title: MYR1-dependent effectors are the major drivers of a host cell’s early response to Toxoplasma including counteracting MYR1-independent effects

city: Stanford

first: Adit

last: Naor

state: CA

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

institute: Stanford

summary: The intracellular parasite Toxoplasma gondii uses a diverse repertoire of effector molecules to manipulate its host cell. The first effectors to be introduced into the host cell derive from rhoptries (ROPs) and are secreted exclusively during invasion. Once the parasite has established a parasitophorous vacuole, a subset of secreted dense granule effector proteins (GRAs) are then translocated across the parasitophorous vacuolar membrane in a MYR1-dependent manner to enter the host cell cytoplasm and nucleus. Translocation of these GRA effectors is also dependent on the activity of Toxoplasma Aspartyl protease 5 (ASP5) which either directly cleaves the effectors or potentiates translocation in some other way. To determine the totality of MYR1-dependent (predominantly GRA) and MYR1-independent (e.g., ROP) host responses as well as the degree of overlap between MYR1- and ASP5-dependent effectors, we analyzed the RNAseq expression profile of human foreskin fibroblasts infected with wild type (RH strain) Toxoplasma gondii tachyzoites, RHΔmyr1, RHΔasp5 and their respective complements. We show that a majority subset of the differentially regulated host gene responses during infection with wild type parasites are modulated in a MYR1-dependent manner. Gene set enrichment analysis of the MYR1-dependent host responses indicates that, among others, there is a clear up-regulation related to E2F transcription factors and the cell cycle and a clear down-regulation in expression related to interferon signaling. The ASP5-dependent host gene responses were less numerous and encompassed fewer gene sets than the MYR1-dependent responses, indicating that translocation and/or activity of a subset of effectors is MYR1- but not ASP5-dependent. Consistent with this, we show that even though MYR1 is normally cleaved by ASP5, such cleavage is not necessary for MYR1’s role in translocation. Interestingly, some responses were seen upon infection with RHΔmyr1 but not RH-WT; these previously “hidden” responses are likely due to the normally counter-balancing action of MYR1-dependent and -independent activities. The host genes and gene sets revealed here to be MYR1-dependent provide new insight into the relative contribution of GRA- vs. ROP-mediated effectors in co-opting host cell functions.

overall_design: RNASeq of human foreskin fibroblasts, infected with Toxoplasma, harvested 6 hours post infection. Samples are: Mock infected, infected with a WT RH, RH∆myr1,  RH∆myr1::MYR1, RH∆asp5, RH∆asp5::ASP5.

first: John

last: Boothroyd


title: Effect of ablation of the alternative NF-kB pathway on the regulatory T cell (Treg) transcriptome

status: Public on Jan 31 2018

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

country: France

institute: Cancer Research Center of Lyon

type: Expression profiling by high throughput sequencing

summary: We report here the transcriptome analysis of in-vitro stimulated WT, nfkb2-/-, Relb-/- and nfkb2-/-Relb-/- murine Treg cells

overall_design: RNA-sequencing (30 million reads/sample) on Foxp3+ murine Treg, stimulated overnight with antiCD3/CD28/OX-40 and IL-2. The experiment was performed in duplicates.

first: Sankar

last: Ghosh


title: RNA seq analysis of regenerating hearts from three models of successful cardiac regeneration

status: Public on Feb 01 2018

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

country: USA

institute: University of Pittsburgh

summary: Defining conserved molecular pathways in animal models of successful cardiac regeneration could yield insight into why adult mammals have inadequate cardiac regeneration after injury. Here we describe a cross-species transcriptomic screen to identify evolutionarily conserved pathways in the early events of cardiac regeneration in three species that can regenerate myocardium after a major injury.  In this study, we performed RNA-seq on regenerating hearts from three model organisms - axolotl, zebrafish and mouse. Apical resection was performed to amputate ~10 - 20% of the left ventricle in all three model organisms. Following resection, hearts were harvested at 12, 24 and 48 hours post-resection and subjected to RNA-seq. RNA-seq on sham controls (no ventricular amputation) was used as interanal control. This approach revealed upregulation of inflammatory genes in all three organisms during regeneration. Furthermore, upregulation of Complement 5a receptor1 (C5aR1) expression in the regenerating hearts of zebrafish, axolotls and mice was observed.

sample_organism:
Danio rerio
Ambystoma mexicanum
Mus musculus

overall_design: Examination of differentially expressed genes in early cardiac regeneration in three model organisms - zebrafish, axolotl and mouse.

first: Richard

middle: T

last: Lee


title: Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [RNA-seq]

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Transcriptome levels of matched patient-derived xenograft (PDX) in vitro-in vivo models.

overall_design: Comparison of gene expression levels between matched patient-derived xenograft in vitro-in vivo models.

first: Eliza

middle: L

last: Fong

first: Tan

middle: B

last: Toh

first: Xiaoxuan

last: Lin

first: Zheng

last: Liu

first: Lissa

last: Hooi

first: Masturah

last: Mohd Abdul Rashid

first: Edward

middle: K

last: Chow

first: The

middle: H

last: Huynh

first: Hanry

last: Yu


title: Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression profiling from high-fat medium (HFM)-treated and growth medium (GM)-treated Sk-hep1 cells

city: Taipei City

first: WEI-JIA

last: LUO

address: Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist.

country: Taiwan

institute: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University.

summary: Non-alcoholic fatty liver disease (NAFLD) is a major problem in obese peoples and caused by unbalanced uptake of fatty acid. Novel drug identification is necessary to develop effective therapies. We combine LOPAC® and High-Content system to identify compounds significantly reducing intracellular lipid droplets after high fat medium (HFM) treatment. Among 1280 compounds, 5 show efficacy in lipid droplet reduction. To construct the underlying regulatory network, whole-genome transcriptomic, pathway, and connectivity map analysis are performed.

overall_design: To know the gene expression profiles after high-fat environment incubation, total RNAs from the following 4 groups were extracted for whole trancriptomic analysis : (1)Sk-hep1 cells treated with 12 hr GM; (2) Sk-hep1 cells treated with 12 hr HFM; (3) Sk-hep1 cells treated with 24 hr GM; (4) Sk-hep1 cells treated with 24 hr HFM.

first: KANG-YI

last: SU


title: The AP-1 -BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

summary: Transcription factor AP-1 is constitutively activated and IRF4 drives growth and survival in ALK+ and ALK– Anaplastic Large Cell Lymphoma (ALCL). Here we demonstrate high-level expression of BATF and BATF3 in ALCL, irrespective of the ALK-status. Both BATFs bind classical AP-1 motifs and interact with in ALCL deregulated AP-1 factors. Together with IRF4, they co-occupy AP-1-IRF composite elements (AICE), differentiating ALCL from non-ALCL. Gene-specific inactivation of BATFs by CRISPR/Cas9 or siRNAs, or global AP-1 inhibition by the dominant-negative A-Fos results in ALCL growth retardation and/or cell death in vitro and in vivo. Furthermore, the AP-1-BATF module establishes TH17 / innate lymphoid cell type 3 (ILC3)-associated gene expression in ALCL, including marker genes such as AHR, IL17F, IL22, IL26, IL23R, IL18R1 and RORγt. Elevated IL-17A and IL-17F levels were detected in pretreatment sera of a subset of children and adolescents with ALK+ ALCL. Finally, pharmacological inhibition of RORC as single treatment leads to cell death in ALCL cell lines, and, in combination with the ALK inhibitor crizotinib, enforces death induction in ALK+ ALCL. Our data highlight the crucial role of AP-1 / BATFs for ALCL biology and lead to the concept that ALCL might originate from ILC3 cells.

overall_design: This GEO dataset consists of 10 measured cell lines, including 6 ALCL cell lines (4 ALK+, 2 ALK-) and 4 control samples.

first: Stephan

last: Mathas

first: Martin

last: Janz

first: Georg

last: Lenz


title: The microglial reaction signature revealed by RNAseq from individual mice

city: Montpellier

first: Helene

last: Hirbec

address: 141, rue de la Cardonille

department: Neuroscience

institute: IGF CNRS UMR5203

summary:
Expression profiling by high throughput sequencing
Microglial cells have a double life as the immune cells of the brain in times of stress but have also specific physiological functions in homeostatic conditions. In pathological contexts, microglia undergo a phenotypic switch called “reaction” ’that promotes the initiation and the propagation of neuro-inflammation. Reaction is complex, molecularly heterogeneous and still poorly characterized, leading to the concept that microglial reactivity might be too diverse to be molecularly defined. However, it remains unknown whether reactive microglia from different pathological contexts share a common molecular signature. Using improved flow cytometry and RNAseq approaches we studied, with higher statistical power, the remodeling of microglia transcriptome in a mouse model of sepsis. Through bioinformatic comparison of our results with published datasets, we defined the microglial reactome as a set of genes discriminating reactive from homeostatic microglia. Ultimately, we identified a subset of 86 genes deregulated in both acute and neurodegenerative conditions. Our data provide a new comprehensive resource that includes functional analysis and specific molecular makers of microglial reaction which represent new tools for its unambiguous characterization.

overall_design: Whole transcriptome RNA sequencing was performed on acutely isolated microglia from 2-3 months old female CX3CR1+/egfp mice(C57BL6/J bacground) which received either intraperitoneal LPS (4 mg/kg; LPS group) or saline solution injection (control group). The mice were eutanized 24h after the injection. 5 LPS and 5 control biological replicates were sequenced, each replicate corresponds to a single mouse.

first: Hirbec

last: Helene

first: Marmai

last: Camille

first: Croze

last: Severine

first: Lachuer

last: Joel

first: Rassendren

last: Francois


title: Telomerase-mediated Strategy for Overcoming Non-Small Cell Lung Cancer Targeted Therapy and Multi-drug Chemotherapy Resistance

status: Public on Jan 30 2018

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

summary: Standard and targeted therapies almost universally fail due to tumor heterogeneity/plasticity leading to intrinsic or acquired drug resistance. We used the telomerase substrate precursor 6-thio-2’-deoxyguanosine (6-thio-dG) to target telomerase-expressing targeted therapy and platin-doublet chemotherapy resistant cells. We observed that erlotinib, paclitaxel/carboplatin and gemcitabine/cisplatin resistant cells are sensitive to 6-thio-dG in xenograft, syngeneic immunocompetent and genetically engineered mouse models. We also show sensitivity to 6-thio-dG on a large panel of non-small cell lung cancer cell lines (73 of 77). The 4 resistant NSCLC lines clustered together, providing a molecular signature for patients that may not respond to 6-thio-dG. We find SLC43A3 as a top candidate in this molecular signature. Thus, 6-thio-dG may prolong disease control of therapy-resistant lung cancer patients.

overall_design:
Gene expression from microarray and RNAseq data was used to compare resistant and sensitive NSCLC lines. The microarray data was a subset from GSE32036. RNA-seq raw data are only available for samples GSM2970438-GSM2970449 (those produced at GeneWiz). The submitter states that the raw data for samples GSM2970450-GSM2970491 will be made available under controlled access at dbGaP.  The RNAseq data for GeneWiz samples is linked to Bioproject PRJNA431789 with SRA accession SRP131505

Microarray samples from GSE32036 were not re-analyzed. The log2 quantile-normalized values were used directly.  Gene expression of 6-thio-dG sensitive and resistant cell lines was analyzed using a subset of 40 NSCLC samples from GSE32036 (sensitive lines had IC50 < or equal to 1.55 microM, resistant lines cells had IC50 > or equal to 10 microM). Using the processed data from the subset of 40 samples, statistically significant genes were determined using unpaired t-tests with Bonferroni correction (p<0.01). The data matrix of these re-used microarray data are included here for convenience. Also included is a text file with the 6-thio-dG status of the cell lines from the microarray study.

first: Ilgen

last: Mender

first: Ryan

last: LaRanger

middle: G

first: Krishna

last: Luitel

last: Peyton

first: Luc

last: Girard

first: Tsung-Po

last: Lai

first: Crystal

last: Cornelius

first: Maithili

middle: P

last: Dalvi

last: Ramirez

first: Wenting

last: Du

first: Lani

middle: F

last: Wu

first: Steven

middle: J

last: Altschuler

first: Rolf

last: Brekken

first: Elisabeth

middle: D

last: Martinez

first: David

last: Wheeler

first: John

last: Minna

first: Woodring

middle: E

last: Wright

first: Jerry

middle: W

last: Shay


title: Polycomb Group Protein YY1 is an Essential Regulator of Hematopoietic Stem Cell Quiescence

status: Public on Feb 02 2018

city: Madison

first: Xuan

last: Pan

state: Wisconsin

address: 2015 Linden Drive

institute: University of Wisconsin-Madison

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify Yy1 regulated genetic network by comparing transcriptome in Yy1 deficient HSCs with wild-type HSCs.
Methods: Total RNA was purified from bone marrow HSCs (Lin-Sca1+c-Kit+ CD48-CD150+and Lin-Sca1+c-Kit+CD48-CD150-) sorted from Yy1-/- versus Yy1+/+ mice using RNeasy Micro kit (Qiagen).  Sequencing libraries were prepared by using Ovation RNA-Seq System V2 (NuGen) according to the manufacturer’s specifications and were sequenced by an Illumina HiSeq 2000. Sequencing reads were adapter and quality trimmed using the Skewer trimming program.  Quality reads were subsequently aligned to the annotated reference genome using Subjunc aligner from subread package. qRT–PCR validation was performed using SYBR Green assays.
Results: This analysis identified a small cohort of 100 significantly upregulated and 49 downregulated genes in Yy1-/- HSCs (FDR<0.05, logFC>=1).  Among them, many genes involved in cell cycle were deregulated in Yy1-/- HSCs .  Gene ontology analysis of the upregulated cohort revealed a significant enrichment of genes involved in cell cycle, cell division, chromosome condensation and segregation, cytoskeleton and spindle organizations.  Gene Set Enrichment Analysis (GSEA) revealed cell cycle gene sets associated with pre-replication complex (RC) assembly, degradation of p27, DNA replication, G1 to S phase, and M to G1 phase transitions were significantly enriched.  The RNA-seq analysis revealed that YY1-deficient HSCs had an aberrant genetic network associated with G0 to G1 phase entry.

overall_design: Total RNA was purified from bone marrow HSCs (Lin-Sca1+c-Kit+CD48-CD150+and Lin-Sca1+c-Kit+CD48-CD150-) sorted from Yy1-/- versus Yy1+/+ mice, and used for RNA-seq analysis.

first: Courtney

last: Hong

first: Zhanping

last: Lu

first: Guangyao

last: Kong

first: Anna L.

last: F. V. Assumpção


title: DNA methylation patterns separate senescence from malignant transformation potential in human cells

city: Baltimore

first: Wenbing

last: Xie

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Department of Oncology

institute: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine

type:
Expression profiling by array
Methylation profiling by array


title: Methylome analysis of non syndromic cleft lip and palate in comparison to control samples

city: Sao Paulo

first: Lucas

last: Alvizi

state: Sao Paulo

address: Rua do Matao 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profilinf from 67 non syndromic cleft lip and palate samples and controls using whole-blood DNA and Illumina Infinium Human Methylation 450K Bead array, in which over 485000 CpGs sites were analysed per sample

overall_design: Bisulfite converted DNA from all 126 samples were hybridised to the Illumina Infinium Human Methylation 450K Bead array

first: Maria

middle: R

last: Bueno


title: Role of skeletal muscle in mandible development.

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

institute: Dalhousie University

summary:
Previous analysis of Myf5-/-:MyoD-/- mouse fetuses lacking skeletal muscle demonstrated the importance of muscle contraction and static loading in mouse skeletogenesis. Previous analysis of Myf5-/-:MyoD-/- mouse fetuses lacking skeletal muscle demonstrated the importance of muscle contraction and static loading in mouse skeletogenesis. Among abnormal skeletal features, micrognathia (mandibular hypoplasia) was detected: small, bent and posteriorly displaced mandible. As an example of Waddingtonian epigenetics, we suggest that muscle, in addition to acting via mechanochemical signal transduction pathways, networks and promoters, also exerts secretory stimuli on skeleton. Our goal is to identify candidate molecules at that muscle-mandible interface. By employing Systematic Subtractive Microarray Analysis approach, we compared gene expression between mandibles of amyogenic and wild type mouse fetuses.
We identified a set of candidate genes with involvement in mandibulardevelopment: Cacna1s, Ckm, Des, Mir300, Myog and Tnnc1. We also performed mouse-to-human translational experiments and found analogies. In the light of our findings we discuss various players in mandibular morphogenesis and make an argument for the need to consider mandibular development as a consequence of reciprocal epigenetic interactions of both skeletal and non-skeletal compartments.

overall_design: Mouse embryos were obtained at E18.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Irene

last: Rot

first: Snjezana

last: Mardesic-Brakus

first: Willard

last: Costain

first: Mirna

last: Saraga-Babic


title: Transcriptome study of colon epithelial cells in Reg3a-transgenic mice

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
The human C-type lectin Reg3a (HIP/PAP) is an antimicrobial peptide that kills Gram-positive bacteria. Reg3a preserves gut microbiota homeostasis, reinforces intestinal barrier function and thereby helps to fight induced colitis in mice.
Transcriptomic data revealed an upregulation of numerous genes involved in the robustness of the intestinal barrier, and the biosynthesis pathway of mucin core 1 and 3 O-glycans.

overall_design: Transcriptome analysis was performed on colon sections from wild-type and Reg3a-transgenic C57BL/6N mice non-treated or treated with 3% dextran sodium sulfate using  GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).

first: Marion

last: Darnaud

first: Sandrine

last: Augui

first: Alexandre

last: Dos Santos

first: Christophe

last: Desterke

first: Emilie

last: Braun

first: Nicolas

last: Moniaux

first: Gert

last: De Hertogh

first: Jinzi

last: Zheng

first: Raphael

last: Boisgard

first: Christel

last: Neut

first: Frank

last: Chiappini

first: Francesca

last: Guerrieri

first: Didier

last: Samuel

first: Patricia

last: Lepage

first: Joel

last: Doré

first: Christian

last: Bréchot

first: Jamila

last: Faivre


title: LSK cells transfected with Hhex retrovirus

city: Melbourne

first: Ashley

last: Ng

state: Victoria

address: 1G Royal Parade, Parkville

department: Cancer and Haematology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: The Hematopoietically-expressed homeobox (Hhex) transcription factor is overexpressed in human myeloid leukemias. Conditional knockout models of murine acute myeloid leukemia (AML) indicate that Hhex maintains leukemia stem cell self-renewal by enabling Polycomb-mediated epigenetic repression of the Cdkn2a tumor suppressor locus, encoding p16Ink4a and p19Arf. However, whether Hhex overexpression also affects hematopoietic differentiation is unknown. To study this, we retrovirally overexpressed Hhex in hematopoietic progenitors. This enabled serial replating of myeloid progenitors, leading to the rapid establishment of IL-3-dependent promyelocytic cell lines. Use of a Hhex-ERT2 fusion protein demonstrated that continuous nuclear Hhex is required for transformation, and structure function analysis demonstrated a requirement of the DNA binding and N-terminal repressive domains of Hhex for promyelocytic transformation. This included the N-terminal Pml interaction domain, although deletion of Pml failed to prevent Hhex-induced promyelocyte transformation, implying other critical partners. Furthermore, deletion of p16Ink4a or p19Arf did not promote promyelocyte transformation, indicating that repression of distinct Hhex target genes is required for this process. Indeed, transcriptome analysis showed that Hhex overexpression resulted in repression of several myeloid developmental genes. To test potential for Hhex overexpression to contribute to leukemic transformation, Hhex-transformed promyelocyte lines were rendered growth factor-independent using a constitutively active IL-3 receptor common b subunit (bcV449E). The resultant cell lines resulted in a rapid promyelocytic leukemia in vivo. Thus Hhex overexpression can contribute to myeloid leukemia via multiple mechanisms including differentiation blockade and enabling epigenetic repression of the Cdkn2a locus.

overall_design: 3 biological replicates of MIG-Hhex transduced LSK cells and 3 biological replicates of MIG transduced LSK cells as controls. Differential gene expression analysis of LSK cells from C57BL/6 mice transduced with either MIG or MIG-Hhex retrovirus and cultured for two days.

first: Jacob

last: Jackson


title: RNA-sequencing of mouse adult hippocampal progenitor cells in which Nfix was deleted.

city: Brisbane

first: Michael

last: Piper

address: St Lucia

institute: The University of QUeensland

summary: RNA-sequencing of mouse adult hippocampal nestin+ progenitor cells & dcx+ progenitor cells from wild-type animals, and animals in which the gene Nfix was deleted.

overall_design: Hippocampal nestin+ flox-reporter progenitor cells (3 wt, 3 kos - 60 days post tamoxifen adminstration), dcx+ flox-reporter progenitor cells (3 wt, 3 kos - 7 days post administration)

first: Lachlan

last: Harris


title: Role of skeletal muscle in ear development.

first: Boris

last: Kablar

summary:
Here, we show lists of 10 up- and 87 down-regulated genes obtained by a cDNA microarray analysis that compared developing Myf5-/-:Myod-/- (and Mrf4-/-) petrous part of the temporal bone, containing middle and inner ear, to the control, at embryonic day 18.5. Myf5-/-:Myod-/- fetuses entirely lack skeletal myoblasts and muscles. They are unable to move their head, which interferes with the perception of angular acceleration. Previously, we showed that the inner ear areas most affected in Myf5-/- :Myod-/- fetuses were the vestibular cristae ampullaris, sensitive to angular acceleration. Our finding that the type I hair cells were absent in the mutants’ cristae was further used here to identify a profile of genes specific to the lacking cell type.
Microarrays followed by a detailed consultation of web-accessible mouse databases allowed us to identify 6 candidate genes with a possible role in the development of the inner ear sensory organs: Actc1, Pgam2, Ldb3, Eno3, Hspb7 and Smpx. Additionally, we searched for human homologues of the candidate genes since a number of syndromes in humans have associated inner ear abnormalities. Mutations in one of our candidate genes, Smpx, have been reported as the cause of X-linked deafness in humans. Our current study suggests an epigenetic role that mechanical, and potentially other, stimuli originating from muscle, play in organogenesis, and offers an approach to finding novel genes responsible for altered inner ear phenotypes.

first: Irene

last: Rot

first: Mark

last: Baguma-Nibasheka

first: Willard

last: Costain

first: Paul

last: Hong

first: Robert

last: Tafra

first: Snjezana

last: Mardesic-Brakus

first: Natasa

last: Mrduljas-Djujic

first: Mirna

last: Saraga-Babic


title: GRO-seq analysis of control and senescent BJ and TIG3 cells

status: Public on Jan 29 2018

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We used GRO-seq to examine transcriptional activities in BJ and TIG-3 cells under control conditions and after activation of oncogenic RAS_V12 that leads to Oncogene-Induced Senescence (OIS)

overall_design: Examination of transcriptional changes upon oncogene-induced senescence (OIS) in two normal human diploid fibroblast cell lines: BJ and TIG-3

first: R

last: Agami


title: Ang II type 1a receptor in Marfan syndrome

city: New York

first: Josephine

last: Galatioto

state: New York

address: 1468 Madison Avenue

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Using Cdh5-Cre and Sm22-Cre transgenes to characterize the impact of disruption of the angiotensin II type 1a receptor (AT1ar) in vascular endothelial and smooth muscle cells, respectively, of wild type (WT) mice compared to fibrillin-1 hypomorphic mice (Fbn1mgR/mgR mice) that replicate early onset progressively severe Marfan syndrome (MFS) with dissecting thoracic aortic aneurysm (TAA).

overall_design: Comparing biological processes identified from transcriptomic analyses of aortic tissue harvested from either WT (at1Rfl) mice or mice with a knockout of AT1ar in either endothelial cells (at1Rcdh5) or smooth muscle cells (at1Rsm22).


title: Retinal Cell Type Epigenetic Memory Predicts Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures [RNA-Seq_Mm]

status: Public on Jan 28 2018

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Diverse cell types can be reprogrammed into pluripotent stem cells by ectopic expression of Oct4 (Pou5f1), Klf4, Sox3 and Myc. Many of these induced pluripotent stem cells (iPSCs) retain an epigenetic memory of their cellular origins and this in turn may bias their subsequent differentiation. Differentiated neurons are difficult to reprogram and there has not been a systematic side-by-side characterization of reprogramming efficiency or epigenetic memory across different neuronal subtypes. We have recently developed a new method for reprogramming retinal neurons and successfully reprogrammed rod photoreceptors from the murine retina. Here we extended our retinal reprogramming to cone photoreceptors, bipolar neurons, amacrine/horizontal cell interneurons and Müller glia at two different stages of development. We scored the efficiency of reprogramming across all 5 retinal cell types at each developmental stage and we measured retinal differentiation from each iPSC line using a quantitative standardized scoring system called STEM-RET. We discovered that the rod photoreceptors and bipolar neurons had the lowest reprogramming efficiency but iPSCs derived from rods and bipolar cells had the best retinal differentiation. Epigenetic memory was analyzed by characterizing DNA methylation and performing ChIP-seq for 8 histone marks, Brd4, PolII and CTCF. The epigenetic data were integrated with RNA-Seq data from each iPSC line. Retinal cell types with a greater epigenetic barrier to reprogramming (rods and bipolars) are more likely to retain epigenetic memory of their cellular origins. In addition, we identified biomarkers of iPSCs that are predictive of retinal differentiation. This work will have implications for selection of cell populations for cell based therapy and for using reprogramming of purified cell populations to advance our understanding of the role of the epigenome in normal differentiation.

overall_design: Examination of 8 different histone modifications and 3 transcription factors, transcriptome, DNA methylation in 33 different iPSC cell lines along with mESC Eb5

first: Lu

last: Wang

first: Daniel

last: Hiler

first: Issam

last: Aldiri

first: Xiang

last: Chen

first: Lyra

last: Griffiths

first: Marc

last: Valentine

first: Abbas

last: Shirinifard

first: Andras

last: Sablauer

first: Suresh

last: Thiagarajan

first: Marie-Elizabeth

last: Barabas

first: Jiakun

last: Zhang

first: Dianna

last: Johnson

first: Sharon

last: Frase

middle: A

last: Dyer


title: DNA methylation patterns separate senescence from malignant transformation potential in human cells [methylation]

first: Wenbing

last: Xie

summary: Replicative senescent cells reportedly share similar DNA methylation changes with cancer cells, which are purported to facilitate tumorigenesis in cells bypassing senescence. However, we now report biologically critical and distinct patterns of DNA methylation evolution between replicative and oncogene-induced senescence and transformation in a classic human cell transformation model. While overall DNA methylation losses and gains occur in both replicative senescent and transformed cells, the patterns evolve more programmatically for the former and stochastically for the latter. Oncogene-induced senescence is an acute process involving minimal changes to DNA methylation. The stochastic DNA methylation alterations in transformation mainly involve a set of pro-survival promoter CpG-island methylation events targeting genes controlling development and differentiation processes, while the senescence-specific promoter changes occur in genes involved in positive regulation of cellular biosynthesis and macromolecular metabolism. The above set of pro-survival promoter CpG-island hypermethylation events, but not the senescence-specific events, are prone to occur in primary tumors and aging tissues. Importantly, cells manifest senescence-specific epigenomic patterns very early during commitment to senescence, and while these “near-senescent” cells can be immortalized, they are refractory to transformation by H-Ras oncoprotein (H-rasV12). The senescence-specific methylation is retained during immortalization and transformation attempts, suggesting it does not function to promote tumorigenesis. Thus, abnormalities in cancer-related methylation has their origins in aging and not replicative senescence, and senescence-associated methylation potentially prevents malignant transformation.

overall_design: Bisulphite converted DNA from the 31 samples to test DNA methylation alterations in transformation and senescence

first: Lixia

last: Pan

first: Yang

first: Lauren

last: Murphy

first: Xiangqian

last: Kong

first: Limin

last: Xia

first: Fillipe

last: Carvlho

first: Stephen

last: Baylin

first: Hariharan

last: Easwaran


title: DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

summary: Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342,596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formal mediation analysis. DNAm mediated the association of prenatal famine exposure with adult BMI and TG but not with glucose. DNAm at PIM3 (cg09349128), a gene involved in energy metabolism, mediated 13.4% [95% confidence interval (CI), 5 to 28%] of the association between famine exposure and BMI. DNAm at six CpGs, including TXNIP (cg19693031), influencing β cell function, and ABCG1 (cg07397296), affecting lipid metabolism, together mediated 80% (95% CI, 38.5 to 100%) of the association between famine exposure and TG. Analyses restricted to those exposed to famine during early gestation identified additional CpGs mediating the relationship with TG near PFKFB3 (glycolysis) and METTL8 (adipogenesis). DNAm at the CpGs involved was associated with gene expression in an external data set and correlated with DNAm levels in fat depots in additional postmortem data. Our data are consistent with the hypothesis that epigenetic mechanisms mediate the influence of transient adverse environmental factors in early life on long-term metabolic health. The specific mechanism awaits elucidation.

overall_design: Comparison of DNA methylation in  human tissues

first: R

middle: C


title: Gene expression data from WM983B melanoma cells treated with vehicle or 2.5 µM inhibitor (corin2 or MS-275) for 24 h

first: Jay

middle: Hans

last: Kalin

address: 725 N. Wolfe St., Hunterian 314

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins University

summary:
Epigenetic regulation of gene expression by histone modification has emerged as a major facet of physiologic and disease processes. As a result, there has been intense interest in developing epigenetic therapies leading to the discovery of small molecule agents that target proteins involved in histone modification. Several histone deacetylase (HDAC) inhibitors are now approved drugs for a specialized group of hematologic malignancies but not yet for a wider range of cancer types including solid tumors. One of the conceptual challenges in targeting HDACs is that even selective class I HDAC inhibitors likely impact these deacetylase activities indiscriminately across a range of distinct HDAC-containing multiprotein complexes. Such broad cellular effects may result in a narrow therapeutic window between disease efficacy and toxicity.  Among HDAC complexes, the CoREST complex, which includes HDAC1 or its close paralog HDAC2, the scaffolding protein CoREST, and lysine specific demethylase 1 (LSD1) has attracted special interest. Here we report corin2, designed to dually inhibit the CoREST complex major enzymatic activities, lysine specific demethylase 1 (LSD1) and HDACs 1/2. Corin2 is a synthetic hybrid agent derived from the class I HDAC inhibitor (entinostat) and an LSD1 inhibitor (tranylcypromine analog). Enzymologic analysis reveals that corin2 selectively targets the CoREST complex and shows more sustained inhibition of the CoREST complex HDAC activity than entinostat.  Cell-based experiments demonstrate that corin2 exhibits a superior anti-proliferative profile against several melanoma lines compared to its parent monofunctional HDAC and LSD1 inhibitors (alone or in combination) but is less toxic to non-cancerous primary human melanocytes.  Transcriptomics analysis shows that corin2 is a more powerful inducer of tumor suppressor genes relative to the parent HDAC and LSD1 compounds (alone or in combination).  Genetic knockdown of CoREST or LSD1 in cancer cell lines abolishes the differences in potency of corin2 vs. entinostat, suggesting that corin2's favorable pharmacologic effects rely on an intact CoREST complex. Corin2 was also effective in slowing tumor growth in a melanoma mouse xenograft model. These studies highlight the promise of a new class of two-pronged hybrid agents that selectively target particular epigenetic regulatory complexes and offer unique therapeutic opportunities.
We characterized the gene expression changes uniquely related to dual inhibition of HDAC1/2 and LSD1 as part of the CoREST complex to identify genes associated with our dual inhibitor's (corin2) antiproliferative mechanism of action in melanoma cells.   Transcriptomics analysis shows that corin2 is a more powerful inducer of tumor suppressor genes relative to the parent HDAC and LSD1 compounds (alone or in combination).

overall_design: Three experimental conditions were run in biological triplicate for a total of nine samples. Gene expression changes ≥ 2-fold were considered significant for subsequent analysis.

first: Muzhou

last: Wu

first: Nkosi

last: Adejola

first: Byungwoo

last: Ryu

first: Rhoda

middle: M

last: Alani

first: Philip

last: Cole


title: Retinal Cell Type Epigenetic Memory Predicts Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures [ChIP-seq_Mm]

first: Beisi

last: Xu

type: Genome binding/occupancy profiling by high throughput sequencing

first: Lu

last: Wang

first: Daniel

last: Hiler

first: Issam

last: Aldiri

first: Xiang

last: Chen

first: Lyra

last: Griffiths

first: Marc

last: Valentine

first: Abbas

last: Shirinifard

first: Andras

last: Sablauer

first: Suresh

last: Thiagarajan

first: Marie-Elizabeth

last: Barabas

first: Jiakun

last: Zhang

first: Dianna

last: Johnson

first: Sharon

last: Frase

first: Michael


title: Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors [4C]

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system consisting of ~200kb human bacteria artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) replication origin elements (E-BACs). E-BACs were stably maintained as autonomous mini-chromosomes in both HeLa and human induced pluripotent stem cells (hiPSCs) and established their RT de novo. We applied 4C-seq to evaluate E-BACs' sub-nuclear compartment.

overall_design: 4C-seq profiles of E-BAC transfected K3-EBNA1 cells

last: Bartlett


title: Retinal Cell Type Epigenetic Memory Predicts Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures [TEBS_Mm]

type: Methylation profiling by high throughput sequencing

last: Dyer


title: HOXA9 cooperates with activated JAK/STAT signaling to drive leukemia development

status: Public on Jan 26 2018

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: Leukemia is caused by the accumulation of multiple genomic lesions in hematopoietic precursor cells. However, how these events cooperate during oncogenic transformation remains poorly understood. We studied the cooperation between activated JAK3/STAT5 signaling and HOXA9 overexpression, two events identified as significantly co-occuring in T-cell acute lymphoblastic leukemia. Expression of mutant JAK3 and HOXA9 led to a rapid development of leukemia originating from multipotent or lymphoid-committed progenitors, with a significant decrease in disease latency compared to JAK3 or HOXA9 alone. Integrated RNA-seq, ChIP-seq and ATAC-seq revealed that STAT5 and HOXA9 have co-occupancy across the genome resulting in enhanced STAT5 transcriptional activity and ectopic activation of Fos/Jun (AP-1). Our data suggest that oncogenic transcription factors such as HOXA9 provide a fertile ground for specific signaling pathways to thrive, explaining why JAK/STAT pathway mutations accumulate in HOXA9 expressing cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA-sequencing and ChIPmentation sequencing on mouse thymus samples
ChIPmentation sequencing on xenograft sample

first: Charles

last: de Bock

first: Jan

last: Cools


title: Transcriptome analysis of E. coli strain MG1655 on exposure to glutathione (GSH) and/or ciprofloxacin

city: MUMBAI

first: Manish

last: Goswami

state: Maharashtra

address: Mod Labs, trombay

department: Molecular Biology Division

country: India

institute: Bhabha Atomic Research Centre

summary:
Expression profiling of wild type E. coli K-12 strain MG1655 with exogenous glutathione (GSH) supplementation, sub-inhibitory ciprofloxacin concentration and GSH with inhibitory ciprofloxacin concentration.
We used microarrays to detail the global gene expression program underlying ciprofloxacin exposure and glutathione mediated abrogation of ciprofloxacin's anti-bacterial action.

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

overall_design: An eight-chip study with one E. coli strain under four separate culture conditions (two biological replicates for each condition).

first: Akkipeddi

middle: V

last: Rao


title: On the design of CRISPR-based single cell molecular screens

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: We demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity.

overall_design: Experiments were conducted with FACs followed by NGS to quantify the rate of template switching. single-cell RNA-seq experiments were performed on the 10X Genomics platform for mock and doxorubicin treated MCF10a cells that had been tranduced with a CRISPR KO library (targeting tumor suppressors) that allowed for readout of the KO via a linked distal barcode using both an arrayed lentivirus production strategy and a pooled lentivirus production strategy. single-cell RNA-seq was also performed on mock and doxorubicin cells tranduced with a CRISPR KO library targeting tumor suppressors using a CROP-seq vector as the backbone.

first: A

last: Hill

first: J

middle: L

last: McFaline-Figueroa

first: C

last: Trapnell


title: Marfan syndrome in mice

status: Public on Jan 27 2018

first: Josephine

last: Galatioto

summary: Comparison of whole genome expression profiles to characterize gene expression during development of thoracic aortic aneurysm in fibrillin-1 hypomorphic mice (Fbn1mgR/mgR).

overall_design: We compared biological processes identified from transcriptomic analyses of aortic tissue harvested from Fbn1mgR/mgR mice, a validated model of early onset, progressive, severe Marfan syndrome (MFS).


title: Single cell transcriptomic analysis of mouse FoxP3- CD4+ Tconv cells and FoxP3+ regulatory CD4+ T cells isolated from secondary lymphoid organs, colon, muscle, visceral adipose tissue [CelSeq]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation

last: Zemmour

first: Christophe

last: Benoist


title: Primary cilia sensing-regulated transcriptome in the collecting duct

city: Nijmegen

first: Joost

last: Hoenderop

state: Gelderland

address: Geert Grooteplein Zuid 30

department: Physiology

institute: Radboud Institute for Molecular Life Sciences

summary: RNA-seq technology was used to reveal the transcriptome changes of tubular epithelia in response to fluid flow and determine the role of primary cilia in this process. Many fluid flow-sensitive genes were identified, among which are those regulated by primary cilia sensing of fluid flow. These genes were further validated by RT-qPCR.

overall_design: Ciliated and non-ciliated IMCD3 (inner-medullary collecting duct) cells were exposed to fluid flow followed by RNA isolation and sequencing.

first: Sami

last: Mohammed

first: Francisco

last: Arjona

first: Eric

last: Verschuren

first: Zeineb

last: Bakey

first: Wynand

last: Alkema

first: Sacha

last: Van hijum

first: Miriam

last: Schmidts

first: René

last: Bindels


title: RNA-seq analysis of colon tumors collected from St2-/- and WT reciprocal bone marrow chimeric mice treated with azoxymethane.

city: Heidelberg

first: Moritz

middle: Falk

last: Eissmann

address: 145 Studley Road

institute: Olivia Newotn-John Cancer Research Institute

summary: Interleukin 33 (IL33) is an inflammatory cytokine released during necrotic cell death. The epithelium and stroma of the intestine express large amounts of IL33 and its receptor St2. IL33 is therefore continuously released during homeostatic turnover of the intestinal mucosa. Although IL33 can prevent colon cancer associated with inflammatory colitis, the contribution of IL33 signaling to sporadic colon cancer remains unknown.  Here, we utilized a mouse model of sporadic colon cancer to investigate the contribution of IL33 signaling to tumorigenesis in the absence of pre-existing inflammation. We demonstrated that genetic ablation of St2 enhanced colon tumor development. In reciprocal bone marrow (BM) chimeras, the concurrent loss of IL33 signaling within radioresistant nonhematopoietic, and the radiosensitive hematopoietic, compartments was associated with increased tumor burden. To elucidate the molecular mechanisms underpinning the tumor-suppressing effect of IL33 signaling in sporadic colon cancer, we performed whole transcriptome analysis of tumors collected from each of the four cohorts of the 6xAOM-treated BM chimeras. We discovered that St2 deficiency within the nonhematopoietic compartment coincided with suppression of an IFN gene expression signature. The decrease of this IFN gene expression signature was associated with more aggressive disease in human colon cancer patients, suggesting that lack of IL33 signaling impaired the generation of a potent IFN-mediated antitumor immune response. Collectively, our data reveal that IL33 functions as a tumor suppressor in sporadic colon cancer.

overall_design:
Reciprocal bone marrow chimeras were established by reconstituting lethally irradiated (2x 5 Gy) WT or St2-/- recipient mice with 5-10x 10^6 bone marrow cells from either WT or St2-/- mice and allowed to reconstitute for 8 weeks. 4 groups of BM chimeras were generated:
1. WT bone marrow into WT host (WT => WT)
2. WT bone marrow into St2-/- host (WT =>St2-/-)
3. St2-/- bone marrow into WT (St2-/- => WT)
4. St2-/- bone marrow into St2-/- host (St2-/-=>St2-/-).
Sporadic colon cancer was then induced by intraperitoneal injections of azoxymethane (AOM; 10 mg/kg) once weekly for 6 consecutive weeks. Mice were monitored for tumor development for up to 20 weeks after the last AOM injection. Total RNA was extracted from snap-frozen tumors collected from BM chimeras using Trizol®Reagent (Life Technologies). Extracted RNA was then further purified using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were generated using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s instructions. Three biological replicates were generated and sequenced for each group of BM chimeras by subjecting 1μg of RNA to single-end (50 pb) sequencing on an Illumina HiSeq 2500 instrument at the Australian Genome Research Facility.
3 biological replicates are provided for each of the 4 group of bone marrow chimeras.

first: Christine

last: Dijkstra

first: Merridee

last: Wouters

first: David

last: Baloyan

first: Dmitri

last: Mouradov

first: Paul

last: Nguyen

first: Mercedes

last: Davalos-Salas

first: Tracy

last: Putoczki

first: Oliver

last: Sieber

first: John

last: Mariadason

first: Matthias

last: Ernst

first: Frederick

last: Masson


title: Differential gene expressions of human pluripotent stem cells derived cells in different culture system

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Human pluripotent stem cells (H9s) were differentiated into endothelial cells (ECs), neural stem cells (NSCs) and vascular smooth muscle cells (VSMCs) in 2 dimentional, 3 dimensional PEG hydrogel and alginate hydrogel culture system, and we compared their differential gene expression in different culture system, respectively.

overall_design:
RNA deep sequencing
H9s were maintained in E8 medium for routine culture. Then H9s were differentiated into ECs, NSCs and VSMCs in 2D, 3D PEG hydrogel and alginate hydrogel cell culture system according to their differentiation protocol. mRNAs were sequenced.

first: Lei

last: Yuguo

first: Lin

last: Haishuang

first: Zhang

last: Chi


title: Transcriptional profiling of pre- and post-natal glutamatergic progenitors and nascent neurons by single cell RNA sequencing

status: Public on Jan 25 2018

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

institute: Universite Lyon 1

summary:
Purpose: We labeled synchronous cohorts of prenatal and postnatal glutamatergic progenitors to study their lineage relationship and transcriptional  specificities.

Method and results: We performed scRNA-seq of postnatal glutamatergic progenitors isolated from microdissected pallium at E15.5 or dorsal subventricular zone at P2 in the mouse. Our results highlight transcriptional dysregulation at P2 which includes genes involved in metabolism, differentition and migration.

overall_design: tdTom+ cells (glutamatergic progenitors) were isolated from E15 and P2 transgenic mice expressing a tamoxifen inducible Cre-recombinase under Neurog2 genomic regulatory sequences. A total of 230 cells were obtained (121 at E15.5 and 109 at P2). Following tissue dissociation, single cells were isolated by flow cytometry and processed with the C1 Single-Cell Auto Prep System (Fluidigm). RNA-sequencing libraries were muliplexed and sequenced at 75bp single reads using the Illumina HiSEQ500 platform at a depth of 7M reads. Every sample in this series represents a single cell.

first: Olivier

last: Raineteau

first: Quentin

last: Lo Giudice

first: Vanessa

last: Donega


title: The chromatin remodeler Bptf activates a stemness gene-expression program essential for the maintenance of adult hematopoietic stem cells

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

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

overall_design: Refer to individual Series


title: The chromatin remodeler Bptf activates a stemness gene-expression program essential for the maintenance of adult hematopoietic stem cells [RNA-Seq]

summary: Bptf, a component of NURF chromatin-remodeling complex, is essential for maintaining the pool size and function of hematopoietic stem cells (HSCs). Genome-wide transcriptome profiling revealed that Bptf loss caused down-regulation of HSC-specific gene-expression programs, which included master transcription factors (such as Meis1, Pbx1, and Lmo2) known to be required for HSC maintenance and self-renewal. Bptf directly bound to the promoter of ‘stemness’ TF genes, potentiating their transcription and DNA accessibility.

overall_design: To dissect the gene-regulatory role of Bptf in HSPCs, we sorted out phenotypically identical LSK cells from the bone marrow of Bptf conditional KO mice and littermate controls, followed by ACAT-seq and RNA-seq studies. We also performed H3K4me3 ChIP-seq using HPC7 cells, a murine HSPC-mimicking cell line.

first: Bowen

last: Xu

first: Gang


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [TRAP-Seq SER_Meth]

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: The adult brain is composed of hundreds of different neuronal subtypes, which retain their differentiated traits and identity throughout the lifespan of the organism. Nevertheless, in part due to technical limitations, the mechanisms governing this stability are not fully understood. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in sparse neuronal populations in vivo, we present, to our knowledge, the first comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons and embryonic neural progenitors. Our results support a model wherein a sequential deposition of the repressive modifications H3K27me3 and H3K9me3 occur on developmental genes in a neuronal subtype specific manner. We furthermore show that aberrant gene expression during dopaminergic stress in a mouse model of Parkinson’s disease, or after methamphetamine injection, is characterized by the de-repression of genes with promoter regions that are dually marked by H3K4me3 and H3K27me3, whereas the induction of genes with promoter regions marked by any other combination of H3K27me3 and H3K9me3 occur less frequently. Our study provides to our knowledge the first genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare but clinically relevant neuronal subtypes. This strategy can be generalized for the identification and functional characterization of molecular determinants involved in the maintenance of gene expression in other classes of neurons.

overall_design: 16 samples in total from 8 mice. 8 TRAP-seq samples: 4 from methamphetamine treated mice, 4 from saline treated mice. 8 RNA-seq samples performed on total RNA from the unbound fraction of each TRAP sample.

first: Erik

last: Södersten

first: Konstantinos

last: Toskas

first: Vilma

last: Rrakli

first: Katarina

last: Tiklova

first: Åsa

last: Björklund

last: Ringnér

first: Thomas

last: Perlmann

first: Johan

last: Holmberg


title: The chromatin remodeler Bptf activates a stemness gene-expression program essential for the maintenance of adult hematopoietic stem cells [ChIP-Seq]


title: Differential gene expression pattern of mouse livers transfected with dual oncogenes (day-7 post-injection data set)

city: La Jolla

first: Jijun

last: Liu

state: CA

address: Rm1220 Bay-C, Biomedical Research Facility II, 9500 Gilman Drive

department: Pathology

institute: UC San Diego

summary: To understand global gene expression patterns of mouse livers upon dual-oncogene transfection, RNA sequencing and analysis were conducted on liver samples from Shp2F/F or Shp2∆H (Shp2F/F:Alb-cre) mice hydrodynamically injected with the combination of Met/β-Catenin or Met/PIK3CA .

overall_design: 18 mice from 6 experimental groups (n=3 for each group) were included in the experiment. Group1: GFP hydrodynamically injected Shp2F/F control mice; Group2: GFP hydrodynamically injected Shp2ΔH control mice; Group3: Met/β-Catenin hydrodynamically injected Shp2F/F mice;  Group4: Met/β-Catenin hydrodynamically injected Shp2ΔH mice; Group5: Met/PIK3CA hydrodynamically injected Shp2F/F mice; Group6: Met/PIK3CA hydrodynamically injected Shp2ΔH mice. Total RNA was extracted on day-7 post-injection from liver of each mouse.

first: Jacey

first: Yanjie

last: Li

first: Gen-Sheng

last: Feng


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [TRAP-Seq mDA_Meth]


title: The chromatin remodeler Bptf activates a stemness gene-expression program essential for the maintenance of adult hematopoietic stem cells [ATAC-Seq]


title: TFAM binding analysis at mitochondrial genome between Wild Type (Wt) and Actb-/- (KNO) Mouse Embryonic Fibroblast

status: Public on Jan 24 2018

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Using Chromatin-immunoprecipitation and NGS, we investigated the binding of TFAM protein at mitochondrial genome between Actb+/+ Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast

overall_design: Examination of TFAM binding at mitochondrial genome between Actb+/+Wild Type (WT) and Actb-/- (KNO) Mouse Embryonic Fibroblast

first: Xin

last: Xie

first: Nizar

last: Drou


title: Microarray analysis of gene expression during ESC cell competition

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

country: United Kingdom

institute: NHLI Imperial College London

summary: A fundamental question in developmental biology is whether there are mechanisms to detect stem cells with mutations that, although not adversely affecting viability, would compromise their ability to contribute to further development. Here, we show that cell competition is a mechanism regulating the fitness of embryonic stem cells (ESCs). We find that ESCs displaying defective bone morphogenetic protein signaling or defective autophagy or that are tetraploid are eliminated at the onset of differentiation by wild-type cells. This elimination occurs in an apoptosis-dependent manner and is mediated by secreted factors. Furthermore, during this process, we find that establishment of differential c-Myc levels is critical and that c-Myc overexpression is sufficient to induce competitive behavior in ESCs. Cell competition is, therefore, a process that allows recognition and elimination of defective cells during the early stages of development and is likely to play important roles in tissue homeostasis and stem cell maintenance.

overall_design: GFP labelled Bmpr1a-/-  embryonic stem cell (ESCs) and unlabelled wild-type (WT)  ESCs were mixed in equal proportions and co-cultured for 3 days in N2B27. As a control, the two cell types were grown separately in the same conditions. After 3 days of mixed culture, the two cell types were FACS sorted (based on GFP expression of the Bmpr1a-/- cells) and RNA was extracted from each of the two subpopulations at this time-point.

first: Margarida

last: Sancho


title: Per2 regulation of mammary gland development and branching morphogenesis via cell fate determination

city: College Station

first: Cole

last: McQueeen

address: 4467 VMRB

institute: Texas A&M University

summary: Circadian rhythms play key roles in daily physiological functions, development, and cancer.  Period 2 (PER2) is a repressive element which inhibits transcription activated by positive clock elements resulting in diurnal cycling of genes.  Here we show, that outside of time keeping, PER2 has a non-circadian function that is critical to mammary gland development. Virgin Per2 deficient mice, Per2ldc, have underdeveloped glands containing fewer bifurcations and terminal ducts. Using a transplantation model, we show that these changes are intrinsic to the gland and furthermore identify changes in cell fate commitment.  Per2ldc mouse mammary glands have a luminal/basal bi-potent phenotype in cells of the ductal epithelium. We identified co-localization of E-cadherin and Keratin 14 in luminal cells and decreased p63 staining and gene expression in myoepithelial cells. Moreover, Per2ldc mice overexpress SLUG, which is related to mammary stem cell maintenance and EMT.  Similar results were demonstrated using MCF10A and shPER2 MCF10A cell lines.  Collectively this study reveals a critical non-circadian function of PER2 in mammary gland development, validates the Per2ldc model, and describes a potential role for PER2 in breast cancer.

overall_design: Analysis of RNA expression from wild type and Per2ldc mice

last: McQueen

first: Emily

last: Schmitt

first: Tapasree

last: Sarkar

first: Jessica

last: Elswood

first: Richard

last: Metz

first: David

last: Earnest

first: Monique

last: Rijnkels

first: Weston

last: Porter


title: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [TRAP-Seq mDA_6-OHDA]

first: Markus

last: Ringner

overall_design: 20 samples in total from 5 mice. 10 TRAP-seq samples: TRAP was performed in the 6-OHDA lesioned (R) and control (L) side of the midbrain of each mouse. 10 RNA-seq samples: RNA-seq was performed on total RNA from the unbound fraction of each TRAP sample.

first: Erik

last: Södersten

first: Konstantinos

last: Toskas

first: Vilma

last: Rrakli

first: Katarina

last: Tiklova

first: Åsa

last: Björklund

last: Ringnér

first: Thomas

last: Perlmann

first: Johan

last: Holmberg


title: Next-generation RNA-sequencing data of models of Ewing sarcoma with modulated expression of the lncRNA HOTAIR

city: Columbus

first: Nilay

last: Shah

state: Ohio

address: 700 Children’s Dr.

department: Center for Childhood Cancer and Blood Diseases

institute: The Research Institute at Nationwide Children’s Hospital

summary:
Purpose: Our experimental results demonstrate an essential role for the lncRNA HOTAIR in Ewing sarcoma. We have repressed HOTAIR expression in three Ewing sarcoma cell lines and overexpressed HOTAIR, alone and with EWS-FLI1, in htert-immortalized human mesenchymal stem cells to evaluate its effects on gene expression in this cancer.
Methods: RNA-Seq of Ewing sarcoma cell lines with HOTAIR represssed by GapmeR or treated with nonsilencing control, and hTERT-immortalized hMSCs with expression of control GFP, HOTAIR, or HOTAIR and EWS-FLI1, was used for gene expression analysis.
Results: Defined gene expression signatures were defined as driven by HOTAIR in each cell line model, with a consensus set of gene identified in the Ewing sarcoma cell lines. Additionally, a set of genes regulated by HOTAIR independently of EWS-FLI1 was identified in the hTERT-hMSC models.
Conclusions: HOTAIR expression regulates a set of genes critical to viability, cell adhesion, cell motility, and other markers of EMT and metastasis in Ewing sarcoma, independently of EWS-FLI1.

overall_design: Ewing sarcoma cell lines SKES, ES2, and A673 were treated with locked nucleic acic antisense oligonucleotides (GapmeR, Exiqon) against either HOTAIR or a nonsilencing control for 48 hours, then had RNA isolated using the Nucleospin RNA isolation kit. hTERT-immortalized human mesenchymal stem cells were obtained from Applied Biological Materials and infected with lentivirus expressing GFP and PuroR with or without HOTAIR, then subsequently with lentivirus expressing either BFP and PuroR with or without EWS-FLI1, and stable clones were selected by puromycin treatment. RNA was isolated as above and used for RT-qPCR, by which expression of HOTAIR and EWS-FLI1 was confirmed. RNA from these samples was then used for quality assessment, then for RNA-Seq in quadruplicate for each sample, using the Illumina HiSeq4000.


title: Single cell transcriptomic analysis of mouse FoxP3- CD4+ Tconv cells and FoxP3+ regulatory CD4+ T cells isolated from secondary lymphoid organs, colon, muscle, visceral adipose tissue

first: CBDM

last: Lab


title: Next Generation Sequencing based on the DNA fragment pulled down by p53 antibody (Santa Cruz, sc-126) from MCF7 wile type and MCF7 MDMX-C463A/WT cells.

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

institute: Harvard University

summary: Hypothesis: Based on gene chip results and further investigation, MDMX C463A/WT cells shows large portion of transcripts change at p53 dependent manner. As transcriptional factor, p53 regulates those genes could be related to DNA binding status change. ChIP-seq was used to test this hypothesis and figure out global map of p53 binding in MCF7 C463A/WT MCF7 cells by using MCF7 parental cells as reference.

overall_design: Examination of p53 genomic DNA binding affinity change in MCF7 C463A/WT cells comparing to parental cells.

first: Weiqi

last: Zeng


title: Expression data and ChIP-seq from MCF7 wildtype and MCF7 MDMXC463A/WT cells


title: RBX2 maintains final retinal cell position in a DAB1-dependent and -independent fashion

status: Public on Jan 23 2018

city: Davis

first: Sergi

last: Simo

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: Purpose: Understanding the role of RBX2 neuron migration in the retina and cone photoreceptor function

overall_design: Methods: Retinal mRNA profiles of pooled 15-day-old wild-type (WT), using Illumina NextSeq 500 (Illumina, San Diego, CA) with paired-end 40bp reads.

first: Corinne

last: Fairchild

first: Keiko

last: Hino

first: Jisoo

middle: S

last: Han

first: Adam

last: Miltner

first: Gabriel

last: Peinado Allina

first: Caileigh

last: Brown

first: Marie

last: Burns

first: Anna

last: La Torre

last: Simó


title: Dual inhibition of G9a and DNMT1 Enhances Cell Reprogramming Promoting Induction of Mesenchymal-to-Epithelial Transition and Facilitating Transcription Factor Engagement in the Genome.

status: Public on Jan 22 2018

city: Pamplona

first: Juan Roberto

last: Rodriguez-Madoz

state: Navarra

address: PIO XII 55

department: Cell Therapy Program

country: Spain

institute: Foundation For Applied Medical Research

summary: The combination of defined factors with small molecules targeting epigenetic factors is a strategy that has been shown to enhance optimal derivation of human iPSCs and could be used for therapeutic and regenerative medicine applications. In this study, we showed that a new first-in-class dual G9a/DNMT inhibitor CM272 compound improves the standard four-factor reprogramming efficiency of human fibroblast. The use of CM272 facilitates the generation of iPSC with only two factors, OCT4 and SOX2, allowing the removal of potentially oncogenic factors such as cMYC or KLF4. Taking a closer look at the early events occurring during cell reprogramming we demonstrated that treatment with our G9a/DNMT dual inhibitor induces heterochromatin relaxation, facilitates the engagement of OCT4 and SOX2 transcription factors to the genome and promotes mesenchymal to epithelial transition during cell reprogramming. Thus, the use of this new G9a/DNMT dual inhibitor compound may represent an interesting alternative for improving cell reprogramming.

overall_design: BJ cell and BJ cells treated with CM272by triplicate

first: Juan

first: Edurne

last: San Jose-Eneriz

first: Obdulia

last: Rabal

first: Xabier

last: Agirre

first: Julen

last: Oyarzabal

first: Felipe

last: Prosper


title: ROP: Dumpster Diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

city: Los Angeles

first: Harry

middle: Taegyun

last: Yang

address: Engineering VI 286

department: Computer Science

institute: University of California, Los Angeles

summary: High-throughput RNA sequencing technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at http://smangul1.github.io/rop/.

overall_design:
19 nasal epithelium RNA-Seq, 9 ashmatic, 10 normal/control. 18 peripheral blood RNA-Seq, 9 ashmatic, 9 normal/control.
Please note our analysis identifies the origin of unmapped read, hence Read Origin Protocol, by aligning the unmapped reads to elements that are not on human reference genome. The elements include bacterial and viral genome database as well as immune variable regions, and repeat elements.

first: Serghei

last: Mangul

middle: T

first: Nicolas

last: Strauli

first: Franziska

last: Gruhl

first: Hagit

last: Porath

first: Kevin

last: Hsieh

first: Linus

last: Chen

first: Timothy

last: Daley

first: Stephanie

last: Christenson

first: Agata

last: Wesolowska-Andersen

first: Roberto

last: Spreafico

first: Cydney

last: Rios

first: Celeste

last: Eng

first: Andrew

last: Smith

first: Ryan

last: Hernandez

first: Roel

last: Ophoff

first: Jose

last: Santana

first: Erez

middle: Y

last: Levanon

first: Prescott

last: Woodruff

first: Esteban

last: Burchard

first: Max

last: Seibold

first: Sagiv

last: Shifman

first: Eleazar

last: Eskin

first: Noah

last: Zaitlen


title: Myeloid-targeted immunotherapies act in synergy to induce inflammation and anti-tumor immunity

first: Robert

middle: Anthony

last: Amezquita

address: 1100 Fairview Ave. N.

department: Integrated Immunotherapy Research Center

institute: Fred Hutchinson Cancer Research Institute

summary:
Purpose: Eliciting effective anti-tumor immune responses in patients who fail checkpoint inhibitor therapy is a critical challenge in cancer immunotherapy, and in such patients, tumor-associated myeloid cells and macrophages (TAMs) are promising therapeutic targets. We demonstrate in an autochthonous, poorly immunogenic mouse model of melanoma that combination therapy with an agonistic anti-CD40 mAb and CSF1R inhibitor potently suppressed tumor growth. Microwell assays to measure multiplex protein secretion by single cells identified that untreated tumors have distinct TAM subpopulations secreting MMP9 or co-secreting CCL17/22, characteristic of an M2-like state. Combination therapy reduced the frequency of these subsets, while simultaneously inducing a separate polyfunctional inflammatory TAM subset co-secreting TNF, IL-6, and IL-12. Tumor suppression by this combined therapy was partially dependent on T cells, TNF and IFN. Together, this study demonstrates the potential for targeting TAMs to convert a “cold” into an “inflamed” tumor microenvironment capable of eliciting protective T cell responses.
Methods: Total RNA was purified with the use of QIAzol and RNeasy Mini kit (QIAGEN), in which an on-column DNase treatment was included. Purified RNA was submitted to the Yale Center for Genomic Analysis where it was subjected to mRNA isolation and library preparation. Non-strand specific libraries were generated from 50ng total RNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit.  Libraries were pooled, six samples per lane, and sequenced on an Illumina HiSeq 2500 (75-bp paired end reads), and aligned using STAR to the GRCm38 (mm10) reference genome. A count-based differential expression protocol was adapted for this analysis(Anders et al., 2013); mappable data were counted using HTSeq, and imported into R for differential expression analysis using the DESeq2.To find differentially regulated sets of genes for signature generation, a 1.5-Log2 fold-change difference between samples and p-adjusted (Holm-Sidak) ≤ 0.01 was used.
Results: To begin to understand how these treatments modulated TAMs to control tumor growth, and to possibly illuminate additional biomarkers of response, we examined the transcriptomes of CD11b+ Ly6G- cells treated with CD40 or CSF1Ri, alone or in combination, relative to control, using high throughput RNA-sequencing. Principal components analysis (PCA) on the genome-wide dataset demonstrated that treating with CD40 and CSF1Ri individually caused largely non-overlapping changes in transcription, as indicated by their movement along orthogonal principal components (PC) relative to the control. Importantly, combination therapy was visualized as a systems-level combination of each individual treatment in PC space.     We then examined the mRNAs most altered by either treatment alone or in combination relative to Controls (Log2FC>1.5, p<.01) by unsupervised hierarchical clustering. Five major gene patterns emerged from the clustering of genes. Cluster #1 comprises genes that are upregulated by CD40 and CSF1Ri+CD40 treatment but are mostly unaffected by CSF1Ri, suggesting that CD40 is the primary driver of this cluster in the combination treatment. Notable genes in this cluster include Tnfa, IfngIl12b and Cxcl9; interestingly, for Tnfa and Il12b, CSF1Ri+CD40 appears to have a synergistic effect on expression. In contrast to Cluster #1, Cluster #5 contains genes substantially downregulated by CSF1Ri and CSF1Ri+CD40 treatments, but are largely unaffected by CD40, suggesting that CSF1Ri is the driver of this cluster in the combination treatment. Cluster #5 genes include Cd36 and Fabp4, suggesting alterations in lipid homeostasis in the TAMs after treatment. Cluster #2 includes genes that are modestly upregulated by CD40 and CSF1Ri individually, leading to a stronger upregulation when combined. Finally, Clusters #3 and #4 include, for the most part, genes that are differentially affected by CD40 versus CSF1Ri and for which the combination treatment yields an intermediate response. In summary, these data show that CSF1Ri and CD40 agonism elicit predominantly distinct changes in gene expression in the CD11b+ cells, indicating they target different biological processes in myeloid cells. The net result of the changes in myeloid gene expression from the combination of CSF1Ri+CD40 treatment reveal additive effects by the individual treatments, but also synergy in the expression of several pro-inflammatory genes (e.g., Tnfa, Ifng, Il6 and Il12b).   We further examined our dataset with Gene Set Enrichment Analysis (GSEA). Although CSF1Ri and CD40 treatments did not closely match any immunological signatures in the immunological database of MSigDb, combined CSF1Ri+CD40 had a strikingly similar signature to myeloid cells exposed to a variety of inflammatory stimulants, most closely reflected by BMDMs treated with lipopolysaccharide (LPS). This motivated us to look specifically at categories of NF-κB target genes that are significantly affected by LPS treatment, including transcription factors, cytokines and chemokines. Indeed, most of these NF-κB target genes associated with inflammation were strongly upregulated by CSF1Ri+CD40 treatment. Finally, Ingenuity Pathway Analysis identified TNFR1 and TNFR2 signaling and Acute phase response signaling among the top genetic signatures produced by the CSF1Ri+CD40 treatment combination, matching what we observed with GSEA. Thus, gene expression analysis not only revealed several biomarkers of response that may be relevant for assessing therapeutic activity in ongoing clinical trials using these drugs, but illuminated lead biological factors that may cause tumor regression.
Conclusions: myeloid-targeted immunotherapies anti-CD40+CSF1R inhibition synergistically induce a pro-inflammatory microenviroment

overall_design: mRNA profiles of tumor associated macrophages (TAMs) mice were generated by deep sequencing, in triplicate, using Illumina.

first: Curtis

last: Perry

first: Andrés

last: Muñoz-Rojas


title: Exploring Six2 distal enhancer interactome in developing mouse kidney

status: Public on Jan 18 2018

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: The Six2 distal enhancer regulates expression of the 60 kb-downstream gene Six2, but does not regulate the Six3 gene which is 70 kb further downstream. CTCF ChIP-Seq and Hi-C data points to a chromatin domain boundary between Six2 and Six3 which may intervene interaction between Six2-DE and Six3. The irradiation-induced Brachyrrhine (Br) mutant allele was found to carry a 320 kb genomic inversion that includes Six2 and Six3, but not Six2DE. This repositioned Six2 under Six3 enhancer control and Six3 under Six2 distal enhancer control. Consistent with this, Six3 is ectopically expressed in Br/+ kidneys and Six2 expression is reduced. To test whether there is a change of interaction between Six2 distal enhancer and Six2 or Six3 promoters, we performed 4C-Seq in E16.5 wildtyp or Br/+ mice nephron-genic zone cells.

overall_design: The nephron genic zone cells from E16.5 wildtype or Br/+ kidneys were dissociated following Brown et al., 2015 and subject to 4C-Seq using Dpn II and NlaIII as primary and secondary digest enzyme, with Six2DE as view point.

first: Qiuyu

last: Guo

first: Ben

last: Fogelgren

first: Ramya

last: Raviram

first: Bing

last: Ren


title: Single cell RNA-seq analysis of freshly isolated synovial fibroblasts in patients with rheumatoid arthritis or osteoarthritis

status: Public on Jan 19 2018

city: Charlestown

first: Kamil

last: Slowikowski

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

summary: Transcriptomics of distinct subpopulations of synovial fibroblasts from osteoarthritis and rheumatoid arthritis arthroplasty tissues.

overall_design:
We gated synovial fibroblasts by protein surface markers and used RNA-seq to profile gene expression in 96 cells from each patient. This data includes 384 cells from 2 osteoarthritis patients and 2 rheumatoid arthitis patients.

*** Raw data are not available for this Series due to patient privacy concerns. The raw data will not be available through controlled-access resources such as dbGaP. The patients did not consent to genomic data sharing. ***

first: Fumitaka

last: Mizoguchi


title: The translation termination factor GSPT1 is a phenotypically relevant off-target of heterobifunctional phthalimide degraders

status: Public on Jan 20 2018

city: Wien

first: Georg

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

summary: Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase cereblon (CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. While both series failed to induce degradation of their consensus targets, individual molecules displayed pronounced efficacy in leukemia cell lines. Orthogonal target identification supported by molecular docking led us to identify the translation termination factor G1 to S phase transition 1 (GSPT1) as a converging off-target resulting from inadvertent E3 ligase modulation. This research highlights the importance of monitoring degradation events that are independent of the respective targeting ligand as a unique feature of small-molecule degraders.

overall_design: RNA-seq of MOLT4 cells treated with sunitinib and the phthalimide conjugate MI-389

first: James

last: Bradner


title: Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells

status: Public on Jan 17 2018

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

first: Stephen

last: Clark

first: Ricard

last: Argelaguet

first: Chantriolnt-Andreas

last: Kapourani

first: Thomas

last: Stubbs

first: Heather

last: Lee

first: Celia

last: Alda-Catalinas

first: Guido

last: Sanguinetti

first: Gavin

last: Kelsey

first: John

last: Marioni

first: Oliver

last: Stegle

first: Wolf

last: Reik


title: Mutant p53 controls tumor metabolism and metastasis by regulating PGC-1α

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Mutant forms of p53 protein often possess pro-tumorigenic function, conferring increased survival and migration to tumor cells via its “gain of function” activity.  Whether and how a common polymorphism in TP53 at amino acid 72 (Pro72Arg, hereafter P72 and R72) impacts this gain of function has not been determined.  We show that mutant p53 enhances migration and metastasis of tumors through the ability to bind and regulate PGC-1α, and that this regulation is markedly impacted by the codon 72 polymorphism.  Tumor cells with the R72 variant of mutant p53 show increased PGC-1α function, along with greatly increased mitochondrial function and metastatic capability.  Breast cancers containing mutant p53 and the R72 variant show poorer prognosis compared to P72.  The combined results reveal PGC-1α as a novel “gain of function” partner of mutant p53, and indicate that the codon 72 polymorphism influences the impact of mutant p53 on metabolism and metastasis.

overall_design: RNA-seq analysis of R175H and R273H mutant, P72- and R72-polymorphism H1299 cells

first: Maureen

last: Murphy

first: Subhasree

last: Basu


title: Microarray analysis of freshly isolated synovial fibroblast subsets in patients with rheumatoid arthritis or osteoarthritis

first: Kamil

last: Slowikowski

overall_design: We gated 7 subsets of synovial fibroblasts by protein surface markers and used microarrays to profile gene expression of cells taken from each gate. This data includes 37 samples from 3 osteoarthritis donors and 3 rheumatoid arthritis donors.

first: Fumitaka

last: Mizoguchi


title: Mapping open chromatin in mouse nephron progenitor cells

first: Andrew

last: McMahon

summary: To delineate the epigenomic profile of the Six2+ mouse nephron progenitor cells, we mapped open chromatin using ATAC-Seq in Six2+ cells from E16.5 mouse kidneys.

overall_design: Using Six2TGC/+ transgenic mice, we isolated Six2+ cells by FACS enriching for GFP+ cells from dissociated kidney cortex, then use 50,000 cells for each ATAC-Seq reaction following Buenrostro et al, 2013.

first: Qiuyu

last: Guo


title: H3K27me3 ChIP-Seq in LCLs cells with conditionally activated EBNA3C

city: Madsion

first: Duy

last: Nguyen

state: WI

address: 1300 University Ave

department: Statistics

institute: University of Wisconsin, Madison

summary: Epstein-Barr virus (EBV) is a herpesvirus that establishes lifelong asymptomatic infection in up to 95% of the human population. In vitro EBV infection of resting B lymphocytes drives them to proliferate as lymphoblastoid cell lines (LCLs). EBV expresses limited genes, which include six nuclear proteins (EBNAs), three integral membrane proteins (LMPs), and more than 30 micro RNAs in LCLs. EBNA3C, one of the six nuclear proteins, is transcription factor and regulates host cell genes. The growth effects of EBNA3C appear to be primarily due to suppression of the CDKN2A gene products, p16INK4A and p14ARF. Conditional inactivation of EBNA3C results in increasing p16 expression and this is accompanied by the substantial reduction of the repressive H3K27me3 modification at the CDKN2A promoter and cell cycle arrest. To further elucidate the relationship between EBNA3C and H3K27me3 modification, we profiled H3K27me3 by ChIP-seq in CDKN2A knockout EBNA3CHT LCLs in the presence (4HT+) or absence (4HT-) of 4-hydroxytamoxifen, with a total of 4 biological replicates per condition.

overall_design: We profiled H3K27me3 by ChIP-seq in CDKN2A knockout EBNA3CHT LCLs in the presence (4HT+) or absence (4HT-) of 4-hydroxytamoxifen, with a total of 4 biological replicates per condition.

first: Makoto

last: Ohashi

first: Anqi

last: Wang

first: Eric

last: Johannsen


title: Transcriptome analysis of iPSC-derived keratinocytes with or without a disease-associated TP63 mutation

status: Public on Jan 16 2018

city: Aurora

first: Maranke

last: Koster

address: 12800 E19th Avenue

department: Dermatology

institute: University of Colorado-Anschutz Medical Campus

summary: Induced pluripotent stem cells (iPSC) were generated from two patients affected by ankyloblepharon ectodermal dysplasia and clefting (AEC), an ectodermal dysplasia caused by mutations in TP63. The two TP63mutations(I537T and R598L) were corrected using Crispr/Cas9- mediated homologous recombination. The resulting conisogenic iPSC pairs were differentiated into keratinocytes and subjected to RNA-sequencing.

overall_design: 2 conisogenic pairs of AEC and gene-corrected iPSC-derived keratinocytes were analyzed (4 samples total)

middle: I

first: Peter

last: Koch


title: Calorie restriction governs intestinal epithelial regeneration through cell autonomous regulation of mTORC1 in reserve stem cells

status: Public on Jan 15 2018

city: Phiadelphia

first: Corbett

last: Berry

address: 3800 Spruce St

institute: University of Pennsylvania

summary: Here, we show that CR enhances regenerative capacity of the intestinal epithelium as a result of increased number of reserve ISCs. We observe that precise regulation of mechanistic target of Rapamycin complex 1 (mTORC1) signaling plays a significant role in regulation of sensitivity of reserve intestinal stem cells to injury and that premature activation of mTORC1 signaling through nutrient modulation, at the time of damage, leads to poor regeneration outcome. These data delineate a critical role for mTORC1 signaling in epithelial regeneration and inform clinical strategies based on nutrient modulation of mTORC1 activity.

overall_design: mRNA-Sequencing of FACS sorted murine intestinal reserve stem cells (Hopx-CreER) or active stem cells (Lgr5-eGFP-CreER) isolated from mice fed ad libitium or under calorie restriction. Cells were isolated in 5 batches from 10 different animals.

first: Maryam

last: Yousefi

first: Christopher

last: Lengner


title: Integrated approach reveals diet, APOE genotype and sex affect immune response in APP mice

status: Public on Jan 13 2018

city: Pittsburgh

first: Iliya

last: Lefterov

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

summary: Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder that is influenced by genetic and environmental risk factors, such as inheritance of ε4 allele of APOE (APOE4), sex and diet. Here, we examined the effect of high fat diet (HFD) on amyloid pathology and expression profile in brains of AD model mice expressing human APOE isoforms (APP/E3 and APP/E4 mice). APP/E3 and APP/E4 mice were fed HFD or Normal diet for 3 months. We found that HFD significantly increased amyloid plaques in male and female APP/E4, but not in APP/E3 mice. To identify differentially expressed genes and gene-networks correlated to diet, APOE isoform and sex, we performed RNA sequencing and applied Weighted Gene Co-expression Network Analysis. We determined that the immune response network with major hubs Tyrobp/DAP12, Csf1r, Tlr2, C1qc and Laptm5 correlated significantly and positively to the phenotype of female APP/E4-HFD mice. Correspondingly, we found that in female APP/E4-HFD mice, microglia coverage around plaques, particularly of larger size, was significantly reduced. This suggests altered containment of the plaque growth and sex-dependent vulnerability in response to diet. The results of our study show concurrent impact of diet, APOE isoform and sex on the brain transcriptome and AD-like phenotype.

overall_design: HFD increases amyloid load in male and female APP/E4 but not in APP/E3 mice. Immune response network with a hub gene Tyrobp correlates to female APP/E4-HFD mice. HFD affects genes involved in transcription and cell migration in male APP/E4 mice. Microglia barrier around amyloid plaques is reduced in female APP/E4 mice fed HFD.

first: Kyong

middle: N

last: Nam

first: Cody

last: Wolfe

first: Nicholas

middle: F

last: Fitz

first: Florent

last: Letronne

first: Emilie

last: Castranio

first: Anais

last: Mounier

first: Jonathan

last: Schug

first: Radosveta

last: Koldamova


title: PRKCI regulates tumor microenvironment through YAP1 [Affymetrix]

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: A key feature of serous ovarian cancer is frequent amplification in the 3q26 locus, which harbors the PRKCI gene. Here we show that PRKCI is amplified and overexpressed in a 78% of high-grade serous ovarian carcinoma. Our in vivo studies with orthotopic mouse models establish it as an ovarian cancer oncogene. This oncogenic property of PRKCI is mediated by regulation of YAP1 activity. Accordingly YAP1 knockdown partially rescues PRKCI mediated tumorigenesis. Integrated gene expression profiling and YAP1 promoter occupancy analyses reveal that PRKCI and YAP1 cooperate to transcriptionally regulate genes affecting the tumor immune microenvironment. Consistently, CD11b+Gr1+Ly6G+ MDSCs are increased in the tumor microenvironment of PRKCI over-expressing tumors. Importantly, we show that elevated PRKCI expression in high-grade serous ovarian carcinomas strongly correlated with assignment to immunoreactive subtype.  In summary, we identify PRKCI and YAP1 as key mediators of a tumor-promoting immunosuppressive microenvironment in ovarian cancers.

overall_design: Affymetrix U133 Plus 2.0 microarrays were performed for each condition (WT, YAP1sh2, YAP1sh1, PRKCI sh2 and PRKCI sh3) in triplicates. Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package

first: Sharmistha

last: Sarkar

first: Lynda

last: Chin


title: Next Generation Sequencing Facilitates Quantitative Analysis of the Effect of GM-CSF on the Transcriptomes of Alveolar and Exudative Lung Macrophages from Influenza-infected C57BL/6 Mice

status: Public on Jan 12 2018

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: The transcriptomes of FACS-sorted siglec-F+ alveolar macrophages and siglec-f- CD11b+ exudative macrophages from inducible airway GM-CSF over-expressing transgenic mice (DTGM) were compared to non-inducible littermate controls during influenza A virus infection.

overall_design: Examination of effect of GM-CSF on airway macrophages during influenza A virus infection

first: E

last: Halstead

first: Todd

last: Umstead

first: Michael

last: Davies

first: Patricia

last: Silveyra

first: Judie

last: Howyrlak

first: Linlin

last: Yang

first: Weichao

last: Guo

first: Sanmei

last: Hu

first: Eranda

last: Kurundu Hewage

first: Zissis

last: Chroneos


title: Transcriptome profiling of de-differentiated chondrocytes over-expressing miR-138 or miR-181ab1 during osteogenic induction

city: St Louis

first: Audrey

last: McAlinden

state: MO

address: 660 South Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University

summary: The goal of this study was to investigate the effects of miR-138 or miR-181ab1 on regulating osteogenesis. Gene expression profiles were analyzed in human de-differentiated chondrocytes (DDCs) over-expressing either miR-138 or miR-181ab1 following day 2 or day 7 of osteogenic induction. DDCs were isolated from human osteoarthritic articular cartilage and over-expression of miR-138 or miR-181ab1 was induced following lentiviral transduction of DDCs over-expressing the precursor form of miR-138 or miR-181ab1. Control DDCs were transduced with lentivirus expressing a non-silencing (NS) control RNA. Total RNA was harvested at day 2 or day 7 following osteogenic induction and subjected to RNA-Seq analysis.

overall_design: Triplicate samples of de-differentiated chondrocytes at P3-4 were transduced with lentivirus expressing either precuror miR-138, precursor miR-181ab1 or lentivirus expressing a non-silencing (NS) control precursor RNA. Transuced cells were then induced to undergo ostegenic differentiation. At days 2 and 7 following osteogenic induction, total RNA was isolated and processed for high throughput RNA sequencing.

first: A

first: H

last: Zheng


title: RNAseq analyze global transcriptome of changes between siIRF3 and siYAP in Gastric cancer cells

status: Public on Jan 10 2018

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

country: China

institute: Shanghai Institutes of Biological Sciences

summary:
Purpose: To investigate the signal crosstalk between IRF3 and YAP, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of IRF3 or YAP in HGC-27 cells.
Methods: Total RNA was extracted from HGC-27 cell after transfection with negative control siRNA (n.c.), IRF3 siRNA (siIRF3) or YAP siRNA (siYAP). Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina  HiSeq 2500 platform.
Results: Approximately approximately one thousand transcripts showed differential expression between the siIRF3/siYAP and n.c., with a Fold-change>=2 and q-value <= 0.05. Gene ontology (GO) and gene set enrichment analysis (GSEA) showed a significant negative enrichment of YAP target genes identified by three independent studies in IRF3-knockdown condition.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding the signal crosstalk between IRF3 and YAP.

overall_design: RNA was extracted from HGC-27 cells transfected with siRNAs for 48 h. The quality assessed on the Agilent 2100 and sequencing on the Illumina Hiseq2500.

first: Jingmin

last: Guan

first: Zhaocai

last: Zhou


title: DNA methylation in hESC derived brain organoids and iPSC derived neurons, astrocytes and neural progenitors

city: New York City

first: Sylvie

last: Janssens

state: NY

address: 1452 Madison Avenue

department: Department for Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

summary: We studied the impact of ZIKA virus infection on DNA methylation in whole organoids, organoid derived astrocytes, neurons neural progeniotors and  hESC or iPSC derived astrocytes, neurons, neural progenotor cells

overall_design: Examination of differences in DNA methylation upon ZIKV infection in whole organoid samples or specific cell types

last: Schotsaert

first: Rahul

last: Karnik

first: Vinod

last: Balasubramaniam

first: Marion

last: Dejosez

first: Alexander

last: Meissner

first: Adolfo

last: García-Sastre

first: Thomas

last: Zwaka


title: Expression data for hiPSC-derived RPE treated with 10mM Nicotinamide or vehicle

city: Rensselaer

last: Kiehl

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

summary:
Nicotinamide (NAM) inhibited the expression of Age related macular degeneration (AMD) associated proteins in hiPSC-derived retinal pigment epithelium (RPE).
We did the microarray analysis to examine the global impact of NAM on hiPSC-derived RPE transcriptome in order to better understand the mechanism of action of NAM.

overall_design: Three hiPSC-RPE lines that had been cultured with 10mM NAM or vehicle for three weeks were used for RNA extraction and hybridization on affymetrix microarrays. We treated 2 AMD hiPSC-RPE and 1 Control hiPSC-RPE line with 10mM NAM or vehicle.

first: Janmeet

last: Saini

first: Sally

last: Temple