title: Unraveling the Plasmodium vivax sporozoite transcriptional journey from mosquito vector to human host

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

summary: Malaria parasites transmitted by mosquito bite are remarkably efficient in establishing human infections. The infection process requires ~30 minutes and is highly complex as quiescent sporozoites injected with mosquito saliva must be rapidly activated in the skin, migrate through the body, and infect the liver. This process is poorly understood for Plasmodium vivax due to low infectivity in the in vitro models. To study this skin-to-liver stage of malaria, we developed quantitative bioassays coupled with transcriptomics to evaluate parasite changes linked with mammalian microenvironmental factors. Our in vitro phenotype and RNA-seq analyses revealedkey microenvironmental relationships with distinct biological functions. M ost notable, preservation of sporozoite quiescence by exposure to insect-like factors coupled with strategic activation limits untimely activation of invasion-associated genes to dramatically increase hepatocyte invasion rates. We also report the first transcriptomic analysis of the P. vivax sporozoite interaction in salivary glands identifying 118 infection-related differentially-regulated Anopheles dirus genes. These results provide important new insights in malaria parasite biology and identify priority targets for antimalarial therapeutic interventions to block P. vivax infection.

sample_organism:
Plasmodium vivax
Anopheles dirus

platform_organism:
Plasmodium vivax
Anopheles dirus

overall_design: Examination of media components and temperature on Plasmodium vivax sporozoites

first: Alison

last: Roth

first: Swamy

last: Adapa

first: Min

last: Zhang

first: Xiangyun

last: Liao

first: Vishal

last: Saxena

first: Raaven

last: Goffe

first: Suzanne

first: Ratawan

last: Ubalee

first: Gagandeep

last: Saggu

first: Zarna

last: Pala

first: Shilpi

last: Garg

first: Silas

last: Davidson

first: Rays

first: John

last: Adams


title: Affymetrix Gene Expression array data for Tcl1 mouse model samples

status: Public on Aug 10 2018

city: Roma

first: Elisabetta

last: Caprini

state: Italy

address: Via dei Monti di Creta 104

country: Italy

institute: IDI-IRCCS

summary:
Tcl1 is known to be involved in survival, proliferation and differentiation of human lymphocytes and mouse embryonic stem cells. Loss of Tcl1 gene in the KO mouse model affects skin integrity inducing alopecia and ulcerations.
The study used epidermal keratinocytes from wild type (WT), Tcl1 knock down (KO) and K14-driven TCL1 transgenic (TGKO) mouse models to investigate the role of Tcl1 gene in the skin homeostasis. Our data indicate that Tcl1 loss mainly induces a decrease in the gene expression of keratinocytes, which is largely rescued by K14-TCL1. GO analysis revealed Tcl1 to be involved in the proliferation and differentiation of mouse keratinocytes. Moreover, pathway analysis identifies growth factor and MAPK signaling to be highly implicated.

overall_design: Affymetrix Gene Expression arrays were performed, according to the manufacturer's directions, on RNA extracted from freshly isolated keratinocytes. Skin specimens were excised three days post depilation and epidermal sheet was separated from the dermis through incubation with 1U/mL of dispase. Gene Expression, GO and pathway analyses were performed for 3 Tcl1-/-, 3 K14-TCL1 and 2 WT samples used as references.

first: Diego

last: Arcelli


title: Enduring Histone Methylation Changes at Proteoglycan Network Genes following Ethanol Exposure

status: Public on Aug 01 2018

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

country: USA

institute: Oregon Health & Science University; Portland VA Research Service

summary: Alcohol use disorder (AUD) is a chronic mental illness in which patients often achieve protracted periods of abstinence prior to relapse. Epigenetic mechanisms may provide an explanation for the persisting gene expression changes that can be observed even after long periods of abstinence and may contribute to relapse. In this study we examined two stable histone modifications, histone 3 lysine 4 tri-methylation (H3K4me3) and histone 3 lysine 27 tri-methylation (H3K27me3), in the prefrontal cortex of Withdrawal Seizure Resistant (WSR) mice 21 days after 72 hours of ethanol vapor exposure. These histone modifications were selected because they are associated with active promoters (H3K4me3) and repressed gene expression in a euchromatic environment (H3K27me3). We performed a genome-wide analysis to identify differences in H3K4me3 and H3K27me3 levels in post-ethanol exposure vs. control mice by ChIP-seq. We detected a global reduction in H3K4me3 peaks and increase in H3K27me3 peaks in post-ethanol exposure mice compared to controls, these changes are consistent with persistent reductions in gene expression and suggest differential epigenetic regulation of genes during this post-exposure period. We also examined the correspondence between genes that displayed changes in H3K4me3 and/or H3K27me3 and were differentially expressed. The expression of 52% of the genes with altered H3K4me3 binding and 40% of genes with H3K27me3 differences found here  is altered by ethanol exposure based on analysis of prior studies. Finally, pathway analysis of genes displaying changes in H3K4me3 and H3K27me3 revealed enrichment for genes involved in proteoglycan and calcium signaling pathways, respectively. The chromatin changes associated with the 21-day post-exposure period suggest that this period is a unique state in the addiction cycle that differs from ethanol intoxication and acute withdrawal. These results provide insights into the enduring effects of ethanol on proteoglycan and calcium signaling genes in the brain.

overall_design: Four control and five ethanol treated arrays were run using total RNA isolated from the Prefrontal Cortex of Withdrawal Seizure Resistant (replicate lines 1 & 2) mice 21 days following a single 72 hour chronic vapor inhalation exposure.

first: Joel

middle: G

last: Hashimoto


title: Expression data after PAK2 knockdown in head and neck cancer cells

status: Public on Aug 07 2018

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary:
Epigenetic mechanisms play an important role in the cellular development and maintenance of cellular homeostasis. Any alteration of epigenetic mechanisms via the changes in DNA methylation and histone modification may lead to various diseases including cancer. The differential expression of histone modifiers has been observed in various malignancies.
We used microarray to detail the differential gene-expression pattern of head and neck (HNC) cancer cells upon depletion of p21 activated kinase (PAK2). we identified distinct class of downregulated genes, majorly associated with cellular proliferation and tumorigenesis.

overall_design: In this study, we have analyzed the global expression pattern upon PAK2 depletion compared to shControl cells using Affymetrix Human Transcriptome 2.0 platform. Array data was processed by Transcriptome Analysis Console (TAC). The experiment was performed with biological replicates.

first: Amit

last: Gupta

first: Athira

last: Ajith

first: Smriti

last: Singh

first: Rajendra

middle: K

last: Panday

first: Atul

last: Samaiya


title: Small RNA sequencing in asexual stages of Plasmodium falciparum NF54

status: Public on Aug 22 2018

city: Berlin

first: Christian

last: Schmitz-Linneweber

address: Granseer Str. 7

department: Faculty of Life Sciences

country: Germany

institute: Humboldt University Berlin

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the accumulation of non coding small RNAs we performed high throughput RNA sequencing on size selcted total RNA from malaria parasite Plasmodium falciparum

overall_design:
Total RNA was used with the NEBNext small RNA seuqencing kit to create a sequencing library with size selction <100nt. Resulting sequencing library was mapped to organellar genomes (apicoplast and mitochondria) to determine clusters of organellar small RNAs.
In a second experiment, RNA from enriched Plasmodium falciparum organelles was subjected to the same library preparation, sequencing scheme, and mapping analysis.

first: Arne

last: Hillebrand


title: Single cell RNA seq for Ciona late tailbud embryos

status: Public on Jul 31 2018

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

type: Expression profiling by high throughput sequencing

summary: We applied single cell RNA seq with 10x genomics platform to study the cell identity change in Ciona late tailbud embryos. By comparing single cell data from Pax3/7>Foxc amd control embryos, we found ectopic expression of FoxC in BTN cells transformed into PSC cells, which suggest common shared origin of BTNs and PSCs.

overall_design: we injected Pax3/7>Foxc construct into Ciona oocytes, fertilized and let them developed into late tailbud stage along with control. Embryos were dissociated into single cells and loaded into 10x platform for single cell RNA-seq. reads are aligned to Ciona genome with Cell Ranger pipeline.

first: Kai

last: Chen


title: Sperm Epimutation Biomarkers of Obesity and Pathologies following DDT Induced Epigenetic Transgenerational Inheritance of Disease

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Gestating F0 generational female rats were transiently exposed to DDT during fetal gonadal sex determination and the incidence of adult onset pathologies was assessed in the subsequent F1, F2, and F3 generations. In addition, sperm differential DNA methylation regions (DMRs) that were associated with specific pathologies in the F3 generation males were investigated. No pathology was observed in the F1 generation DDT lineage males or females compared with F1 generation controls (vehicle exposure). There was an increase of testis disease and early onset puberty in the F2 generation DDT lineage males. The F3 generation DDT males had significant increases in testis disease, prostate disease, and late onset puberty. The F3 generation DDT females had significant increases in ovarian and kidney disease. Both the F3 generation males and females had significant increases in the frequency of obesity and multiple disease. The F3 generation sperm was collected to examine DMRs for the ancestrally exposed DDT male population. Unique sets of DMRs were associated with late onset puberty, kidney disease, and multiple disease pathologies.

overall_design: Outbred gestating female rats were transiently exposed to a vehicle control or DDT The F1 generation offspring were bred to generate the F2 generation and then the F2 generation bred to generate the F3 generation. The F3 generation control and DDT lineage rats were aged and various pathologies investigated. The male sperm were collected to investigate DNA methylation differences between the DDT lineage sperm from samples with different disease outcomes. MeDIP-seq was used to measure methylation in each sample.

first: Setphanie

last: King

first: Margaux

last: McBirney

first: Daniel

last: Beck

first: Ingrid

last: Sadler-Riggleman

first: Eric

last: Nilsson


title: Differentiation-dependent regulation of human endogenous retrovirus K sequences and neighbouring genes in germ cell tumour cells

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary: By using high-density DNA microarrays, we analyzed the gene-expression profile in a panel of germ cell tumour cell lines

overall_design: RNA was extracted from established cell lines and analyzed with Affymetrix HG_U133A microarrays.

first: Thomas

last: Müller

first: Claudia

last: Hantsch

first: Ines

last: Volkmer

middle: S


title: miRNA profiles in invasive front of pT1 colorectal cancer

city: Herlev

first: Rikke

middle: Karlin

last: Jepsen

state: Danmark

address: Herlev Ringvej 75

department: Dept. Pathology

country: Denmark

institute: University Hospital of Copenhagen, Herlev and Gentofte Hospital

summary:
The goal of the study was to identify miRNAs differentially expressed in the invasive front of early and more advanced colorectal cancers, and to determine wheter miRNA profiles could differentiate between colorectal cancers with and without early metasttic progression.
miRNA array data was used for analyses of associations beteen metastatic status and for associations to histopathological risk factors for metastatic progression.

overall_design: We used RNA extracted from formalin fixed paraffin embedded colorectal adenocarcinoma tissue from invasive front of 56 matched pT1 and 20 matched pT3 colorectal cancers. Additionally three random normal colorectal mucosa samples and three stroma samples were analyzed.

first: Estrid

last: Høgdall


title: 4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

status: Public on Aug 02 2018

city: Baton Rouge

first: Craig

middle: M.

last: Hart

state: Louisiana

address: 202 Life Science Building, LSU Campus

institute: Louisiana State University

summary: Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis- and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell.

overall_design: 4C-seq analysis of four viewpoints each having two biological replicates

first: Shraddha

last: Shrestha

first: Dong-Ha

last: Oh

first: J

last: Keller McKowen

first: Maheshi

last: Dassanayake

middle: M


title: Selection and Gene Flow Shape Genomic Islands that Control Floral Guides

status: Public on Aug 18 2018

city: Cambridge

first: Yrjö

last: Helariutta

address: 47 Bateman Street,

department: Sainsbury Laboratory

country: United Kingdom

institute: University of Cambridge

summary: Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands.  It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow.  Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone.  We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies.  The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact.  This barrier affects the selected flower color genes and tightly linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome.  Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence while heterogeneous gene flow flattens the surrounding “sea”, making the island of divergence stand out.   By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.

overall_design: A total of 21 samples from 7 different genotype combinations for the linked ROSEA and ELUTA flower colour loci. Each genotype has 3 replicates.

first: Hugo

last: Tavares

first: Annabel

last: Whibley

first: David

middle: L

last: Field

first: Desmond

last: Bradley

first: Matthew

last: Couchman

first: Lucy

last: Copsey

first: Joane

last: Elleouet

first: Monique

last: Burrus

first: Christophe

last: Andalo

first: Miaomiao

last: Li

first: Qun

first: Yongbiao

last: Xue

first: Alexandra

middle: B

last: Rebocho

first: Nick

last: Barton

first: Enrico

last: Coen


title: Analysis of the mRNA content of bovine oviductal extracellular vesicles during the estrous cycle

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary:
The success of the early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (e.g. proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviduct EVs composition and their implications in reproductive success. The objective of our study was to determine the changes of oviductal EVs mRNA content under the hormonal influence during the estrous cycle.
Methods: EVs, exosomes and microvesicles, were isolated from  bovine oviductal fluid at different stages of the estrous cycle (postovulatory-stage, early luteal phase, late luteal phase and pre-ovulatory stage). Total RNA was isolated and used for the preparation of RNA-seq libraries. RNA-sequencing was performed on an Illumina HiSeq 2500. The obtained sequence reads that passed quality filters were mapped to the bovine genome sequence using Hisat 2. Read counts were calculated with QuasR Qcount and statistical analysis with EdgeR to identify differential mRNA abundance across the different stages of the estrous cycle.
Results: RNA-sequencing identified 903 differentially expressed transcripts (FDR<0.001) in bovine oviductal EVs across the estrous cycle. Major differences were found between post-ovulatory and the rest of the stages analyzed.Functional annotation of the differentially abundant mRNAs identified functions related to cilia expression, exosome/vesicles, and many transcripts encoding ribosomal proteins.
Conclusions: Our findings represent the first extensive oviductal signature of bovine oviductal EVs mRNA content and contribute to a better understanding of the role of EVs as modulators of gamete/embryo-maternal interactions.

overall_design: Messenger RNA profiles of bovine oviductal extracellular vesicles during the estrous cycle were generated by RNA-sequencing of samples collected from 4 stages with 5 replicates per stage, using Illumina HiSeq 2500

first: Carmen

last: Almiñana


title: Analysis of the mRNA and small non-coding RNA content of bovine oviductal extracellular vesicles during the estrous cycle

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

overall_design: Refer to individual Series


title: Nicaragua Dengue Natural Infection

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

summary: These 40 microarray datasets represent whole blood samples from 31 primary dengue infection patients and 9 healthy volunteers from Managua, Nicaragua. The dengue infection patients include both primary dengue fever (DF) and primary dengue hemorrhagic fever (DHF) cases.


title: Expression data of H2O2 responding genes at Arabidopsis root tip

city: Nagoya

first: Hironaka

last: Tsukagoshi

state: Aichi

address: 1-501 Shiogamaguchi, Tempaku-ku

department: Faculty of Agriculture

country: Japan

institute: Meijo University

summary: To identify genes that regulate root development in a hydrogen peroxide devendent manner, we performed a time course microarray analysis of root treated with 1mM H2O2.

overall_design: We isolated RNA of non-treated roots and roots treated for 1, 3, and 6 hours. To assess expression responses of proliferating and elongating cells, we dissected each harvested the meristematic and elongation zones of root tips separately.

first: Wolfgang

last: Busch


title: ChIP-Chip tiling array for H3k27ac in mouse β-TC3 cells over panel of genes including Pax6, Sox2, Otx2, Sox9.

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

type: Genome binding/occupancy profiling by genome tiling array

summary:
Enhancer identification using H3k27ac ChIP-ChIP in mouse β-TC3 cells, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9.
Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000),  Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

overall_design: Two biological replicates of β-TC3 H3K27ac ChIP hybridized versus input DNA.

first: Adam

last: Buckle

first: Ryu-Suke

last: Nozawa

first: Dirk

middle: A

last: Kleinjan

last: Gilbert


title: Analysis of the small non-coding RNA content of bovine oviductal extracellular vesicles during the estrous cycle

summary:
The success of the early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (e.g. proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviduct EVs composition and their implications in reproductive success. The objective of our study was to determine the changes of oviductal EVs small ncRNA content under the hormonal influence during the estrous cycle.
Methods: EVs, exosomes and microvesicles, were isolated from bovine oviductal fluid at different stages of the estrous cycle (postovulatory-stage, early luteal phase, late luteal phase and pre-ovulatory stage). RNA enriched for short molecules was isolated and used for the preparation of small RNA-seq libraries. RNA-sequencing was performed on an Illumina HiSeq 2500. The obtained sequence reads that passed quality filters were annotated by BLAST alignment to various sets of non-coding and coding RNAs. Read counts were calculated based on the frequency of unique sequences after removal of PCR duplicates. Statistical analysis was done with EdgeR to identify differential small ncRNA abundance across the different stages of the estrous cycle.
Results: Small RNA-Seq identified the presence of different types of ncRNAs (miRNAs, rRNA fragments, tRNA fragments, snRNA, snoRNA, and other ncRNAs), which were partially also under hormonal influence. Major differences were found between post-ovulatory and early luteal and the rest of the stages for small ncRNAs. Interesting miRNAs identified in oviductal EVs, miR-34b and miR-449a, showed differential abundance among stages. Dysregulation of these miRNAs has been associated with defective cilia in the oviduct and infertility.
Conclusions: Our findings represent the first extensive oviductal signature of bovine oviductal EVs miRNA content and contribute to a better understanding of the role of EVs as modulators of gamete/embryo-maternal interactions.

overall_design: Small ncRNA profiles of bovine oviductal extracellular vesicles during the estrous cycle were generated by small RNA-sequencing of samples collected from 4 stages with 5 replicates per stage, using Illumina HiSeq 2500.


title: The Epigenetic Factor Landscape of Developing Neocortex is Regulated by Transcription Factors Pax6→Tbr2→Tbr1

status: Public on Jul 30 2018

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Epigenetic factors (EFs) regulate multiple aspects of cerebral cortex development, including proliferation, neuronal differentiation, laminar fate, and regional identity. The same neurodevelopmental processes are also regulated by transcription factors (TFs), notably the Pax6→Tbr2→Tbr1 cascade expressed sequentially in radial glial progenitors, intermediate progenitors, and postmitotic projection neurons, respectively. Here, we studied the EF landscape and its regulation in embryonic mouse neocortex. Microarray and in situ hybridization assays revealed that many EF genes are expressed in specific cortical cell types, such as intermediate progenitors, or in rostrocaudal gradients. Furthermore, many EF genes are directly bound and transcriptionally regulated by Pax6, Tbr2, or Tbr1, as determined by chromatin immunoprecipitation-sequencing and gene expression analysis of TF mutant cortices. The results demonstrated that Pax6, Tbr2, and Tbr1 form a direct feedforward genetic cascade, with direct feedback repression. Results also revealed that each TF regulates multiple EF genes that control DNA methylation, histone marks, chromatin remodeling, and noncoding RNA.

overall_design: Tbr1 knockout (KO), Tbr2 conditional knockout (cKO), and Tbr1/2 double KO/cKO (dKO) mouse embryos were produced as described (Bedogni et al., 2010a; Elsen et al., 2013). The Tbr1/2 double mutants were generated by breeding to combine the necessary alleles (Tbr1/;Tbr22F/2F;Nes11Cre). On E14.5, embryos were harvested, and neocortex was immediately dissected and frozen. Genotypes were determined by PCR 216 of tail DNA. Controls were wild type (+/+) for Tbr1 and non-recombined for Tbr2. Each embryonic neocortex was an independent biological replicate. For each genotype, n = 4 samples of neocortex were analyzed by microarray (Affymetrix ST 1.0). The microarray results were analyzed statistically as described (Elsen et al., 2013). In the current paper, we also analyzed previous microarray data from Tbr1 KO (Bedogni et al., 2010a) and Tbr2 cKO (Elsen et al., 2013) neocortices, designated microarray 1 (MA1); the new microarray data were designated microarray 2 (MA2). Tbr1/2 dKO neocortex was analyzed only in MA2.

first: Gine

middle: E

last: Elsen

first: Francesco

last: Bedogni

first: Rebecca

middle: D

last: Hodge

first: Theo

last: Bammler

middle: W

first: Susan

last: Lindtner

first: John

last: Rubenstein

first: Robert

middle: F

last: Hevner


title: Decoding the regulatory logic of the Drosophila male stem cell system

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

institute: Universität Heidelberg, Centre for Organismal Studies

summary: The importance of the niche to provide regulatory inputs to balance stem cell self-renewal and differentiation has become clear. However, the regulatory interplay between stem cells and their niche at the whole genome level is still poorly understood. To elucidate the mechanisms controlling stem cells and their progenies as they progress through development at the transcriptional level, we recorded the regulatory program of two independent cell lineages in the Drosophila testis. We identified genes active in the soma or germline as well as genome-wide binding profiles of two transcription factors, Zfh-1 and Abd-A, expressed in somatic support cells and crucial for fate acquisition of both cell lineages. In order to uncover gene activities in the testis soma, we first determined the transcriptome of the somatic and germline lineages by RNA polymerase II Targeted DamID (TaDa) (Southall et al., 2013), followed by the identification of genes bound by two regulators active in somatic sub-populations and controlling their development using regular DNA adenine methyltransferase identification (DamID) (Van Steensel et al., 2001). For identifying abd-A and Zfh1 binding regions in the Drosophila testis the fusion protein was expressed from the uninduced minimal Hsp70 promoter of the UAS vector pUAST. As a control for nonspecific Dam activity, transgenic flies expressing the Dam alone were used (Choksi et al., 2006). To express the AbdA-Dam fusion protein, we first generated a pNDam-Myc-abdA construct by cloning abdA in the pNDam-Myc vector (van Steensel et al., 2001) and then subcloned the NDam-Myc-abdA fragment into the pUAST-attB and to express the Zfh1-Dam fusion protein, we first generated a pNDam-Myc-zfh1 construct by cloning zfh1 in the pNDam-Myc vector (van Steensel et al., 2001) and then subcloned the NDam-Myc-zfh1 fragment into the pUAST-attB. For targeted DamID (TaDa) in Drosophila 3rd instar testes cyst and germline cells. Cell-type specific DamID was performed in cyst cells (CySCs and SCCs) and early germline of 3rd instar larval testes for profiling RNA Pol II occupancy in these cells by crossing UAS-LT3-Dam-Pol II and UAS-LT3-Dam control flies to c587-GAL4 (somatic lineage) or Nanos-GAL4 (early germline) drivers. For Dam-ID two individual replicates of Dam-abd-A, Dam-Zfh1 and Dam alone have been generated whereas for TaDa, two individual replicates of c587>UAS-LT3-Dam-PolII, Nanos>UAS-LT3-Dam-Pol II and c587>UAS-LT3-Dam (control), Nanos>UAS-LT3-Dam (control) have been used. Following a methylation-sensitive DNA digestion and PCR amplification, DNA fragments from the above samples were labeled and hybridized to genomic Affymetrix arrays in duplicates (Protocol available at “www.flychip.org.uk”).

overall_design: Samples from testis.

first: Eugen

last: Rempel

first: Olga

last: Ermakova

first: Srividya

last: Tamirisa

first: Fani

last: Papagiannouli

first: Nils

last: Trost

first: Juliane

last: Mundorf

first: Samantha

last: Brunel

first: Naima

last: Ruhland

first: Jun

last: Zhou

first: Jan

first: Micheal

last: Boutros


title: Differential transcriptional responses of stem and differentiated non-stem cells to ionizing radiation exposure.

city: St. Louis

first: Girdhar

last: Sharma

state: MO

address: 4511 Forest Park

department: Radiation Oncology - Cancer Biology

institute: Washington University School of Medicine

summary: Cells differ in their response to ionizing radiation (IR) depending on the cell type, proliferation rate and cell cycle stage. Normal stem cells exhibit a radiosensitive phenotype contributing to normal tissue injury following radiotherapy, whereas differentiated cells are comparably resistant to IR-induced programmed cell death. An improved understanding of differential radiation responses in varying cellular contexts and their mechanistic distinction is imperative for efficient treatment of malignancies by radiotherapy. Low dose IR induced apoptosis is exclusively confined to the normal stem cells in multiple stem cell niches in vivo and the radiation hypersensitivity is recapitulated in primary stem cell culture models of embryonic and neuronal stem cells contrasting their isogenic differentiated non-stem radioresistant progeny. Transcriptional profiles of primary, early passage, mouse embryonic stem cells and isogenic differentiated non-stem cells were compared to discover genes that are selectively induced in stem cells, but not in differentiated cells; to characterize potential molecular regulators of stem cell radiosensitivity. These molecular insights may contribute to the development of therapeutics that minimize normal tissue injury.

overall_design: Mouse embryonic Stem Cells (ES) and isogenic differentiated non-stem cells (ED) were irradiated with 10Gy. Total RNA samples for expression profiling was obtained from ES & ED cells after 15minutes (ESRE and EDRE) and 4 hours (ESRL and EDRL) post IR. Irradiated sample was analyzed in triplicates along with unirradiated ES and ED control cells.

first: Sandeep

last: Misri

first: Keith

last: Jacobs

first: Dennis

last: Hallahan


title: Effect of DGAT knockdown on gene expression in A498 xenograft tumors

status: Public on Jul 28 2018

city: Philadelphia

first: Daniel

last: Ackerman

state: PA

address: 421 Curie Blvd, BRB II/III, Rm 646

institute: University of Pennsylvania

summary:
The metabolic enzyme diglyceride acyltransferase (DGAT) is responsible for the synthesis of triglycerides. Loss of its expression may sensitize cells to conditions of nutrient and oxygen that are commonly present in tumors. This study is designed to identify stress response pathways that may be induced following the shRNA-mediated knockdown of the two genes coding for the DGAT enzymes.
We used microarrays to detail the global programme of gene expression following DGAT knockdown in vivo and identified differentially regulated gene sets.

overall_design: A cell line was created from A498 ccRCC cells that effectively knocks down DGAT levels upon doxycycline administration. This cell line was used to grow subcutaneous tumors in NIH-III mice, which were then treated with doxycycline containing chow (200mg/kg) or control chow for 5 days before tumors were harvested and RNA was isolated for this microarray study.


title: Queen and worker honeybee castes are defined by alternative chromatin states during larval development. [ChIP-Seq]

status: Public on Jul 27 2018

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We use chromatin immunoprecipitation and high throughput sequencing to produce the first genome-wide maps of chromatin structure in the honeybee at a key larval stage where developmental canalization into queen or worker is irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification that most robustly defines caste and suggest that these regions may harbour caste-specific cis-acting elements such as enhancers.

overall_design: Replicate pools of 96hW and 96hQ for H3K36me3, H3K4me3, H3K27ac

first: Rob


title: Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression during blue light exposure in Arabidopsis

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

summary: uORF-mediated translation reguration

overall_design: Ribosome profiling

first: Yukio

last: Kurihara

first: Yuko

last: Makita

first: Mika

last: Kwashima

first: Tomoya

last: Fujita

first: Shintaro

last: Iwasaki

first: Minami

last: Matsui


title: NanoString comparison of immune gene expression between AIR patients, RP patients and controls

city: Ann Arbor

first: Steven

last: Lundy

state: MI

address: 4043 Biomedical Sciences Research Bldg 109 Zina Pitcher Place

department: Internal Medicine

institute: University of Michigan Medical School

summary: Autoimmune retinopathy patient whole blood mRNA was compared to patients with retinitis pigmentosa and non-eye disease controls.

overall_design: NanoString Human Immunology panel was performed on whole blood RNA (PAXgene) on untreated non-paraneoplastic AIR patients (n=14) selected based on clinical diagnosis. Clinically-defined RP patients with normal progression (n=14) and age/gender matched controls were compared.

first: Mohammad

middle: I

last: Othman

first: Rebecca

last: Tagett

first: John

middle: R

last: Heckenlively


title: Effect of DGAT loss on hypoxic tumor cells growing under serum-deprived conditions

summary:
The metabolic enzyme diglyceride acyltransferase (DGAT) is responsible for the synthesis of triglycerides. Loss of its expression may sensitize cells to conditions of nutrient and oxygen that are commonly present in tumors. This study is designed to identify stress response pathways that may be induced following the shRNA-mediated knockdown of the two genes coding for the DGAT enzymes. In vitro growth conditions lacking serum and oxygen were used to mimic growth conditions commonly found in poorly perfused tumor domains
We used a microarray study to identify global transcriptional changes in kidney cancer cells (A498) grown under serum deprived conditions. DGAT was knocked down using doxycycline, which induced DGAT1/2 shRNA expression. The effects of both DGAT loss and oxygen deprivation on the transcriptome were tested.

overall_design: Cells were grown under normoxia and serum replete conditions initially and plated onto all replicate plates. After overnight adherence, media was changed to low serum media and plates were randomly assigned to either vehicle or doxycycline treatment. Following 5 days of treatment, cells were exposed to 2 days of either normoxia or hypoxia (0.5% O2). Cells were collected in Trizol at the end of this 48h period of normoxia or hypoxia.


title: Effect of the genotoxic human lung carcinogen benzo[a]pyrene and its non-carcinogenic isomer benzo[e]pyrene on transcriptomic profiles in HepaRG cells.

status: Public on Jul 24 2018

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with 2 µM benzo[a]pyrene (B[a]P) and benzo[e]pyrene (B[e]P) for 72 hours. Following the treatment, the cells were harvested by mild trypsinization, washed in phosphate-buffered saline, and immediately frozen at −80°C for subsequent analyses. Gene expression profiles in the HepaRG cells treated with B[a]P and B[e]P were investigated using Agilent whole genome 8x60K human microarrays according to the manufacturer’s instructions.

overall_design: Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with 2µM B[a]P or 2 µM B[e]P. Gene expression profiles in the HepaRG cells treated with BaP and BaP for 72 hours were investigated.

first: Kostiantyn

last: Dreval

first: Frederick

last: Beland

first: Igor

middle: P

last: Pogribny


title: Circulating Small Noncoding RNAs in Recovery after Exhaustive or Repetitive Exercise, in comparison to PAD patients

status: Public on Jul 26 2018

city: Leiden

first: Anne Yäel

last: Nossent

address: Albinusdreef 2

department: Department of Vascular Surgery

country: Netherlands

institute: Leiden University Medical Center

summary: Focus Panel measurements of Serum microRNAs during different time points before and after strenous exercise in professional athletes, as well as Peripheral Artery Disease patients.

overall_design: Biomarker study using blood samples drawn before strenous exercise, directly after as well as after 2 and 5 hours of restitution. For PAD patients, blood was drawn during hospital admission for leg amputation.

first: Kjell

last: Hakansson

first: Anne

middle: Y


title: Genome-wide maps of STAT1, STAT2 and IRF9 in conjunction with nucleosome occupancy maps at 20 interferon-stimulated gene regions during steady state and after type I interferon stimulation.

city: Evanston

first: Nancy

last: Au-Yeung

state: IL

address: 2200 Campus Dr

institute: Northwestern University

summary: The genome-wide distributions of STAT1, STAT2 and IRF9 in mock and interferon alpha (IFN) stimulated human cells was generated using high throughput sequencing to identify ISGF3 genomic occupancy. In combination, the nucleosome occupancy of 20 select IFN-stimulated gene regions were analyzed by direct selection MNase sequencing to determine the nucleosome positions and changes in nucleosome occupancy levels following IFN treatment over time. IFN stimulation resulted in decreased nucleosome positioning strength, with clear disruption over the course of IFN treatment followed by a return to steady state, and prominently at most ISGF3-bound regions.

overall_design: Examination of 3 proteins genome-wide and nucleosome occupancy at 20 interferon-stimulated gene regions during steady state and after type I interferon stimulation in 1 human cell line.

first: Curt

last: Horvath


title: Queen and worker honeybee castes are defined by alternative chromatin states during larval development

first: Robert

last: Lowe


title: Expression data from MCF-7 breast cancer cells grown in 2D and 3D

city: Farmington

first: Nicole

last: Farra

state: Connecticut

address: 263 FARMINGTON AVE

department: Molecular Biology and Biophysics

institute: University of Connecticut Health

summary: We used a microarray to examine the global gene expression profile of MCF7 cells grown in 2D and 3D culture conditions.  Our goal was to identify changes in the expression of genes that regulate iron metabolism when cellular spatial organization was altered.

overall_design: MCF-7 cells were grown as 2D monolayers or 3D spheroids for 3 days before RNA extraction and hybridization on Affymetrix microarrays. We used three different 3D culture methods: Poly(2-hydroxyethyl methacrylate) (pHEMA) coated U-bottom 96-well plates, Ultra-Low Attachment 96-well plates (Corning), or the additional of methylcellulose as an aggregating agent to U-bottom 96-well plates

last: Blanchette-Farra

first: David

last: Lemler

first: Anna

last: Konstorum

first: Suzy

middle: V

last: Torti


title: Abberant lncRNA expression profiles in recurrent implantation failure endometrium

city: Beijing

first: Fan

middle: Li

last: juan

state: Beijing

address: 11th Xizhimen south street,Xicheng district

department: Reproductive medical Center

country: China

institute: Peking University Peoples' Hospital

summary:
To compare the lncRNA expression profile of RIF (recurrent implantation failure) and normal control endometrium,endometrium samples were collected at window of implantation (LH+6~10 days)
The dysregulated lncRNAs between RIF and control group were deem to be involve in the regulation of endometrium receptivity

overall_design: Compare RIF and control group endometrium lncRNA expression profile at window of implantation

last: Lijuan

first: Shi

last: Cheng


title: Activation of IL5R and CRTH2 on Human Eosinophils Elicit a Similar Molecular Response and Reveal a Synergistic Effect

status: Public on Jul 25 2018

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

institute: Idorsia Pharmaceuticals Ltd.

summary:
Eosinophils represent key cells driving inflammatory processes in asthma and eosinophilic esophagitis (EoE). Eosinophils migration and activation in disease is orchestrated by a myriad of molecules among which prostaglandin D2, the cognate ligand of CRTH2, and interleukin 5 play a crucial role. In clinical studies with CRTH2 antagonists and anti-IL-5 antibodies, a reduction of the number of eosinophils in disease tissue of asthma and EoE patients was demonstrated, validating the pharmacological effects on eosinophils migration. In contrast, activation of eosinophils through IL5 or CRTH2 receptor has not been studied to the same extent. Understanding the molecular CRTH2 and IL5 activation bias in disease would provide a better assessment of pharmacological intervention, or the need for a combination therapy, to block eosinophils efficiently.
We performed gene expression profiling studies with isolated human eosinophils to compare the molecular signatures of CRTH2 and IL5 receptor activation. Furthermore we employed gene set enrichment analysis to query the eosinophils activation bias in asthma and EoE.  We observed that activation of CRTH2 and IL5 on human eosinophils shared a large part of the molecular response but also present distinct molecular signatures. Remarkably, FADS1, involved in the synthesis of prostaglandin D2, was identified as a specific CRTH2-induced gene that is counter-regulated by IL5, potentially representing a feedback loop between CRTH2 and IL5 receptor.
In silico use of the identified gene signatures and FADS1 demonstrated an enrichment of the IL5 activation signature in lung tissue of asthma patients, whereas esophagus tissue of EoE patients presented a CRTH2 bias.

overall_design: Comparison of IL-5 or dk-PGD2 stimulated human eosinophils against vehicle with 6 biological replicates for each condition.

first: Anastasia

last: Murat

first: Virginie

last: Sippel

first: Bérengère

last: Renault

first: Julie

last: Hoerner

first: Peter

last: Groenen

first: Daniel

middle: S

last: Strasser


title: Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary: F0 generation rats were exposed to vinclozolin, and the subsequent F1, F2 and transgenerational F3 generations are evaluated for diseases and pathologies. F3 generation rats showed transgenerational increases in testis, prostate, and kidney disease, changes in the age of puberty onset in males, and an increased obesity rate in females. Overall there was an increase in the rate of animals with disease, and in the incidence of animals with multiple disease. The methylation of the F3 vinclozolin lineage rat samples was determined using MeDIP-seq. Unique signatures of differential DNA methylation regions (DMRs) in sperm were found that associated with testis disease, prostate disease and kidney disease, however, these signatures were not statistically significant.

overall_design: Outbred gestating female rats were transiently exposed to a vehicle control or vinclozolin. The F1 generation offspring were bred to generate the F2 generation and then the F2 generation bred to generate the F3 generation. The F3 generation control and atrazine lineage rats were aged and various pathologies investigated. The male sperm were collected to investigate DNA methylation differences between the vinclozolin lineage sperm from samples with different disease outcomes. MeDIP-seq was used to measure methylation in each sample.

first: Eric

last: Nilsson

first: Setphanie

last: King

first: Margaux

last: McBirney

first: Deepika

last: Kubsad

first: Michelle

last: Pappalardo

last: Beck

first: Ingrid

last: Sadler-Riggleman


title: The role of lncRNA bound to IκBα and p65 in the sensitivity to AICD of tumor-specific T cells

status: Public on Jul 23 2018

city: Guangzhou

first: Di

last: Huang

address: 107 Yanjiang West Road

institute: Sun-Yat-sen Memorial Hospital

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

summary: Analysis of p65 and IκBα binding lncRNA profile in T cells primed by MDA-MB-231-lysate pulsed DCs for 6 days. Results provide insight into the molecular mechanisms underlying tumor-mediated AICD in T cells.

overall_design: Mononuclear cells were obtained from peripheral blood of three HLA-A2+ healthy donors and cultured for 14 d in serum-free X-VIVO 20 medium (BioWhittaker, Walkersville, Maryland) with human GM-CSF (50 ng/ml; Peprotech) and IL-4 (20 ng/ml; Peprotech). Non-adherent DCs were enriched by depletion of contaminating T and B lymphocytes and pulsed for 20 h with lysates (200 μg protein/1 × 10^6 cells/ml) from MDA-MB-231 (HLA-A2+) that were lysed by 5 freeze/thaw cycles. T cells were incubated for 13 d in RPMI-1640 with 10% human AB serum (PromoCell) and IL-2 (25 U/ml; Peprotech) followed by incubation in the same medium with antigen-specific DCs (5:1) for 6 days. T cells were retrieved from the cocultures at day 6.T cells were lysed with RIP lysis buffer supplemented with protease inhibitor cocktail and RNase Inhibitor (1000U/ml, Ambion), followed by incubation with p65,  IκBα or control IgG antibody-coated microbeads at 4℃ overnight.After the immunoprecipitation, the coprecipitated RNA were extracted. The quality of extracted RNA was assessed using the NanoDrop ND-2000 spectrophotometer.


title: Queen and worker honeybee castes are defined by alternative chromatin states during larval development [RNA-Seq]

first: Robert

last: Lowe

overall_design: 96hQ and 96hW larval heads were profiled by RNA-Seq using 4 replicates each

first: Rob


title: RNA-seq transcriptome profiling of 1) C. elegans male germlines vs. oogenic germlines, and 2) male germlines, sperm, and F1 offspring germlines when offspring inherited sperm chromatin lacking H3K27me3.

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Paternal contributions to epigenetic inheritance are not well understood. We report that in C. elegans sperm, the genome is packaged in nucleosomes and carries a histone-based epigenetic memory of gene expressions during spermatogenesis. In mature sperm, genes with spermatogenesis-specific expression are marked with both active and represseive histone modifications and genes with oogenesis-enriched expression are marked with active histone modifications. We showed that genes with oogenesis-enriched expression are in fact transcribed in spermatogenic germlines. We tested if sperm chromatin marking is necessary for germ cell development in offspring that inherit both sperm and oocyte chromosomes, using male parents that either can or cannot generate H3K27me3. Males homozygous for a mutation in mes-3, which encodes a member of the worm PRC2 complex, were mated with feminized mes-3/+ heterozygous worms to produce offspring that inherited sperm chromosomes lacking H3K27me3. We call these offspring M+P- or MpPm (Maternal chromosomes are + or plus for H3K27me3, Paternal chromosomes are - or minus for H3K27me3). Most of the resulting mes-3 homozygous M+P- offspring developed into sterile adults in this sensitized genetic background. In contrast, genetically identical control offspring that received appropriate H3K27me3-marked sperm chromosomes (M+P+ or MpPp) displayed low sterility. We compared genes mis-regulated in mes-3 male germlines versus control him-8 male germlines, mature sperm from those germlines, and germlines of mes-3 mutant F1 offspring that inherited sperm chromatin lacking H3K27me3 (M+P-) versus inherited sperm chromatin with H3K27me3 (M+P+), based on RNA-seq.

overall_design: 1) Transcriptome profiles of male germlines (2 replicates from N2 wild-type males and 4 replicates from him-8 males) vs. oogenic germlines (3 replicates from N2 hermaphrodites and 3 replicates from fem-2 females). 2) mes-3 male germlines (3 replicates) vs. control him-8 male germlines (4 replicates), mes-3 sperm (3 replicates) vs. control him-8 sperm (3 replicates), and F1 M+P- germlines (2 replicates) vs. genetically identical F1 M+P+ germlines (2 replicates).

first: Tomoko

middle: M

last: Tabuchi

first: Andreas

last: Rechtsteiner


title: Nucleosome occupancy of C. elegans wild-type (N2) early stage embryos vs. mature sperm from him-8(e1489) males

summary: To determine how the genome is packaged in C. elegans sperm, we isolated adult him-8(e1489) males and collected mature sperm (~99% purity). We utilized micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq) to evaluate the presence of nucleosomes across the genome in sperm vs. early embryos. We found that the sperm genome retains nucleosomes genome-wide, comparable to wild-type early embryos.

overall_design: Examination of nucleosome occupancy using MNase-seq in 2 replicate samples from C. elegans sperm and early embryos


title: C. elegans germlines that inherited only paternal chromosomes (non-Mendelian inheritance, 'red-head worms') and the germlines of their offspring  vs.  germlines that inherited both maternal and paternal chromosomes (Mendelian inheritance, HBR1280 control)

summary:
RNA-seq transcriptome analysis of C. elegans germlines that inherited only paternal chromosomes (non-Mendelian inheritance, 'red-head worms') and the germlines of their offspring ('offspring of red-head worms') vs. germlines that inherited both maternal and paternal chromosomes (Mendelian inheritance, HBR1280 control).
Given that epigenetic marking of sperm chromosomes is faithfully transmitted through embryo cell divisions, and that sperm epigenetic marking is important in offspring, we tested if sperm epigenetic marking alone is sufficient for proper development of the germline in offspring. We utilized a mutant that, during the first embryonic division, delivers the sperm genome to the daughter cell that generates the germline and the oocyte genome to the other daughter cell (Besseling & Bringmann, 2016). This mutant over-expresses GPR-1, a protein involved in regulation of kinetochore pulling forces. GPR-1 over-expression results in excessive pulling forces, causing the paternal and maternal pronuclei to inappropriately move to opposite poles of the 1-cell embryo instead of merging in the center of the embryo. In this mutant background, ~60% of offspring undergo atypical chromosome segregation, generating mosaic embryos whose germlines are derived entirely from sperm chromosomes (Besseling & Bringmann, 2016). To track the parental genomes, differentially tagged histone transgenes were used: a GFP-tagged histone H2B encoded in the sperm genome, and a TdTomato-tagged histone H2B encoded in the oocyte genome. The mosaic embryos whose germline inherited only sperm chromosomes (‘red-head' worms) develop into fertile adults with a normal brood size, similar to control worms, in which the germline inherited both sperm and oocyte chromosomes. RNA-seq analysis demonstrated that the germline transcriptome of ‘red-head’ worms and their offspring show few (<80 genes) and minor changes compared to control worms. These findings demonstrate that epigenetic information provided by sperm can guide proper germ cell development.

overall_design: Germlines from 'red-head' worms (2 replicates), germlines from offspring of 'red-head' worms (2 replicates) vs. control germlines from HBR1280 (2 replicates)


title: Epigenome of C. elegans sperm, oocytes, and early embryos (MNase-seq, ChIP-seq, RNA-seq)

summary:
This SuperSeries is composed of the SubSeries listed below.
The reanalyzed early embryo ChIP-seq data can be found in the GSE115704 SubSeries.

overall_design: Refer to individual Series


title: Analysis of gene expression in wildtype and PPARdelta knockout naïve CD4+ T cells

status: Public on Jul 21 2018

city: Toronto

first: Shannon

last: Dunn

state: ON

address: 30 Bond Street, Office Location: 209 Victoria Street, 5th floor, 516

department: Keenan Research Centre for Biomedical Research

country: Canada

institute: St. Michael's Hospital

summary:
The goal of this study was to identify differences in gene expression between wildtype and PPARdelta knockout CD4+ T cells. CD62L+CD4+ T cells were magnetically isolated from N=6 WT and N=6 knockout mice per group.
Cells were cryopreserved immediately or after a 20 h stimulation in culture with anti-CD3 and anti-CD28 for total RNA isolation.

overall_design: Total RNA was obtained from naïve CD4+ T cells that were freshly isolated from wildtype and PPARdelta knockout mice or from these cells that had been stimulated for 20 h in vitro with anti-CD3 and anti-CD28.


title: lnc-Mir100HG promotes cell proliferation by modulating the interation between HuR and its target mRNAs

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Long non-coding RNAs (lncRNAs) regulate vital biological processes, including cell proliferation, differentiation and development. A subclass of lncRNAs is synthesized from microRNA host genes (MIRHGs) due to pre-miRNA processing, and is categorized as miRNA-host gene lncRNAs (lnc-miRHGs). Presently, it is not clear whether lnc-miRHG perform additional functions.  We demonstrate a miRNA-independent role for a nuclear-enriched lnc-miRHG in cell cycle progression. MIR100HG produces spliced and stable lncRNAs (lnc-MIR100HG) that display elevated levels during the G1 phase of the cell cycle. Depletion of lnc-MIR100HG in human cells results in aberrant cell cycle progression with out altering the levels of miRNA encoded within MIR100HG. Notably, lnc-MIR100HG interacts with the HuR/Elav as well as with several of HuR-target mRNAs. Further, lnc-MIR100HG-depleted cells show reduced interaction between HuR and its target mRNAs, indicating that lnc-MIR100HG facilitates interaction between HuR and target mRNAs. Our studies have unearthed novel roles played by miRHG-encoded lncRNAs in regulating RNA binding protein activity, thereby underscoring the importance of determining the function of several hundreds of miRHG lncRNAs that are present in human genome.

overall_design: RNA samples were collected in biological triplicates from U2OS control and AS knock down Lnc-MiR100HG.

first: Ling

middle: L

last: Xiao

first: Prasanth

last: Kannanganattu

first: Ashish

last: Lal


title: The mRNA and lncRNA profiles of the T cells activated by breast tumor-specific DCs pulsed by MDA-MB-231 lysates at day 0, day 1 and day 6

summary: Activation induced cell death (AICD) of T lymphocytes may be exploited by cancers to eliminate cytotoxic T cells (CTLs). Here, we demonstrated excessive apoptosis of tumor antigen-specific CTLs in breast and lung cancers. Interestingly, NKILA, an NF-κB interacting lncRNA, sensitizes CTLs to AICD by inhibiting NF-κB activities after their activation. In vivo, administering CTLs with NKILA silencing into immunocompromised mice with breast cancer patient derived xenografts (PDXs) effectively inhibits PDX growth by increasing CTL infiltration. Clinically, NKILA was overexpressed in the tumor specific CTLs of breast and lung cancers, which was associated with less CTL infiltration in the tumors and shorter patient survival. Our findings present the first evidence that AICD in patient tumor-specific CTLs is crucial to cancer immune evasion, and targeting NKILA in CTLs emerges as a novel anti-tumor immunotherapy.

overall_design: Mononuclear cells were obtained from peripheral blood of three HLA-A2+ healthy donors and cultured for 14 d in serum-free X-VIVO 20 medium (BioWhittaker, Walkersville, Maryland) with human GM-CSF (50 ng/ml; Peprotech) and IL-4 (20 ng/ml; Peprotech). Non-adherent DCs were enriched by depletion of contaminating T and B lymphocytes and pulsed for 20 h with lysates (200 μg protein/1 × 10^6 cells/ml) from MDA-MB-231 (HLA-A2+) that were lysed by 5 freeze/thaw cycles. T cells were incubated for 13 d in RPMI-1640 with 10% human AB serum (PromoCell) and IL-2 (25 U/ml; Peprotech) followed by incubation in the same medium with antigen-specific DCs (5:1) for 6 days. T cells were retrieved from the cocultures at day 0, day 1 and day6. Total RNA was extracted from T cells with indicated treatments (5 x 106 cells) using the TRIzol Reagent (Cat#A33251, Thermo Fisher). The quality of extracted RNA was assessed using the NanoDrop ND-2000 spectrophotometer.


title: Distribution of histone modifications across the genome in C. elegans sperm vs. oocytes vs. early embryos

summary: Here we report that the Caenorhabditis elegans sperm genome is packaged in nucleosomes and carries a histone-based epigenetic memory of genes with spermatogenesis-restricted expression and surprisingly genes with oogenesis-enriched expression as well. In sperm, spermatogenesis genes are uniquely marked with both active and repressive marks, which may reflect a sperm-specific chromatin signature.

overall_design: Examination of three histone modifications in 2 replicate samples of C. elegans sperm, oocytes, and early embryos

first: Tess

last: Jeffers

first: Coleen

middle: T

last: Murphy


title: Candida albicans Sfl1/Sfl2 regulatory network drives the formation of pathogenic microcolonies.

city: Buffalo

first: Mira

last: Edgerton

state: New York

address: 3435 Main St

department: Oral Biology

institute: University at Buffalo

summary: Candida albicans is an opportunistic fungal pathogen that can infect oral mucosal surfaces despite being under continuous flow from saliva. Previous studies have shown that under specific conditions C. albicans will form microcolonies that more closely resemble the biofilms formed in vivo than standard in vitro biofilm models. However, very little is known about these microcolonies, particularly genomic differences between these specialized biofilm structures and the traditional in vitro biofilms. In this study, we used a novel flow system, in which C. albicans spontaneously forms microcolonies, to further characterize the architecture of fungal microcolonies and their genomics compared to non-microcolony conditions. Fungal microcolonies arise from radially branching filamentous hyphae that increasingly intertwine with one another to form extremely dense biofilms, and closely resemble the architecture of in vivo oropharyngeal candidiasis. We identified 20 core microcolony genes that were differentially regulated in flow-induced microcolonies using RNA-seq. These genes included HWP1, ECE1, IHD1, PLB1, HYR1, PGA10, and SAP5. To better understand the regulatory elements for microcolonies, we utilized a predictive algorithm to discover ten transcriptional regulators potentially involved in microcolony formation. Of these transcription factors, we found that six played a key role in microcolony formation and development (Rob1, Ndt80, Efg1, Sfl1, Sfl2, and Nrg1). We also found that Hwp1, Sap5, Pga10, and all the microcolony regulators promoted adhesion and invasion of the microcolonies to oral epithelium. Furthermore, epithelial cells infected with deletion mutants of ROB1, NDT80, SFL2, EFG1, and MCM1 had reduced immune response, evidenced by reduced phosphorylation of MKP1 and c-Fos, key signal transducers in the hyphal invasion response. This profile of microcolony transcriptional regulators more closely reflects Sfl1 and Sfl2 hyphal regulatory networks than biofilm regulatory networks, suggesting that hyphal morphogenesis plays a more central role in the development of flow-induced microcolonies.

overall_design: RNA expression profiles of 24 h C. albicansbiofilms grown under flow (at 37 °C or 23 °C) or static (at 37°C) conditions generated by duplicate analyses using Illumina HiSeq 2500

first: Andrew

last: McCall

first: Rohitashw

last: Kumar


title: Genome wide analysis of BCL3 mediated chemotherapy resistance

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

summary: We identify the atypical inhibitor-κB protein, Bcl3, as a novel biomarker in gliomas whose expression level predicts response to therapy. Bcl3 is found at 19q13 and its expression level in glioma is regulated by copy number alteration. Mechanistically, Bcl3 mediates mesenchymal differentiation and its presence promotes resistance to cytotoxic DNA damage.

overall_design: The U87 cells was transfected with siRNA targeting BCL3 (dharmacon) or control siRNA, and followed by temozolomide treatment (100uM) for 24 hr before RNA extraction.

first: Longtao

last: Wu

first: Kirk

last: Cahill


title: The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression II

status: Public on Jul 20 2018

first: Mark

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary:
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARG), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RARG expression, and determine RARG regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARG levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARG cistrome which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARG to regulate androgen signaling, RARG knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARG down-regulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARG expression and function. Capture of the miR-96 targetome by biotin-miR96 identified that RARG and a number of RARG  interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARG  target genes (e.g. SOX15) that significantly associated with worse disease free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p=0.015). In summary, miR-96 targets a RARG network to govern AR signaling, PCa progression and disease outcome.
LNCaP malignant prostate cell line +/- shRARG, +/- 250nM CD437 for 24 hours

overall_design: 12 sample total, 4 experimental conditions (each in triplicate); shCTL-DMSO, shCTL_CD437, shRARG-DMSO, shRARG-CD437

first: Dominic

middle: J

last: Smiraglia

first: Moray

last: Campbell


title: The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression III

summary:
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARG), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RARG expression, and determine RARG regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARG levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARG cistrome which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARG to regulate androgen signaling, RARG knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARG down-regulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARG expression and function. Capture of the miR-96 targetome by biotin-miR96 identified that RARG and a number of RARG  interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARG  target genes (e.g. SOX15) that significantly associated with worse disease free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p=0.015). In summary, miR-96 targets a RARG network to govern AR signaling, PCa progression and disease outcome.
RWPE-1 non-malignant prostate cell line +/- 30nM bi-NC or bi-96, Pulldown & Input (24 hr post-transfection)

overall_design: 12 sample total, 4 groups (each in triplicate); bi-NC PD, bi-96 PD, bi-NC input, bi-96 input


title: The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression IV

summary:
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARG), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RARG expression, and determine RARG regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARG levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARG cistrome which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARG to regulate androgen signaling, RARG knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARG down-regulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARG expression and function. Capture of the miR-96 targetome by biotin-miR96 identified that RARG and a number of RARG  interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARG  target genes (e.g. SOX15) that significantly associated with worse disease free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p=0.015). In summary, miR-96 targets a RARG network to govern AR signaling, PCa progression and disease outcome.
RWPE1 non-malignant, immortalized cell line +/- shRARG, +/- 10nM CD437 for 24 hours


title: The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression I

summary:
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARG), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RARG expression, and determine RARG regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARG levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARG cistrome which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARG to regulate androgen signaling, RARG knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARG down-regulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARG expression and function. Capture of the miR-96 targetome by biotin-miR96 identified that RARG and a number of RARG  interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARG  target genes (e.g. SOX15) that significantly associated with worse disease free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p=0.015). In summary, miR-96 targets a RARG network to govern AR signaling, PCa progression and disease outcome.
LNCaP malignant prostate cell line +/- 30nM bi-NC or bi-96, Pulldown & Input (24 hr post-transfection)


title: In vitro gene signature of keratinocytes

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

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


title: In vitro gene signature of cultured volar or nonvolar keratinocytes

summary:
How cell and tissue identity persist despite constant cell turnover is an important biologic question with cell therapy implications. While many mechanisms exist, we investigated the controls for site-specific gene expression in skin given its diverse structures and functions. For example, the transcriptome of in vivo palmoplantar (i.e. volar) epidermis is globally unique including Keratin 9 (KRT9). While volar fibroblasts have the capacity to induce KRT9 in non-volar keratinocytes, we demonstrate here that volar keratinocytes continue to express KRT9 in vitro solo-cultures. Despite this, KRT9 expression is lost with volar keratinocyte passaging, in spite of stable hypo-methylation of its promoter. Coincident with KRT9 loss is a gain of the primitive Keratin 7 and a signature of dsRNA sensing, including the dsRNA receptor DDX58. Exogenous dsRNA inhibits KRT9 expression in early passage volar keratinocytes or in vivo footpads of wild-type mice. Loss of DDX58 in passaged volar keratinocytes rescues KRT9 and inhibits KRT7 expression. Additionally, DDX58 null mice are resistant to the ability of dsRNA to inhibit KRT9 expression. These results demonstrate that the sensing of dsRNA is critical for loss of cell specific gene expression; our results have important implications of how dsRNA sensing is important outside of immune pathways.
Keratinocytes were expanded from both  the sole and the dorsum of the foot and at passage 4, RNA was extracted and sent for microarray analysis

overall_design: The same single human donor was the source of a single isolate of volar keratinocytes and a single isolate of nonvolar keratinocytes. At passage 4 total RNA was extracted and sent for microarray analysis


title: In vitro gene signature of volar keratinocytes at early vs late passage

summary:
How cell and tissue identity persist despite constant cell turnover is an important biologic question with cell therapy implications. While many mechanisms exist, we investigated the controls for site-specific gene expression in skin given its diverse structures and functions. For example, the transcriptome of in vivo palmoplantar (i.e. volar) epidermis is globally unique including Keratin 9 (KRT9). While volar fibroblasts have the capacity to induce KRT9 in non-volar keratinocytes, we demonstrate here that volar keratinocytes continue to express KRT9 in vitro solo-cultures. Despite this, KRT9 expression is lost with volar keratinocyte passaging, in spite of stable hypo-methylation of its promoter. Coincident with KRT9 loss is a gain of the primitive Keratin 7 and a signature of dsRNA sensing, including the dsRNA receptor DDX58. Exogenous dsRNA inhibits KRT9 expression in early passage volar keratinocytes or in vivo footpads of wild-type mice. Loss of DDX58 in passaged volar keratinocytes rescues KRT9 and inhibits KRT7 expression. Additionally, DDX58 null mice are resistant to the ability of dsRNA to inhibit KRT9 expression. These results demonstrate that the sensing of dsRNA is critical for loss of cell specific gene expression; our results have important implications of how dsRNA sensing is important outside of immune pathways.
Keratinocytes were expanded from  the sole of the foot and at passage 4 or 8, RNA was harvested to identify unique transcripts

overall_design: The same single volar isolate was tested one time at passage 4 and one time at passage 8. Total RNA was extracted and sent for microarray analysis


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [uPBM_Runx1Runx2]

status: Public on Jul 19 2018

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

type: Genome binding/occupancy profiling by array

summary: Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. Our finding was possible due to a unique combination of carefully designed high-throughput assays and rigorous computation modeling, integrated into a unified framework called iMADS. We used iMADS to quantity, model, and analyze specificity differences between 11 paralogous TFs from 4 distinct human TF families. Our finding of differential specificity between closely related TFs has important implications for the interpretation of the regulatory effects of non-coding genetic variants.

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, full-length, human transcription factors Runx1 and Runx2. Briefly, universal PBMs involved binding of GST-tagged transcription factors to double-stranded 44K Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [uPBM_Elk1Ets1Gabpa]

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, full-length, human transcription factors Elk1, Ets1, and Gabpa. Briefly, universal PBMs involved binding of GST-tagged transcription factors to double-stranded 44K Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.


title: Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor

status: Public on Jul 18 2018

city: Cambridge

first: Corinne

last: Pender

state: MA

address: 77 Massachusetts Ave

institute: MIT

summary: The HIF (hypoxia-inducible factor) transcription factor is the master regulator of the metazoan response to chronic hypoxia. In addition to promoting adaptations to low oxygen, HIF drives cytoprotective mechanisms in response to stresses and modulates neural circuit function. How most HIF targets act in the control of the diverse aspects of HIF-regulated biology remains unknown. We discovered that a HIF target, the C. elegans gene cyp-36A1, is required for numerous HIF-dependent processes, including modulation of gene expression, stress resistance, and behavior. cyp-36A1 encodes a cytochrome P450 enzyme that we show controls expression of more than a third of HIF-induced genes. CYP-36A1 acts cell non-autonomously by regulating the activity of the nuclear hormone receptor NHR-46, suggesting that CYP-36A1 functions as a biosynthetic enzyme for a hormone ligand of this receptor. We propose that regulation of HIF effectors through activation of cytochrome P450 enzyme/nuclear receptor signaling pathways could similarly occur in humans.

overall_design: RNA-seq experiment characterizing C. elegans strains mutant for one or more member of the egl-9/hif-1/cyp-36A1 signaling pathway. Experiment was performed with two biological replicates per strain. N2 was used as the wild-type control.

first: H

last: Horvitz


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [uPBM_E2f1E2f3E2f]

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, full-length, human transcription factors E2f1, E2f3, and E2f4. Briefly, universal PBMs involved binding of GST-tagged transcription factors to double-stranded 44K Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.


title: Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation

status: Public on Jul 17 2018

first: Yi

last: Zhang

address: 19 Xie Jie Kou Wai Street, Hai Dian District

institute: Beijing Normal University

summary: Upon illumination, etiolated seedlings experience a transition from heterotrophic to photoautotrophic growth. During this process, the tetrapyrrole biosynthesis pathway provides chlorophyll for photosynthesis. This pathway has to be tightly controlled to prevent the accumulation of photoreactive metabolites and to provide stoichiometric amounts of chlorophyll for its incorporation into photosynthetic protein complexes. Therefore, plants have evolved regulatory mechanisms to synchronize the biosynthesis of chlorophyll and chlorophyll-binding proteins. Two phytochrome-interacting factors (PIF1 and PIF3) and the DELLA proteins, which are controlled by the gibberellin pathway, are key regulators of this process. Here, we show that impairment of TARGET OF RAPAMYCIN (TOR) activity in Arabidopsis (Arabidopsis thaliana), either by mutation of the TOR complex component RAPTOR1B or by treatment with TOR inhibitors, leads to a significantly reduced accumulation of the photoreactive chlorophyll precursor protochlorophyllide in darkness but an increased greening rate of etiolated seedlings after exposure to light. Detailed profiling of metabolic, transcriptomic, and physiological parameters revealed that the TOR-repressed lines not only grow slower, they grow in a nutrient-saving mode, which allows them to resist longer periods of low nutrient availability. Our results also indicated that RAPTOR1B acts upstream of the gibberellin-DELLA pathway and its mutation complements the repressed greening phenotype of pif1 and pif3 after etiolation.

overall_design: Wild type or rb10 plants were grown on half MS media without sucrose under dark for 5 days. The etiolated seedling were exposed to white light for 1 hour or not. Microarray analysis was performed using Affymetrix Gene 1.0 ST Array (Thermo Fisher Scientific) with three biological replicates of WT and rb10 samples. Total RNA was isolated from pools of seedlings and labeling was performed using 1 μg RNA as previously described. Affymetrix Gene 1.0 ST Array hybridizations were performed by Atlas Biolabs.

first: Patrick

last: Giavalisco


title: Global alternative splicing analysis of cryptic splicing suppressors in C. elegans

first: Alan

last: Zahler

address: Sinsheimer Labs

summary: Dominant mutant alleles of prp-8 and snrp-27 were identifed in a forward genetic screen for suppressors of cryptic splice site activation

overall_design: Strains with cryptic splicing suppressor mutations in prp-8 and snrp-27 were compared to wild type strains to identify changes in native gene alternative splicing

first: Sol

last: Katzman

first: Samira

last: Yitiz

first: James

last: Ragle


title: De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

summary: Cornus officinalis Sieb. et Zucc., a perennial woody plant which is recognized with high medicinal, economic and ecological values, has been used as traditional Chinese medicine (TCM) for thousands of years in China. Modern pharmacological research has revealed that cornel iridoid glycosides (CIGs, e.g. loganin and morroniside) in dried pericarp of C. officinalis have significant medicinal activities for strengthening immune functions. However, little is known on the molecular processes responsible for the medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of C. officinalis were first generated and used for transcriptome analysis. A total of 54,827 unigenes with an average length of 817 bp, an N50 of 1,379 bp, and an average GC content of 44.91% were yielded by de novo assembly, of which 31,780 unigenes were successfully annotated. As potential molecular markers, 121, 118, 96, 89, and 82 transcription factors belonged to bHLH, MYB, PHD, WRKY, and AP2-ERF were further analyzed, respectively. The results of qRT-PCR confirmed that geraniol 10-hydroxylase (G10H) and loganin synthase (SLS) were differentially expressed in fruits and leaves during different growing stages. Furthermore, we found that loganin accumulation was positively related to G10H expression but was negatively correlated with SLS expression. Collectively, the genomic information and gene expression results presented in this study will be helpful for future studies on gene discovery and molecular process of loganin synthesis in C. officinalis.

overall_design: Fruit mRNA profiles of Cornus officinalis Sieb. et Zucc. collected in June were generated by deep sequencing, in a mixture of three samples, using Illumina® Hiseq 2000 platform.qRT–PCR validation was performed using SYBR Green assays.

first: Chengke

last: Bai

first: Yongmei

first: Jun

last: Xu

first: Guishuang

last: Li


title: Gene expression data of human airway epithelium following human parechoviruses infection

city: Amsterdam

first: Cosimo

last: Cristella

address: Meibergdreef 9

institute: Academic Medical Center

summary: Human parechoviruses (HPeVs), a poorly studied genus within the Picornaviridae family, are classified into 19 genotypes of which HPeV1 and HPeV3 are the most often detected.  HPeVs pathogenesis is poorly understood as there are no animal models and the previous studies have only been conducted in immortalized monolayer cell cultures which do not adequately represent the characteristics of human tissues. To bridge this gap, we determined the polarity of infection, replication kinetics, and cell tropism of HPeV1 and HPeV3 in the well-differentiated human airway epithelial (HAE) model. We found the HAE cultures to be permissive for HPeVs.  We speculated that differences in the airway epithelium host response may contribute to the distinct clinical outcomes and performed transcriptome analyses to compare the HAE gene expression profiles induced by HPeV1 and HPeV3 infection. Transcriptional profiling suggested that HPeV3 infection induced stronger immune activation than HPeV1. The polarized entry and genotype-specific host responses may contribute to the differences into the pathogenesis and clinical outcomes associated with HPeV1 and HPeV3.

overall_design: HAE (donor 59701) cultures in five technical replicates were basolaterally inoculated with HPeV1 or HPeV3 (or mock). Cultures were lysed and RNA extracted by High Pure RNA Isolation Kit (Roche LifeScience, Penzberg, Germany) 72hrs post-infection. RNA samples concentration and quality was determined by Nanodrop (ThermoFisher Scientific) and BioAnalyzer (Agilent Technologies, Santa Clara, California). Total RNA samples were labeled and hybridized using the Human Clariom S HT microarray platform according to the manufacturer’s guidelines (Affymetrix/ThermoFisher Scientific). The BrainArray (version 22) custom Chip Description File (CDF) was used to re-map probesets on the arrays based on the latest genome and transcriptome information. Probesets normalization was achieved by Robust Multi-array Average (RMA) function in the R programming environment.

first: Eveliina

last: Karelehto

first: Xiao

last: Yu

first: Katja

middle: C

last: Wolthers

first: Menno

middle: D

last: de Jong


title: Expression data of siRNA interfere men1 expression in N2a cell line

city: XiaMen

first: Honghua

last: zheng

state: FuJian

address: XiaMen University xiang’an campus

institute: Institute of Neuroscience xiamen university

summary:
Menin (MEN1) is a critical modulator of tissue development and maintenance.Although menin is abundantly expressed in the nervous system, little is known with regards to its function in the adult brain.
To explore molecular mechanisms associated with the phenotypes observed upon neuronal Men1 deletion, we profiled transcriptomes from the Neuro2a(N2a) cells transfected Men1 siRNA USING NimbleGen Mouse gene expression array [100718_MM9_EXP].

overall_design: Transfected  scramble siRNA and Men1 siRNA into Neuro2a cell line respectively and hybirdzation on Agilent Mouse 4 X 44K microarrays.

last: Zheng

first: Jie

first: Kai

last: Zhuang


title: mRNA and lncRNA expression analysis of irradiated and nonirradiated human HaCaT cells

status: Public on Jul 14 2018

city: Suzhou

first: huimin

last: Jia

address: No.199 Ren'ai Road, Wuzhong District

institute: Soochow University

summary:
This study aims to compare mRNA expression between radiated and non-radiated human keratinocyte HaCaT cells by microarray analysis. Human keratinocyte HaCaT cells were divided into two groups, each group has three repeats. The cells were irradiated with a single dose of 0 or 20Gy of X-ray irradiation. 48 hours post radiation, cells from 0 or 20 Gy groups were collected and subjected to microarray analysis.
mRNA and lncRNA profilings of each group were analyzed by microarray.

overall_design: This study aims to examine mRNA and lncRNA expression spectrum of irradiated and non-irradiated human keratinocyte HaCaT cells. Human keratinocyte HaCaT cells were divided into two groups, each group has three repeats. The cells were irradiated with a single dose of 0 or 20Gy of X-ray irradiation. 48 hours post radiation, the 0 and 20 Gy irradiated cells were collected by Trizol and subjected to microarray analysis.

first: Shuyu

last: Zhang

first: Huimin


title: AAV9 mediated overexpression of Rbm24 in wildtype C57/Bl6 mice

status: Public on Jul 16 2018

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

institute: Institute of Experimental Cardiology

summary: The RNA-binding protein Rbm24 has recently been identified as a pivotal splicing factor in the developing heart. Loss of Rbm24 in mice disrupts cardiac development by governing a large number of muscle- specific splicing events. Since Rbm24 knockout mice are embryonically lethal, the role of Rbm24 in the adult heart remained unexplored. Here, we used adeno-associated viruses (AAV9) to investigate the effect of increased Rbm24 levels in adult mouse heart. Using high-resolution microarrays, we found 893 differentially expressed genes and 1102 differential splicing events in 714 genes in hearts overexpressing Rbm24. We found splicing differences in cardiac genes, such as PDZ and Lim domain 5, Phospholamban, and Titin, but did not find splicing differences in previously identified embryonic splicing targets of Rbm24, such as skNAC, αNAC, and Coro6. Gene ontology enrichment analysis demonstrated increased expression of extracellular matrix (ECM)-related and immune response genes. Moreover, we found increased expression of Tgfβ-signaling genes, suggesting enhanced Tgfβ-signaling in these hearts. Ultimately, this increased activation of cardiac fibroblasts, as evidenced by robust expression of Periostin in the heart, and extensive cardiac fibrosis. These results indicate that Rbm24 may function as a regulator of cardiac fibrosis, potentially through the regulation of TgfβR1 and TgfβR2 expression.

overall_design: 1 week old male C57/Bl6 mice were intraperitonally injected with 4 x 10^12 vg of either AAV9-GFP or AAV9-Rbm24, and were sacrificed 2 weeks later. RNA from left ventricular tissue was subsequently used for analysis with the Affymetrix Mouse Transcriptome Array 1.0

first: Esther

middle: E

last: Creemers


title: Using biopsies to improve risk stratification in patients with prostate cancer treated with radical radiation therapy

status: Public on Jul 12 2018

city: Belfast

first: Suneil

last: Jain

address: 97 Lisburn Road

institute: Queen's University Belfast

summary:
Background: Radiotherapy is an effective treatment of intermediate/high-risk locally advanced prostate cancer,  however,>30% of patients relapse within 5 years. Clinicopathological parameters currently fail to identify patients prone to  systemic relapse and those whom treatment intensification may be beneficial. The purpose of this study was to independently  validate prognostics assays in a cohort of diagnostic biopsies from patients treated with radical  radiotherapy and androgen deprivation therapy.

Patients and methods: Independent clinical validation in a cohort of diagnostic biopsies  from patients treated with radical radiotherapy and androgen deprivation therapy. Multivariable Cox proportional hazard  regression analysis was used to assess assay performance in predicting biochemical failure-free survival (BFFS) and metastasis free  survival (MFS).

Results: Gene expression analysis was carried out in 248 patients from the independent validation cohort and the Metastatic  Assay applied. Ten-year MFS was 72% for Metastatic Assay positive patients and 94% for Metastatic Assay negative patients  [HR 3.21 (1.35–7.67); P=0.003]. On multivariable analysis the Metastatic Assay remained predictive for development of distant  metastases [HR 2.71 (1.11–6.63); P=0.030]. The assay retained independent prognostic performance for MFS when assessed  with the Cancer of the Prostate Assessment Score (CAPRA) [HR 3.23 (1.22–8.59); P=0.019] whilst CAPRA itself was not  significant [HR 1.88, (0.52–6.77); P=0.332].

Conclusions: The Metastatic Assay demonstrated significant prognostic performance in patients treated with radical  radiotherapy both alone and independent of standard clinical and pathological variables. The Metastatic Assay could have  clinical utility when deciding upon treatment intensification in high-risk patients.

overall_design: For this validation cohort, 248 localized/locally advanced prostate cancer patients commencing radical radiotherapy  (with ADT) were included. Patients were treated with 70–74 Gy external beam radiation therapy (EBRT) in 2 Gy fractions with 3D  conformal or intensity modulated techniques over 7–7.5 weeks. Node negative patients received elective pelvic nodal irradiation at the physician’s  discretion; node-positive patients had radiotherapy to pelvic nodal regions. Short (6months) or long (>6–36months) course ADT  commenced at least 3 months before radiation with LHRH agonists or antiandrogens.

first: S

first: C

middle: A

last: Lyons

last: Walker

last: McQuaid

middle: O

last: Hynes

first: D

last: Mitchell

first: B

last: Pang

first: G

last: Logan

first: A

last: McCavigan

last: O'Rourke

middle: G

last: McArt

last: McDade

first: I

last: Mills

first: K

last: Prise

first: L

last: Knight

last: Steele

first: P

middle: W

last: Medlow

first: V

last: Berge

last: Katz

last: Lobaw

last: Harkin

first: J

last: James

last: O'Sullivan

first: R

last: Kennedy

last: Waugh


title: Leukemia hijacks a neural mechanism to invade the central nervous system

first: Dorothy

last: Sipkins

address: 905S La Salle Street

department: Hematological Malignancies and Cell Therapy

summary: Acute lymphoblastic leukemia (ALL) has a striking propensity to metastasize to the central nervous system (CNS).1 In contrast to solid tumor brain metastases, ALL seldom involves the parenchyma but is isolated to the leptomeninges, an infrequent site for carcinomatous invasion.2,3 While CNS metastasis is characteristic across ALL subtypes, a unifying mechanism for invasion has not been determined. Here we show that ALL cells in circulation are unable to breach the blood brain barrier; instead they migrate into the CNS along vessels that passage directly between vertebral or calvarial bone marrow (BM) and the subarachnoid space.  The basement membrane of these bridging vessels is enriched in laminin, known to coordinate neuronal progenitor cell pathfinding in the CNS.4-6 The laminin receptor a6 integrin is expressed by most ALL.7,8 We found that a6/laminin mediated ALL migration toward cerebrospinal fluid (CSF) in vitro. ALL-xenografted mice treated with either a PI3Kd inhibitor that decreased ALL a6 expression or specific a6 neutralizing antibodies showed significantly less ALL transit along bridging vessels, CSF blast counts and CNS disease symptoms despite minimally decreased BM disease burden. Our data suggest that a6 integrin expression, common in ALL, allows cells to coopt neural migratory pathways to invade the CNS.

overall_design: NALM6 ALL cells isolated from the bone marrow (BM) or the cerebrospinal fluid (CSF) of SCID mice treated with control (n=6 mice) or PI3Kd (n=6 mice for BM isolation, n=4mice for CNS isolation).

first: Hisayuki

last: Yao

first: Trevor

last: T Price