title: PU.1 is required for the developmental progression of multipotent progenitors to common lymphoid progenitors.

status: Public on Aug 14 2017

city: Parkville

first: Carolyn

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: The transcription factor PU.1 is a central regulator of hematopoiesis, required for the normal differentiation of the myeloid and lymphoid lineages. Due to its essential role in early development and the importance of PU.1 in regulating several defining markers of lymphoid progenitors, its precise function in early lymphopoiesis has remained unclear. Using conditional mutagenesis and alternative lineage identification strategies, we demonstrate the developmental stage restricted function for PU.1 in early lymphopoiesis. PU.1 was required for efficient generation of “lymphoid primed multipotent progenitors (LMPPs)” from hematopoietic stem cells and was essential for the subsequent formation of “common lymphoid progenitors (CLPs)”. In contrast, further differentiation into the B cell lineage was independent of PU.1. The function of PU.1 was dosage sensitive as loss of one allele decreased all stages of early lymphopoiesis. PU.1 expression mirrored its functional role during lineage differentiation. PU.1 peaked at LMPPs and was maintained in CLPs, before being down regulated in committed pro-B cells. Examination of the transcriptional changes in PU.1 conditionally deficient LSK cells revealed that PU.1 activates lymphoid and dendritic cell associated genes in LMPPs, while repressing genes normally expressed in neutrophils. These data identify PU.1 as a critical regulator of lymphoid priming and the transition between LMPPs and CLPs.

overall_design: Total RNA was obtained from wild type LSKs and LSKs with Pu1 conditionally deleted

first: Swee

middle: H

last: Pang

first: Douglas

last: Hilton

first: Nicholas

last: Huntington

first: Sebastian

last: Carotta

first: Li

last: Wu

first: Stephen

last: Nutt


title: Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [expression microarray]

status: Public on Aug 23 2017

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

country: USA

institute: Cleveland Clinic

summary: Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) mutations drive the development of gliomas and other human malignancies.  Significant efforts are already underway to attempt to target mutant IDH in clinical trials.  However, how mutation of IDH leads to tumorigenesis is poorly understood. Mutant IDH1 promotes epigenetic changes that promote tumorigenesis but the scale of these changes throughout the epigenome and the reversibility of these changes are unknown.  Here, using both human astrocyte and glioma tumorsphere systems, we generate a large-scale atlas of mutant IDH1-induced epigenomic reprogramming.  We characterize the changes in the histone code landscape, DNA methylome, chromatin state, and transcriptional reprogramming that occur following IDH1 mutation and characterize the kinetics and reversibility of these alterations over time.  We discover coordinate changes in the localization and intensity of multiple histone marks and chromatin states throughout the genome.  These alterations result in systematic chromatin states changes, which result in widespread gene expression changes involving oncogenic pathways.  Specifically,  mutant IDH1 drives alterations in differentiation state and establishes a CD24+ population that features enhanced self-renewal and other stem-like properties.  Strikingly, prolonged exposure to mutant IDH1 results in irreversible genomic and epigenetic alterations.  Together, these observations provide unprecedented molecular portraits of mutant IDH1-dependent epigenomic reprogramming at high resolution.  These findings have significant implications for our understanding the mechanisms underlying mutant IDH function and for optimizing therapeutic approaches to targeting IDH mutant tumors.

overall_design: We profiled the kinetics of gene expression reversibility following loss of IDH1 R132H using a doxycycline inducible immortalized human astrocyte cell line. RNA was extracted at various passages following dox withdrawal and hybrized to Affymetrix arrays.

first: Sevin

last: Turcan

first: Timothy

middle: A

last: Chan


title: Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Histone modification ChIP-sequencing of IDH1 R132H expressing astrocyte and tumorsphere models


title: Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium.

status: Public on Aug 02 2017

city: Amsterdam

first: Anna

last: Bennis

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Amsterdam Medical Centre Amsterdam

summary: Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE.We compared the gene expression profiles of RPE and IE.

overall_design: We collected 5 IE and RPE samples from 5 different donors. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays, using a common reference design.

first: Arthur

last: Bergen


title: Genetic profiling of developing human embryonic stem cell derived Retinal pigmented epithelium

summary: Age-related macular degeneration is a progressive disease resulting in impaired central vision. Degeneration of the retinal pigmented epithelial (RPE) monolayer is associated with the progression of the disease. To date no treatment is able to stop this progression, however new cell replacement studies using human embryonic stem cells (hESC) to generate RPE show a promising prospective. To improve cell replacement strategies a better understanding about the development of RPE cells is necessary. In the current study we therefore do extensive genetic profiling of hESC derived RPE cells at different stages during development based on their pigmentation.

overall_design: Start pigmentation samples (n=6, Cy5) were compared with late pigmentation samples (n=6, Cy5). Data was normalized on pooled common reference (Cy3) expression using R LIMMA


title: Cerebellar granule cell replenishment postinjury by adaptive reprogramming of Nestin+ progenitors

status: Public on Aug 01 2017

city: new york

first: alexandre

last: wojcinski

state: NY

address: 430 E. 67th Street

institute: memorial sloan kettering cancer center

type: Expression profiling by high throughput sequencing

summary: We report the application of RNA-sequencing for high-throughput profiling of gene expression in Nestin expressing cells of P5 mouse cerebellum Non-Irradiated or Irradiated at P1. By using the Nes-CFP reporter mouse line, we isolated Nes-CFP positive cells of P5 cerebellum to compare the transcriptomes between Nes-CFP positive cells from Non-irradiated cerebellum and cerebellum irradiated at P1.

overall_design: The mRNA profiles of Nestin expressing cells in P5 Non-Irradiated mouse cerebellum and P5 Irradiated mouse cerebellum were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2500.

first: Alexandre

last: Wojcinski

first: Alexandra

last: Joyner


title: Jak/Stat3 regulated global gene expression dynamics during late-stage reprogramming process

status: Public on Aug 18 2017

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

summary: We performed RNAseq analysis to dissect the dynamic transcriptome change during mouse iPSC induction, with or without blocking the Jak/Stat3 activity. We described Jak/Stat3 activity-specific global gene expression patterns, biological events, and regulation of key pluripotent genes, epigenetic modulators, and non-coding RNAs during the reprogramming process. We further demonstrated that Jak/Stat3 activity is essential for proper imprint of Dlk1-Dio3 region that is necessary for complete pluripotency establishment. Functional analysis revealed that one Jak/Stat3 downstream targets identified in our study - Esrrb significantly rescues reprogramming despite the inhibition of Jak/Stat3 activity. Our data illustrated novel mechanism in Jak/Stat3 promoted pluripotency establishment, which is valuable for further improvement of naïve-state iPSC generation across different species.

overall_design: Examination of the RNA samples collected from reprogrammed cells at 18 days after retroviral OKSM transduction of OG-MEFs and cultured in reprogramming medium with LIF, with either Jaki or DMSO (control) treatment starting at day 3 (named hereafter Jaki-Stage 1 (S1) or DMSO-S1, respectively), or from iPSC colonies picked at day 21 and expanded one more passage (p2) (named hereafter Jaki-S2 or DMSO-S2, respectively)

first: Ling

last: Wang

first: Zongliang

last: Jiang

first: Delun

last: Huang

first: Jingyue

last: Duan

first: Chang

first: Shannon

last: Sullivan

first: Kaneha

last: Vali

first: Yexuan

last: Yin

first: Ming

last: Zhang

first: Jill

last: Wegrzyn

first: Young

last: Tang


title: Expression data from neuroblastoma of TH-MYCN/KI RetM919T mice

status: Public on Sep 15 2017

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type:
Expression profiling by array
Third-party reanalysis

summary:
The RET gene has been identified previously as a target of activated ALK at the mRNA level in both human neuroblastoma cell lines and primary tumors as well as in murine tumors driven by mutated Alk and MYCN. Moreover, it has been shown that tumor growth of murine TH-MYCN/KI Alkmut tumors was impaired upon Ret inhibition by the vandetanib inhibitor, suggesting RET as a therapeutic target in ALK mutated neuroblastoma. To further demonstrate the crucial role of RET in ALK mutated driven neuroblastoma oncogenesis, transgenic TH-MYCN mice were bred with KI RetM919T tumors. We document an oncogenic cooperation between activated Ret and MYCN overexpression in neuroblastoma formation.
We used microarrays to analyze the global programme of gene expression of MYCN/RetM919T tumors and compare these profiles with profiles of MYCN/Alkmut tumors (GSE46583). Altogether, our data show that MYCN/RetM919T tumors present with expression profiles close to MYCN/Alkmut tumors.

overall_design: We selected 6 murine neuroblastoma tumors from MYCN/RetM919T mice for RNA extraction and hybridization on Affymetrix microarrays

first: Lucille

last: Lopez-Delisle

first: Cécile

last: Pierre-Eugène

first: Caroline

last: Louis-Brennetot

first: Olivier

last: Delattre


title: A long and abundant non-coding RNA (lancRNA) in Lactobacillus salivarius

city: Cork

first: Denise

middle: B

last: Lynch

state: Not Applicable

address: College Road

department: APC Microbiome Institute

country: Ireland

institute: University College Dublin

summary: Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbor at least one megaplasmid which encodes functions contributing to contingency metabolism and environmental adaptation. RNA-seq transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel long and unusually abundant non-coding RNA (lancRNA) encoded by the megaplasmid and which represented more than 75% of total RNA-seq reads after depletion of ribosomal RNA species. The expression level of this 550 nt lancRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time, and was also expressed during intestinal transit in a mouse. This lancRNA sequence is specific to the L. salivarius species, however among 45 L. salivarius genomes analyzed, not all (only 34) harbored the sequence for the lancRNA. This lancRNA was produced in 27 tested L. salivarius strains but at strain-specific expression levels. High-level lancRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lancRNA identified altered expression levels of genes in a number of pathways but a definitive function of this new long non-coding RNA was not identified. This lancRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.

overall_design: L. salivarius UCC118 wild-type vs 2 mutants (ΔlancRNA and ΔlancRNA ΔHTH), in exponential and stationnary growth phases

first: Fabien

middle: J

last: Cousin

first: Victoria

last: Chuat

first: Pat

middle: G

last: Casey

first: Marion

last: Dalmasso

first: Hugh

middle: M

last: Harris

first: Angela

last: McCann

first: Paul

middle: W

last: O'Toole


title: Dynamics of RNA polymerase II pausing and bivalent histone H3 methylation during neuronal differentiation in brain development [RNA-seq]

status: Public on Jul 12 2017

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Cell fate specification is accompanied by global changes in gene expression from patterns of maintaining stem/progenitor cells to patterns for supporting differentiation. To ensure a proper transition, it is conceivable that genes important for differentiation are kept silent in stem/progenitor cells yet can be readily activated. RNA polymerase II (Pol II) pausing and bivalent chromatin marks are two paradigms that are suited for establishing such a poised state of gene expression, however, their contributions to gene regulation in development are not well understood. Here, using neural progenitor cells (NPCs) and their daughter neurons co-purified from the embryonic mouse cerebral cortex, we characterized Pol II pausing and H3K4me3/H3K27me3 marks in this in vivo setting of neurogenesis. We show that genes paused in NPCs or neurons are well correlated with their respective cell type-specific functions, but pausing and pause release did not predict gene activation. Bivalent chromatin marks, on the other hand, poised the marked genes in NPCs for activation in neurons. Interestingly, our data also revealed a positive correlation between H3K27me3 and paused Pol II. This study thus reveals cell-type specific Pol II pausing and gene activation-associated bivalency during mammalian neuronal differentiation.

overall_design: Transcriptome analyses in neural progenitor cells (NPCs) and their daughter neurons, and their relationship with RNA polymerase II pausing and histone bivalent mark

first: Jiancheng

last: Liu

first: Qiang

last: Lu


title: Dynamics of RNA polymerase II pausing and bivalent histone H3 methylation during neuronal differentiation in brain development [ChIP-seq]

overall_design: ChIP-seq analyses of RNA polymerase II and histone H3K4me3 and H3K27me3 in neural progenitor cells (NPCs) and their daughter neurons


title: Dynamics of RNA polymerase II pausing and bivalent histone H3 methylation during neuronal differentiation in brain development

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

overall_design: Refer to individual Series


title: Arrayed gene expression analysis of the SETD1A depleted cancer cells

status: Public on Jul 18 2017

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

summary: Investigation of gene expression level changes in the SETD1A depleted cancer cells (shSETD1A), compared to the GFP depleted cancer cells (shGFP) as control. This analysis was performed to gain an understanding of the transcriptional changes induced by chromation modifications through H3K4 methyltransferase SETD1A. Key Word: SETD1A, Epigenetics

overall_design: This series represents a set of experiments performed using RNA isolated from SETD1A depleted cancer cells in human breast cancer MDA-MB-231 cells and lung cancer A549 cells.

first: Ken

last: Tajima

first: Toshifumi

last: Yae

first: Sarah

last: Javaid

first: Oliver

last: Tam

first: Valentine

last: Comaills

first: Ben

middle: S

last: Wittner

first: Mingzhu

first: Amanda

last: Engstrom

first: Fumiyuki

last: Takahashi

first: Joshua

middle: C

last: Black

first: Sridhar

last: Ramaswamy

first: Toshihiro

last: Shioda

first: Molly

last: Hammell

first: Daniel

last: Haber

first: Johnathan

middle: R

last: Whetstine

first: Shyamala

last: Maheswaran


title: Distal-to-Proximal Re-patterning of Small Airway Epithelium in Smoking-associated Chronic Obstructive Pulmonary Disease

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The proximal-distal patterning program determines unique structural and functional properties of proximal and distal airways in the adult lung. Based on the knowledge that remod-eling of distal airways is the major pathologic feature of chronic obstructive pulmonary disease (COPD), and that small airway epithelium (SAE), which covers distal airways, is the primary site of the initial smoking-induced changes relevant to COPD pathogenesis, we hypothesized that in COPD smokers, the SAE transcriptome loses its region-specific biologic identity and takes on the transcriptional pattern of the proximal airways. By analyzing human airway epithelium col-lected by bronchoscopic brushings from proximal and distal airways of healthy smokers, proxi-mal and distal airway epithelial transcriptome signatures were identified. Dramatic smoking-dependent suppression of distal signature paralleled by acquisition of the proximal airway epithe-lial phenotype was found in the SAE of COPD smokers. Distal-proximal re-patterning observed in the SAE of smokers in vivo was reproduced in vitro by stimulating SAE basal cells (BC), the stem/progenitor cells of the SAE, with EGF, a growth factor up-regulated in airway epithelium by smoking. Together, this study identifies distal-proximal SAE re-patterning as a characteristic feature of small airway disordering in COPD smokers potentially driven by EGF/EGFR-mediated reprogramming of SAE BC stem/progenitor cells.

overall_design: In this study, distal and proximal human airway epithelial transcriptome signatures were identified by genome-wide analysis of the epithelial samples obtained by bronchoscopic brushings from the distal and proximal airways of healthy nonsmokers. Expression of the identified distal and proximal signatures were then analyzed in the small airway epithelium (SAE) of smokers with COPD compared to that of healthy smokers and healthy nonsmokers. A dramatic smoking-dependent suppression of the distal signature expression accompanied by up-regulation of the proximal signature genes was observed in the SAE of COPD smokers, a novel pathologic feature of COPD-associated small airway disordering designated “distal-proximal re-patterning” of the SAE.

first: Renat

last: Shaykhiev

first: Jing

last: Yang

first: Wu-Lin

last: Zuo

first: Tomoya

last: Fuhui

first: Ion

last: Chao

first: Michelle

last: Staudt

first: Robert

last: Kaner

first: Jacqueline

last: Salit

first: Ronald

last: Crystal


title: Plant microRNAs in larval food regulate honeybee caste development

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: The major environmental determinants of honeybee caste development come from larval nutrients: royal jelly stimulates the differentiation of larvae into queens, whereas beebread leads to worker bee fate. However, these determinants are not fully characterized. Here we report that plant RNAs, particularly miRNAs, which are more enriched in beebread than in royal jelly, delay development and decrease body and ovary size in honeybees, thereby preventing larval differentiation into queens and inducing development into worker bees. Mechanistic studies reveal that amTOR, a stimulatory gene in caste differentiation, is the direct target of miR162a. Interestingly, the same effect also exists in non-social Drosophila. When such plant RNAs and miRNAs are fed to Drosophila larvae, they cause extended developmental times and reductions in body weight and length, ovary size and fecundity. This study identifies an uncharacterized function of plant miRNAs that fine-tunes honeybee caste development, offering hints for understanding cross-kingdom interaction and coevolution.

sample_organism:
Camellia japonica
Apis mellifera

platform_organism:
Camellia japonica
Apis mellifera

overall_design: Fresh samples were collected and stored at -80℃. Total RNA of Royal Jelly, Honey, Beebread and Pollen were extracted and solexa sequencing was performed.

first: Kegan

last: Zhu

first: Zheng

last: Fu

first: Xi

last: Chen


title: The efficiency of Xist-mediated silencing of X-linked and autosomal genes is determined by the genomic environment

status: Public on Jul 04 2017

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

summary: Xist is indispensable for X chromosome inactivation (XCI) in female mammalian cells. However, how Xist RNA directs chromosome-wide transcriptional inactivation of the X chromosome is largely unknown. Here, to study chromosome inactivation by Xist, we generated a system where ectopic Xist expression can be induced from several genomic contexts in aneuploid mouse ES cells. We found that ectopic Xist expression from any location on the X chromosome faithfully recapitulated endogenous XCI, showing the potency of Xist to initiate XCI. Genes that escape XCI remain consistently transcriptionally active upon ectopic XCI, regardless of their position relative to Xist transgenes, and the enrichment of CTCF at their promoters is implicated in directing XCI escape. Xist expression from autosomes facilitates their transcriptional silencing to different degrees, and gene density in proximity of the Xist transcription locus plays a central role in determining the efficiency of gene inactivation. We also show that the enrichment of LINE elements together with a specific chromatin environment facilitates Xist-mediated silencing of both X-linked and autosomal genes. These findings provide new insights into the epigenetic mechanisms that mediate XCI and identify genomic features that promote Xist-mediated chromosome-wide gene inactivation

overall_design: 60 RNA-seq from mouse embryonic stem cells and fully differentiated neurons in which ectopic Xist epression is either triggered (plus samples) or not (minus samples) upon doxycycline treatment.

first: Agnese

last: Loda

first: Ivaylo

last: Vassilev

first: Johan

last: Brandsma

first: Wilfred

last: van IJcken

first: Edith

last: Heard

first: Joost

last: Gribnau


title: Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [patients RNA-Seq]

status: Public on Jul 01 2017

city: Philadelphia

first: Yu

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary: The goal of this study is to investigate if endogenous RNA in exosomes activates RIG-I through unshielding.

overall_design: transcription profiling of exosomal RNA isolated from breast cancer patients before, during and after radiation therapy.

first: Barzin

middle: Y

last: Nabet

first: Jacob

middle: E

last: Shabason

first: Tony

last: Wu

first: Taewon

last: Yoon

first: Christina

middle: T

last: Victor

first: Brian

last: Kim

first: Joseph

last: Marcotrigiano

first: Andy

last: Minn


title: Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes


title: Disrupted prenatal RNA processing and myogenesis in congenital myotonic dystrophy

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

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

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

summary: Myotonic dystrophy type 1 (DM1) is a CTG microsatellite expansion (CTGexp) disorder caused by expression of CUGexp RNAs. These mutant RNAs alter the activities of RNA processing factors, including MBNL proteins, leading to reversion to specific fetal isoforms in adult tissues and DM1 pathology. While this pathogenesis model accounts for adult-onset disease, the molecular basis of congenital DM (CDM) is unknown. Here, we test the hypothesis that disruption of developmentally regulated RNA alternative processing pathways contributes to CDM disease. Analysis of alternative splicing (AS) transitions during human myogenesis reveals hundreds of AS events that undergo prenatal isoform transitions and both AS and alternative polyadenylation abnormalities are prominently detectable in infant CDM muscle biopsies. While the majority of RNA targets are also mis-regulated in adult-onset DM1, splicing dysregulation is significantly more severe in CDM. Since many of these mis-processing events are MBNL-regulated, we generated mouse Mbnl double (Mbnl1; Mbnl2) and triple (Mbnl1; Mbnl2; Mbnl3) muscle-specific knockout models that recapitulate the congenital myopathy, gene expression and spliceopathy defects characteristic of CDM. This study demonstrates RNA mis-processing is a major pathogenic factor in CDM and provides novel mouse models to further examine roles for co/post-transcriptional gene regulation during tissue development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Disease-control (SMA type 1) and CDM skeletal muscle (biceps brachii) was used for RNA-seq and polyA-seq and transcriptome analysis (gene expression, alternative splicing, and alternative cleavage and polyadenylation) was performed to identify RNA mis-processing associated with disease. Newborn (P0) quadriceps muscle from wild-type, double (Mbnl1; Mbnl2) knockout (DKO), and TKO (Mbnl1; Mbnl2; Mbnl3) knockout (TKO) muscle and wild-type and Mbnl3 knockout (3KO) myoblasts were also used for transcriptome analysis to test the contribution of MBNL loss-of-function to disease features.

middle: D

first: Eric

last: Wang


status: Public on Jul 06 2017

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

summary:
Gene expression profiling of ISWI chromatin remodeler mutants before and after DNA damage BAZ1A is a regulatory subunit within the ISWI family of chromatin remodelers in humans. We and others have shown that BAZ1A is required for efficient recovery from DNA damage.  The DNA damage hypersensitivity caused by BAZ1A* is as severe as the deletion of the entire gene. This is striking given that BAZ1A* contains only two substitutions (K1181A and K1183Y) within a poorly characterized domain of BAZ1A. We find that this domain can interact with DNA, and that the mutations present in BAZ1A* hinder DNA binding.
We used transcriptional profiling to identify molecular events leading to the DNA damage hypersensitivity of BAZ1A* cells.

overall_design:
HeLa cells (CL132529) were subjected to genome editing using the Cas9 technology to abrogate expression of the chromatin regulator BAZ1A. Lentiviral transduction was then used to re-express either BAZ1A wild-type or the BAZ1A* mutant in BAZ1A knockout cells. All genome edited cell lines have been cloned and passed in-house QC (mycoplasma-free and cell line authenticated).
Cells were either unchallenged (control) or subjected to UVC irradiation (200 J/m2) to cause DNA damage.  One hour after irradiation, total RNA was extracted in triplicate.  Gene expression was measured by RNA-sequencing.
In total there are 8 conditions: 4 cell lines (parental (HeLa), BAZ1A knockout, re-express BAZ1A, re-express BAZ1A* mutant), with or without DNA damage. Each condition includes triplicate RNA extractions, for a total of 24 samples.


title: Mitochondrial DNA drives tumor dormancy escape in ER+ breast cancer

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Although the estrogen receptor (ER) positive variant of breast cancer is touted as the most indolent and favorable, the majority of breast cancer deaths are in fact from this subtype. There are several features of this category of breast cancers that likely account for this outcome. The first is that metastatic relapse can occur many years after initial diagnosis of primary disease. The second is that once the cancer cells awaken into full-blown metastatic disease, they are largely resistant to ER-directed therapies (i.e. hormonal therapy, HT). The third is that when metastases do occur, they are invariably in many locations. This observation suggests that these dormant/sleeping metastatic cells are “globally” awakened as if by a “systemic” infection. We suggest that these three processes be not only linked, but underlie the lethal features of metastatic disease. We hypothesized that mtDNA is necessary for the escape from therapy induced tumor dormancy of luminal breast cancer cells

overall_design: Total RNA was isolated after 2 months of treatment of breast cancer cell lines MCF7 cells with hormonal therapy (tamoxifen, 1uM) and biologically CTRL replicates are also present. Treatments with HT led to tumor dormancy in vitro. Samples for each group were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Pasquale

last: Sansone

first: Jaqueline

last: Bromberg


title: Setaria viridis (A10.1) circadian expression after light or temperature entrainment

city: St. Louis

first: Malia

last: Gehan

state: Missouri

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

overall_design: Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.

first: Todd

last: Mockler


title: Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [ppp5end RNA-Seq]

first: Yu

last: Qiu

overall_design: 5' triphosphate end profiling of  exosomal RNA isolated from stroma/breast cancer cell co-culture (MRC5 and 1833).


title: Microenvironmental regulation by miRNAs in pancreatic cancer.

status: Public on Jul 29 2017

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

summary: To demonstrate the role of miRNAs in desmoplastic stroma of pancreatic cancer patients sample, we compared the miRNA expression patterns in tumor, stroma  and normal tissue.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was extracted from formalin fixed paraffin embedded samples from the pancreatic cancer patients samples. The miRNA expression profiling is done on tumor, stroma and normal tissues seperately using miRCURY LNATM microRNA Array 7'th arrays (Exiqon, Denmark). The expression profiles were background corrected and quantile normalized. Filtering of controls and low expressed probes was done. 755 miRNAs were used to demonstarte the role of miRNAs in tumor and stroma interaction and in carcinogenesis.

first: Elin

last: Kure


title: Components of the ESCRT machinery act downstream of MLKL to regulate necroptotic cell death and its consequences

status: Public on Jun 16 2017

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

summary: The activation of Mixed Lineage Kinase-Like (MLKL) by Receptor Interacting Protein Kinase-3 (RIPK3) results in plasma membrane (PM) disruption and a form of regulated necrosis, called necroptosis. Here we show that during necroptosis, MLKL-dependent calcium (Ca++) influx and phosphatidylserine (PS) exposure on the outer leaflet of the plasma membrane preceded loss of PM integrity. Activation of MLKL results in the generation of broken, PM “bubbles” with exposed PS that are released from the surface of the otherwise intact cell. Components of the ESCRT machinery are required for formation of these bubbles, and act to sustain survival of the cell when MLKL activation is limited or reversed. Under conditions of necroptotic cell death, ESCRT controls the duration of plasma membrane integrity. As a consequence of the action of ESCRT, cells undergoing necroptosis can express chemokines and other regulatory molecules, and promote antigenic cross-priming of CD8+ T cells.

overall_design: hMLKL1-181-2Fv-NIH3T3 cells were stimulated with or w/o 50 nM B/B for 1h, plus/minus 3000 nM washout for 6h

first: Yi-Nan

last: Gong

first: Melanie

last: Loyd

first: Douglas

last: Green


title: Genome-wide identification of genes involved in phytochrome (phy)-mediated anther development in rice

city: Jinan

first: Xiao Hui

last: Xu

address: No. 202, Gongyebei Road

institute: Shandong Academy of Agricultural Sciences

summary: This study is the first research that provides valuable insight into the complex regulation networks underlying phytochrome-mediated anther development in plant. Furthermore, the results also provide new clues for cultivating new male sterile lines in hybrid rice breeding.

overall_design: Phytochromes (phy) are the main plant photoreceptors that sensing and transducing red and far-red light signals to regulate multiple developmental processes. Previous studies mainly focused on their roles in photomorphogenesis, such as seed germination, de-etiolation and shade avoidance. However, the regulatory network of phytochrome-mediated anther development was largely unknown. There are three genes encoding phytochromes in rice, phyA, phyB and phyC. The single mutant of each phy gene has no effects on rice fertility, but the fertility of phyA phyB double mutant was decreased significantly. Histological and cytological analysis revealed that the reduced fertility in phyA phyB double mutant was due to defects in anther development and dehiscence. To identify genes involved in phytochrome-mediated anther development, the transcriptomes of anthers in phyA, phyB single and double mutant, and wild-type rice were compared. The results showed that carbohydrate metabolism and heat-shock responses were activated in the anther of phyA phyB double mutant. Sugar contents analysis indicated that the abnormal anther development in phyA phyB double mutant was partially caused by the increased hemicellulose content and decreased cellulose content. Quantitative reverse transcription-PCR results confirmed that the expression of most of heat-shock factors and proteins were up-regulated in phyA phyB double mutant.

first: Xiao


title: Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [RNA-Seq]

overall_design: transcription profiling for exosomal RNA and cellular RNA with and without micrococcal nuclease treatment

first: Barzin

last: Nabet

first: Jacob

last: Shabason

first: Tony

last: Wu

first: Taewon

last: Yoon

first: Christina

last: Victor

first: Brian

last: Kim

first: Joseph

last: Marcotrigiano

first: Andy

last: Minn


title: Hepatic transcriptome in CUGBP1 S302A knock-in mice highlights CUGBP1 degradation by Gankyrin through diethylnitrosamine (DEN) activation, leading to fatty liver and liver cancer

status: Public on Jun 12 2017

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: CUGBP1 is an important regulator of liver homeostasis, through splicing regulation, stability, and mRNA translation. To aim to characterize the transcriptome of DEN-mediated liver cancer in CUGBP1 knock-in mice with Ser302 mutated to Ala (which mimics unphosphorylated CUGBP1 isoform) through RNA sequencing. Specifically, we compared gene expression levels to identify the impact of DEN-driven activation in both wildtype and CUGBP1 Ser302-to-Ala knock-in mice, focusing on downstream CUGBP1 targets and tumor activating pathways.

Methods: Hepatic mRNA profiles were obtained through RNA sequencing of flash-frozen samples obtained at time of sacrifice.

Results: We observe an augmentation of up- and downregulated cancer-related genes and pathways in CUGBP1 s302a knock-in mice compared to WT mice. We observe not only changes in expression related to oncogenesis, but also in splicing. Reduction of CUGBP1 protein due to the s302a variant leads to higher sensitivity to the development of liver cancer as a result of alterations in expression of down-stream mRNAs at both the splicing and expression levels.

Conclusion: CUGBP1 is a strong tumor suppressor in the liver, and reduction of the CUGBP1 protein accelerates the development of liver cancer.

overall_design: RNA sequencing was performed on livers from WT and CUGBP1 s302a knock-in mice following treatment with DEN.

first: Nickolai

last: Timchenko


title: Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [exoRNA-Seq]

first: Yu

last: Qiu

overall_design: transcription profiling for exosomal RNA isolated from stroma cell (MRC5) or stroma/breast cancer cell co-culture (MRC5 and 1833).


title: Genome-wide analysis of human iPS cell-derived hepatocyte-like cells induced by methoxamine treatment.

status: Public on Jun 17 2017

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Analysis of whole gene expression during differentiation from hiPS cells into hepatocyte-like cells. The hypothesis tested in the present study was that the hepatocyte-like cells induced with adrenergic receptor agonists were identical to those induced with conventional growth factors (hepatocyte growth factor and oncostatin M). Results provide the important information of the differentiation mechanisms from hepatoblasts into hepatocytes.

overall_design: Total RNA obtained from undifferentiated hiPS cells, hiPS cell-derived hepatoblast-like and hepatocyte-like cells. The hiPS cells were induced to differentiate into hepatoblast-like cells, then the cells were treated with methoxamine or growth factors (hepatocyte growth factor and oncostatin M) to induce the differentiation into hepatocyte-like cells.

first: Maki

last: Kotaka

first: Chihiro

last: Okada

first: Masahiro

last: Nakamura

first: Kenji

last: Osafune


title: Global transcriptional responce in C.elegans on a high glucose diet

status: Public on Jul 26 2017

first: Ivan

last: Gusarov

address: 450E 29th street

department: Biochemistry

institute: NYU School of Medicine

summary: We compared differential gene expression in C. elegans on a regular and 2% glucose supplemented diet.

overall_design: Worms grown on NGM plates seeded with E.coli OP50 till L4 stage, trensferred on NGM or NGM+2% glucose, incubated over night at 20oC, and collected for RNA-seq library preparation.

first: Ilya

last: Shamovsky


title: Genetically distinct parallel pathways in the entopeduncular nucleus for limbic and sensorimotor output of the basal ganglia

status: Public on Jun 01 2017

city: Boston

first: Arpiar

last: Saunders

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: We report single-cell transcriptional assessment and functional circuit characterization of neuron types within the mouse entopeduncular nucleus (EP)

overall_design:
Transcriptional profilingof EP neurons from P60-70 C57BL/6 male mice; three types were identified, characterized, and incorporated into a synaptic-circuit model of basal ganglia
please note that Replicate 2 was lost experimentally and not included, so n=3 replicates total

first: Bernardo

last: Sabatini


title: De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

status: Public on Jun 20 2017

city: Hilo

first: Monika

last: Frazier

state: HI

address: 200 West Kawili Street

department: Tropical Conservation Biology and Environmental Science

institute: University of Hawaii at Hilo

summary:
Purpose: There is a dearth of knowledge regarding the molecular pathology of growth anomaly in corals.  We investigated the gene expression profile of Montipora capitata metatranscriptomes from healthy and diseased (growth anomaly) coral colonies to elucidate differentially expressed genes.
Methods: mRNA profiles of coral tissue (including symbionts) were generated from three different tissue states: healthy, affected and unaffected. Healthy tissue was collected from coral colonies not affected by growth anomaly.  Affected tissue was collected from coral growth anomaly lesions.  Unaffected tissue was collected from coral colonies affected by growth anomaly.

overall_design: Three distinct tissue types were sampled for this study: (1) healthy tissue from healthy corals, (2) diseased tissue from coral with growth anomaly, (3) apparently healthy tissue from coral with growth anomaly.

first: Martin

last: Helmkampf

first: Renee

last: Bellinger

first: Scott

last: Geib

first: Misaki

last: Takabayashi


title: High-throughput screening of gene expression in the patient's cholangiocarcinoma biopsy

status: Public on Nov 22 2017

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) patient’s tumor biopsy sample, obtained at the time of the first CCA diagnosis. We next used bioinformatical software Oncobox to analyze gene expression data and to identify molecular pathways differentially regulated in the patient’s tumor sample.

overall_design:
Microarray analysis was performed for single biopsy sample. Sample was evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers (sample should contain at least 80% of tumor cells).

Gene expression data from the cholangiocarcinoma sample was merged with gene expression data from adult liver control samples from GSE61276 (GSM1503734-GSM1503825) and quantile normalized using R statistical programming language and 'preprocessCore' library. The supplementary file 'GSE107233_complete_normalized_data.txt' includes the quantile normalized data from the cholangiocarcinoma Sample and Samples GSM1503734-GSM1503825.

first: Elena

last: Ilnitskaya


title: Unique liver transcriptomics profiles in chronic HBV: intrinsic intrahepatic functional clusters discriminate distinct clinical phases

status: Public on Jun 10 2017

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

summary: Since little information is available on the processes in the liver associated with the natural history during chronic HBV infections, we now examined hepatic transcriptomes to identify distinctive gene expression profiles in the HBV clinical phases.  We show that the transcriptomes of mild fibrotic, HBV-infected livers were significantly different from those with comorbidities. Across the clinical HBV phases, comparable intrahepatic ISG expression was observed. However, global transcription was most distinctive between the immunotolerant and the immunoactive phases (n=92 genes), followed by the immunotolerant and the HBeAg-negative hepatitis phase (n=71 genes), and the immunotolerant and the inactive carrier phase (n=46 genes). Among these were CD19, TNFRSF13C, granzyme H, and KIR2DS3. Moreover, during these clinical phases, 4 intrinsic functional clusters (IFC) with distinctive transcriptional activity were identified by combined global module analysis. These discriminative clusters contained B-cell and cell cycle-related genes, which were highly expressed in liver during the immunoactive phase; and NK-cell and mitochondria respiration-related genes in the HBeAg-negative hepatitis phase. Our data define distinctive transcriptomes in the liver during HBV clinical phases. We observed important differences between the liver and blood in transcription levels of ISG and cell cycle genes, but, strikingly, also a high degree of overlap in expression patterns of B- and NK-cell genes during the immune active phases.

overall_design: we analyzed a cohort of FFPE biopsies collected from the livers of well-characterized chronic HBV patients (n=74) and archived for up to 30 years. Differential gene expression analysis , global module analysis, and unsupervised clustering analysis were performed by employing the WG-DASL assay on liver transcriptomes from chronic HBV patients with and without concomitant NASH or advanced fibrosis, or between different HBV clinical phases.

first: Jun

last: Hou

first: Willem

middle: P

last: Brouwer

first: Kim

last: Kreefft

first: Lucio

last: Gama

first: Sarah

middle: L

last: Price

first: Harry

last: Janssen

first: Pim

last: French

first: Thomas

last: Vanwolleghem


title: Gene expression profiling of KSHV-infected periodontal ligament cells

city: Guangzhou

first: Yuqing

last: Li

address: North campus of Sun Yat-sen University, No.74 of Zhongshan 2nd road, Yuexiu Distinct, Guangzhou, Guangdong

institute: Sun Yat-sen University

summary: We reported the potential and mechnism of oral mesenchymal stem cell to become Kaposi Sarcoma progenitor cell. Human periodontal ligament cells were infected for 48 hours and 96 hours, then subjected to RNA extraction and sequencing. We found that KSHV-infected PDLSC shared a better similarity with KS biosies in cytokine production, including chemotaxis, angiogenesis, inflammation and differentiation. Furthermore, infection of PDLSC upregulated a spectum of genes involving mesenchymal-to-endothelial differentiation, a process which has been revealed in KS spindle cells. This study reveals the potential and mechnism in which oral mesenchymal stem cell is transformed by KSHV to KS progenitor cell.

overall_design: Gene expression profiling of uninfected PDLSC and KSHV-infected PDLSC after 48h and 96h.

first: Yan

last: Yuan


title: Exosomal microRNAs in the giant panda (Ailuropoda melanoleuca) breast milk: the potential maternal regulators for the development of newborn cubs

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

summary:
Purpose:To present the miRNA expression profiles in giant panda milk exosomes across five lactation stages (0, 3, 7, 15 and 30 days after birth), aiming to provide new information for investigations into the physiological functions of the giant panda milk
Methods: Three females were sampled in all, and each individual were sampled over multiple lactations, including 0, 3, 7, 15 and 30 days after delivery. Breast milk samples (5-10 ml) were collected from each stages. Total RNA isolated from individuals in five lactation stages (0, 7, 15 and 30 days after delivery) were pooled in equal quantities for each stage
Results: Here, we illustrated the species and expression characteristics of exosome-loaded miRNAs existing in giant panda breast milk during distinct lactation periods, and highlighted the enrichment of immune- and development-related endogenous miRNAs in colostral and mature giant panda milk, which are stable even in certain hash conditions, like low pH and high concentration of RNAase, by the protection of extracellular vesicles.These findings indicate that breast milk may allow dietary intake of maternal miRNAs by infants for the regulation of postnatal development. We also demonstrated that the exogenous plant miRNA from the primary food source of giant panda (bamboo) were detected in the exosomes of giant panda breast milk, which were predicted to be of regulatory role in basic cell metabolism and neuron development. This result suggested that the dietary plant miRNAs were able to be absorbed by host cell and then secreted to body fluids as potential cross-kingdom regulators.
Conclusions: Exosomal miRNAs in the giant panda breast milk may be the crucial maternal regulators for the development of intrinsic ‘slink’ newborn cubs.

sample_organism:
Ailuropoda melanoleuca
Bambusa vulgaris

platform_organism:
Ailuropoda melanoleuca
Bambusa vulgaris

overall_design: Three females were sampled in all, and each individual were sampled over multiple lactations, including 0, 3, 7, 15 and 30 days after delivery. Breast milk samples (5-10 ml) were collected from each stages. Total RNA isolated from individuals in five lactation stages (0, 7, 15 and 30 days after delivery) were pooled in equal quantities for each stage.

first: Jideng

last: Ma

first: Chengdong

last: Wang


title: Microarray profiling of lncRNA expression in MCF-7 and MDA-MB-231 cells

city: Beijing

first: Wanjin

address: No. 38, Xueyuan road.

institute: Peking University Health Science Center

summary: Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs that are over 200 nucleotides in length. In the past years, those molecules have emerged as important components of the epigenetic regulatory network to influence transcription as well as other nuclear activities, and their dysregulation underlies several pathologic states including cancer. To determine which lncRNA participates in the interaction between FOXN3 and SIN3A, we performed a comparative analysis of the expression profiles of lncRNAs in MCF-7 and MDA-MB-231 cells using lncRNA microarrays.

overall_design: Total  RNAs containing non-coding RNAs were extracted  from  MCF-7  cells  and  MDA-MB-231  cells  with  Trizol  Reagent  (Life  Technology) for reverse  transcription  in  the  presence  of   Cy3-dCTP  (GE  Healthcare).  Amplified/Cy3-labeled  cDNAs  were  hybridized  onto   oligonucleotide  microarrays  containing  40,916  probes of  lncRNAs  (CapitalBio  Human   lncRNA 4.0 Array).

first: Zihan

last: Zhang


title: FOXN3 and SIN3A ChIP-Seq; FOXN3 and IgG iRIP-Seq

summary: The forkhead box (FOX) family of proteins is composed of more than 50 members that are phylogenetically classified into 19 subclasses (A to S). These transcription factors all share a homology in their DNA-binding domain, the forkhead domain, also known as winged helix due to its butterfly-like structural appearance.FOX proteins have been implicated in a broad spectrum of cellular processes including cell proliferation, differentiation, DNA repair, metabolism, and aging. However, the biological function of the mammalian forkhead transcription factors of the N class including FOXN3 remains to be investigated. The SIN3A complex is a large protein assembly consisting of over a dozen of proteins including SIN3A, HDAC1/2, RBBP4/7 and etc. This complex is recruited by multiple transcription repressors and impacts on multifaceted biological functions ranging from development, differentiation, and senescence to oncogenic transformation. Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs that are over 200 nucleotides in length. In the past years, these molecules have emerged as important components of the epigenetic regulatory network to influence transcription as well as other nuclear activities, and their dysregulation underlies several pathologic states including cancer. One of the lncRNAs, NEAT1 (nuclear paraspeckle assembly transcript 1), is a highly abundant lncRNA initially described as a structural component of nuclear paraspeckles. Subsequent studies suggest that NEAT1 also influences transcription through either an indirect mechanism or a direct way. In this study, we investigated the function and the underlying mechanism of FOXN3 in breast cancer cells. We showed that FOXN3 is physically associated with the SIN3A complex and identified that NEAT1, which is induced by estrogen in breast cancer cells, is required for this interaction. We analyzed the genomic targets of the FOXN3/SIN3A/NEAT1 complex and demonstrated that estrogen receptor (ER) itself is regulated, through negative feedback, by the FOXN3/SIN3A/NEAT1 complex. We investigated the role of the FOXN3/SIN3A/NEAT1 complex in breast cancer metastasis and explored the clinicopathological significance of the ER-NEAT1-FOXN3/NEAT1/SIN3A-GATA3 axis in breast cancer.

overall_design: The Genome-wide binding profiles of FOXN3 and SIN3A in MCF-7 cells were determined by Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Besides, the potential lncRNAs that is required for the interaction of the SIN3A complex with FOXN3 were identified by an Improved RNA ImmunoPrecipitation-coupled high-throughput sequencing (iRIP-seq) method with antibodies against FOXN3.


title: FOXN3 Enlists NEAT1-containing SIN3A Complex to Regulate Mammary Epithelium Differentiation and Promote Breast Cancer Metastasis

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

overall_design: Refer to individual Series


title: Genome-wide analysis of nucleus accumbens gene expression after ethanol consumption in rat

city: Gothenburg

first: Julia

last: Morud

address: Beroendemedicin, Box 410

country: Sweden

institute: University of Gothenburg

summary:
The study investigated ethanol-induced alterations in the transcriptome of adult male Wistar rats. The study was divided into two parts. Part 1: 10 animals were single housed during 8 weeks and exposed to 6% ethanol solution and water simultaneously or just water (24 hours/day, 7 days/week). Fluid intake and body weight were recorded twice weekly during 8 weeks. Animals were sacrificed immediately after the last consumption measurement and the nucleus accumbens were dissected and snap frozen until further processing. Part 2: 12 rats were single housed and exposed to continuous access to ethanol and water (24 hours/day, 7 days/week). After 4 weeks, animals were divided into 2 groups, equally balanced based on previous ethanol intake, and were given additional ethanol or water through a gavage tube daily during 3 weeks. This was followed by an additional 2 weeks of continuous ethanol access and then animals were immediately sacrificed and the nucleus accumbens were dissected and snap frozen until further processing. Next, the RNA was extracted from the cells using Qiagen RNeasy Lipid tissue mini kit and the RNA concentration and quality was measured using a BioAnalyzer. RNAseq was performed using standard Illumina protocols in collaboration with SciLifeLab, Stockholm, Sweden. No difference in gene expression was detected between any groups.

Keywords: RNAseq, Gene expression profiles, Ethanol consumption, Rat.

overall_design: Five samples from water consuming controls (experiment-1_water) and five from voluntary ethanol consuming (experiment-1_ethanol) rats. Six samples from ethanol consuming rats that received excessive amounts of water (experiment-2_water-gavage) or ethanol (experiment-2_ethanol-gavage) trough a gavage tube.

first: Arghavan

last: Ashouri


title: MiRNAs regulate dynamic transcriptional changes of broiler embryos in response to modification of the incubation temperature

status: Public on May 31 2017

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf


title: MiRNAs regulate dynamic transcriptional changes of broiler embryos in response to modification of the incubation temperature (Musculus pectoralis)

summary: miRNA expression was analysed of samples derived from M. pectoralis of day 10 and day 13 chicken embryos and day 35 broiler after variation of incubation temperature

overall_design: Broiler eggs were incubated at a lower or higher temperature (36.8°C, 38.8°C) relative to control (37.8°C) over two developmental intervals, embryonic days (ED) 7-10 and 10-13. MicroRNA expression of Musculus pectoralis  was assayed at ED 10, ED 13, and slaughter age [post-hatch day (D) 35] (6 groups; 3 time points) by microarray analysis and treated samples were compared to controls within each time point

first: Watcharapong

last: Naraballobh

first: Nares

last: Trakooljul

first: Eduard

last: MurÃ¡ni

first: SiriluckÂ

last: Ponsuksili


title: Bioenergetic Alterations in Colorectal Polyp and Cancer

status: Public on May 23 2017

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background: The change of cellular energy metabolism in colorectal carcinogenesis is poorly understood. It is widely accepted tht most, if not all, colorectal cancers (CRCs) arise from adenomatous polyps (APs). Our aim was to characterize the mitochondrial and bioenergetic alternations in the adenoma-carcinoma sequence.
Results: Two glycolysis-related genes, aldolase B (ALDOB) and solute carrier family 16 member 4 (SLC16A4), were upregulated in polyps. This result was further confirmed by the real-time PCR analysis showing that the both ALDOB and SLC16A4 mRNA expressions were higher in the polyps with villous component compared with their adjacent normal mucosa.

overall_design: 5 colon polyps with villous component and adjacent normal mucosa were included. Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA). Gene expression profiles of the human polyps and adjacent normal mucosa were analyzed with a human gene 2.0 array (Affymetrix, Santa Clara, CA). For real-time Q-PCR, first strand cDNA was synthesized with an oligo-T primer using superscript III first strand synthesis kit (Invitrogen, Carlsbad, CA). Gene expression of ALDOB, SLC16A4 and GAPDH mRNA were analyzed with the TaqMan® GENE expression assay (Applied Biosystem, Foster City, CA).

first: Wey-Ran

last: Lin

first: Jy-Ming

last: Chiang

first: Siew-Na

last: Lim

first: Ming-Yao

last: Su

first: Tsung-Hsing

last: Chen

first: Shu-Wei

last: Huang

first: Kung-Hao

last: Liang

first: Ren-Chin

last: Wu

first: Chia-Lung

last: Tsai

first: Chau-Ting

last: Yeh

first: Cheng-Tang

last: Chiu


title: Crebbp deletion cooperates with Bcl2 over-expression to promote B-cell lymphoma in mice

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: We confirmed that common CREBBP mutations in human FL result in reduced acetyltransferase activity of the protein, and modeled this loss of function by B-cell-specific deletion of one or both alleles of Crebbp in transgenic mouse models. We show that Crebbp deletion results in deficits in B-cell development, and provide the first evidence from transgenic mouse models that Crebbp inactivation can cooperate with Bcl2 over-expression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B-cells we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the regulatory regions of these genes. In contrast, B-cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions that were enriched for Myc DNA binding motifs and Myc binding. These transgenic models therefore provide important links between Crebbp inactivation and Bcl2 dependence, and a potential role for Crebbp inactivation in the induction of Myc expression.

overall_design: B-cells were isolated from the spleens of 3 mice per strain by magnetic bead selection and interrogated by gene expression microarray

first: Isidro

last: Sanchez-Garcia


title: MiRNAs regulate dynamic transcriptional changes of broiler embryos in response to modification of the incubation temperature (Musculus gastrocnemius)

first: Klaus

last: Wimmers

summary: miRNA expression was analysed of samples derived from M. gastrognemius of day 10 and day 13 chicken embryos and day 35 broiler after variation of incubation temperature

overall_design: Broiler eggs were incubated at a lower or higher temperature (36.8°C, 38.8°C) relative to control (37.8°C) over two developmental intervals, embryonic days (ED) 7-10 and 10-13. MicroRNA expression of Musculus gastrocnemius was assayed at ED 10, ED 13, and slaughter age [post-hatch day (D) 35] (6 groups; 3 time points) by microarray analysis and treated samples were compared to controls within each time point

first: Watcharapong

last: Naraballobh

first: Nares

last: Trakooljul

last: Muráni

first: Siriluck


title: Skeletal muscle gene expression in the wild type and the GAA knock-out mice, a model of Pompe disease

status: Public on May 13 2017

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Pompe disease is a Lysosomal glycogen storage disorder due to the deficiency of acid alpha glucosidase. The enzyme degrades glycogen to glucose and its deficiency results in progressive enlargement of glycogen-filled lysosomes in multiple tissues with skeletal and cardiac muscle most severely affected clinically. Clinical spectrum ranges from most severe infantile cardiomegally and skeletal muscle myopathy to milder late onset forms with only skeletal muscle pathology. The currently available enzyme replacement therapy has only limited effect in skeletal muscle. Here we use RNA sequencing of therapy-resistant skeletal muscle (white part of gastrocnemius muscle) to identify the differencies between the diseased and healthy muscle.

overall_design: Total RNA was obtained from gastrocnemius muscle (white part) of acid alpha glucosidase knock-out and wild-type mice.

first: Nina

last: Raben

first: Gustavo

last: Gutierrez-Cruz

first: Jeong-A

first: Hong-Wei


title: Expression data from gall bladder and cystic duct in wild type and Sox17+/-mice at 15 dpc

status: Public on May 30 2017

city: Tokyo

first: AIsa

last: Ozawa

address: Yayoi 1-1-1,Bunkyo-ku

institute: The university of Tokyo

summary:
Sox17 expression is important for development of gallbladder and bile duct systems in embryo, and it is reported that gallbladder hypoplasia in Sox17 hetero genic embryo. Additionally it was reported that hepatitis was occurred in Sox17 hetero genic newborn by gallbladder hypoplasia. So, we examined Sox17 gene cascade and the role for the formation of gallbladder and bile duct systems by microarray analysis on Sox17 hetero genic gallbladder in day 15 of pregnancy when Sox17 express and gallbladder epithelium alternated morphology.
We detected that expression of Sonic hedgehog (shh) signal genes decreased in sox17+/- gallbladder and cysticduct as compared with the wildtype gallbladders.These arry analysis in gallbladder and cysticduct reveal expression of shh in developmental gallbladder is downstream in sox17+/- and gene expression in sox17+/- gallbladder was similar in cysticduct .

overall_design: Total RNAs from gallbladder and cysticduct of wildtype and Sox17+/- mice at 15dpc were subjected to microarray analyses. Two biological replicates of each genotype were analyzed.

first: Aisa


title: Effect of human genetic variability on gene transcription in dorsal root ganglia and association with pain phenotypes [exon-level]

status: Public on May 10 2017

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

country: Canada

institute: McGill University

summary: Single nucleotide polymorphisms (SNP) can affect mRNA gene expression, in a tissue-specific manner. In this work we survey association of SNP alleles with mRNA gene expression in human dorsal root ganglions (DRG) to gain insights into pathophysiology of pain phenotypes.

overall_design: DNA and RNA was extracted from dorsal root ganglions of deceased human patients; the DNA used for genotyping and the RNA used for mRNA expression level measurement. Expression quantitative trait loci analyses were performed between SNP alleles and mRNA levels to evaluate strength of association between minor allele content at a given SNP and mRNA level of a given gene/exon.

first: Samar

last: Khoury

first: Anne-Julie

last: Chabot-Doré

first: Gary

last: Slade

first: Shad

middle: B

last: Smith

first: Roger

last: Fillingim

first: Richard

last: Ohrbach

first: Joel

last: Greenspan

first: William

last: Maixner

first: Inna

last: Belfer

first: J

last: Mogil

first: Luda

last: Diatchenko


title: Effect of human genetic variability on gene transcription in dorsal root ganglia and association with pain phenotypes [transcript-level]


title: MCF7 cells: empty vector  (Neo) vs. PAR4 overexpression vector transfected before and after 100nM docetaxel treatment

status: Public on May 04 2017

city: São Paulo

first: Simone

middle: Aparecida

last: de Bessa Garcia

state: São Paulo

address: Av. Dr. Arnaldo, 251

department: Radiologia e Oncologia

country: Brazil

institute: ICESP

summary:
The aim of this study was evaluate the transcriptome changes in the comparison between MCF7 cells with increased expression of PAR-4 and the control cells before and after docetaxel treatment .
The results generated could be of particular interest for the understanding the action of PAR-4 in chemosensitivity, especially to increase the specificity and effectiveness of drug treatment and overcoming resistance to chemotherapy.

overall_design: Four-condition experiment, MCF7 Neo vs. MCF7 over PAR4 cells before (control) and after 100nM docetaxel treatment. Biological replicates: 2 control replicates (Neo and over PAR4 before treatment) and 4 docetaxel treated replicates (2 Neo and 2 over PAR4 100nM).

first: Ana

last: Pavanelli

middle: A

first: Natalia

last: Cruz e Melo

first: Maria

last: Nagai


title: Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes


title: Affymetrix SNP array data of melanoma cell lines II

status: Public on May 24 2017

city: Essen

first: Klaus

middle: Georg

last: Griewank

address: Hufelandstr. 55

department: Dermatology

institute: University of Duisburg-Essen

summary: Genetic alterations lead to resistance to immunotherapy

overall_design:
Cell lines were generated from tumor material, differences in Immune profiles were observed and Affymetrix SNP arrays performed according to the manufacturer's directions on DNA extracted from cell lines
SNP analysis of different melanoma cell lines obtained from three melanoma patient

first: Annette

last: Paschen


title: Comparative gene expression profiling of serum-free and FBS treated adherent primary pancreatic TIC cultures

status: Public on May 16 2017

city: Heidelberg

first: Hanno

last: Glimm

address: Im Neuenheimer Feld 460

department: Translational Oncology

institute: National Center for Tumor Diseases

summary: To induce a differentiated phenotype, primary pancreatic TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and parallel control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed.

overall_design: RNA was obtained from four different patient derived cultures grown in serum-free or 10% FBS containing culture medium at passage 3 and passage 8

first: Felix

last: Oppel

first: Claudia

last: Ball


title: RNA-Seq analysis of alveolar macrophages from normal and fibrotic mouse lungs

status: Public on May 03 2017

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

summary: We performed gene expression profiling of alveolar macrophages from mice that were intratracheally instilled with saline or bleomycin. We identified a number of differentially expressed genes in the two groups of cells.

overall_design: Expression profiling of alveolar macrophages from mice that were intratracheally instilled with saline or bleomycin.

first: Gang

last: Liu


title: Genome-wide DNA methylation in Tibetan chicken and Chahua chicken embryos

city: beijing

first: Yawen

last: Zhang

address: No. 2 Yuanmingyuan West Rd.

institute: china agriculture university

type: Methylation profiling by high throughput sequencing

summary: In this study, methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to provide an atlas of DNA methylomes in the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos.A total of 31.2 gigabases (Gb) of sequence data were generated from six MeDIP-seq libraries. We identified 1049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs were involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB, BMPR1B, BMPRII, and ITGA2) might have key regulatory functions for hypoxia adaptation in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.

overall_design: we use MeDIP-seq to generate an atlas of DNA methylomes in heart tissue of hypoxic chicken embryos to investigate the difference in DNA methylation between Tibetan chickens and their lowland counterparts.

first: Hao


title: RNAseq changes in mouse skin after treatment with external light

status: Public on May 09 2017

city: Taipei

first: Mai-Yi

last: Fan

address: No1, Sec. 1, Jen - Ai Rd.

institute: National Taiwan University

summary: To identify the cellular processes upregulated in skin after treatment with external light

overall_design: skin mRNA profiles of mouse with treatments; SRP106582; PRJNA385557

first: Sung-Jan

last: Lin


title: Transcription and chromatin determinants of the rate of de novo DNA methylation in oocytes

status: Public on May 15 2017

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

summary: We generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation.  We find that the major transitions in the oocyte transcriptome occur well before the de novo methylation phase; nevertheless, transcription level does correlate with rate of methylation. Conversely, timing of methylation of CpG islands (CGIs) correlates inversely with enrichment of histone modifications inhibitory to DNA methylation and dependence on histone 3 lysine-4 demethylases, implicating chromatin remodelling as a major determinant of methylation timing.

overall_design: RNA-Seq, PBAT and RRBS in mouse oocytes at different stages of folliculogenesis

first: Lenka

last: Veselovska

first: Shinichi

last: Tomizawa

first: Sebastien

last: Smallwood

first: Heba

last: Saadeh


title: Transcriptional profiling of the pest Bactrocera oleae feeding on phenolic rich green olives

status: Public on May 12 2017

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
The strictly monophagous olive fruit fly, Bactrocera oleae, represents the major pest of olive orchards worldwide.
It has the unique ability to hydrolyze olive proteins as well as to overcome olive defenses, especially the high levels of phenolic compounds present in the green olive mesocarp.
In this study, we aimed to identify specific genes potentially implicated in overcoming green olive defense and the utilization of the flesh, by examining larval responses to green olives on the transcript level.
Focusing on the up-regulated gene set, we identified two putative serine proteases and one putative UDP-glycosyltransferase possibly associated with these traits. Serine proteases could be involved in the digestion of dietary proteins but also could represent a mechanism to overcome the effect of trypsin inhibitors induced by the olive fruit upon attack.
UDP-glycosyltransferase may be implicated in the sequestration and/ or direct detoxification of phenolic compounds highly present in green olives.

overall_design: Two major comparisons were performed: four biological replicates of green olive reared larvae (GO) were compared to either four biological replicates of black olive reared larvae (BO) or four replicates of artificial diet reared larvae (AD).

first: N

last: Pavlidi

first: W

last: Dermauw

first: A

last: Kampouraki

first: T

last: Van Leeuwen

first: J

last: Vontas


title: Genome-wide maps of the total and lysine methylated enriched pools of peroxisome proliferating activated receptor gamma (pparg) co-activator 1 alpha (ppargc1a)  in Hepa 1-6 cells

status: Public on May 01 2017

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

summary: We report the application of single nucleotide sequencing technology for high-throughput profiling of ppargc1a  in mouse hepatome cells (Hepa1-6). By obtaining 1.2 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide maps of ppargc1a sin mouse hepatoma cells. We identify novel non- coding sites of ppargc1a occupation in hepatic cells for Sirt5, Idh3b, Pfkl, and Hmox2 strongly corresponds with the enrichment of enhancer -associated RNAs.

overall_design: Examination of the genomic disttribution of the total pool of ppargc1a and the lysine methylated (K779me) enriched pool of ppargc1a in mouse Hepa1-6 hepatoma cells.

first: Francesca

last: Aguilo

first: Fan

first: Weijia


title: Silencing of KDM2B leads to deregulation of apoptosis related genes in GBM

city: Istanbul

first: Tugba

last: Bagci-Onder

state: Sariyer

address: Koc University School of Medicine

department: School of Medicine

country: Turkey

institute: Koc University

summary: Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising anti-cancer protein that can specifically kill tumor cells while sparing healthy ones. Emerging evidences suggest that TRAIL resistance in cancers is associated with aberrant expression of the key components of the apoptotic program. However, how these components are regulated at the epigenetic level is not understood. In this study, we aimed to identify novel epigenetic mechanisms regulating TRAIL response in Glioblastoma Multiforme (GBM) by a short-hairpin RNA (shRNA) screen. We employed an shRNA-mediated loss of function approach to interrogate the role of 48 genes in DNA and histone modification pathways. From this we identified KDM2B, an H3K36-specific demethylase, as a novel regulator of TRAIL response. Accordingly, silencing of KDM2B significantly enhanced TRAIL sensitivity, the activation of Caspase-8, Caspase-3, Caspase-7, and cleavage of PARP. KDM2B knockdown also accelerated the apoptosis process, as revealed by live cell imaging experiments. Moreover, simultaneous knockdown of the methyltransferases responsible for generating the histone marks removed by KDM2B significantly recovered the cell death phenotype observed with KDM2B inhibition. To decipher the downstream molecular pathways regulated by KDM2B, levels of apoptosis-related genes were examined by RNA-sequencing and quantitative PCR upon KDM2B loss, which revealed de-repression of pro-apoptotic genes HRK, caspase-7, and DR4 and repression of anti-apoptotic gene Mcl-1. The apoptosis phenotype was dependent on HRK upregulation, as HRK knockdown significantly abrogated the sensitization. In vivo, KDM2B-silenced tumors exhibited slower growth and reduced angiogenic capacity compared to controls. Taken together, our findings suggest a novel mechanism regulating apoptotic response, where the key apoptosis components are under epigenetic control of KDM2B in GBM cells.

overall_design: mRNA profiles of U87MG GBM cells transduced either by control shRNA or shRNA targeting KDM2B were generated by RNA-seq (Illumina HiSeq 2500). 2 biological replicates of shControl and shKDM2B total RNAs were barcoded individually and deep sequenced as 3 technical replicates each in 3 lanes.

first: Zeynep

middle: H

last: Gumus

first: Ibrahim

middle: C

last: Kurt


title: Inhibiting the oncogenic translation program is an effective therapeutic strategy in multiple myeloma

city: Boston

first: Irene

last: Ghobrial

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Multiple Myeloma (MM) is a frequently incurable hematological cancer in which over activity of MYC plays a central role, notably through upregulation of ribosome biogenesis and translation. To better understand the oncogenic program driven by MYC and investigate its potential as a therapeutic target, we screened a chemically diverse small molecule library for anti-MM activity. The most potent hits identified were rocaglate-scaffold inhibitors of translation initiation. Expression profiling of MM cells revealed reversion of the oncogenic MYC-driven transcriptional program by CMLD010509, our most promising rocaglate. Proteome-wide, reversion correlated with selective depletion of short-lived proteins key to MM growth and survival, most notably MYC, MDM2, CCND1, MAF and MCL-1. The efficacy of CMLD010509 in mouse models of MM confirmed the therapeutic relevance of these findings in vivo and supports the feasibility of targeting the oncogenic MYC-driven translation program in MM with rocaglates.

overall_design: RNA sequencing of 5 cell lines (NCI-H929, NAMALWA, U266, MM1S and OPM2) treated with CMLD010509 or vehicle control (DMSO)

first: Salomon

last: Manier

middle: M


title: Analysis of gene expression  from fbn5-1 T-DNA insertion mutant of Arabidopsis

status: Public on Apr 30 2017

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes in fbn5-1 T-DNA insertion Arabidopsis mutant.
Fibrillins are lipid-associated proteins in plastids and are ubiquitous in plants. Fibrillins are known to accumulate and sequester carotenoids in chromoplasts during the development of flowers and fruits; however, little is known about the function of fibrillins in leaf tissues. Here we identified a novel protein fibrillin5 (FBN5) that is essential for plastoquinone-9 (PQ-9) biosynthesis in Arabidopsis thaliana. We showed that homozygous fbn5-1 plants were seedling-lethal, and XVE:FBN5-B transgenic plants expressing low levels of FBN5-B showed a lower growth rate and were smaller than wild-type. In chloroplasts, FBN5-B physically interacts with solanesyl-diphosphate synthase (SPS) 1 and 2, which synthesize the solanesyl moiety of PQ-9. Plants containing defective FBN5-B accumulated less PQ-9 and its cyclized product, plastochromanol-8, which is consistent with mutant phenotypes showing lower photosynthetic performance and higher levels of hydrogen peroxide. The role of FBN5-B in the FBN5-B/dimeric SPS complex is discussed with respect to biosynthesis of the solanesyl moiety.

overall_design: 4 replicats of wild-type as control and fbn5-1 T-DNA insertion mutants were analized.

first: Hyun

middle: U


title: Expression data from 48 hpf WT and mne mutant zebrafish

status: Public on Apr 28 2017

city: Flora Hill

first: M Cristina

last: Keightley

state: VIC

address: Edwards Rd

department: Rural Clinical Sciences

country: Australia

institute: La Trobe University

summary:
We sought to identify new factors important for myeloid development. From a forward genetic screen in zebrafish we identified the transciptional repressor Zbtb11.
To understand pathways regulated by Zbtb11 we profiled gene expression in 48 hpf WT and mne mutant zebrafish. We identified TP53 as a significantly upregulated gene in mne compared to WT.

overall_design: Total RNA was isolated from three biologically independent pools of WT and marsanne embryos (total = 6 samples). Input was 100 ng of total RNA, samples were processed using the Affymetrix WT Plus kit with no amplification and hybridization was to Affymetrix Zebrafish Gene Array 1.0 ST (Affymetrix). Data were analysed using Bioconductor and R packages (http://www.bioconductor.org). Expression values for all genes were calculated using the robust multi-array average method.

first: Maria-Cristina

first: Graham

middle: J

last: Lieschke


title: The m6A pathway facilitates sex determination in Drosophila

status: Public on Apr 22 2017

first: Eric

last: Lai

state: New York

address: 430 E 67th Street

department: Department of Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: N6-methyladenosine (m6A) has recently emerged as a widespread and conserved RNA modification that modulates messenger RNA (mRNA) processing and activity. As most m6A studies have been conducted in cultured cells, we established Drosophila as a model system that combines molecular and genomic analyses of m6A with investigations of organismal biology. We first apply miCLIP sequencing to map m6A modifications at single-nucleotide resolution during Drosophila embryogenesis. We next characterize Drosophila components of the m6A "writer" methyltransferase complex [MTC factors, METTL3/IME4, METTL14, FL(2)D and Nito], and characterize m6A-binding properties of the YTH domain-containing proteins, YT521-B and CG6422. We complement this by generating a collection of mutants in m6A writer and reader components. While Drosophila orthologs of mammalian MTC factors that have additional roles in splicing are lethal, our mutants in METTL and YTH factors are viable but present specific developmental and behavioral defects. We note that several mammalian m6A factors were originally identified as Drosophila regulators of Sxl splicing, which generates the master determinant of female identity. While our mutants in dedicated writer and reader machinery are not required to accumulate Sxl protein in the ovary, maternal loss of m6A writers and readers collaborates with reduction of Sxl to induce female lethality. Our data indicate Sxl is directly regulated by the m6A pathway, since miCLIP data show Sxl is a substantial target of intronic m6A in early embryos, in addition to bearing exonic m6A. Consistent with this, female-specific Sxl splicing is defective in m6A pathway mutants. YT521-B appears to be the major effector of m6A for Sxl regulation, as it shows much stronger genetic interactions with Sxl than CG6422 and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit for studying the m6A pathway in Drosophila reveals a major biological utilization in establishing sex-specific splicing.

overall_design: UV-crosslinking and immunoprecipitation with m6A-antibodies was used to map m6A sites with single nucleotide resolution

first: Lijuan

last: Kan

first: Anya

middle: V

last: Grozhik

first: Jeffrey

last: Vedanayagam

first: Deepak

last: Patil

last: Pang

first: Kok-Seong

last: Lim

first: Yi-Chun

last: Huang

first: Brian

last: Joseph

first: Ching-Jung

last: Lin

first: Vladimir

last: Despic

first: Jian

last: Guo

first: Dong

last: Yan

first: Shu

last: Kondo

first: Wu-Min

last: Deng

first: Peter

last: Dedon

first: Samie

middle: R

last: Jaffrey


title: NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia [mRNA]

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

institute: National Taiwan University Hospital

summary: Mutation in the nucleophosmin (NPM1) gene is frequent in acute myeloid leukemia (AML). This mutation has remarkable prognostic significance and correlates with distinct biological features. Our data from the sample-paired microRNA (miRNA) and mRNA microarrays of de novo AML patients strongly indicated that miRNA−mRNA regulation (MMR) may be dynamic and can be modulated by NPM1 mutation. We identified 493 NPM1 mutation-modulated MMR pairs by a systematic framework, in which MMR was attenuated specifically in patients carrying NPM1 mutations. The involved miRNAs/mRNAs were associated with cancer and hematological diseases, as well as known functions of NPM1 mutation including cell death and cellular response to therapeutics. The NPM1 mutation modulation could be validated with three approaches, including two independent cohort datasets, a high-throughput dataset derived from cell line-based experiments, and two in vitro models. Our study provides novel biological insights into the role of NPM1 mutation as a modulator of MMR, based on which novel prognostic markers are derived in AML.

overall_design: Cryopreserved bone marrow cells were obtained from 109 de novo AML patients. Each sample was analyzed with Illumina HumanHT-12 V4.0 expression beadchip.

first: Hwei-Fang

last: Tien


title: NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia [miRNA]

overall_design: Cryopreserved bone marrow cells were obtained from 109 de novo AML patients. Each sample was analyzed with nCounter® Human miRNA Expression Array.


title: Analysis of IgM and IgG Autoatibodies NOD.B10Sn-H2b/J female mice and age and gender-matched C57BL/10 controls

status: Public on Apr 18 2017

city: Dallas

first: yun

last: lian

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: NOD.B10Sn-H2b/J mice are a mouse model of primary Sjogren's syndrome.  We compared IgM and IgG autoantibody levels from NOD.B10Sn-H2b/J females with clinical disease to those of healthy controls.

overall_design: We collected serum from female NOD.B10Sn-H2b/J and C57BL/10 mice at 26 weeks of age. We performed autoantigen arrays at the Microarray Core Facility of the University of Texas Southwestern Medical Center

first: Daniel

last: Gaile

first: Jill

last: Kramer


title: Gene expression analysis of different subtypes of GSCs upon miR-128 overexpression or downregulation and after knockdown of Polycomb components BMI1 and SUZ12

first: Arun

middle: Kumar

last: Rooj

state: Massachusetts

address: 4 Blackfan Circle

department: Neurosurgery

institute: Brigham and Women's Hospital

summary: To analyze the change of global transcriptome landscape among proneural and mesenchymal GSCs, after the transient knockdown of polycomb repressor complex and upon deregulations of miR-128 in different subtypes of GSCs

overall_design: Pateient derived GSCs were classified among Proneural and Mesenchymal subtypes. Stable GSC were prepared with either overexpression or downregulation of miR-128. The polycomb repressor components BMI1 and SUZ12 were downregulated using siRNA.

middle: K

first: Agnieszka

last: Bronisz

first: Jakub

last: Godlewski


title: NPM1 mutation-modulated microRNA-mRNA regulation in acute myeloid leukemia

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

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

overall_design: Refer to individual Series


title: Liver fibrosis model of  hepatocyte-specific FOXA2 knockout mice

status: Public on Apr 04 2017

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: Liver firbrosis model of  hepatocyte-specific FOXA2 knockout mice. Adeno-associated virus AAV8-TBG-Control or AAV8-TBG-Cre was injected via the tail vein of FOXA2flox/flox (FOXA2f/f) mice 2 weeks prior to CCl4 administration. Hepatic fibrosis was induced by injection of CCl4 twice per week for 4 weeks.

overall_design: Adeno-associated virus AAV8-TBG-Control or AAV8-TBG-Cre was injected via the tail vein of FOXA2flox/flox (FOXA2f/f) mice 2 weeks prior to CCl4 administration. Hepatic fibrosis was induced by injection of CCl4 twice per week for 4 weeks. The mice were sacrificed on the third day after the last injection of CCl4 (0.25ml/kg BW). Total RNA was extracted from primary hepatocytes.

first: Lijia

last: Yao

first: Xin

last: Zhang

first: Weifen

last: Xie


title: Development of gene expression signatures for CXXC5 in pDCs

status: Public on Apr 07 2017

city: shanghai

first: Hui

last: Xiao

address: 320 Yueyang Road, Life Science Research Building B

institute: Institut Pasteur of Shanghai

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by CXXC5 in pDCs. pDCs (CD11c+B220+CD11b-) were differentitated from wild-type and CXXC5-deficient bone marrows by FLT3L for 6 days and sorted by FACS. Expression of five genes (Irf7,Ccl1,Smtn,Dppa2,Ifnab) from this signature was quantified in the same RNA samples by real-time PCR.

overall_design: Gene expression was measured in WT and CXXC5-deficient pDCs.

first: Shixin

last: Ma


title: Global gene expression of various tissues with different treatments of deciduous dioecious tree, Eucommia ulmoides

city: Suita

first: Yoshihisa

last: Nakazawa

state: Osaka

address: 8, Yamadaoka-2

department: Graduate School of Engineering

institute: Osaka University

summary:
To obtain the global gene expression of Eucommia ulmoides, microarray analyses based on EST was conducted. We used 5 kinds of samples (inner stem, outer stem, immature fruit, flower, and leaf) with hormon (IAA, NPA, ABA), light (dark, bright field) & temperature (27, 37, 42°C) treatmens.
In total, 102 independent samples were analysed.

overall_design: Gene expression of various plant tissues including inner and outer stems, female and male reproductive organs and leaves with hormon, heat, light treatments.


title: Two microRNA Signatures for Malignancy and Immune Infiltration Predict Overall Survival in Advanced Epithelial Ovarian Cancer

status: Public on Apr 01 2017

first: Ilya

last: Korsunsky

address: 77 Avenue Louis Pasteur

department: Genetics

summary: MicroRNAs have been established as key regulators of tumor gene expression and as prime biomarker candidates for clinical phenotypes in epithelial ovarian cancer (EOC). We analyzed the coexpression and regulatory structure of microRNAs and their colocalized gene targets in primary tumor tissue of 20 advanced epithelial ovarian cancer patients in order to construct a regulatory signature for clinical prognosis. We performed an integrative analysis to identify two prognostic microRNA/mRNA coexpression modules, each enriched for consistent biological functions. One module, enriched for malignancy related functions, was found to be upregulated in malignant versus benign samples. The second module, enriched for immune related functions, was strongly correlated with intratumoral immune infiltrates of T cells, NK cells, Cytotoxic Lymphocytes, and Macrophages. We validated the prognostic relevance of the immunological module microRNAs in the publically available TCGA dataset. These findings provide novel functional roles for microRNAs in the progression of advanced EOC and possible prognostic signatures for survival.

overall_design: 27 samples from Primary EOC tumor Ovarian masses were assayed.


title: Liver Clock Rescue

status: Public on Mar 31 2017

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

summary:
Circadian clocks drive 24-h rhythms of physiology and behavior. The circadian clock of hepatocytes has been shown to regulate glucose metabolism, and we were interested if rescuing liver clock function can reverse metabolic impairments in hyperphagic/obese Clock-D19 mutant mice.
We compared transcripomte regulation in livers (at Zeitgeber time ZT10) of wild-type (C57BL/6J) and Clock-D19 mice and Clock-D19 mice with genetic rescue of liver clock function using hydrodynamic tail vein injection of a WT-CLOCK expression plasmid

overall_design: Animals (n = 3 per group) were kept under 12h:12h light-dark cycle with ad libitum access to a 45% high-fat diet for 5 weeks and then sacrificed at ZT10 by cervical dislocation and livers isolated.

first: Judit

last: Meyer-Kovac


title: Genome-wide transcriptome analysis during differentiation of human embryonic stem (hES) cells into cardiac lineage

city: Mumbai

first: Deepa

last: Bhartiya

state: Maharashtra

address: Opposite Ramesh Bhavan, Jehangir Merwanji Street, Parel East

department: Stem Cell Biology

country: India

institute: National Institute for Research in Reproductive Health

summary: hES cells display an excellent model to study the developmental mechanisms occuring in vivo both at genetic and epigenetic levels. hES cell line were subjected to global transcriptome analysis to study the differentiation patterns during differentiation of pluripotent hES cells into cardic progenitors and beating cardiomyocytes.

overall_design: In-house derived hES cell line KIND1 was subjected to cardiac directed differentiation protocol leading to derivation of cardiac progenitors on day 12 and beating cardiomyocytes on day 20 of differentiation. With an aim to understand the global transcriptome of differentiated progenies cardiac progenitors (day 12) and beating cardiomyocytes (day 20) were harvested and subjected to microarray analysis. Each of the differentiated progeny was compared to undifferentiated hES cells as day 0 versus day 12, day 0 versus day 20 and day 12 versus day 20

first: Varsha

last: Pursani


title: A MicroRNA Associated With Caste Determination in a Bumblebee is Expressed from a Mirtron Within a Homologue of Vitellogenin

city: Norwich

first: Matthew

last: Beckers

state: Norfolk

address: Norwich Research Park

institute: University of East Anglia

summary: Our aim was to use next-generation sequencing to identify the miRNAs associated with caste determination in queen-destined and worker-destined larvae of the bumble bee, Bombus terrestris. We found that two miRNAs (miR-6001-5p and miR-6001-3p) were upregulated in queen-destined larvae that had passed the critical developmental period when caste becomes irreversible in this species. The two miRNAs form a duplex that is expressed from the gene VHDL, a homologue of Vitellogenin. This finding suggests a new connection between miRNAs and a key protein known to play multiple roles in regulating reproductive division of labour in eusocial Hymenoptera .

overall_design: We made miRNA profiles from two development points (termed early-instar and late-instar) in queen-destined and worker-destined larvae of Bombus terrestris (four replicates per phenotype, making 16 libraries in total). Early-instar larvae are still capable of developing into either queens or workers, while the caste of late-instar larvae has already been determined. We then used bioinformatics methods to compare the miRNA profile between each phenotype, and isolated miRNAs that were differentially expressed.

first: David

last: Collins

first: Irina

last: Mohorianu

first: Vincent

last: Moulton

first: Tamas

last: Dalmay

first: Andrew

middle: G

last: Bourke


title: Expression of the maize Dof1 transcription factor in wheat and sorghum

status: Public on Mar 30 2017

city: Lincoln

first: Pamela

middle: A.

last: Pena

state: NE

address: 1901 Vine St

department: Agronomy

institute: University of Nebraska-Lincoln

summary: Nitrogen is essential for plant growth and development. Improving the ability of plants to acquire and assimilate nitrogen more efficiently is a key agronomic parameter that will augment sustainability in agriculture. A transcription factor approach was pursued to address improvement of nitrogen use efficiency in two major commodity crops. To this end, the Zea mays Dof1 (ZmDof1) transcription factor was expressed in both wheat (Triticum aestivum) and sorghum (Sorghum bicolor) either constitutively, UBI4 promoter from sugarcane, or in a tissue specific fashion via the maize rbcS1 promoter. The primary transcription activation target of ZmDof1, phosphoenolpyruvate carboxylase (PEPC), is observed in transgenic wheat events. Expression ZmDof1 under control of the rbcs1 promoter translates to increase in biomass and yield components in wheat. However, constitutive expression of ZmDof1 led to the down-regulation of genes involved in photosynthesis and the functional apparatus of chloroplasts, and an outcome that negatively impacts photosynthesis, height, and biomass in wheat. Similar patterns were also observed in sorghum transgenic events harboring the constitutive expression cassette of ZmDof1. These results indicate that transcription factor strategies to boost agronomic phenotypic outcomes in crops need to consider expression patterns of the genetic elements to be introduced.

overall_design: The wheat independent event pPTN1034 NN569-3-5-1 T2 (UD-2) carrying the ZmDof1 cassette driven by the constitutive promoter UBI4 was selected for microarray analysis. Transgenic progeny and wild type (CBO37) were grown side by side under greenhouse conditions (10/14 h photoperiod and day/night temperatures of 29°C/24°C ). A total of 4 samples were obtained for microarray analysis (2 transgenic and 2 wild type). Each sample consisted of pooled RNA from flag leaves at anthesis from 3 different plants.

last: Peña

first: Truyen

last: Quach

first: Shirley

last: Sato

first: Zhengxiang

last: Ge

first: Natalya

last: Nersesian

first: Taity

last: Changa

first: Ismail

last: Dweikat

first: Madhavan

last: Soundararajan

first: Tom

middle: E

last: Clemente