title: Estrogen-related receptors are targetable ROS sensors

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

summary: Excessive reactive oxygen species (ROS) can cause oxidative stress and consequently cell injury contributing to a wide range of diseases. Addressing the critical gaps in our understanding of the adaptive molecular events downstream ROS provocation holds promise for the identification of druggable metabolic vulnerabilities. Herein, we unveil a direct molecular link between the activity of two estrogen-related receptor (ERR) isoforms and the control of glutamine utilization and glutathione antioxidant production. ERRα downregulation restricts glutamine entry into the TCA cycle while ERRγ upregulation promotes glutamine-driven glutathione production. Notably, we identify increased ERRγ expression/activation as a hallmark of oxidative stress triggered by mitochondrial disruption or chemotherapy. Enhanced tumor antioxidant capacity is an underlying feature of human breast cancer (BCa) patients that respond poorly to treatment. We demonstrate that pharmacological inhibition of ERRγ with the selective inverse agonist GSK5182 increases antitumor efficacy of the chemotherapeutic paclitaxel on poor outcome BCa tumor organoids. Our findings thus underscore the ERRs as novel redox sensors and effectors of a ROS defense program and highlight the potential therapeutic advantage of exploiting ERRγ inhibitors for the treatment of BCa and other diseases where oxidative stress plays a central role. In this study, ERRγ ChIP-seq analysis was performed under normal conditions in the breast cancer cell line BT-474.

overall_design: Duplicate ChIP-seq experiments of ERRgamma (ERRγ, ESRRG) were performed in BT-474 breast cancer cells under basal conditions with input DNA as a control ChIP-seq.

first: Étienne

last: Audet-Walsh

first: Mathieu

last: Vernier

first: Catherine

last: Dufour


title: Gene Expression Timecourse of WT, DUBmut, and EndoUmut Mouse Hepatitis Virus Strain A59 infected C57bl/6 Bone Marrow derived macrophages

status: Public on Feb 07 2020

city: MAYWOOD

first: Susan

last: Baker

state: IL

address: 2160 S. 1st Ave, Bldg 115 Rm 270B Baker

department: Microbiology & Immunology

country: USA

institute: Loyola University Chicago

type: Expression profiling by high throughput sequencing

summary: We report the differences in innate immune activation in the comparison of wild type and mutant Mouse Hepatitis Virus Strain A59 infection of bone marrow derived macrophages.  We infected BMDMs and harvested RNA at 3, 6, 9, and 12 hpi while comparing changes in host gene expression compared to mock infected cells. Here, using a transcriptomics approach, we compared the scope and kinetics of the host response to the wild type, DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response, predominantly involving type I interferons and a subset of interferon-responsive genes, within 12 hours after infection. In contrast, the wild type and DUBmut viruses stimulate the upregulation of over 2,800 genes, including the activation of unfolded protein response (UPR) pathways and a proinflammatory response associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in modulating the kinetics and magnitude of the host response during virus infection and demonstrates that inactivation of a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages and the disease process.

overall_design: Examination of 3 different Mouse Hepatitis Virus Strain A59 infecting C57bl6 BMDMs at 4 different timepoints. Each sample was done in triplicate with a mock infected control.

first: Xufang

last: Deng

first: Aaron

last: Volk

first: Matthew

last: Hackbart

first: Robert

middle: C

last: Mettelman

first: Amornrat

last: O'Brien


title: Expression data of mice ovarian tissue cell treated with Red Ginseng Extract fraction (RGE)

status: Public on Feb 08 2020

city: seongnam si,

first: Boo-yong

last: Lee

state: kyungggi do

address: pangyoro 335, seongnam si, kyungggi do

country: South Korea

institute: CHA university

summary: Female infertility and subfertility have been increasing in prevalence worldwide. One contribuing factor is the health of the ovary, the function of shich is directly related to maternal age. In this report, we investigated the effecte of Korea Red Ginseng Extract Fraction on ovarian function in female mice

overall_design: 6 month and 12 month age mice ovarian tissue were isolated and treated with DMSO or 10mg/mL RGE for 24 hours. Total RNA was extracted using TRIzol reagent and processed for quality control of total RNA. The microarray is performed.

first: Boo-Yong

first: Sungwoo

last: Chei


title: Epithelial planar bipolarity emerges from Notch-mediated asymmetric inhibition of Emx2

status: Public on Feb 06 2020

city: Neuherberg

first: Hernán

last: López-Schier

address: Ingolstaedter Landstr. 1

department: Research Unit Sensory Biology and Organogenesis

country: Germany

institute: Helmholtz Zentrum München

summary: This dataset consists of single-cell RNA-seq (10X) data of neuromast cells from zebrafish larvae. Posterior lateral-line neuromast cells were isolated by fluorescence activated cell sorting (FACS) from the dissociated trunks of Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae expressing the green fluorescent protein (EGFP) in hair cells and unipotent hair-cell progenitors (UHCPs), and from Tg[Et(krt4:EGFP)sqgw57A] larvae expressing EGFP in supporting cells.

overall_design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells.

first: Eva

middle: L

last: Kozak

first: Subarna

last: Palit

first: Jerónimo

middle: R

last: Miranda-Rodríguez

first: Aleksandar

last: Janjic

first: Anika

last: Böttcher

first: Heiko

last: Lickert

first: Wolfgang

last: Enard

first: Fabian

last: Theis


title: JUN induction in osteoprogenitors

city: Palo Alto

first: Pablo

last: Domizi

state: CA

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

summary: Different osteoprogenitors (SSC, BCSP, Thy+) were sorted after 2 days of JUN induction, followed by RNA extraction and microarray analysis

first: Tristan

last: Lerb

first: Gerlinde

last: Wernig


title: Molecular profile of apocrine glands in hidradenitis suppurativa

city: Dessau

first: Christos

last: Zouboulis

address: Auenweg 38

department: Departments of Dermatology, Venereology, Allergology and Immunology

institute: Dessau Medical Center, Brandenburg Medical School Theodor Fontane

summary: Molecular taxonomy and key signaling pathways of apocrine glands of patients with hidradenitis suppurativa were studied by whole transcriptome profiling. Dysregulated genes were detected by comparing lesional and non lesional skin obtained from male and female HS patients using the Agilent array platform.

overall_design: Total RNA was obtained from apocrine glands isolated by laser capture microscopy from full thickness skin specimens taken from both lesional and non lesional sites in 16 patients (8 male 8 female) diagnosed with Hurley stage II hidradenitis suppurativa.

first: André

middle: N

last: da Costa

first: Sabine

last: Fimmel

first: Konstantin


title: Global expression analysis of primary endothelial cells before and after TNFa stimulation

city: New York

first: Anne

middle: M

last: Bowcock

state: New York

address: One Gustave L. Levy Place, Box 1130

institute: Icahn School of Medicine at Mount Sinai

summary: Endothelial cells are a primary site of leukocyte recruitment during inflammation. An increase in tumor necrosis factor-alpha (TNFa) levels as a result of infection or some autoimmune diseases can trigger this process. Several autoimmune diseases are now treated with TNFa inhibitors. However, genomic alterations that occur as a result of TNF-mediated inflammation are not well understood. To investigate molecular targets and networks resulting from increased TNFa, we measured DNA methylation and gene expression in 40 human umbilical vein endothelial cell primary cell lines before and 24 hours after stimulation with TNFa via microarray.

overall_design: After quality control, 39 sample pairs (treated and untreated) remained for analysis, and 18,937 probes were collapsed to 14,019 genes by selecting the probe with the maximum mean intensity value for each gene

first: Brooke

last: Rhead

first: Xiaorong

last: Shao

first: Hong

last: Quach

first: Poonam

last: Ghai

first: Lisa

middle: F

last: Barcellos


title: Global CpG methylation analysis of primary endothelial cells before and after TNFa stimulation

overall_design: The final dataset used for analysis consisted of 37 sample pairs and 818,391 CpG sites.


title: The effect of IL-37 in HCC cell line Sk-hep1

city: singapore

first: Yu

last: Mei

state: Singapore

address: 28 medical drive, center for life sciences, 03/09

country: Singapore

institute: NUS

summary:
We performed whole microarray expressiong prolife of Sk-hep1 cells which could over-express IL-37.
This project is to explore the effect of interleukin-37 on hepatocellular carcinoma(HCC) development. We transfected human HCC cell line Sk-hep1 with lentiviral vector encoding IL-37 or control. The successfully transfected cells were sorted by FACS and the cells were further cultured for 24 hours. The cells were harvested and send for microarray analysis.

overall_design: Sk-hep1 cells transfected with control empty lentivrus or IL-37-encoding lentivrus were harvesed for microarray assay

first: Haiyan

last: Liu


title: Analysis of primary endothelial cells before and after TNFa stimulation

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing quantitative analysis of PBMC transcriptomes from dogs with atopic dermatitis and healthy dogs

status: Public on Feb 05 2020

city: Seattle

first: Elia

last: Tait Wojno

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

summary: We used Drop-seq and next generation sequencing to determine gene expression differences in dogs with atopic dermatitis and healthy dogs in peripheral blood mononuclear cells in an unbiased way. Using Seurat, we find 13 discrete immune cells clusters, including a cluster enriched for Gata3 expressing T cells with 95 differentially expressed genes between healthy and allergic dogs.

overall_design: PBMCs from 5 dogs diagnosed with atopic dermatitis and 5 matched healthy dogs were analyzed using Drop-seq and Seurat, and analyzed on a NextSeq500.

middle: T

last: Wojno

first: Simon

last: Früh


title: The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [BiSulfite-seq]

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

type: Methylation profiling by high throughput sequencing

summary: Although much research has been done on the diversity of gut microbiome, little is known about the way it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested as operating at the interface between the microbiota and the intestinal epithelium cells (IECs). Using genome-wide analyses, we discovered that exposure to microbiota induced both global DNA hypomethylation and localized changes at regulatory elements, which culminates in activation of a set of “early sentinel” response genes that play a role in maintaining gut homeostasis. Furthermore, we demonstrated that exposure to microbiota in acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements leading to alterations in the gene expression program in colitis and colon cancer. Our studies add a new dimension to our understanding of the cross talk between the microbiota and IECs, and provide the foundation for how microbiota impact epigenetic programming.

overall_design: Whole genome methylation analysis of M. musculus. Four conditions were sequenced and analyzed, the first is an untreated control, the second corresponds to inflammation, the third mice with a germ-free condition and the fourth to a germ-free condition in combination with inflammation

first: F

last: Lyko

first: Y

last: Bergman


title: RNA-sequencing of human peripheral blood mononuclear cells from Tanzanian children

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Total RNA sequencing of peripheral blood mononuclear cells (PBMC) from Tanzanian children from the Phase 3 trial of the RTS,S (Mosquirix) vaccine (ClinicalTrials.gov NCT00866619). At baseline (B0) children were between 5-17 months of age at baseline (B0), and were 32 months older at B32.

overall_design: The RNA-sequencing data compliments a much larger immune-phenotyping study. Where there was sufficient cells remaining after flow-cytometry experiments, cells were stored in RNA-later. Samples from time-points B0 (n=21) and B32 (n=9) were then sequenced to determine how the blood transcriptome changes over time. Three participants had samples were sequenced at both B0 and B32.

first: Danika

last: Hill

first: Michelle

last: Linterman

first: Edward

last: Carr


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [B16-OVA treated with MEKi, CD40, in vivo]

first: Michael

last: Volkmar

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

institute: German Cancer Research Center (DKFZ)

summary:
Cancer types with lower mutational load and a non-permissive tumor microenvironment are intrinsically resistant to immune checkpoint blockade. While the combination of cytostatic drugs and immunostimulatory antibodies constitutes an attractive concept for overcoming this refractoriness, suppression of immune cell function by cytostatic drugs may limit therapeutic efficacy. Here we show that targeted inhibition of mitogen-activated protein kinase (MAPK) kinase (MEK) does not impair dendritic cell-mediated T-cell priming and activation. Accordingly, combining MEK inhibitors (MEKi) with agonist antibodies (Abs) targeting the immunostimulatory CD40 receptor resulted in potent synergistic anti-tumor efficacy. Detailed analysis of the mechanism of action of MEKi GDC-0623 by means of flow cytometric analysis of the tumor immune infiltrate and whole tumor transcriptomics showed that, in addition to its cytostatic impact on tumor cells, this drug exerts multiple pro-immunogenic effects, including the suppression of M2-type macrophages, myeloid derived suppressor cells and CD4+ T-regulatory cells. In addition, MEKi was found to induce tumor-cell intrinsic interferon signaling, which contributed to antigen presentation by tumor cells. Finally, the tumoridical impact of MEKi involves the activation of multiple pro-inflammatory pathways involved in immune cell effector function in the tumor microenvironment. Our data therefore indicate that the combination of MEK inhibition with agonist anti-CD40 Ab is a promising therapeutic concept, especially for the treatment of mutant Kras-driven tumors such as pancreatic ductal adenocarcinoma.
We used microarrays to monitor transcriptional and cell-type composition changes in murine transplantable tumor models of pancreatic ductal adenocarcinoma (PDA30364), colon cancer (MC38) and melanoma (B16-OVA) upon treatment with MEK inhibitor (GDC-0623), anti-CD40 antibody or the combination of GDC-0623 and anti-CD40 antibody.

overall_design: RNA was isolated from B16-OVA tumor pieces of at least four animals per treatment group at the end of the treatment period and subjected to transcriptome analyses. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

first: Daniel

last: Baumann

first: Rienk

last: Offringa


title: Analysis of ARID3A and ARID3B regulated genes by RNA-seq

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: In ovarian cancer cells ARID3A, ARID3B, or both genes were expressed exogenously with lentivirus. Cells were sorted based on expression level using fluoescent tags. RNA was isolated and RNA-sequencing was conducted to identify ARID3 regulated genes.

overall_design: Cells were transduced with ARID3A-GFP, ARID3B and RFP, or GFP and RFP.  Cells were FACS sorted, cells were collected, and RNA was isolated for RNA-seq.

first: Kirthi

last: Pulakanti


title: A common molecular mechanism underlies the role of Mps1 in chromosome biorientation and the spindle assembly checkpoint

city: Montpellier

first: Giorgia

last: Benzi

address: 1919 route de mende

country: France

institute: CRBM-CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The conserved Mps1 kinase corrects improper kinetochore-microtubule attachments, thereby ensuring chromosome biorientation. Yet, its critical targets in this process remain elusive. Mps1 is also involved in the spindle assembly checkpoint (SAC), the surveillance mechanism halting chromosome segregation until biorientation is attained. Its role in SAC activation is antagonized by the PP1 phosphatase and involves phosphorylation of Knl1/Spc105, which recruits Bub1 to kinetochores to promote assembly of SAC effector complexes. A crucial question is whether error correction and SAC activation are part of a single device or separable pathways. Here we characterise a novel yeast mutant, mps1-3, defective in chromosome biorientation and SAC activation. Through an unbiased screen for suppressors, we found that mutations lowering PP1 levels at Spc105 or forced association of Bub1 with Spc105 reinstate both chromosome biorientation and SAC signalling in mps1-3 cells. Our data strongly argue that Mps1-dependent phosphorylation of the Knl1/Spc105 kinetochore scaffold is critical for Mps1 function in both chromosome biorientation and SAC activation, thus supporting the idea that a common sensory apparatus simultaneously elicits error correction and SAC signalling.

overall_design:
ChIP-seq analysis to study the centromeric localization of Mps1 in the mps1-3 mutant and in the external suppressors spc105-18 mps1-3 and GLC7-24 mps1-3.

Mps1 and Mps1-3 have been tagged at the C-ter of the protein with 3HA (3-Hemagglutinin)

first: Yoshimura

last: Atsunori

first: Yuki

last: Katou

first: Katsuhiko

last: Shirahige


title: Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system

status: Public on Feb 04 2020

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent


title: Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (bulk)

summary: We performed ontogenic, transcriptomic and spatial characterization of sciatic nerve Macs (snMacs). Using multiple fate-mapping systems, we show that snMacs do not derive from the early embryonic precursors colonizing the CNS, but originate primarily from late embryonic precursors and get replaced by bone marrow-derived Macs over time. Using single-cell profiling, we identified a tissue-specific core signature of snMacs and found two spatially-separated snMacs: Relmα + Mgl1 + snMacs in the epineurium and Relmα Mgl1 snMacs in the endoneurium. Globally, snMacs lack most core signature genes of microglia, with only the endoneurial subset expressing a restricted number of these genes. Single-cell transcriptomics revealed that in response to injury both snMacs respond differently and that the PNS, in contrast to the CNS, is permissive to prolonged engraftment of monocyte-derived Macs recruited upon injury.

overall_design:
Microarray = Sciatic Nerve macrophages in steady state and different time points (1.5, 5, 10 and 37 days) after nerve crush. This data was compared to previously published data (GSE75225  and GSE117080) and to other tissue resident macrophages from the Immgen Consortium Database (GSE15907).
Bulk RNA Seq = Brain microglia, Optic Nerve macrophages and Sciatic Nerve macrophages. For each cell type there are 4 replicates, expect for the Brain microglia there are 5 replicates.
Single cell RNA Seq = on steady state Sciatic Nerve macrophages and at different time points (1 day and 5 days) after nerve crush.

first: Elke

last: Ydens

first: Lukas

last: Amann

first: Bob

last: Asselbergh

first: Charlotte

last: Scott

first: Dorine

last: Sichien

first: Omar

last: Mossad

first: Thomas

last: Blank

first: Sofie

last: De Prijck

first: Donovan

last: Low

first: Takahiro

last: Masuda

first: Yvan

last: Saeys

first: Vincent

last: Timmerman

first: Ralf

last: Stumm

first: Florent

last: Ginhoux

first: Marco

last: Prinz

first: Sophie

last: Janssens

first: Martin

last: Guilliams


title: RNA sequencing analysis of  WT- and Tet2-/-G17VRHOA-CD4 splenocytes

city: Tsukuba

first: Mamiko

last: Sakata-Yanagimoto

state: Ibaraki

address: 1-1-1 Tennodai

department: Hematology

country: Japan

institute: University of Tsukuba

summary: Angioimmunoblastic T-cell lymphoma, a subtype of T-cell lymphoma, is a disease with relative poor outcome. Genetic analysis in human samples showed the co-existence of common mutations in TET2 and RHOA genes. We have made a mouse model resembling the genetic lesions in human AITL. Our mice developed  AITL-like lymphoma after 40 weeks old.  We analyzed the expression of transcriptomes in WT- and Tet2-/-G17VRHOA-CD4 splenocytes to find out the underlying pathogenesis mechanism of AITL.

overall_design: We examine 4 mice of WT group and 3 mice of Tet2-/-G17VRHOA group.

first: Tran

middle: B

last: Nguyen

first: Shigeru

last: Chiba


title: Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (single cells)

first: Liesbet

last: Martens

first: Elke

last: Ydens

first: Lukas

last: Amann

first: Bob

last: Asselbergh

first: Charlotte

last: Scott


title: IκBα deficiency imposes a fetal phenotype to intestinal stem cells

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar


title: IκBα deficiency imposes a fetal phenotype to intestinal stem cells [RNA-seq]

summary: The intestinal epithelium is a paradigm of adult tissue in constant regeneration that is supported by intestinal stem cells (ISCs). The mechanisms regulating ISC homeostasis after injury are poorly understood.  We previously demonstrated that IκBa, not only controls NF-κB activation, but also exerts nuclear functions as cytokine sensor in a subset of PRC2-regulated genes. We now uncover nuclear phosphorylated IκBa (P-IκBa) in the ISC compartment where it binds highly histone methylated genomic regions. Mice deficient for IκBa show aberrant distribution of H3K27me3 mark, and altered intestinal differentiation with persistence of a fetal-like ISC signature. In vitro, IκBa deficient intestinal cells produced morphologically aberrant organoids carrying a PRC2, Notch and IFN-dependent fetal-like transcriptional signature. Induction of the fetal-like phenotype by DSS treatment is associated with loss of nuclear P-IκBa in the damaged colonic epithelium and it subsequent accumulation in early CD44 positive regenerating areas. Importantly, IκBa deficient animals showed higher resistance to damage, likely due to persistent fetal-like phenotype. These results point out intestinal IκBa as chromatin sensor of inflammation in the ISC compartment.

overall_design: 9 samples analyzed

last: Espinosa Blay

first: Laura

last: Marruecos Aylagas


title: In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [Cut&Run]

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: In most cancers, only a few genes are mutated at high frequencies, while the vast majority are mutated at low frequencies. The functions of these recurrent but infrequent ‘long-tail’ mutations remain largely elusive. Here, we develop in vivo CRISPR screens to assess the transforming potential of 484 long-tail genes in human Head and Neck Squamous Cell 5 Carcinoma (HNSCC).

overall_design: Differential Rbpj cut and run peaks for Ajuba WT vs. Knockout Cells.

first: Sampath

middle: K

last: Loganathan

first: Ahmad

middle: A

last: Malik

first: Ricky

last: Tsai


title: IκBα deficiency imposes a fetal phenotype to intestinal stem cells [ChIP-seq]

overall_design: 16 samples analyzed, plus two different inputs


title: Single-Cell Chromatin Accessibility Maps Reveal the Regulatory Programs Driving Early Mouse Organogenesis

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: During early mouse embryonic development, pluripotent cells rapidly divide and diversify to construct the developing foetus, yet the underlying regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes of mammalian lineages during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos collected at 8.25 days post-fertilisation. Identification of cell type-specific regions of open chromatin pinpointed known regulatory regions and two new TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted known and previously unrecognised cell type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a powerful role for the ETS transcription factor FEV in endothelial identity. Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.

overall_design: 10 mouse embryos were processed using single-nucleus ATAC-seq protocol (Preissl et al., 2018).

first: Blanca

last: Pijuan-Sala

first: Rebecca

last: Hannah


title: Comparison of Prox1 expressing and Prox1 knockout intestinal tumors and the effect of A2V+CD40

city: Epalinges

first: Tatiana

last: Petrova

state: VD

address: 155, Chemin des Boveresses

department: Oncology

country: Switzerland

institute: University of Lausanne

summary: Control or A2V+CD40 treated Prox1-proficient (AP) and Prox1-deficient (APP) tumors

overall_design: Tumors induced in Apcflox/flox;Tp53flox/flox;villin-CreERT2 (AP) or Apcflox/flox;Tp53flox/flox;Prox1flox/flox;villin-CreERT2 (APP) mice for two weeks. Mice were randomized and treated with PBS, control IgG, or A2V+CD40 for two weeks.

first: Simone

last: Ragusa

first: Sina

last: Nassiri

middle: V


title: RNA helicase DDX21 mediates nucleotide stress responses (ChIP-Seq)

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: The RNA helicase DDX21 acts as trancriptional sensor for nucleotide lowering

overall_design: ChIP-seq analysis of DDX21 and CDK9 in human A375 melanoma cells treated with DMSO, 25 uMA77 1726 and 25uM A771726 plus nucleotides

first: Cristina

last: Santoriello

first: Yang

last: Song


title: Profile of mRNA transcriptomes of E. coli affected by antifungal agent ciclopirox

city: Busan

first: Kwang-sun

last: Kim

address: 63 beon-gil 2, Jangjeon-dng, Geumjeong-gu

department: Chemistry

institute: Pusan National University

summary:
Purpose: The identification of genes and regulatory pathways involved in the susceptibility to ciclopirox activity

Methods: mRNA profiles of ciclopirox treatment in wild-type strain using Illumina sequencing.

Results: Using an optimized data analysis workflow, we mapped about 1 million sequence reads per sample to the E. coli K-12 genome and identified 4,290 transcripts in  wild-type with our without sublethal concentration of ciclopirox (12.5 ug/mL). Overall, this is the first genome-wide level analysis of ciclopirox as an antibacterial against Gram-negative bacteria and shown that >13 pathways were affected by ciclopirox with the change of expression level of >10 genes.  Data analysis with CLRNASeq showed some differently expressed transcripts by ciclopirox treatment.

Conclusions: Our study represents the first detailed analysis of ciclopirox-affected transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

sample_organism:
Escherichia coli
Escherichia coli K-12

platform_organism:
Escherichia coli
Escherichia coli K-12

overall_design: mRNA profiles of ciclopirox treatment with or without sublethal concentration in wild type (WT) were generated by deep sequencing using Illumina HiSeq 2500.


title: Polycomb dysfunctional transcriptional repression in muscle stem cells contributes to lamin dependent muscular dystrophy [RNA-seq]

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

summary: Polycomb group of proteins (PcG) and the nuclear Lamin A are key factors in the maintenance of chromatin higher order structures required for preserving cell identity. Mutations in the Lamin A/C gene cause several diseases, belonging to the class of laminopathies, including Emery-Dreifuss Muscular Dystrophy. Nevertheless, epigenetic mechanisms involved in the pathogenesis of lamin-dependent dystrophy are still largely unknown. We show that Lamin A loss causes deregulated PcG positioning in muscular stem cells followed by upregulation of adipogenic markers and induction of the senescence’s driver p16INK4a from Cdkn2a locus.  This aberrant transcriptional programme causes impairment in self-renewal, loss of cell identity and premature exhaustion of quiescent satellite cell pool. Genetic ablation of Cdkn2a locus restores muscle growth and muscle stem cell properties in Lamin A/C null dystrophic mice. In conclusion, our findings suggest that Lamin A has an essential role in preserving satellite cell self-renewal capacity and indicate that Lamin A-dependent muscular dystrophy can be ascribed to intrinsic epigenetic dysfunctions of muscle stem cells

overall_design: Transcriptional and epigenetic profiling of Lmna Δ8-11 +/+ and Lmna Δ8-11 -/- mice

first: Andrea

last: Bianchi

first: Federica

last: Lucini


title: FarS target identification

status: Public on Feb 03 2020

city: Jena

first: Malte

last: Siemers

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

summary: In this study we determined the target spectrum of Vibrio cholerae FarS sRNA via pulse-expression followed by RNA-sequencing.

overall_design: V. cholerae wild-type cells carrying pBAD-ctr (empty control vector) or pBAD-farS (inducible sRNA expression vector) were grown to exponential phase (OD600=0.5). Expression of FarS was induced by L-arabinose and total RNA samples were collected 15 minutes after induction. The experiment was performed with three independent biological replicates.

first: Michaela

last: Huber

first: Kai

last: Papenfort


title: Polycomb dysfunctional transcriptional repression in muscle stem cells contributes to lamin dependent muscular dystrophy

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

overall_design: Refer to individual Series


title: RNAseq analysis of 5week old islets from murine Abca12 KO pancreas

city: Clayton

first: Ian

last: Smyth

state: Victoria

address: Wellington Rd

department: Department of Biochemistry & Molecular Biology, Department of Anatomy & Developmental Biology

country: Australia

institute: Monash University

summary: The goal of this study was to identify changes in the transcriptome that occur following Abca12 gene deletion relative to Control islets

overall_design: Islets were isolated from 5 week old mice from two groups, 1) KO (Abca12 tm1d) animals with a conditional Abca12 floxed allele deleted by the action of Rip1-Cre, or 2) control animals heterozygous for Abca12 floxed allele with Rip1-Cre.

first: Gloria

last: Ursino

first: Denny

last: Cottle

first: Partha

middle: P

last: Das


title: Hfq RIP-seq analysis

summary: In this study we used RNA co-immunoprecipitation followed by RNA-sequencing (RIP-seq) to identify Hfq-binding RNAs in Vibrio cholerae.

overall_design: V. cholerae wild-type and hfq::3XFLAG-tagged strains were cultivated in LB medium to low (OD600 of 0.2) and high cell densities (OD600 of 2.0). Cells were subjected to RNA co-immunoprecipitation and RNA was isolated. The experiment was performed with two independent biological replicates.


title: Drosophila YBX1 homolog YPS promotes ovarian germline stem cell development by preferentially recognizing 5-methylcytosine RNAs

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: 5-Methylcytosine (m5C) is one of the most abundant RNA modifications, but its function in adult stem cell development remains poorly defined. This study shows that Ypsilon schachtel (YPS) promotes germ line stem cell (GSC) maintenance, proliferation, and differentiation in the adult Drosophila ovary by preferentially binding to m5C-containing RNAs. Highly conserved cold-shock domains (CSDs) of YPS and its human homolog Y box binding protein 1 (YBX1) exhibit preferential binding to m5C-containing RNAs through hydrophobic interactions. Human YBX1 can functionally replace YPS to promote GSC development in the Drosophila ovary, and overexpressing RNA-binding–defective YBX1 and YPS mutant proteins disrupts normal GSC development. Thus, this study provides insight into the importance of m5C RNA modification in adult stem cell development.

overall_design: Pull down m5C RNA with specific 5-methylcytosine (5-mC) monoclonal antibody, pull down RNA/Protein complexes via Flag tagged Yps overexpressed proteins.

first: Fan

last: Zou

first: Renjun

last: Tu

first: Bo

last: Duan

first: Zhenlin

last: Yang

first: Zhaohua

last: Ping

first: Xiaoqing

first: Andrew

last: Price

first: Hua

last: Li

first: Allison

last: Scott

first: Anoja

last: Perera

first: Sisi

first: Ting

last: Xie


title: In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice

first: Daniel

last: Schramek


title: RNAseq analysis of 8week old islets from murine Abca12 KO pancreas

first: Ian

overall_design: Islets were isolated from 8 week old mice from two groups, 1) KO (Abca12 tm1d) animals with a conditional Abca12 floxed allele deleted by the action of Rip1-Cre, or 2) control animals with wild type Abca12 alleles and Rip1-Cre or heterozygous for Abca12 floxed allele with Rip1-Cre.

first: Gloria


title: Arabidopsis thaliana analysis of the shade avoidance response in Col-0, rev5, and wox4 mutants

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

summary: Plants were germinated in white light and then either grown in WL (white light) or far-red enriched white light (WL+FR)

overall_design: Examination of four genotypes in two different conditions


title: Tissue determinants of human NK cell development, function and residence

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

institute: University of Pittsburgh

summary: Immune responses in diverse tissue sites are critical for protective immunity and homeostasis. Here, we investigated how tissue localization regulates the development and function of human Natural Killer (NK) cells, an innate lymphocyte important for anti-viral and tumor immunity. Integrating high dimensional analysis of NK cells from blood, lymphoid organs and mucosal tissue sites from 48 individuals, we identify tissue-specific patterns of NK cell subset distribution, maturation and function across age and genetic diversity. Mature and terminally differentiated NK cells with enhanced effector function predominate in blood, bone marrow, spleen and lungs, exhibiting shared transcriptional programs across sites. By contrast, precursor and immature NK cells with reduced effector capacity prevail in lymph nodes and intestines, exhibiting tissue resident signatures and site-specific adaptations. Together, our results reveal anatomic control of NK cell development and maintenance as tissue resident populations, while mature, terminally differentiated subsets mediate immunosurveillance through diverse peripheral sites.

overall_design: mRNA profiling of CD56brightCD16- and CD56dimCD16+ NK cells from blood, bone marrow (BM), spleen, lung, lung lymph node (LN) from 4 individual donors.

first: Pranay

last: Dogra

first: Donna

last: Farber


title: RNA-seq analysis after IRF4 and p65 knockdown in TL-Om1 cells

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

institute: National University of Singapore

summary: RNA-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze gene expression changes after IRF4 or p65 knockdown.

overall_design: Lentiviral shRNA transduction was carried out in TL-Om1 cells to knock down control (GFP), IRF4 or p65 gene.  Two different shRNAs were used to target each gene in biological duplicates.  Total RNA was harvested 3 days after knockdown and RNA-seq analysis was performed.

first: Regina

last: Wong

first: Tze

first: Takaomi

last: Sanda


title: ChIP-seq analysis for p65 protein in TL-Om1 cells

summary: ChIP-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze DNA bindings of p65 in TL-Om1 cells.

overall_design: TL-Om1 cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against p65 Antibody  (C-20) (sc-372).


title: The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [RNA-seq]

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: Although much research has been done on the diversity of gut microbiome, little is known about the way it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested as operating at the interface between the microbiota and the intestinal epithelium cells (IECs). Using genome-wide analyses, we discovered that exposure to microbiota induced both global DNA hypomethylation and localized changes at regulatory elements, which culminates in activation of a set of “early sentinel” response genes that play a role in maintaining gut homeostasis. Furthermore, we demonstrated that exposure to microbiota in acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements leading to alterations in the gene expression program in colitis and colon cancer. Our studies add a new dimension to our understanding of the cross talk between the microbiota and IECs, and provide the foundation for how microbiota impact epigenetic programming.

overall_design: Whole transcriptome analysis of M. musculus. Four conditions were sequenced and analyzed, the first is an untreated control, the second corresponds to inflammation, the third mice with a germ-free condition and the fourth to a germ-free condition in combination with inflammation

first: F

last: Lyko

first: Y

last: Bergman


title: RNA-sequencing of CD56dim NK cells from atopic dermatitis and control patients

city: Cambridge

first: Madison

last: Mack

state: Massachusetts

address: 350 Water St

department: Immunology & Inflammation Research

institute: Sanofi

summary:
Purpose: To determine the underlying transcriptional differences between CD56dim NK cells from atopic dermatitis patients
Methods: We sort-purified 30-100,000 CD56dim NK cells from freshly thawed, cryopreserved PBMCs of atopic dermatitis patients and patients undergoing Mohs surgeries. Ribosomal RNA was removed and cDNA was generated with the SMARTer kit (CloneTech) with 10 ng of total RNA per sample.
Samples were sequenced to an average depth of 34 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Ensembl release 76 using STAR, gene counts were determined with Subread:featureCount, and sequence performance was assessed with RSeQC.

overall_design: 5 atopic dermatitis patients and 5 control patients were sorted and sequenced, then their transcriptomes were compared to each other using DESeq2 in R v3.5.1 with a single-variable design. Alpha was set to 0.05

first: Brian

middle: S

last: Kim


title: IRF4 ChIP-seq analysis in TL-Om1 cells

summary: ChIP-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze DNA bindings of IRF4 in TL-Om1 cells.

overall_design: TL-Om1 cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.  ChIP was performed using an antibody against IRF-4 Antibody (M-17): sc-6059

first: Phuong

last: Ngoc

first: Wei

last: Leong


title: RNA-seq analysis after BATF3 knockdown in TL-Om1 cells

status: Public on Feb 02 2020

summary: RNA-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze gene expression changes after BATF3 knockdown.

overall_design: Lentiviral shRNA transduction was carried out in TL-Om1 cells to knock down control (GFP) and BATF3.  Two different shRNAs were used to target each gene in biological duplicates.  Total RNA was harvested 3 days after knockdown and RNA-seq analysis was performed.

middle: W


title: Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (microarray)

first: Liesbet

last: Martens

institute: VIB-University of Ghent

type:
Expression profiling by array
Third-party reanalysis

summary: We performed ontogenic, transcriptomic and spatial characterization of sciatic nerve Macs (snMacs). Using multiple fate-mapping systems, we show that snMacs do not derive from the early embryonic precursors colonizing the CNS, but originate primarily from late embryonic precursors and get replaced by bone marrow-derived Macs over time. Using single-cell profiling, we identified a tissue-specific core signature of snMacs and found two spatially-separated snMacs: Relmα + Mgl1 + snMacs in the epineurium and Relmα Mgl1 snMacs in the endoneurium. Globally, snMacs lack most core signature genes of microglia, with only the endoneurial subset expressing a restricted number of these genes. Single-cell transcriptomics revealed that in response to injury both snMacs respond differently and that the PNS, in contrast to the CNS, is permissive to prolonged engraftment of monocyte-derived Macs recruited upon injury.

overall_design:
Microarray = Sciatic Nerve macrophages in steady state and different time points (1.5, 5, 10 and 37 days) after nerve crush. This data was compared to previously published data (GSE75225  and GSE117080) and to other tissue resident macrophages from the Immgen Consortium Database (GSE15907).
Bulk RNA Seq = Brain microglia, Optic Nerve macrophages and Sciatic Nerve macrophages. For each cell type there are 4 replicates, expect for the Brain microglia there are 5 replicates.
Single cell RNA Seq = on steady state Sciatic Nerve macrophages and at different time points (1 day and 5 days) after nerve crush.

first: Elke

last: Ydens

first: Lukas

last: Amann

first: Bob

last: Asselbergh

first: Charlotte

last: Scott

first: Dorine

last: Sichien

first: Omar

last: Mossad

first: Thomas

last: Blank

first: Sofie

last: De Prijck

first: Donovan

last: Low

first: Takahiro

last: Masuda

first: Yvan

last: Saeys

first: Vincent

last: Timmerman

first: Ralf

last: Stumm

first: Florent

last: Ginhoux

first: Marco

last: Prinz

first: Sophie

last: Janssens

first: Martin

last: Guilliams


title: CD44s regulated miRNAs in head and neck cancer cells.

status: Public on Feb 01 2020

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: To investigate the function of the  microRNAs involved in drug resistance in head and neck cancer, we overexpressed CD44s gene and GFP gene into oral squamous cancer cell line, SAS-3.4 cells. The phenotypes were analyzed and transcriptome of them were investigated.

overall_design: Two genes (CD44s, GFP) were overexpressed into SAS-3.4 cells that are head and neck cancer cells. And then, we extracted RNA and did microarray.

first: Junichiro

last: Chikuda

first: Hiroaki

last: Miyazaki

first: Ryou-u

last: Takahashi

last: Ochiya


title: Allelic silencing analysis for A-repeat and m6A region in mouse Xist

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: We show that a deletion encompassing the entire Xist 5’ m6A region results in a modest reduction in Xist-mediated silencing.

overall_design: We isolated chromatin-associated RNA (ChrRNA) to analyze the allelic ratio, aiming to understand Xist-mediated Silencing. The ChrRNA was isolated from cells iXist-ChrX derived from mouse embryonic stem cells. Xist is composed of several repetitive elements, which act by interacting with different factors. Cell lines with Xist domain deletions were generated. The allelic ratios were systematically and comprehensively compared.

first: H

last: Coker

first: G

first: T

last: Nesterova

first: N

last: Brockdorff


title: Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [RNAseq]

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

summary: Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differential gene expression programs enriched in the primary tumor is able to distinguish patients that experience relapse to different organs. Epigenomic changes often underlie transcriptomic differences and give rise to stable phenotypes. However, the epigenomic differences present in organotropic metastasis remains underexplored. Here we profile the active chromatin landscape of the claudin-low cell line MDA-MB-231 and its metastatic subpopulations that preferentially grow in the brain (BrM2), and lung (LM2). We find that metastatic cells harbor increased promoter and enhancer activation. Using ATAC-seq, we also define transcription factors that are enriched in an organotropic manner. Chromatin accessibility of metastatic cells correlates with shorter progression-free survival and is enriched in patients who have more aggressive subtypes of breast cancer.

overall_design: RNAseq, ChIPseq (H3K4me3, H3K27ac) and ATACseq of MDA-MB-231 Par, LM2, and BrM2 cell lines

first: Wesley

last: Cai

first: Don

middle: X

last: Nguyen


title: piRNA-independent Function of PIWIL1 as a Novel co-activator for Anaphase Promoting Complex/Cyclosome (APC/C) to Drive Pancreatic Cancer Metastasis

city: Shanghai

first: Li

last: Feng

address: 320 Yue Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology, CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: Piwi proteins are normally restricted in germ cells to suppress transposons through association with piRNAs, but are also frequently activated in many types of human cancers. Of great puzzle is the lack of induction of corresponding piRNAs in cancer cells, as we document here in human pancreatic ductal adenocarcinomas (PDAC), implying that such germline-specific proteins are somehow hijacked to promote tumorigenesis through different mode of action. To pursue the underlying mechanism, we now demonstrate that in the absence of piRNAs, the aberrantly induced human PIWIL1 in PDAC functions as an oncoprotein by activating the Anaphase Promoting Complex/Cyclosome (APC/C), which then targets a critical cell adhesion-related protein Pinin to enhance PDAC metastasis. This is in contrast to piRNA-dependent PIWIL1 ubiquitination and removal by APC/C during late spermiogenesis. These findings thus unveil an piRNA-dependent mechanism to switch PIWIL1 from a substrate in spermatids to a co-activator of APC/C in human cancer cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Small RNA profiling of cancer cell line BxPC-3, with NaIO4 oxidization or not. Oxidation with NaIO4 is used  to enrich piRNAs as they are protected from periodate oxidation by their terminal 2'-O-methyl modification while RNAs with a terminal 2′,3′-hydroxyl are modified and depleted during cDNA library preparation. Mouse testis is positive control.

first: Feng

last: Li

first: Shuang

last: Zhao

first: Mofang

last: Liu


title: Oncogenic Regulatory Network Driven by IRF4 and NF-kappaB in Adult T-cell Leukemia/Lymphoma

first: Tze King

last: Tan

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

overall_design: Refer to individual Series


title: Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing the Drosophila Segmentation Network

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary: Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC seq on Drosophila embryos over the period spanning the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the segmentation network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of segmentation network CRMs. While opa is necessary to drive late opening of segmentation network cis-regulatory elements, competence for opa to pioneer is regulated over time. These results indicate that dynamic systems for chromatin regulation directly impact the interpretation of embryonic patterning information.

overall_design: This study contains four distinct experiments. Experiment 1: ATAC-seq comparing wild-type and bicoid oskar capicua torsolike Toll[RM9] mutant embryos, staged either at 12 or 72 minutes into nuclear cycle 14. Three biological replicates (individual embryos) were collected per genotype and timepoint and subjected to ATAC library preparation. Samples were subjected to paired-end sequencing on an Illumina HiSeq2500 (2 x 63 bp reads). Experiment 2: ATAC-seq on a collection of embryos produced from a cross between opa[IIP32]/+ adults. Embryos were staged at 72 minutes into nuclear cycle 14. Twenty two embryos in total were collected and subjected to paired-end sequencing on an Illumina HiSeq 2500 (2 x 63 bp reads). Experiment 3: ChIP-seq for myc-tagged Opa. 200 cellular blastoderm stage embryos were collected from opa-myc homozygous adults and ChIPped with an anti-myc antibody. The control sample was an equivalent number of staged 'wild-type', i.e., not-myc-tagged embryos. The wild-type genotype is w[1118]. Three independent biological replicates were performed for experimental and control samples. ChIP-seq libraries were subjected to single-end sequencing on an Illumina HiSeq4000 (1 x 50 bp reads). Experiment 4: ATAC-seq comparing wild-type and maternal misexpression of odd-paired (tub>opa), staged at 12 minutes into nuclear cycle 13. Six biological replicates (individual embryos) were collected per genotype and subjected to ATAC library preparation. Samples were subjected to paired-end sequencing on an Illumina NextSeq500 (2 x 36bp reads).


title: Polycomb dysfunctional transcriptional repression in muscle stem cells contributes to lamin dependent muscular dystrophy [ChIP-seq]

first: Chiara

last: Lanzuolo

summary: Polycomb group of proteins (PcG) and the nuclear Lamin A are key factors in the maintenance of chromatin higher order structures required for preserving cell identity. Mutations in the Lamin A/C gene cause several diseases, belonging to the class of laminopathies, including Emery-Dreifuss Muscular Dystrophy. Nevertheless, epigenetic mechanisms involved in the pathogenesis of lamin-dependent dystrophy are still largely unknown. We show that Lamin A loss causes deregulated PcG positioning in muscular stem cells followed by upregulation of adipogenic markers and induction of the senescence’s driver p16INK4a from Cdkn2a locus.  This aberrant transcriptional programme causes impairment in self-renewal, loss of cell identity and premature exhaustion of quiescent satellite cell pool. Genetic ablation of Cdkn2a locus restores muscle growth and muscle stem cell properties in Lamin A/C null dystrophic mice. In conclusion, our findings suggest that Lamin A has an essential role in preserving satellite cell self-renewal capacity and indicate that Lamin A-dependent muscular dystrophy can be ascribed to intrinsic epigenetic dysfunctions of muscle stem cells

overall_design: Transcriptional and epigenetic profiling of Lmna Δ8-11 +/+ and Lmna Δ8-11 -/- mice

first: Andrea

last: Bianchi

first: Federica

last: Lucini


title: Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

summary: We reported a 28-day Intermittent fasting (IF) regimen improved cognitive deficits in db/db mice via a microbiota-metabolites-brain axis assessed by behavioral tests and multiple-omics analysis (transciptomics, 16S rRNA sequencing and metabolomics). Here we present transcriptomics data of mice hippocampus. A total of 310.85Gb clean RNA-SEQ reads of all mice with an average depth of 3.86x were obtained and were then mapped against the Mus musculus genome to obtain the gene expression FPKM values for each sample. We detected 27,094 genes (including 1,345 new predicted genes with no annotation) with FPKM value. Among them, 1,181 genes were found to be only highly expressed in db/db-IF mice compared to db/db and db/m mice, using Differentially Expressed Genes (DEG) analysis, most of which enriched in mitochondrial-related GO terms. Besides, IF strongly elevated genes related to KEGG pathway of oxidative phosphorylation (OXPHOS) via up-regulating mitochondrial located genes expression. In consistent with results from RNA-sequencing analysis, the qPCR analysis confirmed that mitochondrial and metabolic genes expressed were upregulated by IF in db/db mice. In conclusion, IF regimen significantly enhanced mitochondrial and energy metabolism related genes expressions in diabetic mice hippocampus.

overall_design: 11 db/m mice,10 db/db mice,10 db/db-IF mice

first: Zhigang

first: Xin

last: Jin


title: Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain


title: RNAseq of whole striatum from hypothyroid mice, and hypothyroid mice treated with thyroid hormone for 2 days.

status: Public on Jan 31 2020

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

summary: Striatum in rich in GABAergic neurons which require thyroid hormone for their maturation. We used propyl thio uracyl to make mice hypothyroid, and then restored the hormonal level using thyroid hormone. This provided 3 groups of mice for striatum RNAseq analysis. Our results point to GABAergic neurons as direct targets of thyroid hormone during brain development and suggest that many defects seen in hypothyroid brains may be secondary to GABAergic neuron malfunction.

overall_design: All mice treated with PTU and then some treated with T3

first: S

last: Richard

first: F


title: Next Generation Sequencing Facilitates Quantitative Analysis of  E. coli K-12 LE392,  P. putida KT2440, and RP4 plasmid Transcriptomes under AgNP and silver ion exposure

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of  E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0 and 1 μg/L AgNPs or silver ion for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism:
Escherichia coli K-12
Pseudomonas putida KT2440

overall_design: Bacterial mRNA profiles of E. coli K-12 LE392  in response to 0and 1 μg/L AgNPs and silver ion for 2 h, in duplicate, using Illumina HiSeq 2500

first: Ji

last: Lu


title: Connectivity mapping of a chronic kidney disease progression signature identified lysine deacetylases as novel therapeutic targets

city: Toronto

first: Vanessa

last: Williams

state: Ontario

address: 1 King's College Circle

department: Institute of Medical Science

institute: University of Toronto

summary:
Motivation and design: Renal tubulointerstitial injury is an important determinant of chronic kidney disease (CKD) progression, yet treatment is limited to renin angiotensin system blockade. Accordingly, we performed global expression profiling in a 2 × 2 factorial design (N = 8 in each group) on RNA extracted from male Col4a3–/– mice and littermate controls on a 129X1/SvJ background at 4 and 7 weeks of age. Col4a3–/– mice have a mutation in the gene encoding the α3 chain of type IV collagen, associated with proteinuria and progressive loss of kidney function. We analyzed expression with Affymetrix GeneChip Mouse Gene 2.0 ST Arrays and derived a novel CKD progression signature based on aging and disease in Col4a3–/– mice. Using our progression signature, we sought to repurpose existing drugs for the treatment of progressive CKD.
Results: Computational drug repurposing with the Connectivity Map identified lysine deacetylase inhibitor, vorinostat, as a novel candidate treatment for this murine model of CKD. Treatment with vorinostat attenuated tubulointerstitial injury, fibrosis, and altered inflammation. Vorinostat administration significantly increased the lifespan of Col4a3–/– mice although effects on urinary albumin excretion, plasma creatinine, and blood urea nitrogen were modest.
Conclusions: Our data suggest that expression profiling and computational drug repurposing can be used to identify novel drugs that may reverse gene expression changes in experimental CKD. Lysine deacetylase inhibition may be a novel treatment approach to CKD associated with proteinuria and progressive tubulointerstitial injury.

overall_design: Kidney tissue from 4- and 7-week-old male Col4a3–/– mice and littermate controls was analyzed using Affymetrix GeneChip Mouse Gene 2.0 ST Arrays. A total of 32 mice were studied with 8 mice per group.

first: Ana

last: Konvalinka

first: Xuewen

last: Song

first: Xiaohua

last: Zhou

first: Rohan

last: John

first: York

last: Pei

first: James

last: Scholey


title: Comprehensive transcriptome analysis regarding CDR1AS expression

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: We determined the gene expression changes by CDR1AS expression in colon cancer cells

overall_design: CDR1AS RNA was expressed in colon cancer cell lines. To determine the gene expression changes dependent on this circular RNA, we used control cells and DR1AS-expressing cells for the cDNA microarrya analyses.

first: Eri

last: Tanaka

first: Motoyuki

last: Otsuka

first: Kazuhiko

last: Koike


title: Comprehensive transcriptome analysis of the synthetic auxin herbicide response in the problematic weed species Erigeron canadensis

city: West Lafayette

first: Cara

last: McCauley

state: INDIANA

address: 915 West State Street

department: Botany and Plant Pathology

institute: Purdue University

summary:
Background: The auxin herbicides 2,4-D and dicamba are commonly used for management of horseweed (Erigeron canadensis L, (syn: Conyza canadensis L)). Halauxifen-methyl is a new auxin herbicide and recently commercialized to control several broadleaf weed species under a range of sites and environmental conditions. While synthetic auxin herbicides have been used for over 70 years, the precise mode of action that leads to plant death has yet to be clearly characterized. As new chemical families are discovered and the use of these herbicides continues to increase, it is imperative to understand how synthetic auxin active ingredients work within the plant to cause an herbicidal effect.
Results: At 1 hour after treatment (HAT), 48 genes were consistently upregulated across the three herbicides, many of which are involved in the auxin-activated signaling pathway and response to auxin. At 6 HAT, 735 genes were upregulated by all herbicide treatments including genes associated with hormone signaling, metabolism, transport, senescence, and gene expression. The GO terms representing the 501 genes downregulated in all herbicide treatments were broadly categorized under two major groups: ATP and photosynthesis. At 6 HAT, over 50% of the genes differential expressed among the three herbicide treatments were unique to a single active ingredient.
Conclusion: This research presents a first look into the differential gene expression profiles in horseweed following a foliar application of synthetic auxin compounds that represent three unique chemical families. While there are an abundance of transcriptome similarities induced by each herbicide that accounts for the general auxin herbicide response, distinct gene expression changes exclusive to each compound cannot be ignored as a contributor to the mode of action.

overall_design: Effects of 2,4-D, dicamba, and halauxifen-methyl on horseweed (Erigeron canadensis L.)

first: Bryan

middle: G

last: Young

first: Jo

last: Banks


title: Tacrolimus- and sirolimus-induced human b cell dysfunction is reversible and preventable

city: Nashville

first: Alvin

middle: C

last: Powers

state: TN

address: 7465 MRBIV 2215 Garland Avenue

institute: Vanderbilt University

summary: We used RNA-seq to investigate transcriptional changes in human islet grafts that were treated in vivo with tacrolimus or sirolimus. We show that this treatment induces broad transcriptional dysregulation related to peptide processing, ion/calcium flux, and the extracellular matrix.

overall_design: Human islets were tranplanted under kidney capsule of NSG mouse. After two weeks engraftment period, the mice were treated with tacrolimus, sirolimus, or PBS-control  for 4 weeks. The grafts were then removed for analysis.

first: Chunhua

last: Dai

first: John

last: Walker

first: Nripesh

last: Prasad


title: Transcriptional analysis of tendons from mice with a targeted deletion of scleraxis

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report RNA sequencing data from the plantaris tendons of adult male mice in the C57Bl/6 background that either have the scleraxis gene (Scx+) or mice in which scleraxis has been deleted using CreERT2 driven from the Rosa26 locus (Scx-). Mice in which scleraxis was deleted were created by crossing scleraxis-floxed mice with Rosa26-CreERT2 mice. Rosa26-CreERT2 mice that did not have a floxed scleraxis allele served as controls. Mice were treated with tamoxifen for 5 days to induce recombination at the scleraxis locus, and then subjected to a synergist ablation procedure in which the Achilles tendon is removed, resulting in compensatory growth of the plantaris tendon. Mice were analyzed either 7 or 14 days after synergist ablation. Control mice that did not undergo tamoxifen treatment or synergist ablation were also studied (NOC).

overall_design: Differential expression of mRNAs were evaluated from the plantaris tendons of Scx+ and Scx- mice subjected to a growth stimulus for either 7 or 14 days, along with control mice that did not undergo a growth stimulus.


title: High-throughput profiling of mRNA from parental and Enzalutamide resistant C4-2b prostate cancer cell lines

city: Seoul

first: Kyoung-Hwa

last: Lee

address: 101 Daehak ro

department: Urology

institute: Seoul National University Hospital

summary: We established an enzalutamide-resistant C4-2b prostate cell line that has an active androgen receptor by maintaining the C4-2b cell line in serially increasing concentrations of enzalutamide. Among the CRPC cell lines, we selected the C4-2b cell line because it is known to have AR variants, and we desired to identify enzymes with the ability to regulate the activity of AR variants as well as the wild type AR. After 2 months, we acquired resistant cells in even 10 uM enzalutamide. After validation of enzalutamide-resistant character, we analyzed global changes in mRNA expression by using quantitative mRNA-sequencing analysis.

overall_design: mRNA profile from prostate cancer cell line C4-2b and its enzalutamide resistant derivative cell line

first: Cheol

last: Kwak


title: The circadian movement of flowers in the wild tobacco reveals a role for ZEITLUPE in the temporal gating of auxin responses

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how  collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of the movement of flowers we used a whole genome microarray  as a discovery platform to identify genes differentially expressed in adaxial and abaxial sides of the floral peduncle at different stages of the movement.

overall_design: Adaxial and abaxial sides of peduncles of WT plants collected at ZT0, ZT6 and ZT14. Each replicate is a pool of half peduncles collected at same timepoint. Three replicate samples for each condition were used for the analysis. Total RNA was extracted from floral peduncles using the Plant RNeasy kit (Qiagen) and quality checked by spectrophotometry (NanoDrop). Genomic DNA was removed by DNAse treatment (Ambion) following manufacturer instructions. RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent) in the Agilent 2100 Bioanalyzer (Agilent). RNA was labeled with Cyanine-3 (Cy3) with the Quick Amp labeling kit (Agilent) according to manufacturer instructions and followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer. Samples were hybridized in a N. attenuata whole genome single color array (Agilent 8×60K; GPL19764). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting. Probe feature extraction was performed with the feature extraction software (Agilent). Quality control, data filtering and normalization were performed in Genespring GX (Agilent). Probe filtering was performed in Genespring GX using the flag (gIswellAboveBG). Probes that did not pass the condition in all replicates for one of the conditions were filtered out. Probe signals were trssholded to 1, log2 transformed and normalized to the 75th percentile. Differential expression analysis between adaxial and abaxial sides of the peduncles was performed with the Bayesian estimation of temporal regulation algorithm in Multi experiment viewer (MeV). Probe to gene association and gene annotations were based in the N. attenuata genome assembly v2.5.

first: Lucas

last: Cortes-Llorca

first: Sang-Gyu

last: Kim

first: Ian

last: Baldwin


title: B2 and ALU retrotransposons are self-cleaving RNAs whose activity is enhanced by EZH2

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

institute: University of Manitoba

summary: More than 98% of the mammalian genome is noncoding and approximately half is made up of transposable elements. One of the most abundant is the short interspersed nuclear elements (SINE). Among the million copies of SINEs, B2 accounts for ~350,000 in the mouse genome and have garnered special interest because of emerging roles in gene regulation. Our recent work demonstrated that B2 RNA normally binds stress genes to retard transcription elongation. Though epigenetically silenced, B2s become massively upregulated during thermal stress. Specifically, an interaction between B2 RNA and the Polycomb protein, EZH2, results in cleavage of B2 RNA, release of B2 RNA from RNA Polymerase II, and activation of the stress genes. Although an established RNA-binding protein and histone methyltransferase, EZH2 is not known to be a nuclease. Here, we provide evidence for the surprising conclusion that B2 is a self-cleaving RNA. Contact with EZH2 accelerates cleavage rate by >100-fold, suggesting that EZH2 may assist cleavage as an RNA chaperone. Modification-interference analysis demonstrate that phosphorothioate changes at A and C nucleotides can substitute for EZH2’s function. B2 mutagenesis indicate that nucleotides around positions 45-55 and 100-101 are critical for cleavage reaction. Finally, we demonstrate that another family of SINEs, the ALU elements  produce also a self-cleaving RNA. ALUs are intrinsically more auto-reactive than B2s. We propose that the B2/ALU SINEs are a new class of ribozymes whose activity is accelerated by EZH2.

overall_design: Sample from HeLa cells was subjected to heat shock and subsequently RNA was extracted and submitted to short-RNA-seq.

first: Jeannie


title: 5-Hydroxymethylcytosines in Circulating Cell-free DNA Reveal Vascular Complications of Type 2 Diabetes

city: Chicago

first: Wei

last: Zhang

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

summary:
BACKGROUND: Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, non-invasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions.
METHODS: A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design.
RESULTS: Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without (testing set: AUC = 0.85, 95%CI, 0.73-0.96), outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84, 95%CI, 0.68-0.99), showing superiority over conventional clinical variables.
CONCLUSIONS: The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, non-invasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.

overall_design: Differential 5hmC markers between T2D patients with and without macrovascular/microvascular complications were analyzed in a Chinese patient cohort (n = 62).

first: Songmei

last: Liu

first: Chuan

last: He

first: Ying

last: Yang

first: Chang

last: Zeng


title: Shared PPARα/γ target genes regulate brown adipocyte thermogenic function

status: Public on Jan 30 2020

city: Philadelphia

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania


title: Shared PPARα/γ target genes regulate brown adipocyte thermogenic function (RNA-Seq)

summary:
Purpose: To study the role of PPAR nuclear receptors in brown fat.
Methods: mRNA-sequencing was performed on brown adipose tissue from mice on diets with or without added rosiglitazone or fenofibrate.  Sequence reads that passed quality filters were analyzed at the transcript isoform level with RNA-Seq Unified Mapper.
Results: We identified genes that were induced or repressed by either PPAR agonist, and approximately three-fold more genes were significantly regulated by rosiglitazone (rosi, a PPARg agonist) than by fenofibrate (feno, a PPARa agonist). Those genes induced by either drug were enriched for expected lipid metabolic pathways, while down-regulated genes fell in pathways of uncertain relevance. Most genes were selectively regulated by one of the two PPAR agonists, with few regulated by both. Only 34 genes were induced by both PPAR agonists (~10% of rosi-induced genes and ~25% of feno-induced genes), and these were enriched for mitochondrial functionrelated pathways, including fatty acid β-oxidation.
Conclusions: These data suggest that PPARγ agonists have stronger effects on BAT than PPARα agonists, yet those genes activated by both PPAR agonists may be particularly relevant to BAT function.

overall_design: Brown adipose tissue mRNA profiles of control and PPAR agonist-treated mice were generated by deep sequencing

first: Raymond

last: Soccio


title: Analysis of RNA-seq of human neuroblastomas from mouse-human neural crest chimeric mice model and in other neuroblastoma models

status: Public on Jan 29 2020

city: Cambridge

first: Malkiel

last: Cohen

address: 455 Main St

institute: Whitehead Institute

summary: To  confirm the neuroblastomas (NB) identity of human neuroblastomas from mouse-human neural crest chimeric mice model (CHNBs) we characterized their gene expression profiles by RNA-Seq (CHNBs MYCN+ALKF1174L; n=8). For a global comparison of gene expression profiles of CHNBs with  other NB models, we further collected RNA-seq data from patient derived xenografts of neuroblastoma (PDX NBs ; MYCNamp+ALKwt PDX; n=2, and MYCNamp+ALKF1174L PDX; n=3), neuroblastomas from genetically engineered mouse model  (GEMM NBs; Th-MYCN+ALKF1174L; n=3), neuroblastoma established cell lines (n=2; Kelly, MYCNamp+ALKF1174L; SH-SY5Y, MYCNwt+ ALKF1174L), human pluripotent derived human neural crest cells (hNCCs; wt hNCCs; n=2, and MYCN+ALKF1174L hNCCs, with Dox; n=2) and from hNCC xenografts (MYCN+ALKF1174L; n=5).

overall_design: RNA samples were collectd from 28 biological samples, including: 8 samples for CHNB (4 with technical replicates), 5 samples of PDX NBs (with technical replicates), 3 samples of mouse GEMM NBs (with technical replicates), 2 samples of NB cell lines,  5 samples of hNCCS xenografts (one with biological replicate and 2 with  technical replicates) and 4 samples of hNCCs (2 with oncogenes and Dox, and 2 wt with technical replicates), and one mouse wt adernal gland (control) .

first: Rudolf

last: Jaenisch


title: The shared PPARα/γ target genes regulate brown adipocyte thermogenic function (ChIP-Seq)

summary: We report the application of sequencing technology for high-throughput profiling of PPARα/γ in mammalian cells. By obtaining over 3 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse brown adipose tissue. We find that PPARα binds to a subset of PPARγ sites, suggesting a potential redundancy in which PPARα function may not be necessary in brown adipose tissue.While PPARα may not itself be necessary for BAT function, shared targets regulation by PPARα and PPARγ may nonetheless reveal relevant biology in this tissue.This study provides a framework for the application of comprehensive chromatin profiling towards characterization of PPARα/γ regulation in mouse brown adipose tissue.

overall_design: Examination of 2 different transcription factors in 2 cell types.


title: RNAseq analysis of islets from murine Abca12 KO pancreas

city: Clayton

last: Smyth

address: Wellington Rd

institute: Monash University

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

overall_design: Refer to individual Series


title: Transcriptional profile of migrating GABAergic progentitors in the E14 mouse brain following maternal exposure to cypermethrin and restraint stress

city: Iowa City

first: Hanna

middle: E

last: Stevens

state: IA

address: 169 Newton Road

department: Psychiatry

institute: University of Iowa

summary: The goal of this experiment was to assess transcriptional changes in isolated GABAergic progenitors to determine the mechanism by which prenatal exposure to cypermethrin and maternal stress alter their migration

overall_design: RNA was sequenced from GABAergic progentitors isolated via laser capture microdissection from PFA-fixed E14 mouse brain tissue following maternal exposure to cypermethrin (E11-E14) and restraint stress (E12-E14)

first: Benjamin

last: Elser


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [PDA30364 treated with MEKi, in vitro]

status: Public on Jan 24 2020

city: Heidelberg

first: Michael

last: Volkmar

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

institute: German Cancer Research Center (DKFZ)

summary:
Cancer types with lower mutational load and a non-permissive tumor microenvironment are intrinsically resistant to immune checkpoint blockade. While the combination of cytostatic drugs and immunostimulatory antibodies constitutes an attractive concept for overcoming this refractoriness, suppression of immune cell function by cytostatic drugs may limit therapeutic efficacy. Here we show that targeted inhibition of mitogen-activated protein kinase (MAPK) kinase (MEK) does not impair dendritic cell-mediated T-cell priming and activation. Accordingly, combining MEK inhibitors (MEKi) with agonist antibodies (Abs) targeting the immunostimulatory CD40 receptor resulted in potent synergistic anti-tumor efficacy. Detailed analysis of the mechanism of action of MEKi GDC-0623 by means of flow cytometric analysis of the tumor immune infiltrate and whole tumor transcriptomics showed that, in addition to its cytostatic impact on tumor cells, this drug exerts multiple pro-immunogenic effects, including the suppression of M2-type macrophages, myeloid derived suppressor cells and CD4+ T-regulatory cells. In addition, MEKi was found to induce tumor-cell intrinsic interferon signaling, which contributed to antigen presentation by tumor cells. Finally, the tumoridical impact of MEKi involves the activation of multiple pro-inflammatory pathways involved in immune cell effector function in the tumor microenvironment. Our data therefore indicate that the combination of MEK inhibition with agonist anti-CD40 Ab is a promising therapeutic concept, especially for the treatment of mutant Kras-driven tumors such as pancreatic ductal adenocarcinoma.
We used microarrays to monitor transcriptional changes in murine tumor cell lines of pancreatic ductal adenocarcinoma (PDA30364), colon cancer (MC38) and melanoma (B16-OVA) upon treatment with MEK inhibitor GDC-0623.

overall_design: RNA was isolated from PDA30364 tumor cells of 3 biological replicates per conditions (DMSO vs. 100 nM GDC-0623) 24 and 72h after inhibitor/DMSO addition. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

first: Daniel

last: Baumann

first: Rienk

last: Offringa


title: BMP9 signaling promotes the normalization of tumor blood vessels

status: Public on Jan 26 2020

city: Montreal

first: claire

last: viallard

state: QC

address: 5690 rosemont boulevard

institute: HMR

summary: We sought to evaluate the effects of BMP9 on tumor vascular formation. We observed that BMP9 promotes vascular normalization with decreased permeability and increased perfusion and perivascular cell coverage. Gene expression analysis of CD31-positive cells isolated from control and BMP9-overexpressing tumors revealed enrichment of pathways involved in Notch signaling and vascular quiescence.

overall_design: mRNA profiles of CD31-positive cells isolated from control and BMP9-overexpressing Lewis Lung Carcinoma tumors.

first: Bruno

last: Larrivee

first: Claire

last: Viallard


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [MC38 treated with MEKi, in vitro]

overall_design: RNA was isolated from MC38 tumor cells of 3 biological replicates per conditions (DMSO vs. 100 nM GDC-0623) 24 and 72h after inhibitor/DMSO addition. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.


title: Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary: The advent of cell culture-based methods for the establishment and expansion of human corneal endothelial cells (CEnC) has provided an available source of transplantable corneal endothelium, with a significant potential to challenge the one donor-one recipient paradigm. However, concerns over cell state identity remain, and a comprehensive characterization of the cultured CEnC has not been performed. To this end, we compared two established CEnC culture methods by assessing cell function and characterizing the transcriptomic changes that occur during in vitro expansion. In confluent monolayers, low mitogenic culture conditions preserved corneal endothelial cell state identity better than culture in high mitogenic conditions. Expansion by continuous passaging induced replicative cell senescence. Transcriptomic analysis of the senescent phenotype identified a cell senescence signature distinct for CEnC. We identified activation of both classic and new cell signaling pathways that may be targeted to prevent senescence, a significant barrier to realizing the potential clinical utility of in vitro expansion.

overall_design: Seven independent primary CEnC cultures were established from donor corneas. For each culture, half the cells were prepared and isolated using Tryp-LN-F99 protocol and the other half of cells were isolated and prepared using ColA-ColIV-M4M5. Five passages (P0-P4) were established and total RNA was collected from 70 samples.

first: Ricardo

last: Frausto

first: Vinay

last: Swamy

first: Marco

last: Morselli

first: Matteo

last: Pellegrini

middle: J


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [B16-OVA treated with MEKi, in vitro]

overall_design: RNA was isolated from B16-OVA tumor cells of 3 biological replicates per conditions (DMSO vs. 100 nM GDC-0623) 24 and 72h after inhibitor/DMSO addition. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.


title: Transcriptional regulation of Th17 differentiation by mitochondrial oxidative phosphorylation

status: Public on Jan 28 2020

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

summary: We found that mitochondrial oxidative phosphorylation (OXPHOS) plays a critical role in Th17 lineage specification.  CD4 T cells differentiated under OXPHOS inhibited conditions show altered metabolic gene profiles (mitochondrial function, glycolysis, and TCA cycle) and pathways associated with cell proliferation.  Furthermore, gene set enrichment analysis (GSEA) revealed that mitochondrial respiration impacts transcriptional profiles related to Th17 pathogenic signatures and BATF-sensitive gene clusters.  Our study reveals a regulatory role of mitochondrial OXPHOS in transcriptional programming of Th17 lineage commitment.

overall_design: Naïve CD4 T cells were differentiated into Th17 cells in the presence of vehicle (DMSO) or oligomycin (OXPHOS inhibitor) for 48 hours.  Total mRNA profiles were generated by RNA sequencing in triplicate.

first: Gloria

last: Benavides

first: Jianlin

last: Geng

first: Hui

last: Hu

first: Victor

middle: M

last: Darley-Usmar

first: Sergei

last: Koralov

first: Laurie

last: Harrington


title: Acetylation of histone H3K27 signals the transcriptional elongation for estrogen receptor alpha

city: Houston

first: Qin

last: Feng

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: As approximately 70% of human breast tumors are estrogen receptor α (ERα)-positive, estrogen and ERα play essential roles in breast cancer development. By interrupting the ERα  signaling pathway, endocrine therapy has been proven to be an effective therapeutic strategy. In the present study, we identified a novel mechanism by which Transcription Start Site (TSS)-associated histone H3K27 acetylation signals the Super Elongation Complex (SEC) to regulate transcriptional elongation of the ERα  gene. The SEC interacts with H3K27ac on ERα TSS through its scaffold protein AFF4. Depletion of AFF4 by siRNA or CRISPR/Cas9 dramatically reduces expression of ERα and its target genes, consequently inhibiting breast cancer cell growth. More importantly, AFF4 mutant which lacks H3K27ac interaction failed to rescue ERα gene expression, suggesting H3K27 acetylation at TSS region is a key mark bridging the transition from transcriptional initiation to elongation, and perturbing SEC function can be an alternative strategy for targeting ERα  signaling pathway at the level of chromatin.

overall_design: Examination of chromatin association of AFF4 and histone H3K27 acetylation in MCF7 breast cancer cell line

first: Zhu

last: Bokai

first: Feng

last: Qin


title: Metabolic control over mTOR dependent diapause-like state

status: Public on Jan 14 2020

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

summary: Regulation of embryonic diapause, dormancy that interrupts the tight connection between develop- mental stage and time, is still poorly understood. Here, we characterize the transcriptional and metabolite profiles of mouse diapause embryos and identify unique gene expression and metabolic signatures with activated lipolysis, glycolysis, and metabolic pathways regulated by AMPK. Lipolysis is increased due to mTORC2 repression, increasing fatty acids to support cell survival. We further show that starvation in pre-implantation ICM-derived mouse ESCs induces a reversible dormant state, transcriptionally mimicking the in vivo diapause stage. During starvation, Lkb1, an upstream kinase of AMPK, represses mTOR, which induces a revers- ible glycolytic and epigenetically H4K16Ac-negative, diapause-like state. Diapause furthermore activates expression of glutamine transporters SLC38A1/2. We show by genetic and small molecule inhibitors that glutamine transporters are essential for the H4K16Ac-negative, diapause state. These data sug- gest that mTORC1/2 inhibition, regulated by amino acid levels, is causal for diapause metabolism and epigenetic state.

overall_design: We did RNA-seq of Inner cell mass (ICM), diapause (dICM) and post-implantation (EPI) mouse embryos.

first: Yuliang

last: Wang


title: H3122, in vitro resistance to ALK inhibitors

city: Tampa

first: Robert

last: Vander Velde

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures

overall_design: 6 samples comparing drug naïve cells to cells resistant to various ALK inhibitors, no replicates

first: Andriy

last: Marusyk


title: Gene expression analysis of third instar larvae ski3 mutants

city: Tokyo

first: Toshiro

last: Aigaki

address: 1-1, Minami-oosawa, Hachioji-shi

department: Biological Sciences

institute: Tokyo Metropolitan University

summary:
Purpose: To identify genes that are differentially expressed between control and ski3 mutants
Methods: Gene expressions of control and ski3 mutants of third instar larvae  were generated by deep sequencing, in two replicates, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Bowtie2 and TopHat followed by Cufflinks.
Results: We mapped 800,000-1,200,000 sequence reads per each sample to the fruit fly genome (BDGP6) and identified 93,606 transcripts in the whole body of control and ski3[f03251] with TopHat workflow. Analysis of RNA-seq data idnetified 32 differentially expressed genes relevant to mitochondrial function between control and ski3 mutants with FDR <0.05. The mutation affected over 600 genes, which are involved in many different cellular functions. The results were complex: among 32 affected genes, half of them were upregulated, and the remaining half were downregulated. Six genes were related to the TCA cycle. Of these, the downregulated genes include CG9582 (alpha-ketoglutarate transmembrane transporter), CG32832 (mitochondrial pyruvate carrier), and CG7514 (oxoglutarate:malate antiporter). On the other hand, upregulated genes include AcCoAS (Acetyl-CoA synthase), Sirup (Succinate dehydrogenase), and Men-b (malate dehydrogenase), all of which were directly involved in the TCA cycle.
Conclusions: Our study represents the first detailed analysis of ski3 mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. In order to examine the effects of ski3 mutations on gene expression, we performed RNA-seq analyses of wild-type and mutant larvae.  Downregulation of transporter, carrier and antiporter suggested a chronic undersupply of TCA cycle substrates, while some of the TCA cycle enzymes were upregulated.

overall_design: Whole body mRNA profiles of third instar larvae control (w1118) and ski3[f03251] homozygotes were generated by deep sequencing, in two replicates, using Illumina NovaSeq 6000.

first: Kohei

last: Ohnuma

first: Yoshihito

last: Kishita

first: Hiromi

last: Nyuzuki

first: Masakazu

last: Kohda

first: Yuta

last: Ohtsu

first: Satomi

last: Takeo

first: Tsunaki

last: Asano

first: Yukiko

last: Miyata-Sato

first: Akira

last: Ohtake

first: Kei

last: Murayama

first: Yasushi

last: Okazaki


title: BCL9/STAT3 Regulation of Transcriptional Enhancer Networks Promote DCIS Progression

status: Public on Jan 09 2020

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

summary: There is limited research on which specific Wnt targets are regulated by B-Cell Lymphoma-9 (BCL9) and whether BCL9 regulates other signaling pathways to drive cancer malignancy. Here, using ChIP-Exo we have demonstrated that BCL9 in a protein complex with STAT3 drives DCIS invasive progression by regulation of enhancers and enhancer associated target genes involved in cellular growth, invasion and migration.

overall_design: Chromatin immunoprecipitation (ChIP)-exo experiments were performed on the DCIS cell line (DCIS.COM) control and BCL9-knockdown (BCL9 KD) using anti-BCL9 and anti-PS-727-STAT3 antibodies. ChExMix was utilized to analyze the ChIP-exo data.

first: Yan

last: Hong

first: Jeffrey

last: Thompson

first: Fariba

last: Behbod