title: Single-cell RNA-sequencing of CD14+ monocyte differentiation with M-CSF stimulus

city: Cambridge

first: Brian

last: Hie

state: MA

address: 77 Massachusetts Ave

institute: MIT

summary:
We obtained single-cell RNA-sequencing (scRNA-seq) profiles of CD14+ monocytes isolated from human peripheral blood at 0, 3 and 6 days after M-CSF stimulation (to differentiate the cells into macrophages) across multiple donors.

Integration of single-cell RNA sequencing (scRNA-seq) data from multiple experiments, laboratories, and technologies can uncover biological insights, but current methods for scRNA-seq data integration are limited by a requirement for datasets to derive from functionally similar cells. We use a novel algorithm, Scanorama, to identify and merge the shared cell types among all pairs of datasets and to accurately integrate heterogeneous scRNA-seq datasets. Scanorama is sensitive to subtle temporal changes within the same cell lineage, successfully integrating functionally similar cells across time series data of CD14+ monocytes at different stages of differentiation into macrophages. Scanorama is not only able to differentiate between completely disparate cell types but is also sensitive to subtler transcriptional changes within a cell type due to processes like stimulation.

overall_design: scRNA-seq of human CD14+ monocytes at 0, 3, and 6 days after M-CSF stimulation in multiple donors

first: Bryan

last: Bryson

first: Bonnie

last: Berger


title: Continued activity of the pioneer factor Zelda is required to drive zygotic genome activation

status: Public on Feb 06 2019

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

country: USA

institute: University of Wisconsin Madison

type: Expression profiling by high throughput sequencing

summary: Reprogramming cell fate during the first stages of embryogenesis requires that transcriptional activators gain access to the genome and remodel the zygotic transcriptome. Nonetheless, it is not clear if the continued activity of these pioneering factors is required throughout zygotic genome activation or if they are only required early to establish cis-regulatory regions. To address this question, we developed an optogenetic strategy to rapidly and reversibly inactivate the master regulator of genome activation in Drosophila, Zelda. Using this strategy, we demonstrated that continued Zelda activity is required throughout genome activation. We showed that Zelda binds DNA in the context of nucleosomes and suggest that this allows Zelda to occupy the genome despite the rapid division cycles in the early embryo. These data identify a powerful strategy to inactivate transcription factor function during development and suggest that reprogramming in the embryo may require specific, continuous pioneering functions to activate the genome.

overall_design: RNA-seq transcriptomic profiling of Drosophila melanogaster embryos either wild-type or with optogenetically inactivated Zelda.

first: Stephen

middle: L

last: McDaniel

first: Tyler

middle: J

last: Gibson

first: Katherine

middle: N

last: Schulz

first: Meilin

middle: F

last: Garcia

first: Markus

last: Nevil

first: Siddhant

middle: U

last: Jain

first: Peter

middle: W

last: Lewis

first: Kenneth

middle: S

last: Zaret


title: NCR- and Dal80-sensitive genes in Saccharomyces cerevisiae

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: GATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis. However, although their consensus binding sites have been well defined in vitro, the in vivo selectivity for recognition by GATA factors remains poorly characterized. Using ChIP-Seq, we identified the Dal80 GATA factor targets in yeast. Our data reveal Dal80 binding to a large set of promoters, sometimes independently of GATA sites, correlating with nitrogen- and/or Dal80-sensitive gene expression. Strikingly, Dal80 was also detected across the body of promoter-bound genes, correlating with high expression. Mechanistic single-gene experiments showed that Dal80 spreading across gene bodies requires active transcription. Consistently, Dal80 co-immunoprecipitated with the initiating and post-initiation forms of RNA Polymerase II. Our work suggests that GATA factors could play dual, synergistic roles during transcription initiation and post-initiation steps, promoting efficient remodeling of the gene expression program in response to environmental changes.

overall_design: Strand-specific total RNA-Seq analysis in wild-type (WT) and dal80-delta (dal80) cells grown in glutamine- and/or proline-containing medium.

first: Aria

last: Ronsmans

first: Ugo

last: Szachnowski

first: Camille

last: Gautier

first: Marc

last: Descrimes

first: Evelyne

last: Dubois

first: Antonin

last: Morillon

first: Isabelle

last: Georis


title: Genome-wide identification of Dal80- and Gat1-bound regions in budding yeast

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-Seq analysis of Dal80 and Gat1 occupancy in S. cerevisiae


title: TCF4 regulatory gene networks in developing dorsal telencephalon

city: New Haven

first: Hong

last: Li

state: CT

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

summary: Haplo-insufficiency of TCF4 induced by mutations or microdeletion of TCF4 gene causes Pitt-Hopkins Diseases. Recent gene association studies revealed that mutations  of TCF4 is significantly associated with schizophrenia. But the role of TCF4 in developing neocortex is not known. The goal of this study is to identify TCF4 itranscriptional regulatory pathways in developing neocortex by analyzing transcriptomes of  dorsal telencephalons of TCF4knockout, TCF4Heterozygote and WT littermates and comparing differential expressed genes between these genotypes.

overall_design: Dorsal telencephalons were collected from TCF4 knockouts, TCF4 heterozygotes, WT brains at P0, three replicates for each genotypes.

first: Pasko

last: Rakic


title: Length-independent telomere damage drives cardiomyocyte senescence

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

summary: Ageing is the biggest risk factor  to cardiovascular health and is associated with increased incidence of cardiovascular disease.  Cellular senescence, a process driven in part by telomere shortening has been implicated in age-related cardiac dysfunction.  However, the role of cellular senescence and its underlying mechanisms in slowly dividing/post-mitotic cardiomyocytes is not understood.

overall_design: We quantify transcription via high throughput RNA sequencing in young (3 months) and old (20 months) mouse cardiomyocytes.

first: Rhys

last: Anderson

first: Damien

last: Maggiorani

first: Jeanne

last: Mialet-Perez

first: Gavin

middle: D

last: Richardson

first: Joao

last: Passos


title: Human monocytes exhibit a functional and transcriptional reprogramming during Acute-on-Chronic-Liver-Failure with a key role for IL-10

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Background and aims:  Acute-on-chronic liver failure (ACLF) is characterized by rapid deterioration of liver function and organ failure, whereby immunoparesis and susceptibility to infections often precipitate this syndrome. Here we characterized the events triggering immune dysfunction in monocytes within alcoholic liver disease. Methods: We evaluated the frequency of monocyte subsets, their intracellular IL10 production, surface HLA-DR expression, and phagocytic and oxidative burst capacity in patients with decompensated cirrhosis, -alcoholic hepatitis or ACLF. RNAsequencing of ACLF patient-derived CD14+ monocytes were performed either immediately or after 12-hour culture in the presence or absence of plasma from ACLF patients. In this in vitro model of ACLF induction in CD14+ monocytes we characterized the early molecular, immunological and functional changes. Results: Besides a redistribution of monocyte subset composition, ACLF patient-derived monocytes featured elevated frequencies of IL-10-producing cells, reduced HLA-DR expression and impaired phagocytic- and oxidative burst capacity. RNAsequencing revealed a reprogramming of ACLF monocytes, whereby they undergo a transition from a pro-inflammatory to an immunosuppressive- and altered metabolic status. Culturing healthy monocytes in the presence of ACLF plasma, blunted their phagocytic capacity and triggered a gene expression pattern comparable to ACLF patients. Conversely, culturing patient monocytes in normal plasma restored their phagocytic capacity.  Finally, plasma IL-10 levels correlated with patient survival.  Conclusion:  ACLF monocytes featured a defective immunosuppressive and -glycolytic profile, an attribute which could be mimicked by culturing healthy monocytes in the presence of ACLF patient plasma. Our data implicate a role for IL-10 signaling pathways in triggering monocytes dysfunction and opens up new avenues for therapeutic targeting.

overall_design: The study included 27 samples, RNA from purified CD14+ monocytes. 5 samples were from ACLF patients (cells immediately after isolation), 4 samples from healthy human controls immediately after isolation, 5 ACLF patients in vitro cultured in the presence of pool of ACLF serum,  5 ACLF patients in vitro cultured in the presence of pool of normal human serum, 4 healthy controls in vitro cultured in the presence of pool of ACLF serum,  4 healthy controls in vitro cultured in the presence of pool of normal human serum.

first: Hannelie

last: Korf

first: Johannie

last: du Plessis

first: Schalk

last: van der Merwe

first: Jos

last: van Pelt


title: Microarray and RNA-Seq profiling of immune cell types and peripheral blood mononuclear cells

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

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

overall_design: Refer to individual Series


title: rDNA chromatin interactions in the MYC-driven Eμ-Myc transgenic mouse model of B-cell lymphoma [RNA-seq]

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: Analysis of gene expression by RNA-seq in mouse wildtype, premalignant and malignant Eμ-Myc cells.

overall_design: RNA-seq in mouse wildtype, premalignant and malignant cells primary preB Eμ-Myc cells.

first: Gretchen

last: Poortinga


title: CD11c+ cells acquire Plasmodium from hepatocytes to prime CD8 T cell immunity to liver-stage malaria

status: Public on Feb 05 2019

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Malaria, caused by Plasmodium parasites is responsible for the illness of millions of individuals each year. Plasmodium sporozoites inoculated by mosquitoes migrate to the liver and infect hepatocytes prior to release of merozoites that initiate symptomatic blood-stage malaria.  Parasites are thought to be restricted to hepatocytes throughout this obligate liver-stage of replication and differentiation. In contrast to this notion, we found that a subset of hepatic dendritic CD11c+ cells co-expressing F4/80, CD103, CD207 and CSF1R, acquired a substantial parasite burden during the liver-stage of malaria, but only after initial hepatocyte infection. These CD11c+ cells found in the infected liver and liver-draining lymph nodes exhibited transcriptionally and phenotypically enhanced antigen-presentation functions; and primed protective CD8 T cell responses against Plasmodium liver-stage restricted antigens. Our findings uncover a novel aspect of Plasmodium biology as well as the fundamental mechanism by which CD8 T cell responses are primed against liver-stage malaria.

overall_design: SRA study accession SRP171171, and BioProject Accession PRJNA507626

first: Samarchith

middle: P

last: Kurup

first: Rahul

last: Vijay

first: Scott

last: Anthony

first: John

middle: T

last: Harty


title: α1ACT is essential for survival and early cerebellar programming in a critical neonatal window

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago


title: RNA-sequencing of formalin fixed human primary melanoma tissue

city: Pittsburgh

first: Yuri

last: Bunimovich

state: PA

address: 580 S. Aiken Avenue, 2nd Floor

department: Department of Dermatology

institute: University of Pittsburgh

summary: We identify the differences in nervous system related genes and pathways inside melanoma and in the tissure adjacent to melanoma tumor.

overall_design: Formalin fixed primary human melanoma tissue sections from a single tumor were microdissected into samples containing tumor center, tumor border or tissue adjacent to the tumor. Three separate areas of the tumor were used to generate nine samples, which were analyzed by RNA sequencing.

first: Michael

middle: R

last: Shurin

first: Fei

last: Ding

last: Lin

first: William

last: LaFramboise


title: Regulation ot TAM gene expression by Pi3K (WT vs p110d-/-)

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

institute: DKFZ

summary:
Gene expression was analyzed in peritoneal macrophages and TAM from mice injected with ID8 ovarian cancer cells intraperitoneally 28 days after tumor implantation.
Tumor-associated macrophages (TAM) have been shown to have important roles in the malignant progression of various cancers. However, macrophages also posses intrinsic tumoricidal activity and can promote the activity of cytotoxic lymphocytes, but they rapidly adopt an alternative phenotype within tumors, associated with immune-suppression and trophic functions that support tumor growth. The mechanisms that promote TAM polarization in the tumor-microenvironment remain poorly understood, these mechanisms may represent important therapeutic targets to block the tumor-promoting functions of TAM and restore their anti-tumor potential. Here we have characterized TAM in a mouse model of metastatic ovarian cancer. We show that ovarian cancer cells promote membrane-cholesterol efflux and the depletion of lipid rafts from macrophages. Increased cholesterol efflux promoted IL-4 mediated reprogramming while inhibiting IFNg-induced gene expression. These studies reveal an unexpected role for tumor-induced membrane-cholesterol efflux in driving the IL-4 signaling and the tumor-promoting functions of TAM, while rendering them refractory to pro-inflammatory stimuli. Thus, preventing cholesterol efflux in TAM could represent a novel therapeutic strategy to block pro-tumor functions and restore anti-tumor immunity.

overall_design: In total 8 samples; 4 WT, 4 p110d-/- chimeric mice

first: Pieter

last: Goossens

first: Anders

last: Etzerodt

first: Marion

last: Masse

first: Olivia

last: Rastoin

first: Victoire

last: Gouirand

first: Miranda

last: Van Eck

first: Thomas

last: Ulas

first: Olympia

last: Papantonopoulou

first: Magali

last: Bebien

first: Martin

last: Turner

first: Thien

last: Manh

first: Marc

last: Dalod

first: Nathalie

last: Auphan-Anezin

first: Joachim

last: Schultze

first: Toby

last: Lawrence


title: Gene expression data from human primary cultured Schwann cells

first: Yuri

last: Bunimovich

summary:
Schwann cells undergo reprogramming after nerve injury, switching to immature repair phenotype. The goal was to test what genetic perturbations are triggered in Schwann cells with the stimulus from melanoma cell secreted factors.
We used microarrays to detail the changes in gene expression of Schwann cells treated with human melanoma conditioned medium.

overall_design:
Primary human Schwann cells were cultured in triplicates to 90% confluence and treated for 48 hours with 20% (v/v) of either control medium (control) or melanoma conditioned medium (cell lines: 1. 526-mel, 2. 397-mel and 3. 624-mel cell). Schwann cells were washed and collected, total RNA extracted, convereted to cDNA library and analyzed with Affymetrix Human genome U133A 2.0 Array.
Please note that the 'Internal control' sample was only used for data processing (i.e. no processed data).

first: Fei

last: Ding

first: Yan

last: Lin

first: Michael

last: Shurin

first: William

last: LaFramboise


title: Regulation ot TAM gene expression by ABCA1 and ABCG1 (4 Cre- and 4 Cre+)

first: Juan

last: Rodriguez-Vita

summary:
Gene expression was analyzed in TAM from mice injected with ID8 ovarian cancer cells intraperitoneally in ABC a1/g1 fl/fl-LysM-Cre mice.
Tumor-associated macrophages (TAM) have been shown to have important roles in the malignant progression of various cancers. However, macrophages also posses intrinsic tumoricidal activity and can promote the activity of cytotoxic lymphocytes, but they rapidly adopt an alternative phenotype within tumors, associated with immune-suppression and trophic functions that support tumor growth. The mechanisms that promote TAM polarization in the tumor-microenvironment remain poorly understood, these mechanisms may represent important therapeutic targets to block the tumor-promoting functions of TAM and restore their anti-tumor potential. Here we have characterized TAM in a mouse model of metastatic ovarian cancer. We show that ovarian cancer cells promote membrane-cholesterol efflux and the depletion of lipid rafts from macrophages. Increased cholesterol efflux promoted IL-4 mediated reprogramming while inhibiting IFNg-induced gene expression. These studies reveal an unexpected role for tumor-induced membrane-cholesterol efflux in driving the IL-4 signaling and the tumor-promoting functions of TAM, while rendering them refractory to pro-inflammatory stimuli. Thus, preventing cholesterol efflux in TAM could represent a novel therapeutic strategy to block pro-tumor functions and restore anti-tumor immunity.

overall_design: In total 8 samples; 4 Cre- and 4 Cre+

first: Pieter

last: Goossens

first: Anders

last: Etzerodt

first: Marion

last: Masse

first: Olivia

last: Rastoin


title: Gene expression data of Arabidopsis thaliana yaf9a yaf9b double mutant seedlings

city: Pozuelo de Alarcón

first: Pedro

last: Crevillén

state: Madrid

address: Campus de Montegancedo

institute: CBGP (UPM-INIA)

summary: Post-translational histone modifications and the dynamics of histone variant H2A.Z are key mechanisms underlying the floral transition. In yeast, SWR1-C and NuA4-C mediate the deposition of H2A.Z and the acetylation of histone H4, H2A and H2A.Z respectively. Yaf9 is a subunit shared by both chromatin remodeling complexes. The significance of the two Arabidopsis YAF9 homologs, YAF9A and YAF9B, is unknown. We performed a transcriptomic analysis of wild-type and yaf9a yaf9b double mutant seedlings in order to reveal target genes whose transcription is regulated by YAF9 proteins.

overall_design: Transcriptomic analyses were performed using Affymetrix Microarray (Arabidopsis ATH1 Genome Array) with RNA extracted from 20-day-old wild-type and yaf9a yaf9b double mutant seedlings grown on agar plates under short-day conditions and collected at ZT8. Three independent biological replicates were hybridized.

first: Ángeles

last: Gómez-Zambrano

first: Manuel

last: Piñeiro

first: José

last: Jarillo


title: Regulation of gene expression upon inhibition of ROCK and MLCK in mammary epithelial cells

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
To understand how mechanical cues regulate cell metabolism, we compared early changes in gene expression in Ras-transformed MCF10AtK1 mammary epithelial cells grown in high cytoskeletal tension conditions (plastics) vs. cells grown in low cytoskeletal tension conditions (inhibition of the non-muscle myosin II regulatory kinases ROCK and MLCK with standard small-molecule inhibitors Y27632 and ML7, respectively).

Keywords: Expression profiling by array

overall_design: MCF10ATk1 (also knon as MII) growing at low confluence on plastics in standard growth conditions were treated for 6 hours with DMSO (control) or with 20microM Y27632 and 20microM ML7 to inhibit cell contractility (i.e. ROCK and MLCK kinases, master regulators of non-muscle myosin activity), and then harvested for total RNA extraction. 3 independent biological replicates were performed in parallel for each cell line and experimental condition.

first: Sirio

last: Dupont


title: Gene expression profiles in response to proanthocyanidins in pancreatic cancer cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: Proanthocyanidins (PAs) that are naturally occurring compounds have shown the potential chemopreventive efﬁcacy against various forms of cancers in different tumor models. To elucidate the responsible molecular mechanisms involved in antitumor therapeutic effects of PAs, the transcriptome changes of pancreatic cancer cells exposure to PAs at 3, 12 and 24h were investigated in this study. Through two biological replicate sequencing, 966, 3543 and 4944 differentially expressed genes in response to PAs exposure were detected at 3, 12 and 24h, respectively. GO and KEGG analysis showed that cell cycle checkpoints and DNA repair modulations or inhibition were the mainly mechanisms in PAs anti-cancer. Overall, this study provided novel insights into not only the first integrated overview on global gene expression in pancreatic cancer cells post PAs exposure, but also the underlying mechanisms of anti-cancer effects of PAs for chemotherapy.

overall_design: Transcriptome change of PANC-1 cells post Proanthocyanidins (20 μg/ml) exposure at 3, 12 and 24h  were investigated. A biological replicate sequencing was carried out.

first: Yi

last: Zhang


title: The Transgenerational Effects of Prenatal Synthetic Glucocorticoids on the Prefrontal Cortex

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

summary: First generation animals (F1) were exposed to multiple courses of synthetic glucocorticoids in utero. Animals were then bred to produce second (F2) and third (F3) generation offspring. These animals underwent behavioural assessmenets before sacrifice. In this experiment the prefrontal cortex for F1, F2, and F3 female animals, as well as F1 males (Beta and Control) have been extracted via micro-punch and RNA has been extracted.

overall_design: F1 Female Control n=4 vs F1 Female Beta n=4, F2 Female Control n=4 vs F2 Female Beta n=4, F3 Female Control n=4 vs F3 Female Beta n=4, F1 Males Control n=5 vs F1 Males Beta n=6

first: Andrea

last: Constantinof

first: Vasilis

middle: G

last: Moisiadis

first: Moshe

last: Szyf


title: The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast

first: Maxime

last: Wery

summary: 5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3’-5’ exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU’s cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. However, the effect of 5-FU on long non-coding RNAs (lncRNAs), which include regulatory transcripts important for cell growth and differentiation, is poorly understood. RNA profiling of synchronized 5-FU treated yeast cells and protein assays reveal that the drug specifically inhibits a set of cell cycle regulated genes involved in mitotic division, by decreasing levels of the paralogous Swi5 and Ace2 transcriptional activators. We also observe widespread accumulation of different lncRNA types in treated cells, which are typically present at high levels in a strain lacking EXOSC10/Rrp6. 5-FU responsive lncRNAs include potential regulatory antisense transcripts that form double-stranded RNAs (dsRNAs) with overlapping sense mRNAs. Some of these transcripts encode proteins important for cell growth and division, such as the transcription factor Ace2, and the RNA exosome subunit EXOSC6/Mtr3. In addition to revealing a transcriptional effect of 5-FU action via DNA binding regulators involved in cell cycle progression, our results have implications for the function of putative regulatory lncRNAs in 5-FU mediated cytotoxicity. The data raise the intriguing possibility that the drug deregulates lncRNAs/dsRNAs involved in controlling eukaryotic cell division, thereby highlighting a new class of promising therapeutical targets.

overall_design: Total RNA-Seq analysis

first: Bingning

last: Xie

first: Emmanuelle

last: Becker

first: Igor

last: Stuparevic

first: Ugo

last: Szachnowski

first: Antonin

last: Morillon

first: Michael

last: Primig


title: Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability in Salmonella during growth in LB and mLPM media

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: 2 replicate time courses with 5 time points from wild type and csrA mutant strains were analyzed for both LB and mLPM

middle: H

first: Tony

last: Romeo


title: Axonogenesis is coordinated by alternative splicing programming and splicing regulator PTBP2

status: Public on Feb 04 2019

city: Los Angeles

first: Liang

state: CA

address: 1050 Childs Way

institute: University of Southern California

summary: How a neuron acquires an axon is a fundamental question. Piecemeal identification of many axonogenesis-related genes has been done, but coordinated regulation is unknown. Through unbiased transcriptome profiling of immature primary cortical neurons during early axon formation, we discovered an association between axonogenesis and neuron-specific alternative splicing. Known axonogenesis genes exhibit little expression alternation but widespread splicing changes. Axonogenesis-associated splicing is governed by RNA binding protein PTBP2, which is enriched in neurons and peaks around axonogenesis in the brain. Cortical depletion of PTBP2 prematurely induces axonogenesis-associated splicing, causes imbalanced expression of axonogenesis-associated isoforms, and specifically affects axon formation in vitro and in vivo. PTBP2-controlled axongeneisis-associated Shtn1 splicing determines SHTN1’s capacity to regulate actin interaction, polymerization, and axon growth. Precocious Shtn1 isoform switch contributes to disorganized axon formation of Ptbp2-/- neurons. We conclude that PTBP2-orchestrated alternative splicing programming is required for robust generation of a single axon in mammals.

overall_design: Immature cortical neurons were cultured from embryonic day 14 mouse neocortices at the density of 1 million cells per 35 mm petri dish. At 1 day in vitro (1 DIV), these neurons extend multiple indistinguishable processes in a seemingly random manner, just like pre-axonogenesis neurons in vivo. Around 3 DIV, one of the neurites accelerates its growth to become the axon. We performed unbiased deep RNA sequencing (RNA-Seq) of wildytpe DIV 1, wildtype DIV 3, and Ptbp2-/- DIV1 neurons. There are two biological replicates per sample (specific gentoype and age).

first: Sika

last: Zheng


title: rDNA chromatin interactions in the MYC-driven Eμ-Myc transgenic mouse model of B-cell lymphoma [4C-seq]

first: Jeannine

last: Diesch

summary: Long-range interactions of ribososomal DNA (rDNA) identified by 4C-seq in mouse wildtype, premalignant and malignant Eμ-Myc cells and tissue culture adapated Eμ-Myc-shUbtf and Eμ-Myc-LMP (empty vector) cells.

overall_design: We performed 4C-seq in mouse wildtype, premalignant and malignant cells primary preB Eμ-Myc cells and tissue culture adapated Eμ-Myc-shUbtf and Eμ-Myc-LMP. For this we used multiple bait primers across the rDNA and identified long-range interactions in 5000bp windows. The interaction frequency, represented as read counts per window, was compared between wt, prem and mal cells and only interactions also identified in Eμ-Myc-shUbtf and Eμ-Myc-LMP used for further analysis.

first: Gretchen

last: Poortinga


title: rDNA chromatin interactions in the MYC-driven Eµ-Myc transgenic mouse model of B-cell lymphoma


title: Differential RNA-Seq (dRNA-seq)  of Staphylococcus epidermidis PS2 and PS10 isolates

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: We performed differential RNA-seq of two Staphylococcus epidermidis clinical isolates (PS2 and PS10) to compare their transcription profiles. The isolates were originally obtained from blood cultures during a systemic infection in an immunocompromised patient (Weisser et al. 2010. J Clin Microbiol 48: 2407-2412). They are of clonal origin, but differ phenotypically with respect to extracellular biofilm matrix production. Thus PS2, isolated in the early stage of the infection, forms a weak biofilm mediated by protein-protein interactions, while PS10, which was obtained at the end of the infection course, forms a strong biofilm through production of a polysaccharide intercellular adhesin (PIA) extracellular biofilm matrix. Transcription profiling by dRNA-seq was performed to elucidate differentially expressed metabolic pathways and regulators contributing to the switch in extracellular biofilm matrix producction between the two isolates.

overall_design: Exponentially growing S. epidermidis PS2 and PS10 isolates were subjected to dRNA-seq. A detailed analysis of the transcriptome focusing on metabolic gene expression was performed

first: Sonja

last: Schoenfelder


title: CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary (I)

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

summary: Inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. SCCOHT patient tumors are deficient in cyclin D1 yet retain the retinoblastoma-proficient/p16INK4a-deficient profile associated with positive responses to CDK4/6 inhibitors. Thus, our findings indicate that CDK4/6 inhibitors, approved for a breast cancer subtype addicted to CDK4/6 activation, could be repurposed to treat SCCOHT. Moreover, our study suggests a novel paradigm whereby critically low oncogene levels, caused by loss of a driver tumor suppressor, may also be exploited therapeutically.

overall_design: The role of SMARCA4 in SCCOHT cells. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 250 ng of total RNA using  the TruSeq stranded mRNA Sample Preparation Kit (Illumina), as per the manufacturer’s recommendations. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

first: Yibo

last: Xue

first: Radia

middle: M

last: Johnson

first: William

last: Foulkes


title: SETDB1 controls T helper cell lineage integrity by repressing endogenous retroviruses

city: Toulouse

first: Veronique

last: Adoue

address: CHU Purpan

institute: CNRS

summary: Upon activation, naïve CD4 T cells differentiate into distinct helper or regulatory T cell subsets depending on environmental signals received. This process relies on complex and lineage-specific gene expression programs, whose dynamics and stability are regulated at the level of the chromatin. The epigenetic pathways involved remain, however, largely unknown. Here, we report that the histone methyltransferase SETDB1 critically controls the Th1 gene expression program. Indeed, SETDB1-deficient naïve CD4 T cells show exacerbated Th1 priming, and when exposed to a Th1-instructive signal, SETDB1-deficient Th2 cells cross lineage boundaries and transdifferentiate into Th1 cells. Surprisingly, SETDB1 does not appear to directly control Th1 gene promoter activity. Instead, it deposits the repressive H3K9me3 mark at a restricted and cell type-specific set of endogenous retroviruses (ERVs) located in the vicinity of genes involved in immune processes. Refined bioinformatic analyses indicated that these retrotransposons either repress Th1 gene cis-regulatory elements or behave themselves as Th1 gene enhancers. In conclusion, H3K9me3 deposition by SETDB1 ensures T helper cell lineage integrity by repressing a repertoire of ERVs that have been exapted into cis-regulatory modules to shape and control the Th1 gene network.

overall_design: Transcriptomic and epigenetic data for WT, Setdb1-/- and Suv39h1-/- mice T lymphocytes subsets

first: Véronique

first: Bénédicte

last: Binet

first: Agathe

last: Malbec

first: Joanna

last: Fourquet

first: Paola

last: Romagnoli

first: Joost

last: van Meerwijk

first: Sebastian

last: Amigorena

first: Olivier

last: Joffre


title: DNA methylation change involved in doxorubicin-induced testicular toxicity in mice

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

type: Methylation profiling by high throughput sequencing

summary: Testicular toxicity is one of the frequent adverse effects of cancer chemotherapy and the problem is that there is no effective biomarker. To find effective biomarkers, we focused on epigenetic mechanisms of male germline. Therefore, our study investigated the DNA methylation status of male germline under the testicular toxicity induced by doxorubicin(DXR), a widely used anticancer agent. We established mouse models of initial stage of testicular toxicity and testicular pre-toxicity by administrating 0.2 mg/kg and 0.02 mg/kg of DXR twice a week for 5 weeks. Western blotting analysis revealed the protein expression levels of DNA methyltransferases DNMT3a and DNMT3b were decreased in both the DXR administration groups. Consistently, comprehensive DNA methylation analysis of sperm DNA using MBD-seq revealed that the majority of methylation changes induced by DXR administration were hypomethylation. This study showed the possibility of early diagnosis of testicular toxicity by examining DNA methylation status of sperm.

overall_design: DNA methylation profiles of sperms obtained from Control and doxorubicin(DXR) treated mice were analyzed using MBD2 mediated methylated DNA enrichment followed by next generation sequencing (MBD-seq) with Illumina MiSeq.

first: Kentaro

last: Tanemura

first: Kazuya

last: Sakai

first: Maky

last: Otsuka

first: Katsuhide

last: Igarashi


title: Mutational tolerance of HIV-1 Env in the CD4, VRC01 and PG16 bound states

status: Public on Feb 03 2019

city: Urbana

first: Erik

last: Procko

address: 601 S Goodwin Ave

institute: University of Illinois

summary: HIV-1 infection begins with binding of the viral envelope glycoprotein Env to the host receptor CD4, triggering a series of conformational changes that lead to fusion of the virus and cell membranes. Env, a trimer of gp120 and gp41 subunits, occupies a ‘closed’ conformation with contacts between gp120 subunits at the apex, and transitions through an ‘open’ conformation with the gp120 subunits spread apart following CD4 binding.  Using deep mutational scanning, sequence-fitness landscapes were mapped for full-length Env from the clade B BaL strain interacting with CD4, and broadly neutralizing antibodies VRC01 and PG16, which preferentially bind closed Env.  Contacting residues are conserved for CD4 binding, and glycosylation at N262 is critical for accessing the high-affinity CD4-bound state.  By comparison, VRC01 binding is resistant to most single amino acid substitutions, an ideal quality in a broadly neutralizing antibody.  Also in contrast to CD4 interaction, Env interfacial residues are under tight selection for PG16 binding to maintain a closed conformation.  Screening for mutations that enhanced PG16 binding, we identified several important sites, in particular neutralization of the electropositive apical cavity that we hypothesize promotes trimer opening by electrostatic repulsion.  Mutations were combined to generate Quaternary Epitope Stabilized (QES) mutants with enhanced presentation of the PG16 epitope, and the mutations were partially transferable to other HIV-1 strains.  These mutational analyses offer insight into Env conformational stabilization that may assist immunogen design.

overall_design: Env from the R5-tropic HIV-1 BaL strain was encoded by a synthetic codon-optimized gene with a CD5 leader sequence. The Env sequence was diversified by overlap-extension PCR to generate three single-site saturation mutagenesis libraries spanning the full length of the gene. The libraries were expressed in human Expi293F cells (a HEK293 derivative) and sorted by FACS for binding to soluble CD4 (sCD4) and the broadly-neutralizing antibodies PG16 and VRC01. Enrichment ratios were calculated for all single amino acid substitutions by comparing the frequencies of sequence variants in the sorted cells (from RNA transcripts) with the naive libraries (plasmid DNA). Evolution experiments were duplicated.

first: Jeremiah

last: Heredia


title: Single-cell type transcriptome analysis of maize roothair

status: Public on Feb 02 2019

city: Beijing

first: qi

middle: chuang

last: ye

state: Beijing

address: Yuanmingyuan West Road

department: national maize improvement center

institute: china agriculture university

summary: We investigated root hair-specific transcriptome using RNA-seq in maize. ZmLRL5 was further identified as a key regulator of maize root hair elongation.

overall_design: The maize inbred line B73 were germinated in moist germination paper. 3-day old uniform seedlings were dipped into liquid N and root hairs were scraped off and collected. The remaining root hair less roots were collected. From Total RNA was extracted using the Qiagen RNeasy Plant kit. Libraries were constructed and sequenced on an Illumina HiSeq2500

first: Yan

last: He


title: Bach2 keeps homeostasis in lung by regulating inflammatory response and maintaining function of alveolar macrophage.

city: Sendai

first: Kazuhiko

address: Seiryo 2-1

institute: Tohoku University

summary: Alveolar macrophages (AMs) of Bach2 KO mice show multiple alternations in their functions including lipid metabolism. We aimed to clarify the mechanism whereby deficiency of Bach2 impairs the function of AMs and ruins the homeostasis of lungs. Now we report that some cytokines produced from Bach2-deficient T cells alter the character of AMs and expression of Bach2 is necessary for AMs to maintain the function of lipid metabolism.

overall_design:
mRNA profiling of AMs from 16-week old control mice,  Bach2-floxed CD4cre  mice, WT mice and Bach2 germline KO mice were examined by deep sequencing using HiSeq2500.

Please note that two macrophage populations observed in Bach2-floxed/CD4-cre cKO mice were analyzed;
One with normal surface marker phenotype that was the same as control mice (normal).
The other with aberrant  surface marker phenotype compared with control mice (abnormal).

first: Risa

middle: E

last: Shibuya

first: Mitsuyo

last: Matsumoto

first: Ryo

last: Funayama

first: Keiko

last: Nakayama


title: CircZKSCAN1 suppresses stemness in hepatocellular carcinoma (HCC) by competing against RNA-binding protein FMRP

city: Shanghai

first: Lei

last: Chen

address: Changhai Road 225, YangPu district

department: International Cooperation Laboratory on Signal Transduction,

institute: Eastern Hepatobiliary Surgery Institute, Second Military Medical University

summary: We found that Quaking5 protein, a RNA splicing protein was downregulated in HCC. Collectively, this study uncovers the mechanisms underlying the regulating role of circZKSCAN1 in HCC cancer stem cells and reveals that the new discovered Qki5-circZKSCAN1-FMRP-CCAR1-Wnt signaling axis is of important therapeutic value in improving the treatment of HCC.

overall_design: identify the regulating role of circZKSCAN1 in HCC

first: Yan-Jing

last: Zhu


title: Whole-transcriptome gene expression profiling in TRPC1-silenced human primary aortic smooth muscle cells.

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

summary: Effects of TRPC1 silencing on whole-transcriptome gene expression were determined in human primary aortic vascular smooth muscle cells using whole-transcriptome gene expression profiling.

overall_design: Gene expression profile in TRPC1-silencing vector transfected human vascular smooth muscle cells was compared to control cells transfected with empty vector.

first: Yasemin

last: Erac

first: Metiner

last: Tosun


title: MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. We screened several MRT cell lines each with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers.  We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin and ATSP-7041, we show that MRT cells are more sensitive than other p53 wild-type cancer cell lines to MDM2 and dual MDM2/4 inhibition in vitro. These compounds cause significant upregulation of the p53 pathway in MRT cells, and sensitivity is ablated by CRISPR-Cas9-mediated inactivation of TP53. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRT, sensitizes cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth in vivo, with a five-day idasanutlin pulse causing marked regression of all xenografts including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene p53, and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer.

overall_design: RNA-seq in TTC642 MRT cells treated with idasanutlin compared to DMSO

first: Thomas

last: Howard

first: Su

last: Wang

first: Charles

last: Roberts


title: Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

first: Anastasia

last: Potts

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: 4 biological replicates of ribosome protected fragments and paired RNA samples from wild type and csrA:: mutant strains in mLPM and LB were analyzed

first: Tony

last: Romeo


title: Usp22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta

city: Smithville

first: Evangelia

last: Koutelou

address: 1808 Park Rd 1C

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Usp22, a component of the SAGA complex, is over expressed in highly aggressive cancers, but the normal functions of this deubiquitinase are not well defined.  We determined that loss of Usp22 in mice results in embryonic lethality due to defects in extra-embryonic placental tissues and failure to establish proper vascular interactions with the maternal circulatory system.  These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFβ and several receptor tyrosine kinase (RTK) pathways. Usp22 deletion in endothelial cells and pericytes induced from embryonic stem cells also hinders these signaling cascades with detrimental effects on cell survival and differentiation as well as ability to form vessels.  Our findings provide new insights to Usp22 functions during development that may offer clues to its role in disease states.

overall_design: To determine changes in gene expression profile upon Usp22 loss in the developing placenta, RNA from day E9.5 placentas from wild-type and Ups22-/- mice s was isolated for deep sequencing, in triplicates and duplicates respectively. Key genes identified from RNAseq were validated by qRT-PCR using RNA from the same samples that were used for sequencing.

first: Sharon

middle: Y

last: Dent


title: SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons

first: James

last: Ellis

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary: Heterozygous loss-of-function mutations in the synaptic scaffolding gene SHANK2 are strongly associated with autism spectrum disorder (ASD). To investigate their effect on synaptic connectivity, we generated cortical neurons from induced pluripotent stem cells (iPSC) derived from neurotypic and ASD-affected donors. We developed Sparse coculture for Connectivity (SparCon) assays where SHANK2 and control neurons were differentially labeled and sparsely seeded together on a lawn of unlabeled control neurons. We observed striking increases in total synapse number and dendrite complexity. Dendrite length increases were exacerbated by IGF1 or BDNF treatment. Increased excitatory synapse function in haploinsufficient SHANK2 neurons was phenocopied in gene-edited knockout SHANK2 neurons. Gene correction of an ASD SHANK2 mutation rescued excitatory synapse function supporting a role for SHANK2 as a negative regulator of connectivity in developing human neurons. The transcriptome in these isogenic SHANK2 neurons was deeply perturbed in synaptic and plasticity gene sets and ASD gene modules, and activity dependent dendrite extension was defective. Our unexpected findings provide evidence for hyperconnectivity and profoundly altered transcriptome in SHANK2 neurons derived from ASD subjects.

overall_design: RNA-Seq comparison of isogenic pairs of human induced pluripotent stem cell derived neurons at 4- and 9-weeks of age, with 4 replicates at each time point

first: Kirill

last: Zaslavsky


title: Searching for target genes of miR-508/509/506/514 in HCT116 cells

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To elucidate whether miR-508/508/509/514  plays a role in colorectal cancer tumorigenesis,  RNA-seq analysis was performed to compare the gene expression profiles of miR-508/508/509/514 mimics and control microRNA transfectants.

overall_design: RNA-seq was performed in HCT116 colorectal cancer cells after miR-508/508/509/514 mimics and control microRNA virus infection

first: Jie

last: Hong


title: Whole ovaries RNA sequencing; WT and ghrelin o-acyltransferase (GOAT) knockout mice

city: Bundoora

first: Luba

last: Sominsky

state: VIC

address: RMIT University, Plenty road

country: Australia

institute: RMIT University

summary: Ghrelin, an orexigenic gut-derived peptide, is gaining increasing attention due to its multifaceted role in a number of physiological functions, including metabolism, cardiovascular health, stress and reproduction. Ghrelin exists in circulation primarily as des-acylated and acylated ghrelin. Des-acyl ghrelin, until recently considered to be an inactive form ghrelin, is now known to have independent physiological functionality. However, the relative contribution of acyl and des-acyl ghrelin to reproductive development and function is currently unknown. Here we used ghrelin-O-acyltransferase (GOAT) knockout (KO) mice that have no measurable levels of endogenous acyl ghrelin and chronically high levels of des-acyl ghrelin, to characterise how the developmental and life-long absence of acyl ghrelin affects ovarian development and reproductive capacity. We have combined ovarian transcriptome analysis using RNA sequencing with measures of ovarian morphometry, as well as with the assessment of markers of reproductive maturity and the capacity to breed. Our data show pronounced specific changes in the ovarian transcriptome in the juvenile GOAT KO ovary, indicative of advanced ovarian development. These changes corresponded with diminished ovarian reserve in the juvenile and adult ovaries of these mice, due to a continuous reduction in the number of small follicle populations. These changes did not affect the timing of puberty onset or reproductive capacity under optimal conditions. These data suggest that an absence of acyl ghrelin does not prevent reproductive success but that appropriate levels of acyl and des-acyl ghrelin may be necessary for optimal ovarian maturation.

overall_design: 4 WT and 4 GOAT KO ovaries were used for this analysis

first: Jeferson

middle: F

last: Goularte

first: Zane

middle: B

last: Andrews

first: Sarah

last: Spencer


title: SERINE/THREONINE-PROTEIN PHOSPHATASE7-LIKE PP7L Regulates Chloroplast Development

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: PP7L is Involved in the Regulation of Chloroplast Gene Expression. With 1198 and 1004 genes, whose mRNA levels were significantly more than 2-fold reduced or elevated, respectively, a large number of deregulated genes was identified by lncRNA-Seq in 4-d-old pp7l-1 seedlings.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana pp7l-1 mutant compared to wild type in three replicates


title: Poly(GR) impairs protein translation and stress granule dynamics in C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis

city: Jacksonville

first: Mark

last: Ebbert

address: 4500 San Pablo Rd

department: Neuroscience

institute: Mayo Clinic

summary: We show that GFP-(GR)100-expressing mice developed age-dependent neurodegeneration, brain atrophy, as well as motor and memory impairments through the accumulation of diffuse, cytoplasmic poly(GR).

overall_design: We studied affects from GFP-(GR)100 in mice using RNA-seq

first: Yong-Jie

last: Zhang

first: Tania

last: Gendron

first: Aliesha

last: O'Raw

first: Karen

last: Jansen-West

first: Xu

first: Mercedes

last: Prudencio

first: Jeannie

last: Chew

first: Lillian

last: Daughrity

first: Jimei

last: Tong

first: Mei

last: Yue

first: Yuping

last: Song

first: Monica

last: Castanedes-Casey

first: Aishe

last: Kurti

first: Rosa

last: Rademakers

first: Bjorn

last: Oskarsson

first: Dennis

middle: W

last: Dickson

first: Wenqian

last: Hu

first: Aaron

last: Gitler

first: John

last: Fryer

first: Leonard

last: Petrucelli


title: Expression data of Arabidopsis grown under low or sufficient nitrogen availability

city: Seeland

first: Rhonda

middle: C

last: Meyer

address: Corrensstrasse 3

department: Molecular Genetics

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

summary:
Nitrogen availability in the soil is a major determinant of crop yield. While the application of fertilizer can substantially increase the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing the nitrogen use efficiency in crop plants is a necessary step to implement low input agricultural systems. We exploited the genetic diversity present in the world-wide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, with the aim to identify biomarkers associated with good plant performance under low nitrate availability.
Transcription and epigenetic factors were identified as important players in the adaptatiion to limited nitrogen in a global gene expression analysis using the Affymetrix ATH1 chip.

overall_design: Six lines with contrasting growth characteristics on low N were used for gene expression analysis, the accessions El-0 and Fei-0, and the mixed RILs KB006, NG064, NG087, SG063. For each line, root and shoot samples were taken from plants grown on 0.4 mM or 9 mM nitrate. Three biological replicates were used per organ and treatment, in total 72 samples. One replicate consisted of a pool of 30 plants harvested from three plates.

first: Corina

last: Gryczka

first: Andrea

last: Bräutigam

first: Thomas

last: Altmann


title: AMPK activation protects against diet induced obesity through Ucp1-independent thermogenesis in subcutaneous white adipose

status: Public on Feb 01 2019

city: London

first: David

last: Carling

address: Imperial College London, Hammersmith Hospital Campus, DuCane Road

institute: MRC London Institute of Medical Sciences (LMS)

summary:
Purpose: To investigate alterations in subcutaneous white adipose gene expression induced by genetic AMPK activation in vivo, in mice fed a chow or a high-fat diet.
Methods: Subcutaneous white adipose tissue mRNA profiles of wild-type transgenic (WT-Tg) mice and mice expressing a gain-of-function AMPK mutant gamma1 subunit (D316A-Tg) were generated by deep sequencing.
Results: RNA sequencing revealed over 3000 differentially expressed genes between WT-Tg and D316A-Tg subcutaneous white adipose tissue (WATsc) from mice fed a high fat diet (HFD), of which many were classified as 'skeletal muscle-associated'.  Interestingly, uncoupling protein 1 (UCP1), associated with 'beige' adipocyte formation in WATsc, was not differentially expressed. On a chow diet, many differentially expressed genes were also identified, with gene ontology analysis identifiying glycolysis, TCA cycle and brown fat differentiation as highly enriched; key features of brown adipocyte identity. HFD-associated skeletal-muscle associated gene expression was either not significantly altered, or significantly down-regulated on a chow diet, indicating a diet-induced gene signature in D316A-Tg WATsc.
Conclusions: Our study revealed gene signatures indicative of brown adipocyte development on a chow diet, where no overt metabolic phenotype was observed in gain-of-function animals. When fed a HFD, WATsc from D316A-Tg mice displayed a muscle-like gene signature, expressing key components of creatine and calcium thermogenic cycles including Ckmt2 (creatine kinase, mitochondrial 2) Atp2a1 (SERCA1-sarco/endoplasmic reticulum ATPase 1) and ryr1 (ryanodine receptor 1). UCP1 expression was not altered between WT-Tg and D316A-Tg mice fed a HFD. Our findings suggest a novel role for AMPK in the regulation of white adipocyte identity and a potentially novel cell population that, when metabolically challenged, preferrentially utilise muscle-like thermogenic futile cycles independent of UCP1 to mediate whole organism energy expenditure.

overall_design: Whole subcutaneous white adipose tissue mRNA profiles were generated from mice fed either chow or 45% high-fat diet.

first: Alice

last: Pollard

first: Luís

last: Martins

first: Phillip

last: Muckett

first: Sanjay

last: Khadayate

first: Aurelie

last: Bornot

first: Maryam

last: Clausen

first: Therese

last: Admyre

first: Mikael

last: Bjursell

first: Rebeca

last: Fiadeiro

first: Laura

last: Wilson

first: Chad

last: Whilding

first: Vassilios

middle: N

last: Kotiadis

first: Michael

last: Duchen

first: Daniel

last: Sutton

first: Lucy

last: Penfold

first: Alessandro

last: Sardini

first: Mohammad

last: Bohlooly-Y

last: Smith

first: Jon

middle: A

last: Read

last: Snowden

first: Angela

last: Woods


title: Identifying small proteins by ribosome profiling with stalled initiation complexes

city: Baltimore

first: Allen

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Small proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the true prevalence of these regulators remains unknown because conventional annotation pipelines usually exclude such small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly-initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli. We selected 41 smORFs for chromosomal tagging and detected small protein synthesis for all but 3. The corresponding genes are not only intergenic, but are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling of E. coli MG1655 cultures treated with Onc112, an antibiotic that traps ribosomes at start codons, as a means to identify start sites in intergenic regions.


title: Construction of Mini-Chemostats for High-throughput Strain Characterization

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

country: Sweden

institute: Chalmers tekniska högskola

summary: We developed a mini-chemostat system with 16 reactors, each at a working volume of 40 ml. Sensors measure dissolved oxygen in the reactor, while OD600 is measured in the outflow. We further developed a CO2 and pH sensor array that can be plugged in to the outflow of the reactors. The system was used to characterize yeast physiology at four metabolically different conditions: limitations of glucose, both aerobic and anaerobic, nitrogen, and ethanol. The physiology of yeast cells grown at the four different conditions in the mini-chemostat (MC) system was compared with yeast cells grown in a DASGIP 1L system using RNAseq analysis

overall_design: Cells were grown in Glucose-limited, Nitrogen-limited, Ethanol-limited or Oxygen/Glucose-limited chemostat cultivations were measured in biological triplicates

first: Guodong

last: Liu

last: Hansson

first: Jens

last: Nielsen


title: Single cell RNA seq of long-term 3D culture of mouse primary hepatocytes induced by TNFa

city: Palo Alto

first: Weng Chuan

last: Peng

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

summary: Single cell RNA seq to compare the gene expression profile of  hepatocytes cultured in expansion or differentiation media to primary hepatocytes

overall_design: Gene expression profiling by single cell RNA seq (10x Genomics Chromium System)

first: Roel

last: Nusse


title: Deep mutational scanning of Env from the HIV-1 strain DU422 for binding to CD4 and PG16

first: Erik

last: Procko

address: 601 S Goodwin Ave

institute: University of Illinois

summary: The HIV-1 genome gains access to the inside of a cell via the mechanism of the viral spike protein Env, which undergoes a series of major conformational rearrangements after binding target receptors that ultimately drive virus-cell membrane fusion. Env is expressed as a heterogenous ensemble of conformations, which can inappropriately misdirect the host immune response towards the production of non-protective, strain-specific antibodies.  Potent, broadly neutralizing antibodies (bnAbs) frequently recognize a ‘closed’ Env conformation, and therefore Env has undergone significant engineering to stabilize the closed state for vaccine incorporation.  Previously, we used deep mutational scanning of Env from a prototypical tier 1 clade B strain (BaL) to characterize the sequence-activity landscape for binding to PG16, a bnAb that preferentially binds the closed state.  Mutations were identified that increased expression of closed Env and reduced conformational heterogeneity, but these mutations were only partially transferable to Env sequences from other strains.  To generate an expanded set of mutations that may be broadly applicable to diverse HIV-1 strains, we present here the deep mutational scanning of Env from the tier 2 clade C strain DU422 for interactions with CD4 and PG16.  Residues across the trimerization domain and trimer interface have low mutational tolerance for maintaining PG16 recognition.  New mutations are identified that enhance presentation of the closed Env conformation, and these are applied to Env sequences spanning multiple clades and tiers.

overall_design: The extracellular domains of Env (referred to here as gp140) from the clade C HIV-1 DU422 strain were encoded by a synthetic codon-optimized gene with a CD5 leader sequence, and fused at the C-terminus via a glycine/serine-rich linker to a hexahistidine tag and canonical transmembrane helix from class I MHC for surface display. The Env sequence was diversified by overlap-extension PCR to generate three single-site saturation mutagenesis libraries spanning the full length of gp140. The libraries were expressed in human Expi293F cells (a suspension derivative of HEK 293) and sorted by FACS for binding to soluble CD4 and bnAb PG16. Enrichment ratios were calculated for all single amino acid substitutions by comparing the frequencies of sequence variants in the sorted cell populations (from RNA transcripts) with the naive libraries (plasmid DNA). Experiments were independently duplicated.

first: Jeremiah

middle: D

last: Heredia


title: A high-throughput screening strategy identifies regulators of alternative splicing via interaction with RNA G-quadruplexes

city: Houston

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: RNA secondary structures have been increasingly reported to serve critical regulatory roles in post-transcriptional gene regulation. RNA G-quadruplex secondary structures can serve as cis-elements to recruit splicing factors and regulate alternative RNA splicing. We recently showed that RNA G-quadruplexes play a critical regulatory role in regulating alternative splicing during the epithelial mesenchymal transition.  Due to the critical role alternative splicing plays in human health and disease, an unmet need exists to identify small molecule modulators of alternative splicing. In this study, we performed high-throughput screening using a dual-output splicing reporter to identify small molecules capable of regulating alternative splicing by interacting with RNA secondary structure G-quadruplexes. We identify emetine and its analog cephaeline as small molecules that denature RNA G-quadruplexes in a sequence and location independent manner to modify alternative splicing. Transcriptome analysis reveals that treatment with emetine globally regulates alternative splicing, including events associated with exon-proximal G-quadruplexes. These data suggest a critical role for emetine and cephealine as splicing regulators with the selective ability to disrupt RNA G-quadruplex-associated alternative splicing in vivo.

overall_design: PolyA-RNA-sequencing of control and emetine treated cell lines with two biological replicates each

first: Chonghui

last: Cheng


title: Single-cell chromatin conformation capture of mouse sensory neurons in visual and olfactory systems by Dip-C

city: Cambridge

first: Longzhi

last: Tan

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

summary: We performed single-cell chromatin conformation capture with our recently developed method, Dip-C, on mouse sensory neurons in visual and olfactory systems, and reconstructed their 3D genomes.

overall_design: We performed Dip-C on 132 cells from the retina and 277 cells from the main olfactory epithelium, extracted chromatin contacts, and generated 3 replicates of 3D genome structures per cell.


title: RNA-seq analysis of orthotopic GBM tumours derived from mouse glioblastoma stem-like cells GSC1 and GSC2

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

summary: GFP-labelled tumours were dissected under a fluorescence microscope and sequenced to determine gene expression profiles and assess similarity to human GBM

overall_design: 4 independent GSC1- and 3 independent GSC2-derived tumours were sequenced

first: Simona

last: Parrinello

first: Cristina

last: Ottone


title: Genome-wide analysis of Olig2-positive and Olig2-negative tumors in a glioma mouse model.

city: San Francisco

last: Rowitch

address: 35 Medical Center Way

department: Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine

institute: UCSF

summary: Analysis of genes differentially expressed in Olig2-positive (oligodendrocyte-like) versus Olig2-negative tumors. The hypothesis tested in the present study was that the glial phenotype influence the vasculature and the tumor microenvironment.  Results provide evidence that multiple pathways including angiogenesis and immune response are differentially expressed between the two types of tumors.

overall_design: Total RNA obtained from tumors from animals transplanted with Olig2cre/+;p53fl/fl;hEGFRvIII and Olig2cre/cre;p53fl/fl;hEGFRvIII cells, at the time of neurological symptoms appearance.

first: Amelie

last: Griveau

first: Joseph

last: DeYoung


title: Single-cell RNA-seq reveals cellular heterogeneity of pluripotency transition and X-chromosome dynamics during early mouse development

city: Sha Tin

first: Shangli

address: No. 15 Science Park West Avenue

department: Ming Wai Lau Centre for Reparative Medicine

country: Hong Kong

institute: Karolinska Institutet

summary: Here, we present a comprehensive transcriptome roadmap of the critical developmental time window prior to gastrulation by sequencing and analysis of 1724 individual cells from 28 pregastrula mouse embryos. Our analyses reveal the cellular substructure in EPI through clustering cells into anterior, transition and posterior states. The induction of the primitive streak (PS) is achieved via a transition state of a high cellular variability and up-regulation of the PS signature genes. Moreover, the evolvement of these three cellular states corresponds well with the transition from mouse naïve embryonic stem cells (i.e mESCs) to primed epiblast stem cells (i.e. mEpiSCs).  In addition, dissect the substructure of visceral endoderm (VE) and identify novel markers of anterior VE (AVE). Importantly, we also characterize the lineage-specific dynamics of X-chromosome inactivation (XCI), demonstrating that reversal of XCI (i.e. X reactivation) in the EPI lineage occurs before imprinted silencing of the paternal X-chromosome is completely established, and the ensuing random XCI is highly asynchronous. VE displays faster progression of imprinted XCI compared to the extra-embryonic ectoderm (ExE). In summary, our data not only provide new insight into the regulation of lineage specification and XCI dynamics during the early embryogenesis but also shed light on the in vivo counterparts of stem cells including hypothesized formative pluripotency.

overall_design: In total, 1724 cells with three types of mice crossing were utilized. 21 blastocyst cells used for X-chr interactivation analyses.

first: Qiaolin

last: Deng


title: Gene expression in the small intestine of mice colonized with Pseudomonas aeruginosa

city: Hamilton

first: Alberto

last: Caminero

state: ON

address: 1280 Main St W

institute: McMaster University

summary: Celiac disease (CeD) is a food sensitivity characterized by a breakdown of oral tolerance to gluten proteins in genetically predisposed individuals, although the underlying mechanisms are incompletely understood. To evaluate a functional role of bacterial proteases in CeD, we colonized germ-free or clean SPF mice with P.aeruginosa PA14 or P.aeruginosa PA14 disrupted in lasB gene (elastase). We show gluten-independent, PAR-2 mediated upregulation of inflammatory pathways by LasB in C57BL/6 mice without villus blunting. In mice expressing CeD risk genes, P. aeruginosa elastase synergized with gluten to induce more severe inflammation that was associated with moderate villus blunting.

overall_design: Determination of inflammatory genes in tissue and intraepithelial lymphocytes of mice. For RNA extraction, RNeasy Mini Kit (Qiagen) was used. Gene Expression CodeSet for mouse inflammation genes (Mouse Inflammation panel, 254 genes) were run according to the manufacturer’s instructions (NanoString Technologies Inc.). The results obtained were analyzed with nSolver 2.5 (NanoString Technologies).

first: Elena

last: Verdu


title: Antagonism of IAPs enhances CAR T cell efficacy

city: Melbourne

first: Jane

last: Oliaro

state: Victoria

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Chimeric antigen receptor (CAR) T cell therapy has proven highly successful in the treatment of hematological malignancies, notably acute lymphoblastic leukemia and B cell lymphoma. However, the efficacy of CAR T cells against solid tumors is poor, likely due to tumor-associated immunosuppression. Here, we demonstrate that antagonizing Inhibitor of Apoptosis Proteins (IAPs) with the clinical smac-mimetic, birinapant, significantly enhanced the anti-tumor activity of CAR T cells in a TNF-dependent manner. Enhanced tumor cell death occurred independently of the perforin-mediated granule exocytosis pathway, underscoring the cytotoxic potential of CAR T cell-derived TNF. Importantly, combining CAR T cell therapy with birinapant dramatically reduced established tumor growth in vivo, where either therapy alone was relatively ineffective. Using patient biopsy-derived tumoroids, we demonstrate the synergistic potential of combining CAR T cell therapy with smac-mimetics. Taken together, we identify CAR T cell-derived TNF as a potent anti-tumor effector, which can be further harnessed by smac-mimetics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MC38 HER2/ AU565 cells were either left untreated or incubated with CAR T cells [no smac-mimetics]  (in triplicate/ duplicate) at a 2:1 effector-target ratio for 6 hrs followed by 3’ RNA-Seq of viable cells.

first: Magnus

last: Zethoven


title: Epigenomics signature in X-ALD aligns with impaired oligodendrocyte differentiation

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

summary: X-linked adrenoleukodystrophy (X-ALD) is an inherited disorder characterized by axonopathy and demyelination in the central nervous system and adrenal insufficiency. Main X-ALD phenotypes are: (i) an adult adrenomyeloneuropathy (AMN) with axonopathy in spinal cords, (ii) cerebral AMN with brain demyelination (cAMN) and (iii) a childhood variant, cALD, characterized by severe cerebral demyelination. Loss of function of the ABCD1 peroxisomal fatty acid transporter and subsequent accumulation of very-long-chain fatty acids (VLCFAs) are the common culprits to all forms of X-ALD, an aberrant microglial activation accounts for the cerebral forms. How same mutation in the ABCD1 gene can lead to clinically very distinct phenotypes and what factors account for the dissimilar clinical outcomes and prognosis of X-ALD variants remain elusive. We wonder whether epigenetics mechanisms could answer the lack of genotype-phenotype correlation. We employed Illumina state of the art technology to analyze the differential methylation of over 485,000 CpG sites throughout the entire human genome and used stringent statistical criteria to define differential methylation patterns between brains of cALD, cAMN and age-matched controls. We identified a common X-ALD methylation signature comprising the hypermethylation in genes harboring the trimethylated histone H3K27me3 mark in their promoters, the hypermethylation for genes driven the oligodendrocyte lineage, and the hypomethylation for immune-associated genes. We also examined the methylated differences between cALD and cAMN resulting with differential immune response pathways and concordance methylation levels with phenotype severity. The detected methylation differences correlated with transcriptional and translational consequences, as supported by Affymetrix expression arrays, quantitative PCR and WB changes. The reliability of these changes was further demonstrated by validating DNA methylation by an independent pyrosequencing assay. From these evidences, we propose the altered transcriptional programs in oligodendrocyte differentiation in X-ALD patients. These observations may provide new therapeutic epigenetic agents.

overall_design: Total samples analyzed: 37; 8 control child, 9 control adult, 8 cALD and 8 cAMN

first: Angel

last: Diaz-Lagares

first: Juan

last: Sandoval

first: Manel

last: Esteller


title: Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma [RNA-Seq]

city: San Antonio

first: Chin-Hsing Annie

last: Lin

state: TX

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

summary: Epigenetic modifications in the form of altered DNA or histone methylation can influence gene expression patterns critical for neoplastic initiation and progression. The fact that abnormal gene expression can be driven by epigenetic alterations led us to examine the correlation between DNA methylation, trimethylation of histone 3 lysine 9 (H3K9me3) and lysine 27 (H3K27me3), and gene expression in esophageal adenocarcinoma (EAC). Using genome-wide approaches (chromatin immunoprecipitation/sequencing (ChIP-Seq) and methylation arrays), we identified gene targets that were enriched with the chromatin-repressive marks H3K9me3, H3K27me3, and/or DNA hypermethylation across patients with EAC. Using RNA-Seq, we found genes involved in cellular morphology and movement, epithelial cell differentiation, epithelial junction signaling, as well as genes involved in epithelial-mesenchymal transition (EMT) were down-regulated in patients with poorly differentiated EAC. Additionally, comparative analyses of ChIP-Seq, DNA methylation, and RNA-Seq data allowed us to identify a group of genes downregulated in EAC is associated with aberrant H3K27me3 enrichment or a combination of H3K27me3 and DNA hypermethylation in the poorly differentiated EAC cases. Furthermore, by comparison to TCGA data sets, H3K27me3 enrichment is associated with aberrant DNA methylation across numerous EAC cases, suggesting that dysregulation of H3K27me3 and DNA methylation is crucial in the pathogenesis of EAC.

overall_design: Total RNA was extracted using TRIzol reagent (Invitrogen/Life Technologies #15596-026) and sequencing libraries were generated with Illumina RNA-Seq library preparation kit with Ribozero. RNA deep-sequencing for paired-end 36 base pair reads was run at Illumina HiSeq2500; subsequently, 325 million pass filtered reads of each specimen were aligned to hg19. DESeq was used to normalize raw read counts. Cuffdiff was applied to analyze the differential gene expression between EAC and control (SQ) using a log2(fold change) of 1.0 as a cut-off for gene experssion.

first: Christopher

last: Rhodes

first: Chin-Hsing


title: Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma [ChIP-Seq]

overall_design: Esophageal adenocarcinoma specimens from two patients (both poorly differentiated) and normal  human esophageal tissues were crosslinked in 1.1% formaldehyde before chromatin shearing using the  Diagenode Bioruptor. The resulting sheared 200-500 bp chromatin fragments were incubated with  H3K9me3 (Millipore #07-473) or H3K27me3 (Millipore #07-449) antibody-conjugated Protein A  Dynabeads (Life Technology #10002D) overnight. For normalization, an aliquot of sheared chromatin fragments were incubated with antibody against unmodified H3 antibody-conjugated Protein A Dynabeads. Subsequently, enriched chromatin fragments were eluted, de-crosslinked, and purified for library preparation (Illumina Library Kit, Cat#15026486) for the Illumina HiSeq2000 sequencer. DNA obtained from each ChIP pull-down was sequenced to high depth of 150 million tags with 50 basespair-end sequencing.


title: Next Generation Sequencing Facilitates Quantitative Analysis of ISL1 Regulated Transcriptomes

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

summary: The goals of this study are to analyze the transcriptome profiling (RNA-seq) after ISL1 overexpression in Huh7 cells.

overall_design: Huh7 cells were transfected by ISL1 expression lentivirus and blank lentivirus as control.Total RNA was extraced by Qiagen kit and the mRNA profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.

first: Zhiqian

last: Zhang

first: Haibo


title: Genome-wide maps of ISL1-binding site

summary: We report the high-throughput profiling of ISL1-binding sites in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide ISL1-binding maps of Huh7 cells. This study provides a prediction of regulated genes by the ISL1.

overall_design: Examination of ISL1-binding sites in HuH7 cell with overexpression of ISL1.


title: The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence

city: Taipei

first: Hsing Yi

last: Cho

state: Select One

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: ABRC

country: Taiwan

institute: Academia sinica, Taiwan

summary: The goal of this study is to compare translation regulation in Col-0, SnRK1, and eIFiso4G1 mutants in Arabidopsis under submergence

overall_design:
Examination of the steady-state mRNA and RNA loading on the polysome in 9 days old Col-0, SnRK1, and eIFiso4G1 mutants under submergence.
Two independent biological repeats were conducted.

first: Hsing-Yi

first: Ming-Che

last: Shih


title: ISL1

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

overall_design: Refer to individual Series


title: Hepatic PPARalpha is critical in the metabolic adaptation to sepsis

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

institute: Institut Pasteur de Lille

summary:
Sepsis induces a metabolic shift from glucose to fatty acid utilization that is key to survival for the organism.
Here we used microarray analysis to characterize hepatic gene expression in conditions mimicking sepsis.

overall_design: Wild type or whole-body Ppara-KO mice were infected with E.coli to induce sepsis. Mice were killed 16 hours after infection and livers were removed for transcriptomic analysis. Each array is 1 biological replicate

first: Bart

last: Staels

first: Réjane

last: Paumelle


title: Multi-omic measurements of heterogeneity in HeLa cells across laboratories

city: West Haven

first: Yansheng

last: Liu

state: CT

address: 840 West Campus Drive, Fl 3rd Ste Cancer

department: School of Medicine

institute: Yale

summary: Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.

overall_design: Multi-omic (genome, transcriptome, proteome, protein turnover) analysis of 14 HeLa cell lines obtained from different laboratories but grown under the same conditions.

first: Yang

last: Mi

first: Torsten

last: Muller

first: Saskia

last: Kreibich

first: Evan

middle: G

last: Williams

first: Audrey

last: Van Drogen

first: Christelle

last: Borel

first: Max

last: Frank

first: Pierre-Luc

last: Germain

first: Isabell

last: Bludau

first: Martin

last: Mehnert

first: Michael

last: Seifert

first: Mario

last: Emmenlauer

first: Isabel

last: Sorg

first: Fedor

last: Bezrukov

first: Federique

middle: S

last: Bena

first: Hu

last: Zhou

first: Christoph

last: Dehio

first: Giuseppe

last: Testa

first: Julio

last: Saez-Rodriguez

first: Stylianos

last: Antonarakis

first: Wolf-Dietrich

last: Hardt

first: Ruedi

last: Aebersold


title: Transcriptional profile of LPS-stimulated murine macrophages treated with bacterially derived fatty acid

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

summary: We used RNA-seq to profile the effect of a bacterially derived fatty on LPS-stimulated murine macrophages. From the transcriptional response, there was a significant decrease of inflammatory signals with lipid treatment, and pathway analysis of differentially expressed genes suggests PPAR alpha as potential anti-inflammatory mechanism.

overall_design: examination of anti-inflammatory effects of 10(Z)-hexadecenoic acid on LPS-stimulated murine peritoneal macrophages

first: Christopher

last: Lowry

first: Robin

last: Dowell


title: Hsf1 Chip on chip on wildtype(WT) and iron deprived (BPS) cells of Candida albicans using polyclonal antibody

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

type: Genome binding/occupancy profiling by array

summary: Comparative analysis of genome wide binding sites of Hsf1 in normal and iron-deprived conditions

overall_design: Agilent two-color ChIP-on-Chip experiment, Organism: Candida albicans ,Genotypic Technology designed custom Candida albicans 4X180k ChIP-on-chip Array (AMADID-038045)

first: Remya

last: Nair

first: Mohd

last: Shariq

first: Rajendra

last: Prasad


title: Genome-wide sequencing of male and female TCR1640 immune cells

status: Public on Jan 31 2019

city: Montreal

first: Alexandre

last: Prat

state: Quebec

address: 900 Rue Saint-Denis

department: Neurosciences

institute: CRCHUM

summary: Sequencing of TH1/TH17 differentiated immune cells isolated from secondary lymhoid organs from male and female TCR1640 mice and SJL/j WT mice

overall_design: Examination of differences between male and female gene profile within immune cells  isolated from TCR1640 mice and SJL/j WT mice

first: Tessa

last: Dhaeze


title: A mouse tumor biofilm model and its use for dissecting in vivo anti-bacterial and anti-biofilm activities of anti-pseudomonas drugs

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: Chronic Pseudomonas biofilm infections are commonly associated in patients afflicted with cystic fibrosis (CF) leading to high degree of morbidity. In a murine tumor model we demonstrated that P. aeruginosa efficiently colonizes and forms biofilms in cancerous tissue post intra-venous injection. Several non-biofilm forming mutants have been identified and incorporated in the present study. Biofilm formation by wild type strains was evident in electron microscopy and immuno-histological studies. Efficacy of  currently available CF infection treatment antibiotics such as ciprofloxacin, colistin and tobramycin were tested in this model. We found out that normal doses of these antibiotics were unable to eliminate wild type P. aeruginosa PA14. However, transposon mutants of P. aeruginosa PA14 (pqsA & Pel A) had strong influence on colonization. Subsequently high doses were effective against wild type P. aeruginosa PA14 biofilms.

overall_design:
The samples of P. aeruginosa PA14 wild type strain and the transposon mutant of pqsA were analyzed by RNA-seq. The control samples were cultivated in the LB medium until the exponential or stationary growth phase. Four biological replicas were pooled in pairs to get two replicas for RNA extraction, library preparation and sequencing. Tumor samples were collected from mice infected with PA14 wild type or PA14 pqsA transposon mutants. There were four mice per group and the material of each group was pooled to assure sufficient bacterial RNA. The tumor samples were split into two technical replicas for sequencing library preparation.
Please note that two groups which each processed data file were generated from are indicated in the file names as following;
PA14_exponential growth (PA14_e)
PA14_stationary growth (PA14_s)
WT_murine tumor cells (PA14_t)
pqsA_exponential growth (pqsA_e)
pqsA_stationary growth (pqsA_s)
pqsA_murine tumor cells  (pqsA_t)

first: Vinay

last: Pavar

first: Uliana

last: Komor

first: Piotr

last: Bielecki

first: Mathias

last: Muesken

first: Nadine

last: Kasnitz

first: Agata

last: Bielecka

first: Sebastian

last: Bruchman

first: Manfred

last: Rohde

first: Marina

last: Pils

first: Siegfried

last: Weiss

first: Susanne

last: Häussler


title: HDAC Regulates Transcription at the Outset of Axolotl Tail Regeneration

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

summary: Tissue regeneration is associated with complex changes in gene expression and post-translational modifications of proteins, including transcription factors and histones that comprise chromatin. We tested 173 compounds designed to target epigenetic mechanisms in an axolotl (Ambystoma mexicanum) embryo tail regeneration assay. A relatively large number of compounds (N = 31) reproducibly inhibited tail regeneration, including multiple histone deacetylase inhibitors (HDACi). In particular, romidepsin potently inhibited tail regeneration when embryos were treated continuously for 7 days. Additional experiments revealed that romidepsin acts within a very narrow, post-injury window. Romidepsin treatment for only 1 minute post-amputation inhibited regeneration through the first 7 days, however after this time, regeneration commenced with variable outgrowth of tailfin tissue and abnormal patterning. Microarray analysis showed that romidepsin altered early, transcriptional responses at 3 and 6-hour post-amputation, especially targeting genes that function in the regulation of transcription, cell differentiation, cell proliferation, pattern specification, and tissue morphogenesis. Our results show that HDAC activity is required at the time of tail amputation to regulate the initial transcriptional response to injury and regeneration.

overall_design: Ambystoma mexicanum embryos were first treated by an HDAC inhibitor (10um of Romidepsin or Belinostat) and amputated 2mm from tail tip. After amputation, 1 mm of the distal tail tip was collected at time of amputation (0), 3, 6, 12, 24, 48, or 72 hours post amputation (hpa). Additionally, untreated controls were also collected from animals which were not treated by an HDAC inhibitor. A total of 336 embryos were used, with each replicate representing a pool of 8 embryo tail tips.

first: S

middle: R

last: Voss


title: Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition

city: Boston

first: Andrea

middle: June

last: Kriz

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

summary: The zinc finger CCCTC-binding protein (CTCF) carries out many, at times contradictory, functions in the cell. Although previous studies have sought to explain CTCF multivalency based on sequence composition of binding sites, few have examined how CTCF post-translational modification (PTM) could contribute to the its many functions. Here, we performed CTCF mass spectrometry, identified a novel phosphorylation site at Serine 224 (Ser224-P), and demonstrate that phosphorylation is carried out by Polo kinase 1 (PLK1). CTCF Ser224-P is chromatin-associated, mapping to at least a subset of known CTCF sites. Interestingly, CTCF Ser224-P accumulates during the G2/M transition of the cell cycle and is enriched at pericentric regions.  To test function, we mutated residue 224. The phospho-obviation mutant, S224A, appeared normal. However, the phospho-mimic mutant, S224E, is detrimental to mouse embryonic stem cell colonies.  While ploidy and chromatin architecture appear unaffected, S224E mutants exhibit differential expression of hundreds of genes, including p53 and p21.  We have thus identified a new CTCF PTM and provided evidence of function during cellular growth and gene regulation.

overall_design: CTCF and CTCF Ser224-P ChIP-seq, RNA-seq, Hi-C^2

first: B

last: Del Rosario

first: A

middle: M

last: Anselmo

first: C

last: Fry

first: F

last: White

first: R

middle: I

last: Sadreyev

first: J

middle: T

last: Lee


title: SmE1 is a functional subunit of the Arabidopsis Sm-ring that controls plant development and response to cold stress

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

institute: Centro de Investigaciones Biologicas

summary: We report the role of SmE1 protein in the control of Arabidopsis development and tolerance to abiotic stresses. SmE1 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieve over selected transcripts depending on the stimulus nature.

overall_design: Transcriptomic profiling through RNAseq of Col-0 and sme1-1 plants under control conditions or exposed to low temperatures (4ºC, 24h)

first: Raul

last: Huertas

first: Rafael

first: José

last: Jiménez-Gómez

first: Mar

last: Castellanos

first: Pedro

last: Crevillé

last: Jarillo

first: Manuel

last: Piñeiro

first: Julio

last: Salinas


title: MicroRNA Signature of Central Nervous System-Infiltrating Dendritic Cells in an Animal Model of Multiple Sclerosis

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Innate immune cells are integral to the pathogenesis of several diseases of the central nervous system (CNS), including multiple sclerosis (MS). Dendritic cells (DCs) are potent CD11c+ antigen presenting cells which function as critical regulators of adaptive immune responses, particularly in autoimmune diseases such as MS. The regulation of DC function in both the periphery and CNS compartment has not been fully elucidated. One limitation to studying the role of CD11c+ DCs in the CNS is that microglia have been shown to upregulate CD11c during inflammation, making it challenging to distinguish hematopoietically-derived DCs from microglia. Selective expression of microRNAs (miRNAs) has been shown to distinguish populations of innate cells within the CNS during neuro-inflammation and is proposed as a mechanism for the regulation of innate cell function. Using the experimental autoimmune encephalomyelitis (EAE) murine model of MS, we characterized the expression of miRNAs in CD11c+ cells using a non-biased murine array.  Several miRNAs, including miR-31, were enriched in CD11c+ cells within the CNS during EAE, but not LysM+ microglia. Moreover, to distinguish CD11c+ DCs from microglia that upregulate CD11c, we generated bone marrow chimeras and found that miR-31 expression was specific to bone marrow-derived DCs (BMDCs). Interestingly, miR-31 binding sites were enriched in mRNAs downregulated BMDCs that migrated into the CNS. Finally, miR-31 was enriched in DCs that migrated through an in vitro blood-brain barrier. Our findings suggest that miRNAs, including miR-31, may participate in the regulation of DCs entry into the CNS during EAE  and  could potentially represent therapeutic targets for CNS autoimmune diseases such as MS.

overall_design: Radiation bone marrow chimeras with bone marrow-derived DCs (BMDCs) expressing eYFP were immunized with MOG35-55 to induce active EAE. CD11c+eYFP+ cells were sorted by FACS at day 18 post-immunization from the spleen and perfused CNS.

first: Gregory

middle: F

last: Wu

first: Hoye

middle: L

last: Mariah


title: Study of the signaling modulated by HDAC4 in skeletal muscle in ALS

city: Rome

first: Viviana

last: M

address: Via A. Scarpa 16

department: SAIMLAL

institute: La Sapienza University of Rome

summary: BACKGROUND: Histone deacetylase 4 (HDAC4) has been proposed as a target for the treatment of Amyotrophic Lateral Sclerosis (ALS) because it mediates nerve-skeletal muscle interaction and since its expression in skeletal muscle correlates with the severity of the disease. However, our recent studies on the skeletal muscle response upon long-term denervation highlighted the importance of HDAC4 in maintaining muscle integrity.   METHODS: To fully identify the yet uncharacterized HDAC4 functions in ALS, we genetically deleted HDAC4 in skeletal muscles of a mouse model of ALS. Body weight, skeletal muscle, innervation and spinal cord were analyzed over time by morphological and molecular analyses. A transcriptome analysis was also performed to delineate the signaling modulated by HDAC4 in skeletal muscle of a mouse model of ALS.  FINDINGS: HDAC4 deletion in skeletal muscle caused earlier ALS onset, characterized by body weight loss, muscle denervation and atrophy, and compromised muscle performance in ALS mice, although the main catabolic pathways were not activated. A transcriptome analysis identified the gene networks modulated by HDAC4 in ALS, revealing UCP1 as a top regulator that may be implicated in worsening ALS features.   INTERPRETATION: HDAC4 plays an important role in preserving innervations and skeletal muscle in ALS, likely by modulating the UCP1 gene network. Our study highlights a possible risk in considering HDAC inhibitors for the treatment of ALS.

overall_design: Total RNA was isolated and purified from 6 SOD and 5 SOD HDAC4mKO GA muscles at 14 weeks of age. Samples were pooled together and libraries were generated from duplicates of SOD or SOD HDAC4mKO samples

last: Moresi

first: Eva

last: Pigna

first: Constantin

last: Heil

first: Daniela

last: Palacios


title: Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma

first: Chin-Hsing Annie

last: Lin


title: Distinct gene expression profile of Huh7 cell lines stably overexpressing CRABP1 or 2

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

summary: The metabolism of ROL to the biogenesis of ATRA occurs in the cytoplasms of hepatocytes, which in turn translocates into nucleus upon binding to Cellular Retinoic Acid Binding Proteins, CRABP1 or CRABP2. However, the differential effect of CRABP1 and CRABP2 on the intracellular environment is not well understood.  Here,  we report polyA RNA sequencing data of the CRABP1 or CRABP2 overexpressing Huh7 cells.

overall_design: The RNA sample was collected from CRABP1 or CRABP2 overexpressing Huh7 cells. This study examined the gene expression profile in CRABP1 or CRABP2 overexpressing Huh7 cells.

first: Takeshi

last: Saito

first: Bo-Ram

last: Bang