Tontonoz


title: Global characterization of direct substrates of nonsense-mediated mRNA decay in Caenorhabditis elegans

city: Madison

first: Philip

last: Anderson

state: WI

address: 425-G Henry Mall

department: Genetics

institute: University of Wisconsin-Madison

summary:
Purpose: We present a genome-wide investigation to distinguish mRNA substrates directly regulated by nonsense-mediated mRNA decay (NMD) from indirect secondary effects using true NMD null alleles

Methods: mRNA profiles of wild type (N2), smg-1(r910), and smg-1(r910) smg-2(r915) animals were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.  We further performed deep sequencing in triplicate on RNAs that co-immunoprecipitate with the central effector of NMD, SMG-2, in both smg-1(r910) and smg-1(r910) smg-2(r915) mutant animals. The sequence reads that passed quality filters were analyzed at both the gene level and the intron level using Tophat2 and edgeR.  qRT-PCR validation was performed using SYBR Green assays.

Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.

Conclusions: We found that a significant portion of genes with increased expression in an NMD-deficient background are direct substrates of SMG-2.  Among the list of direct targets, we find many mRNAs from pseudogenes, alternative splice isoforms harboring PTCs, mRNAs encoding RNA processing factors, and two recently expanded gene families are directly regulated by the NMD pathway.

overall_design: mRNA profiles of wild type (N2), smg-1(r910), and smg-1(r910) smg-2(r915) C. elegans were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.  RNAs that co-immunoprecipitate with SMG-2 in smg-1(r910) and smg-1(r910) smg-2(r915) nematodes were also sequenced, in triplicate, using Illumina HiSeq2000.

first: Virginia

last: Muir

first: Audrey

middle: P

last: Gasch


title: Transcriptional profile in dermal fibroblasts from patients with collagen VI related muscular dystrophy

status: Public on Dec 04 2017

city: Salt Lake City

first: Russell

last: Butterfield

state: UT

department: Pediatric Neurology

institute: University of Utah

summary:
Objectives:  The collagen VI related muscular dystrophies (COL6-RD), Ullrich congenital muscular dystrophy (UCMD) and Bethlem myopathy (BM) are among the most common congenital muscular dystrophies, but the pathogenesis, including the role of mutant collagen VI in the matrix is poorly understood. To better define the pathways disrupted by mutations in collagen VI, we have used a transcriptional profiling approach with RNA-Seq to identify differentially expressed genes in COL6-RD patients from controls.
Methods:  We have used RNA-Seq to identify differentially expressed genes in cultured dermal fibroblasts from 13 COL6-RD patients (8 dominant negative and 5 null) and 6 controls.  Sequence reads were analyzed using the TopHat/Cufflinks pipeline.
Results:  Differentially expressed transcripts between COL6-RD patient and control fibroblasts include upregulation of ECM components and downregulation of factors controlling matrix remodeling and repair.  DN and null samples are differentiated by downregulation of genes involved with DNA replication and repair in null samples

overall_design: Expression profiles of dermal fibroblasts from 13 COL6-RD patients with dominant negative (8) or null (5) mutations compared to 6 control fibroblasts.

middle: J

first: Robert

last: Weiss


title: RNA Expression Data from developing enteric nervous system (ENS) and bowel

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary:
The enteric nervous system (ENS) can control most essential gut functions owing to its organization into complete neural circuits consisting of a multitude of different neuronal subtypes.
We used microarrays to identify transcription factor networks and signaling pathways involved in diversification and differentiation of enteric neurons during development of the enteric nervous system.

overall_design: In total four enteric samples and two non-ENS bowel samples were isolated (3-4 replicates of each) by FACS sorting of bowel cells from transgenic mouse reporter lines. Progenitor ENS cells (which express Sox10) were isolated from Sox10CreERT2 x R26ReYFP bowel at E11.5 (S11plus-S14plus) and E15.5 (S51plus-S54plus), 20 hours after YFP-reporter had been induced with 4-OHT. Whole ENS populations were isolated from Wnt1Cre x R26ReYFP bowel at E11.5 (W11plus-W13plus) and E15.5 (W51plus-W53plus). Negative populations in the FACS sorting of Wnt1Cre x R26ReYFP were harvested as non-ENS bowel cells at E11.5 (W11minus-W13minus) and E15.5 (W51minus-W53minus).  Total RNA from each sample was converted to cDNA and hybridized on Affymetrix microarrays.

first: Vassilis

last: Pachnis


title: The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORa/g [array]

status: Public on Dec 03 2017

city: Boston

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: We address the function of ROR in the mouse liver metabolism

overall_design: Microarray profiling of livers of control mice and ROR LDKO mice

first: Yuxiang

last: Zhang

first: Bin

last: Fang


title: Differential Expression of microRNAs in Oral Squamous cell carcinoma (OSCC) [Frozen tissue samples]

city: Santiago de Compostela

first: Cintia

middle: Micaela

last: Chamorro

address: Entrerríos s/n

department: Oral Medicin

country: Spain

institute: Santiago de Compostela University

summary:
Our objective was to analyze with microarray the differential expression of microRNAs in oral squamous cell carcinoma compared with healthy control tissue.
We have obtained a total of 97 genes desregulated, 36 overexpressed and 61 under expressed, where 81 were microRNAs.

overall_design: We have used eight samples from patients diagnosed with oral cancer and eight samples from healthy patients. Total RNA was extracted with miRVana Isolation kit, then we have used Affymetrix® FlashTagTM Biotin HSR RNA Labeling Kit to label the samples, and the plate used in the microarray was Affymetrix®miRNA 4.1 Array Plate. We have followed the manufacturers instructions in all the protocols, except in the miRVana Isolation kit in the first part, where we have disgregated successfully the frozen tissue sample using a diamond drill and a handpiece without liquid nitrogen

first: Mario

last: Perez-Sayáns

first: Elena

last: Padín

first: Xabier

last: Marichalar

first: Abel

last: Garcia

first: M

last: Gallas

first: Jose

last: Suarez


title: The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORa/g [seq]

overall_design: We performed GRO-seq and  RORa/RORc ChIP-seq in livers of control mice and ROR LDKO mice at 5am of the day


title: The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORa/g


title: Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

city: Palo Alto

first: Nian

last: Liu

address: 265 Campus Drive, Rm. G3145

department: Chemical and Systems Biology

summary: Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in shaping genome evolution and providing genetic substrates for evolving new regulatory functions. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease. Nonetheless, our knowledge of how L1 activity is controlled and what function L1s play in host gene regulation remains fragmentary. Here, we use CRISPR/Cas9 screening strategies in two distinct human cell lines to provide the first genome-wide survey of genes involved in L1 retrotransposition control. Through this approach we identified functionally diverse genes that either promote or restrict L1 retrotransposition. These factors control the L1 life cycle at transcriptional or post-transcriptional levels, and in a manner which in some, but not in other cases depends on the endogenous L1 sequence, underscoring the complexity of L1 regulation. We further investigated L1 restriction by three candidate regulators, MORC2 and HUSH (human silencing hub) complex subunits TASOR and MPP8. HUSH/MORC2 selectively bind evolutionarily young, full-length L1s immersed within transcriptionally permissive euchromatic environment, and promote H3K9me3 deposition for transcriptional silencing. Interestingly, these silencing events often occur within introns of transcriptionally active host genes, and lead to down-regulation of host gene expression in a HUSH/MORC2-dependent manner. Together, our data provide a rich resource for studies of L1 retrotransposition, elucidate a novel L1 restriction pathway, and illustrate how epigenetic silencing of TEs can influence host gene expression programs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Identify L1 regulators by one genome-wide CRISPR screen followed by one secondary batch screen in K562 and HeLa cells; Identify the binding profiles of MORC2, MPP8 and TASOR by ChIP-seq in wild type and KO cells; Identify the H3K9me3 methylation changes and RNA polymerase II binding site changes by ChIP-seq and the transcriptional changes by polyA-selected RNA-seq in wild-type and corresponding KO cells.

first: Liu

last: Nian

first: Lee

last: Cameron

first: Swigut

last: Tomek

first: Grow

last: Edward

first: Bassik

last: Michael

first: Wysocka

last: Joanna


title: Transcriptional profile comparing liver tissue in the absence/presence of LKB1 expression

status: Public on Dec 02 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: The aim of this project is to determine the differential expression of genes between liver in the absence or presence of LKB1, leading to mitosis defects observed in absence of LKB1

overall_design: Liver tissues were obtained (+/- LKB1 expression) 48 hours after partial hepatectomy

first: Chantal

last: Desdouets

first: Vanessa

last: Maillet

first: Sébastien

last: Jacques


title: Tamoxifen Resistance in Breast Cancer is Regulated by the EZH2-ERa-GREB1 Transcriptional Axis

status: Public on Dec 01 2017

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio


title: Expression analysis of microRNAs in plasma of new HIV-infected cases, old HIV-infected cases and healthy controls.

city: Nanning

first: Jiegang

last: Huang

state: Guangxi

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

summary:
There are 19 differentially expressed microRNAs among new HIV-infected cases, old HIV-infected cases and healthy controls.
Five microRNAs show trends in healthy controls, new HIV-infected cases and old HIV-infected cases, they are hsa-miR-1291, and hsa-miR-3609 with up-trends, and hsa-miR-3162-3p, hsa-miR-874-5p and hsa-miR-4258 with down-trends.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: A microarray study using total RNA extracted from the plasma of ten new HIV-infected cases (estimated duration of infection <1 year), ten old HIV-infected cases (estimated duration of infection≥ 1 year) and ten healthy controls.  Each array measures the expression level of 3,100 microRNAs annotated in miRBase 18.0, covering all human, mouse and rat, as well as all virus microRNAs related to these species. In addition, this array contains capture probes for 25 miRPlus™ human microRNAs.

first: Hao

last: Liang

first: Li

last: Ye

first: Jingzhen

last: Lai

first: Bingyu


title: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences


title: Inter-individual variation among worms in a shared environment

city: Barcelona

first: Ben

last: Lehner

address: Carrer Doctor Aiguader, 88

department: systems biology

institute: CRG

summary: Isogenic individuals growing in the same environment often show substantial phenotypic variation. The causes, consequences and molecular bases of inter-individual variation are usually poorly understood. To characterize molecular differences between isogenic individuals, we measured genome-wide expression profiles in synchronized single young adult C. elegans worms.

overall_design: 41 individual N2 C. elegans were grown at 20˚C and collected 46h after hatching

first: Mirko

last: Francesconi

first: Marcos

middle: F

last: Perez


title: Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

city: Cambridge

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Eukaryotic genomes must maintain stable inheritance of epigenetic states. In plants, DNA methylation patterns are faithfully inherited over many generations but it is unknown how the dynamic activities of cytosine DNA methyltransferases and 5-methylcytosine DNA glycosylases, which remove 5-methylcytosine by base excision repair, interact to maintain epigenetic homeostasis. Here we show that a methylation-sensing gene regulatory circuit centered on a 5-methylcytosine DNA glycosylase gene is required for long-term epigenetic fidelity in Arabidopsis. Disrupting this circuit causes widespread methylation losses and abnormal phenotypes that progressively worsen over generations. In heterochromatin, these losses are counteracted such that methylation returns to a normal level over four generations. However, thousands of loci in euchromatin progressively lose DNA methylation between generations and remain unmethylated. We conclude that actively maintained equilibrium between methylation and demethylation activities is required to ensure long-term stable inheritance of epigenetic information.

overall_design: Whole genome bisulfite sequencing was used to examine DNA methylation in wild-type (Col-0), ros1, rdr2, and rdr2; ros1 mutant plants. In addition, whole genome bisulfite sequencing was performed on multiple generations of “broken rheostat (BR)” lines, in which expression of the DNA glycosylase ROS1 is decoupled from the methylation state of the genome. “BRmut” denotes control lines in which ROS1 is mutated. T(n) denotes the generation of each BR or BRmut line sample

last: Williams


title: miRNA mobility is a highly regulated process in plants

city: Cold Spring Harbor

first: Damianos

last: Skopelitis

state: NY

address: One Bungtown Rd

department: Cancer Biology

institute: Cold Spring Harbor Laboratory

summary: Small RNAs regulate many important developmental processes by targeting key regulators, such as transcription factor families, for posttranscriptional repression. Although originally assumed to function cell-autonomously, several instances of small RNAs serving as short-range mobile signals have now been reported. The recognition that small RNAs can move from cell-to-cell has broadened our thinking on how these molecules are utilized during development, serving as positional, morphogen-like, signals. However, major questions regarding the properties and function of mobile small RNAs during plant development remain. For example, is miRNA movement a developmentally regulated process? What factors are important for miRNA mobility? In order to address questions regarding the properties of miRNAs mobility, our group has developed a reporter system to assay non-cell-autonomous miRNA activity. In this system an artificial miRNA (MIR-GFP) is expressed from tissue-specific promoters and assayed for its capacity to silence a ubiquitously-expressed, cell-autonomous, nuclear-localized GFP reporter (p35S:3xNLS-GFP). Here we report that miRNA movement is a regulated process, and that competence to move is developmentally determined. In select tissue contexts, miRNAs show differential or directional movement, indicating miRNA mobility to be regulated independently from other signalling molecules.

overall_design: Examination of artificial miRNA (miRGFP) levels in libraries generated from whole seedlings of pCLV3:miRGFP, pSUC2:miRGFP and pRbcS:miRGFP lines and from shoots and roots of pRbcS:miRGFP and the p35S:3xNLS-GFP (no miRGFP) control line. Moreover, in this study we examined the levels of another artificial miRNA (miRGUS), as well as GUS-derived secondary siRNA production, in libraries generated from whole seedlings of p35S:miRGUS line. All lines used to generated small RNA libraries in this study, were made in an rdr6 null mutant background impaired for siRNA production.

first: Kristine

last: Hill

first: Simon

last: Klesen

first: Cristina

last: Marco

first: Anna

last: Benkovics

first: Marja

last: Timmermans


title: B cell presentation of Chlamydia antigen selects out protective CD4ɣ13 T cells; implications for genital tract tissue resident memory lymphocyte clusters

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

summary: Surveillance and defense of the enormous mucosal interface with the nonsterile world is critical to protecting the host from a wide range of pathogens.  Chlamydia trachomatis (Ct) is an intracellular bacterial pathogen that replicates almost exclusively in the epithelium of the reproductive tract.  The fallopian tubes and vagina seem poorly suited to surveillance and defense as they have limited immune infrastructure positioned near the epithelium.  However, a dynamic process during clearing primary infections leaves behind new immune infrastructure positioned near epithelium.  Memory lymphocyte clusters (MLC) harboring tissue resident memory T cells (TRM) are presumed to play an important role in protection from subsequent infections.  Histologically Chlamydia MLC appear to be based on B cells.  We therefore investigated B cell populations in the murine genital tract post-clearance of C. muridarum infections and the nature of T cells recovered from immune mice using immune B cells as antigen presenting cells (APC).  These studies revealed a plasma B cell population in the genital tract consistent with histopathology seen in mouse and human Chlamydia infections, and discovery of a novel CD4 T cell subset based on production of IFN-ɣ and IL-13.   We discuss these results in the context of Trm and previously published data showing that in humans a peripheral blood mononuclear IL-13 response to elementary bodies (EB) predicts resistance to future infection.

overall_design: Modification of T cell expansion using purified immune B cells as APC rather than published unfractionated immune splenocyte APC; resulting T cell clones from immune mice were analyzed to identify subset-specific differences


title: Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models [primary cell lines Hubrecht Institute]

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

summary: Colorectal cancer (CRC) is a highly heterogeneous disease both from a molecular and clinical perspective. Several distinct molecular entities, such as microsatellite instability (MSI), have been defined that make up biologically distinct subgroups with their own clinical course. Recent data indicated that CRC can be best segregated into four groups called Consensus Molecular Subtypes (CMS1-4), which each have a unique biology and gene expression pattern. In order to develop improved, subtype-specific therapies and to gain insight into the molecular wiring and origin of these subtypes, reliable models are needed. This study was designed to determine the heterogeneity and identify the presence of CMSs in a large panel of CRC cell lines, primary cultures and patient-derived xenografts (PDX). We provide a repository encompassing this heterogeneity and moreover describe that a large part of the models can be robustly assigned to one of the four CMSs, independent of the stromal contribution. We subsequently validate our CMS stratification by functional analysis which for instance shows mesenchymal enrichment in CMS4 and metabolic dysregulation in CMS3. Finally, we observe a clear difference in sensitivity to chemotherapy-induced apoptosis, specifically between CMS2 and CMS4. This relates to the in vivo efficacy of chemotherapy, which delays outgrowth of CMS2, but not CMS4 xenografts. This indicates that molecular subtypes are faithfully modelled in the CRC cell cultures and PDXs, representing tumour cell intrinsic and stable features. This repository provides researchers with a platform to study CRC using the existing heterogeneity.

overall_design: Gene expression was analyzed for 18 CRC organoids

first: J

last: Linnekamp

first: S

middle: R

first: P

last: Prasetyanti

first: R

last: Kandimalla

middle: H

last: de Jong

first: K

last: Cameron

last: van Leersum

first: H

last: Rodermond

first: G

last: van Bochove

last: Buikhuisen

first: E

last: Fessler

first: L

last: Vermeulen

first: X

last: Wang

last: Stassi

last: Mangiapane

first: F

last: Nürnberg

last: Clevers

last: Medema


title: Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models [cell line panel]

last: van Hooff

overall_design: Gene expression analysis of 18 CRC cell lines

last: Linnekamp


title: Characterization with age of resident T cells within secondary lymphoid organs in the steady state

first: Franck

last: Letourneur

summary: Using two different experimental approaches, we here highlight the long-term residence of a substantial proportion of CD4 Treg and CD4 Tmem cells within the secondary lymphoid organs of specific pathogen-free mice. Microbiota plays an important role in T-cell residence in Peyer’s patches, but only a minor one, if any, in lymph nodes. Lymph node-resident CD4 Treg and CD4 Tmem cells share many phenotypic and functional characteristics, including a core transcriptional profile, with their cell-counterparts from non-lymphoid tissues. In particular, S1PR1 down-regulation may represent the main mechanism accounting for T-cell residency within secondary lymphoid organs. Strikingly, T-cell residence increases with age, to the point that the majority of CD4 Treg and Tmem cells from lymph nodes are in fact, resident T cells in old mice. Altogether, our results show that T-cell residence is not only a hallmark of non-lymphoid tissues, but can be extended to secondary lymphoid organs.

overall_design: CD4 T cells from lymph nodes (peripheral + mesenteric) of C57BL/6 Foxp3-GFP mice treated or not with anti-LFA-1 and anti-VLA-4 antibodies 2 days before were purified by using Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen). Then, CD4 Treg and Tmem cells were flow-cytometry sorted as CD4+ CD8α- TCRβ+ GFP+ for Treg and CD4+ CD8α- TCRβ+ GFP- CD44hi for Tmem using a FACS-ARIA3 flow cytometer.

first: Aurelie

last: Durand

first: Alexandra

last: Audemard-Verger

first: Vincent

last: Guichard

first: Raphaël

last: Mattiuz

first: Arnaud

last: Delpoux

first: Pauline

last: Hamon

first: Nelly

last: Bonilla

first: Matthieu

last: Rivière

first: Jérome

last: Delon

first: Bruno

last: Martin

first: Cedric

last: Auffray

first: Alexandre

last: Boissonnas

last: Lucas


title: Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models [patient tumors and PDX models]

first: Sander

overall_design: Gene expression analysis of 15 CRC patient tumors and 34 patient derived xenografts established from those tumors

first: J

first: S

first: P

last: Prasetyanti

first: R

last: Kandimalla

last: de Jong

first: K

last: Cameron

last: van Leersum

first: H

last: Rodermond

first: G

last: van Bochove

last: Buikhuisen

first: E

last: Fessler

last: Vermeulen

last: Wang

last: Stassi

last: Mangiapane

last: Nürnberg

last: Clevers

last: Medema


title: The transcriptome effect of overexpressing EZH2 in MCF7

first: Kexin

last: Xu

summary:
Purpose: Increasing evidence suggests that epigenetic reprogramming contributes significantly to the development of endocrine therapy resistance in breast cancer. The goal of this work is to explore how the histone methyltransferase EZH2 interacts with ER signaling and drives the insensitiveness of breast cancer cells to the antagonistic effect of tamoxifen on ER activity. Therefore,  we comprehensively analyzed the transcriptional program regulated by EZH2 in EZH2 overexpressed MCF-7 cells.
Methods: MCF-7 cells between passage 142-144  were used for this assay. For mRNA-Seq, cells are infected with control empty vector (EV) or EZH2 expressing plasmid (EZH2) by lentivirus. Total RNA were extracted by TRIzol (Invitrogen) and libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2 (Cat.# RS-122-2001). Hiseq 3000 was used for sequencing.

overall_design: Transcriptome profiles of tamoxifen sensitive MCF-7 infected with pLenti-CMV-hygro-GFP or pLento-HA-EZH2 were sequenced in at least duplicates using Illumina HiSeq 3000.

first: Yanming

last: Wu

first: Zhao

last: Zhang


title: Human Prostate Cancer Cells: ISL-treated cells vs. Control

city: Shanghai

first: Biyan

address: 1200 Cai Lun Road, Pudong District

department: School of Basic Medicine

institute: Shanghai University of Traditional Chinese Medicine

summary: Transcriptional profiling of human prostate cancer cells comparing Isl-treated cells with untreated cells.

overall_design: LNCaP cells or PC-3 cells treated with ISL (Isoliquiritigenin) or untreated as control samples were used.

first: Zijun

last: Chen


title: Mitochondrial unfolded protein response gene Clpp plays a role in female fertility and reproductive aging

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: We performed RNAseq analysis to determine the effect of ClpP-deletion on cumulus cells global gene expression profile in mature (3 month-old) and (6 month-old) mice. RNA sequencing revealed about 13,000 genes (FPKM > 0.1) expressed in cumulus cells. A total of 1025 genes were significantly differentially expressed (p<0.05) in 3-month ClpP-/- cumulus cells compared to WT (548 up-regulated and 477 down-regulated). At 6-month, a total of 555 genes were significantly differentially expressed in ClpP-/- cumulus cells compared to WT (464 up-regulated and 91 down-regulated). In addition, 1012 and 1034 genes were significantly differentially expressed in both 6 month ClpP-/- and WT cumulus cells compared to younger ClpP-/- cumulus cells, respectively. In this study, we assessed the effect of ClpP global deletion on cumulus cells gene expression. Our findings provide new insight into the role of CLPP in the cumulus cells, and may help understand the potential mechanism of infertility and reproductive aging associated with ClpP-deficiency.

overall_design: Cumulus oophorus complexes (COCs) were collected from 3- and 6-month old ClpP knockout (ClpP-/-) and wild type (WT) female mice (n=3 for each group) 48h after injection with 5IU pregnant mare serum gonadotropin (PMSG, Sigma). Germinal vesicle (GV) oocytes were isolated and 5 oocytes from each mouse were pooled for RNA sequencing analysis. Cumulus cells were isolated and 100 cells from each mouse were pooled for RNA sequencing analysis.

first: Tianren

first: Man

first: Emre

last: Seli


title: Effect of L-tryptophan, tryptamine and indole-3 acetaldehyde on gene expression in Fusarium graminearum

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

summary: Fusarium graminearum is a plant pathogen that can cause the devastating cereal grain disease fusarium head blight (FHB) in temperate regions of the world. Previous studies have shown that F. graminearum can synthetize indole-3-acetic acid (auxin) using L-tryptophan (L-TRP)-dependent pathways. In the present study, Gene expression profiles were obtained using microarray analysis of RNAs from F. graminearum cultures in auxin producing conditions, treated with L-TRP, tryptamine (TAM) and indole-3 acetaldehyde (IAAld).  A comparative expression profiling of all treatments identified candidate genes for auxin production in F. graminearum.  Additional analysis of the expression profiling between L-TRP-treated and control cultures showed that L-TRP treatment induce the up-regulation of a series of genes with predicted function in the metabolism of L-TRP via anthranilic acid and catechol towards the tricarboxylic acid cycle.

overall_design: F. graminearum stain DAOM180378 mycelia samples in 2nd stage media were treated with either 2 mM L-TRP,  0.2 mM TAM, 0.2 mM IAAld or were untreated (NT). Dual-channel, three biological replicated for each treatment with two technical replicates (dye-swaps) for each sample.

first: Caro-Lyne

last: DesRoches

first: Anne

last: Johnston

first: Kun

last: Luo

first: Hui-Yan

last: Zhao

first: Thérèse

last: Ouellet


title: Mining the stiffness-sensitive transcriptome in human vascular smooth muscle cells identifies long non-coding RNA stiffness regulators

city: Philadelphia

first: Daniel

last: Rader

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Vascular extracellular matrix (ECM) stiffening is a risk factor for aortic and coronary artery disease. How matrix stiffening regulates the transcriptome profile of human aortic (Ao) and coronary (Co) vascular smooth muscle cells (VSMCs) is not well understood. Furthermore, the role of long non-coding RNAs (lncRNAs) in the cellular response to stiffening has never been explored. This study characterizes the stiffness-sensitive transcriptome of human Ao and Co VSMCs and identify potentially key lncRNA regulators of stiffness-dependent VSMC functions. Ao and Co VSMCs were cultured on hydrogel substrates mimicking physiologic and pathologic ECM stiffness. Total RNA-seq was performed to compare the stiffness-sensitive transcriptome profiles of Ao and Co VSMCs.

overall_design: 4 unique sample types with 4 replicates (16 total samples). Donor-matched Aortic and Coronary VSMCs were serum starved for 48 hours, then cultured in serum containing media for 24 hours on both soft and stiff fibronectin coated hydrogel matrices.

first: Christopher

last: Yu

first: Richard

last: Assoian


title: Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models [primary cell lines AMC/Palermo]

first: Sander

last: van Hooff

overall_design: Gene expression analysis of 15 CRC primary cell lines grown as spheroids

first: J

last: Linnekamp

first: S

first: P

last: Prasetyanti

first: R

last: Kandimalla

last: de Jong

first: K

last: Cameron

last: van Leersum

first: H

last: Rodermond

first: G

last: van Bochove

last: Buikhuisen

first: E

last: Fessler

first: L

last: Vermeulen

first: X

last: Wang

last: Stassi

last: Mangiapane

first: F

last: Nürnberg

last: Clevers


title: Liver DGE analysis of hemophilia mice (hFIX9-R29X) treated with ASOs inhibiting NMD

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: To evaluate the impact of ASO-mediated depletion of NMD factor Upf1 and Upf3b on the normal transcriptome, we performed digital gene expression analysison hFIX-R29X mouse liver treated with Upf3b-GalNAc-ASO.

overall_design: hFIX-R29X mice 8-14 weeks of age (n=5-6, 2-3 female and 2-3 male mice per group) were treated every 5 days with 6 doses of DPBS, Control-GalNAc-ASO (15 or 20mg/kg), Upf1-GalNAc-ASO (20 mg/kg) and Upf3b-GalNAc-ASO (10 or 20 mg/kg). Animals were sacrificed 48 h after the last dose.

first: Lulu

last: Huang


title: Genome-wide profiling of RNAs reveals novel insights into the immune response between infectious bronchitis virus and avian dendritic cells

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

summary:
Background: Avian infectious bronchitis virus (IBV) was an major respiratory disease-causing agents that lead to significant losses in birds.  Dendritic cells (DCs), an major antigen-presenting cells, influence viruses pathogenicity as well as host immune response. Expression of host non-coding mRNA changes markedly during infectious bronchitis virus (IBV) infection of avian, but their role in regulating host immune function to defend IBV infection has not been explored.  Here, microarray, including mRNAs, miRNAs and lncRNAs, were analysed to better understand the interaction between IBV and avian DCs.

Results: Firstly, we found that IBV infection can effectively induce avian DCs to become mature. Interestingly, inactivated IBV possess high ability in inducing DC maturation and activating lymphocytes than that in actived IBV stimulated group. Then, result identified that IBV infection induced 1093 upregulated and 845 downregulated mRNAs in avian DCs. Analysis of Gene Ontology suggested that celluar macromolecule and protein location (GO-BP), as well as transcription factor binding (GO-MF) were abundance in IBV infected group. Whilst, pathway analyses suggested that oxidative phosphorylation and T cell receptor signalling pathways might activated in IBV group. Moreover, microRNA (miRNA) and long non-coding RNA (lncRNA) alterations in IBV-stimulated avian DCs were observed. A total of 19 significantly altered (7 up and 12 down) miRNAs and 101 (75 up and 26 down) lncRNAs were identified in IBV-stimulated DCs. Furtherly insight analyses not only gain that regulation of actin cytoskeleton and MAPK signal pathway were contributed to IBV stimulated miRNAs target genes, but also build an regulatory networks based on co-expressed lncRNA and mRNA. Finally, our study identified 2 TF-miRNA (CEBPA-miR1772 and CEBPA-miR21), which we based on to constructed 53 transcription factor (TF)–miRNA–mRNA interactions involving 1 TF, 2 miRNAs, and 53 mRNAs in IBV-stimulated avian DCs.

overall_design: In the study presented here, cultured avian BMDCs were randomly divided into control group and IBV stimulated group. Each group consisted of three wells of BMDCs from three chickens.

first: Zhisheng

first: Jingfeng

last: Liang

first: Qian

last: Yang


title: A Bifidobacteria-derived Tight adherence (Tad) pilus-associated protein signals colonic epithelial growth

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

country: Ireland

institute: UCC

summary: Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization, persistence and dialogue with the host remains poorly understood. We previously identified tight adherence (Tad) pili from Bifidobacterium breve UCC2003 as an essential colonisation factor using murine models.We have identified the protein that mediates the proliferation response, and demonstrate that bifidobacteria contribute to the maturation of the naïve gut in early life through the production of specific extracellular protein structures under in vivo conditions. This bifidobacteria-derived signalling protein may represent one of the mechanisms by which members of the early colonising microbiota stimulate growth of the neonatal mucosa

overall_design: Germ free Swiss Webster mice were monocolonised with Bifidobacterium with or without mutant of the bacterial gene,  TadA. The treatment groups and relevant controls were; 1.  Germ Free(GF) Bif UCC 2003  n=4 , 2.  GF and Bif TadA (mutant) n=4, 3. GF 1 n=4, 4.   GF re-conventionalised (CONV) n= 5.  The colons were removed and the RNA extracted (RNAeasy plus universal  kit (Qiagen), quantified and Microarrays were carried out using mouse Exon ST1.0 arrays (Affymetrix) by Almac Group, Craigavon, Northern Ireland. Analysis and pathway mapping was carried out by ALMAC and using Subio Platform software (Subio Inc) and Genesis Software.

first: Mary

middle: O

last: Motherway

last: MacSharry


title: Atac-seq of 2.5 hpf zebrafish embryos

city: Dunedin

first: Michael

last: Meier

address: 1st Floor Hercus Building, Dunedin School of Medicine, Great King Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: Here we analyze the genome-wide accessability during zebrafish embryogenesis before zygotice genome activation 2.5 hours post fertilization

overall_design: Atac-seq to generate genome wide accessibility data pre ZGA zebrafish development at 2.5 hpf, including two biological replicates

first: Amy

last: Dowdle

first: Julia

middle: A

last: Horsfield


title: Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models

first: Sander

last: van Hooff

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

overall_design: Refer to individual Series


title: Transcriptome analysis of rice roots in response to plant growth promoting rhizobacterium Pseudomonas putida RF3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To gain an insight into molecular mechanisms underlying plant-microbe interactions gene expression changes in rice plants in response to a plant growth promoting rhizobacteria such as the Pseudomonas putida, root transcriptome analysis through microarray technology was performed from rice roots in response to P. putida RF3. Species of Pseudomonas are well known as biocontrol agents hence defense response and genes related to root exudation of phytochemicals were analysed in detail. For treatment of rice plants with P. putida, aseptically germinated rice seedlings from half strength MS medium were transferred to flasks containing Hoaglands’ nutrient solution, treated with P. putida and incubated for 48 hours in growth chamber in an orbital shaker. Gene expression changes in rice roots were then analyzed by microarray experiment. Untreated roots served as control. Data analysis revealed defense responsive genes to be upregulated with greater fold changes. In addition to defense response genes, few genes involved in secondary metabolism were also upregulated significantly. Validation of microarray data was performed using real time PCR for defense responsive genes (OsPBZ, OsPR101a, OsCHIA, etc). Detailed analysis of the differentially expressed genes reveal the role of P. putida RF3 in inducing systemic resistance in plants thereby immunizing the rice plants against future attacks by pests/pathogens. Our study enhances the current understanding on gene expression changes occurring during plant-microbe associations and thus demonstrates the potential of P. putida RF3 as a biocontrol agent.

overall_design: control root vs root tissue treated with PGPR

first: B

last: Usha

first: K

last: Rekha


title: Expression data from bovine conceptus during peri-implantation period

city: Tokyo

first: Rulan

last: Bai

address: 1-1-1 Yayoi, Bunkyouku

institute: The University of Tokyo

summary:
Conceptus implantation to the uterine endometrium is required for pregnancy establishment, during which non-invasive trophoblasts attach and adhere to the uterine endometrium or invasive trophoblasts invade into the uterine stroma, followed by placental formation in most mammalian species.
During peri-implantation period, conceptuses must communicate with the uterine endometrium if they are to survive and proceed to attachment to the uterine epithelium. Despite numerous studies performed on the bovine species, molecular mechanisms associated with their attachment processes, particularly the initial attachment to the endometrial epithelium, have not been well characterized.

overall_design: In the bovine species, attachment of conceptus to the uterine endometrium is initiated on day 19.0~19.5 (day 0 = estrus cycle).To study gene expression associated with implanation event in bovine conceptuses, microarray analysis was initially conducted in RNAs isolated from days 20 (start to attchment) and 22 trophoblast (tight attachment) tissues.

first: Kazuya

last: Kusama

first: Kazuhiko

last: Imakawa


title: Genome wide expression analysis of FVB/N Cd151-/- glomeruli

status: Public on Nov 30 2017

city: Ourimbah

first: Judith

last: Weidenhofer

state: NSW

address: 10 Chittaway Rd

department: School of Biomedical Sciences & Pharmacy

institute: University of Newcastle

summary: Analysis of glomerular gene expression levels was performed in 3- to 4-week-old FVB/N Cd151-/-  mice and wild type controls. Identification of the  glomerular gene expression profile at this early stage of disease progression in FVB/N Cd151-/- mice provides insight into the molecular mechanisms associated with glomerular disease development, including thickening and splitting of the glomerular basement membrane

overall_design: Total RNA was obtained from glomeruli isolated from 3-week-old Cd151-/- mice ( 4 mice) and compared to Cd151+/+ controls (4 mice) generated on the FVB/N genetic backgrounds

first: Crystal

last: Naudin

first: Rodney

last: Scott

first: Leonie

last: Ashman

first: Severine

last: Roselli


title: Reduced Representation Bisulfite Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs

city: New York

first: Nipun

last: Verma

address: 430 East 67th St

department: Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit preferential hypermethylation at bivalent promoters without corresponding gene expression changes in undifferentiated hESCs. In the absence of the TET proteins, abnormal accumulation of DNMT3B at bivalent promoters results in hypermethylation and impaired gene activation upon differentiation. Broadly, the competitive balance between the TET proteins and de novo methyltransferases at bivalent promoters could facilitate rapid changes of their methylation state to either activate or silence transcription in a cell-lineage and gene dependent manner.

overall_design: For reduced representation bisulfite sequencing genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. Two replicates were done for each sample.

first: Pan

last: Heng

first: Verma

last: Nipun


title: Selective expression of the transcription elongation factor Eleven Nineteen Lysine-rich Leukemia 3 (ELL3) in actiavted B lymphocytes drives rapid B cell proliferation

city: Tampa

first: Kenneth

last: Wright

state: Florida

address: 12902 Magnolia Dr

department: Immunology

institute: H Lee Moffitt Cancer Center

summary: To identify novel targets of the transcriptional repressor that functions to extinguish the B cell phenotype during terminal plasma cell differentiation, we assessed PRDM1 bound sequences through ChIP-Seq. We prepared PRDM1-enriched chromatin from two PRDM1 positive mutiple myeloma cell lines, U266 and NCI-H929. At least 5 PRDM1- or IgG enrichments were performed per cell line and pooled into the two respective conditions per cell line. The U226 and NCI-H929 revealed respectively, 574 and 2887 association peaks were indentified per cell line. Both cell lines displayed an intense peak at the ELL3 loci, suggesting PRDM1 association. This was validated by ChIP followed by qPCR, confirming PRDM1 association.

overall_design: Examination of PRDM1 binding sites in two Multiple Myeloma cell lines

first: Lou-Ella

last: Alexander

middle: L


title: TET1/2/3


title: Expression data from WT and AIMp1KO mouse bone marrow-derived dendritic cells

city: Houston

first: Dan

last: Liang

address: One baylor plaza, Room N920

department: Pathology and Immunology

institute: Baylor college of medicine

summary:
Dendritic cells are critical regulators of adaptive immune responses which can process and present antigens to effector cells. As a structural component of multi-enzyme aminoacyl tRNA synthetase complex, AIMp1 (p43) is identified to promote type 1 T-cell responses by DCs and play important roles in both antitumor and antiviral immunity.
We use high-throughput microarray analysis to compare the gene expression profiles of WT vs. AIMp1KO bone marrow-derived DCs (BMDC) to study the mechanism by which DC-expressed AIMp1 promote type 1 T-cell immune responses.

overall_design: WT or AIMp1KO BMDCs were loaded with antigens and matured for RNA extraction and hybridization on Affymetrix microarrays. Cells were unloaded or loaded with OVA protein and SIINFEKL peptide (10ug/mL) for 3 hours in media containing 5% serum; then matured with cytokine cocktail (10ng/mL TNFa, 15ng/mL IL-6, 10ng/mL IL-1b, 1ug/mL PGE2) for 48hours prior to harvest.

first: William

middle: K

last: Decker


title: Cohesin facilitates zygotic genome activation in Zebrafish

first: Michael

last: Meier


title: Organotypic three-dimensional cancer cell cultures mirror drug responses in vivo: Lessons learned from the inhibition of EGFR signaling

city: Vienna

first: Thomas

last: Mohr

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

summary: Complex three-dimensional (3D) in vitro model systems that recapitulate human tumor biology are essential to better understand the pathophysiology of the disease and to aid in the discovery of novel anti-cancer therapies. 3D organotypic cultures exhibit intercellula communication, nutrient and oxygen gradients, and cell polarity that is lacking in traditional two-dimensional (2D) monolayer cultures. In the present study, we could demonstrate that 2D and 3D cancer models exhibit different drug sensitivities towards both targeted inhibitors of EGFR signaling and broad acting cytotoxic agents. Changes in the kinase activities of Erb family members and differential expression of apoptosis- and survival-associated genes before and after drug treatment may account for the differential drug sensitivities. Importantly, EGFR oncoprotein addiction was evident only in the 3D cultures mirroring the effect of EGFR inhibition in the clinic. Furthermore, targeted drug efficacy was strongly increased when incorporating cancer-associated fibroblasts into the 3D cultures. Taken together, we could provide conclusive evidence that complex 3D cultures are more predictive of the clinical outcome than their 2D counterparts. In the future, 3D cultures will be instrumental for understanding the mode of action of drugs, identifying genotype-drug response relationships and developing patient-specific and personalized cancer treatments.

overall_design:
6 samples, 3 replicates each.
Cell line: HCC827.  Matrigel coating: yes, no.  Dimensionality: 2D, 3D.

first: Andreas

last: Eger


title: Novel genes and regulators for cell surface of Sinorhizobium meliloti.

city: Stanford

first: Melanie

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: We characterized the transcriptome of a Sinorhizobium meliloti emmA insertion mutant strain.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Gene expression profiling of an Sinorhizobium meliloti Rm1021 emmA mutant was performed using custom Affymetrix GeneChips. Strain MB805, carrying a Tn5-110 insertion in emmA (locus tag = SMb21521) was compared to strain R4A2A, carrying a Tn5-110 insertion in a putative neutral location (locus tag = SMb21477).

first: Sharon

last: Long


title: Caffeine-regulated transcripts in mouse hearts are p27-dependent

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

summary: Overall question: How does caffeine administration for 10 days with the drinking water change the transcriptome of the heart? Are these changes dependent on the protein p27? Results: 242 of the 245 transcripts  differentially regulated after caffeine administration in wildtype animals are p27 dependent, since they are not changed in p27-deficient littermates. Among the most highly enriched gene ontology (GO) categories for biological processes are GO-terms describing pathways, which take place in the mitochondria.

overall_design: Hearts from 4 groups of mice (wt, p27 -/-, wt with caffeine in drinking water for 10 days, p27 -/- with caffeine in drinking water for 10 days), 3 animals per group (one p27-/- untreated control sample had to be disclosed from statistical analysis after failing hybridization QC)

first: Judith

last: Haendeler

first: Joachim

last: Altschmied

last: Köhrer

first: René

last: Deenen

first: Christine

last: Goy

first: Sascha

last: Jakob


title: Expression data from FACS sorted astrocytes FMR1 KO mice vs control

city: Cleveland

first: Ranjan

last: Dutta

state: OH

address: 9500 Euclid Avenue, NC-30

department: Neuroscience

institute: Lerner Research Institute

summary:
Fmr1 mutation results in autistic behaviors and the FMR1 KO mice model is one of the popular methods to study autism spectrum disorders.
In this dataset, we include the expression data obtained from astrocytes isolated from cortex of control and FMR1-KO mice.

overall_design: 10 Total samples were analyzed. We generated the following pairwise comparisons of control vs FMR1 KO using Genespring software V13.1.1

first: G

last: Kidd

first: B

middle: D

last: Trapp


title: Estrogen regulated microRNAs in mouse ovarian cancer cells.

first: Barbara

last: Vanderhyden

address: 501 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

summary:
In a mouse model of ovarian cancer, we have established that prolonged exposure to 17β-estradiol (E2) accelerates tumour onset and increases the incidence of morphologically dysplastic ovarian surface epithelium (OSE). OSE cell proliferation and morphology are tightly regulated by the asymmetrical distribution of polarity proteins that provide positional cues for surface localization and growth inhibition. We hypothesized that E2 causes OSE dysplasia by inhibiting a tumour suppressor gene called Disabled-2 (Dab2). Dab2 is critical in mediating the polarized distribution of cell surface proteins and is highly expressed in normal OSE, but is absent in the majority of ovarian cancers. In this study, Dab2 is shown to be suppressed by E2 and we investigated the possibility that this occurs through E2 up-regulation of microRNAs.
microRNA microarray analysis comparing control vs. E2 treated mouse ovarian cancer cells (MASE) was used to identify candidate miRNAs that have a seeding sequence capable of targeting the 3-prime untranslated region (3’UTR) of both human and mouse Dab2 transcript.

overall_design: MASE ovarian cancer cells were isolated from ascites fluid of estrogen treated tgCAG-TAg mice. Once cells were established in culture, they were treated with 100nM E2 for 24H. An equivalent volume of 100% EtOH (vehicle) was added to control plates for a final concentration of 0.0002% EtOH.

first: Nhung

last: Vuong

middle: C


title: Stranded RNASeq of human mammary primary tumors ER+ and paired adjacent healthy tissues

city: Liege

first: Stephane

last: Wenric

address: Avenue de l'Hopital 1

department: Unit of Human Genetics

country: Belgium

institute: University of Liege

summary: Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which are complementary and overlapping to those of protein-coding transcripts (PCT). NATs were punctually described as regulating gene expression, and are expected to act more frequently in cis than other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired healthy tissues were analyzed by strand-specific RNA sequencing to highlight the potential role of NATs in gene regulations occurring in breast cancer.

overall_design: 22 primary invasive breast cancer carcinoma expressing estrogen receptors and their paired adjacent mammary healthy tissues were analyzed by strand-specific RNA sequencing on a Illumina HiSeq.

first: Sonia

last: El Guendi

first: Guy

last: Jerusalem

first: Claire

last: Josse

first: Vincent

last: Bours


title: A screening system to identify transcription factors that induce binding site-directed DNA demethylation

status: Public on Nov 29 2017

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

type: Methylation profiling by genome tiling array

summary: Background: DNA methylation is a fundamental epigenetic modification which is involved in many biological systems such as differentiation and disease. We and other groups recently discovered that a part of transcription factors (TFs) plays a role for site-specificity determination of DNA demethylation in a binding site-directed manner, although number of reports for such TFs are limited.   Results: Here, we develop a screening system to identify TFs which induce the binding site-directed DNA methylation changes. The system consists of ectopic expression of target TFs in model cells and the DNA methylome analysis followed by overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. Our system successfully identifies binding site-directed demethylation of SPI1 which is known to promote DNA demethylation in a binding-site directed manner. We extend our screening system to 15 master TFs which are involved in cellular differentiations, and identified 8 (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA and TBX5) novel binding site-directed DNA demethylation inducing TFs. Gene ontology and specifically expressing tissue enrichment analysis revealed that those 8 TFs demethylate genome regions which are associated with corresponding biological roles, supporting performance of our system. We also describe characteristics of the binding site-directed DNA demethylation induced by those TFs; targeting highly methylated CpGs, local DNA demethylation, and overlap of demethylated regions between same family TFs.  Conclusion: Thus, our results emphasize usefulness of the developed screening system for identification of TFs which induce DNA demethylation in a site-directed manner.

overall_design: Bisulphite converted DNA from the 17 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Shiori

last: Maeda

first: Erina

last: Furuhata

first: Yuri

last: Shimizu

first: Hajime

last: Nishimura

first: Harukazu


title: Gene expression data of proliferative cells isolated from the adult human peripheral retina, cultured and differentiated

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

summary:
Proliferative cells isolated from the adult human peripheral retina only transiently upregulate key retinal markers upon induced differentiation.
We used microarray to identify gene expression before and after differentiation to evaluate the in vitro retinal differentiation potential of the cells isolated from the adult human peripheral retina using the current cell culture and differentiation protocol.

overall_design: We isolated proliferating cells from the adult human peripheral retina, cultured and differentiated the cells to examine the cells in vitro differentiation potential towards a retinal phenotype.

first: Erik

last: Johnsen

first: Rebecca

last: Frøen

first: Ole

last: Olstad

first: Bjørn

last: Nicolaissen

first: Goran

last: Petrovski

first: Morten

last: Moe


title: Cartilage microRNA dysregulation during the onset and progression of mouse osteoarthritis is independent of aggrecanolysis and overlaps with candidates from end-stage human disease [mRNA]

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

country: Australia

institute: Murdoch Childrens Research Institute

summary: The purpose of this study is to characterize the expression profile of microRNAs and their target mRNAs in cartilage and subchondral bone (SCB) in a mouse model of post-traumatic osteoarthritis (OA).

overall_design: OA was induced in adult male C57BL6 mice by destabilization of the medial meniscus (DMM). RNA from medial tibial cartilage and SCB of DMM and sham-operated mice was isolated by laser micro-dissection at 1 and 6 weeks post-surgery (n=3-4/time point/group). Expression profiling was performed using Agilent microarrays. Joint pathology was scored histologically.

first: Louise

last: Kung

first: Varshini

last: Ravi

first: Lynn

last: Rowley

first: Constanza

last: Angelucci

first: Amanda

last: Fosang

first: Katrina

middle: M

last: Bell

first: Christopher

middle: B

last: Little


title: Different genetic responses to oenological conditions between a flocculent wine yeast and its FLO5 deleted strain: insights from the transcriptome

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

summary: In oenological conditions, yeasts are exposed to several stresses and Saccharomyces cerevisiae strains respond modifying their transcriptional program. Yeast flocculation is a social trait that permits to the cells to escape to hostile conditions by sedimentation. This behaviour is mainly due to the presence in the genome of FLO greenbeards genes. In order to understand the role of flocculation in stress response a flocculent S. cerevisiae wine strain and his FLO5 deleted strain were submitted to standard and second fermentation. At the middle of these two processes a genome wide expression analysis was performed. Results showed that while the FLO5 deleted strain was engaged to a re-organization of cell wall and to find a different way to adhere, flocculent yeast presented a proteic stress response and an up-regulation of genes involved in superior alcohols production. Obtained data confirmed the importance of FLO5 in flocculation phenotype and highlight the role of flocculation in stress response.

overall_design: Two independent experiments were performed with yeasts at 45 g CO2/L  release.  For each experiment, two different strains F6789 and F6789Deltaflo5 growing on sparking wine medium (SW) or synthetic medium (SM) were compared.

first: Paola

last: Di Gianvito

first: Catherine

last: Tesnière

first: Giovanna

last: Suzzi

first: Carole

last: Camarasa

first: Rosanna

last: Tofalo


title: The HPV16-E6 oncoprotein induces the expression of Keratin-6b and 2 delays wound healing by means of its PDZ-ligand domain in vivo

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary:
The K14E6 transgenic mice develop skin hyperplasia, benign tumors, and cancer in the dorsal skin spontaneously. The E6 oncoprotein own its tumorigenic potential to a region located near the C-Terminal domain, better known as the PDZ ligand-domain. The aim of this work was to describe early cellular processes affected by the E6’s PDZ ligand-domain when is expressed in the skin of transgenic mice using microarray technology.
Results. A total of 222 genes were differentially expressed (FC:1.5, Adj.p.value <0.05, and b value > 0.5) in the skin of K14E6 mice as compared to K14E6Δ146-151 mice. Out of those, 70 genes were up-regulated and 151 genes were down-regulated. Enzyme linked receptor protein signaling was the most affected process in our data, followed by cell adhesion, development, and lipid biosynthesis. We also found that the K14E6 strains induces the mRNA of the wound-inducible gene K6b, and delocalizes E-cadherin protein in the entire epidermis. Finally, CD34 and K15 epidermal stem cell marker proteins diminish its expression in the skin, in a PDZ-dependent manner.  Conclusions. The PDZ ligand-domain of HPV16-E6 oncoprotein affects the expression of several genes involved in cellular processes that could be relevant in the HPV-induced carcinogenesis. Since HPV16-E6 oncoproteins lacking the PDZ ligand-domain loose its oncogenic potential, the knowledge of genes transcriptionally affected by the E6’s PDZ ligand-domain will provide valuable information about HPV-induced skin carcinogenesis.

overall_design: We analyzed the expression of 14000 genes with a Mouse Genome 430A 2.0 Affymetrix microarray in dorsal skin biopsies from 1.5 months-old mice for the K14E6, and K14E6delta146-151 (which lacks the PDZ ligand-domain) mice strains. We used two biological replicates for each mouse strain, each replicate consisted on a pool of three different animals.

first: Enoc

last: Bonilla-Delgado


title: Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers

city: Boulder

first: Xuedong

last: Liu

state: CO

address: 3415 Colorado Avenue C318

department: Chemistry and Biochemistry

institute: University of Colorado Boulder

summary: This study aims to address the fundamental mechanism(s) underlying histone deacetylase inhibition in regulating gene expression and cytostatic responses in transformed and normal cells.

overall_design: Examination of epigenetic and transcriptome changes under dose-dependent HDAC inhibition.

first: Gilson

middle: J

last: Sanchez

first: Phillip

last: Richmond

first: Eric

middle: N

last: Bunker

first: Samuel

middle: S

last: Karman

first: Joseph

last: Azofeifa

first: Aaron

middle: T

last: Garnett

first: Quanbin

last: Xu

first: Graycen

middle: E

last: Wheeler

first: Cathryn

last: Toomey

first: Qinghong

last: Zhang

first: Robin

last: Dowell


title: Characterization of  transcripts bound by LARP1 in the free 40S fraction isolated by sucrose gradients

city: L'Hospitalet de Llobregat

first: Francisco

middle: D.

last: Morón-Duran

address: Av. Gran Via de l'Hospitalet, 199

institute: IDIBELL

summary: RNA binding protein LARP1 binds preferentially to mRNAs containing a 5' Tract of Oligo Pyrimidines (5'-TOP) motif

overall_design: RIP-seq performed with anti-LARP1 antibody or Normal Rabbit Serum control IgG from the free 40S fraction isolated from HCT116 cells, background measured with IgG RIP-seq and compared to Input RNA

first: Antonio

last: Gentilella

first: George

last: Thomas


title: Profiling of miRNAs expression in Rag2 KO and wild type mice spleen by miRNA expression microarray analysis

status: Public on Nov 28 2017

city: Seoul

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

country: South Korea

institute: Konkuk University

summary:
Purpose: miRNAs are important fators that are involved in the regulation of at least one third of the total human genes and are involved in the regulation of different biological processes. The purpose of the study was to investigate the differential expression pattern of miRNAs in Rag2 KO mice spleen compared to its wild type counterpart.
Methods: In this study, we have excised the spleen tissues from three Rag2 KO mice and three wild type mice, and then RNA samples were prepared with the spleen tissues for the analysis of miRNAs profiles using the Affymetrix Genechip miRNA 4.0 arrays. The Affymetrix Genechip miRNA 4.0 array offers an updated content without compromising the high performance as the previous-generation arrays, it also provides a comprehensive coverage that is designed to interrogate all mature miRNA sequences in miRBase Release 20, as well as an easily correlate miRNA results having analysis files contain host gene ID, predicted and validated miRNA target genes, and clustered miRNA information.
Result: The miRNAs expression microarray analysis showed that many miRNAs have been expressed differentially between Rag2 KO and wild type  mice spleen. These miRNAs might be involved in the different biological and physiological processes including immune regulations.
Conclusion: miRNAs might be an active player during theprocess of immune regulation.

overall_design: Spleen miRNAs derived from Rag2 KO and wild type mice were profiled by microarray, in triplicates for each sample, by Affymetrix Genechip miRNA 4.0 array platforms.

first: A

first: Y

last: Choi

first: J

middle: H

last: Kim


title: The tumor suppressor Brat controls neuronal lineages by inhibiting the transcription factors Deadpan and Zelda

first: Ilka

last: Reichardt-Gomez

address: Dr. Bohr Gasse 3

institute: Gregor-Mendel-Institute

summary: The TRIM-NHL protein Brain tumor (Brat) acts as a tumor suppressor in the Drosophila brain, but how it suppresses tumor formation is not completely understood. Here, we combine temperature controlled brat RNAi with transcriptome analysis to identify the immediate brat targets in Drosophila neuroblasts. Besides the known target Deadpan (Dpn), our experiments identify the transcription factor Zelda (Zld) as a critical target of brat. Our data show that Zld is expressed in neuroblasts and required to allow re-expression of Dpn in transit amplifying intermediate neural progenitors. Upon neuroblast division, Brat is enriched in one daughter cell where its NHL domain directly binds to specific motifs in the 3’UTR of dpn and zld mRNA to mediate their degradation. In brat mutants, both Dpn and Zld continue to be expressed, but inhibition of either transcription factor prevents tumorigenesis. Our genetic and biochemical data indicate that Dpn inhibition requires higher Brat levels than Zld inhibition and suggest a model where stepwise post-transcriptional inhibition of distinct factors ensures sequential generation of fates in a stem cell lineage.

overall_design: Comparison of transcriptomes of Drosophila melanogaster control and brat RNAi larval brain type II neural stem cell lineages.

last: Reichardt

first: Thomas

middle: R

last: Burkard

first: Juergen

last: Knoblich