title: Time-course inducible NOTCH3-IC expression in SH-SY5Y.

city: Amsterdam

first: Richard

last: Volckmann

address: van der Boechorststraat 6a

institute: msterdam UMC and University of Amsterdam

summary: Expression analysis of ADRN cell line SH-SY5Y with doxycycline-inducible NOTCH3-IC was used to study transcriptional reprogramming to a MES state.

overall_design: Cells were induced with doxycycline for a time-course of 1-7-14-21 days to analyze mRNA.

first: Johan

last: van Nes


title: Whole transcriptome analysis of cadmium sulphide quantum dots response in Saccharomyces cerevisiae

status: Public on Apr 03 2019

city: Parma

first: Luca

last: Pagano

address: Parco Area delle Scienze 11/A

department: Chemistry Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: Cadmium sulphide quantum dots (CdS QDs) are widely used in novel equipment. The relevance of the research lies in the need to develop risk assessments for nanomaterials (ENMs), using baker's yeast as model system. A whole-genome microarray experiment, performed on Saccharomyces cerevisiae (BY4742), showed how genes were regulated in response to CdS QDs.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: A whole-genome microarray experiment, performed on wt strain BY4742, showed how genes were regulated in response to CdS QDs. Wt was treated with different sub-lethal concentrations of nystatin (to increase permeability of cell wall) and CdS QDs.

first: Francesco

last: Pasquali

first: Marta

last: Marmiroli

first: Nelson


title: Wnt1 silences CC/CXC motif chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma

city: Vari

first: Maria

last: Tsoumakidou

state: Attica

address: 34 Fleming Street

country: Greece

institute: B.S.R.C. "Alexander Fleming"

type: Expression profiling by high throughput sequencing

summary: This study showed that the oncogenic ligand Wnt1 silences chemokine genes in dendritic cells, leading to impaired cross-priming of T cells in lung adenocarcinoma. Blocking Wnt1 enhanced rejection of tumors by acting concomitantly at the cancer and immune cell level.

overall_design: 3’ RNA-Seq (QuantSeq) profiling of sorted cDCs populations from WNT1 overexpressing and control (Empty) lung tumors.

first: Dimitra

last: Kerdidani

first: Panagiotis

last: Chouvardas

first: Ares

middle: R

last: Arjo

first: Giopanou

last: Ioanna

first: Ntaliarda

last: Gianna

first: Yu

middle: G

last: Amanda

first: Mary

last: Tsikitis

first: George

last: Kazamias

first: Konstantinos

last: Potaris

first: Stathopoulos

last: George

first: Spyros

last: Zakynthinos

first: Ioannis

last: Kalomenidis

first: Vassili

last: Soumelis

last: Kollias


title: TWIST1 regulated human melanoma transcriptome

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

country: USA

institute: Thomas Jefferson University

summary:
TWIST1 is known to play a role in the metastatic progression of melanoma.  However, the range of TWIST1 targets is poorly charachterized.
Here microarray analysis was used to define the TWIST1 regulated transcriptome in the human melanoma cell line WM793.

overall_design: WM793TR cells expressing a control shRNA, TWIST1 shRNA, or TWIST1 shRNA + TWIST1 rescue construct were treated with doxycycline to induce expression for 96 hours then cells were harvested, RNA isolated and analyzed.

first: Edward

middle: J

last: Hartsough

first: Timothy

last: Purwin


title: Vitamin D globally accelerates growth and regeneration in zebrafish

city: Durham

first: Yanchao

last: Han

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University Medical Center

summary: Animals possess control mechanisms to synchronize organ and organismal size during growth, to maintain tissue integrity through homeostatic cell proliferation, and to counter major injury with regeneration.  A principal research goal is to elucidate mitogenic triggers that underlie these mechanisms.  Here, from a large-scale in vivo chemical screen, we discovered that analogues of the essential nutrient vitamin D potently activate heart muscle cell division in larval zebrafish.  Unexpectedly, loss- and gain-of-function methods to modulate vitamin D signaling altered metabolic and cell cycle gene expression in zebrafish larvae and dictated rates of organismal growth.  Systemic vitamin D treatment sharply increased in vivo cell proliferation in a variety of adult cell types including cardiomyocytes, hepatocytes, osteoblasts, cardiac mesothelium, skin and corneal epithelium, and retina, and enhanced injury-induced heart and appendage regeneration. Our experiments identify vitamin D signaling as a broad growth- and regeneration-initiating influence throughout the life stages of a vertebrate model system.

overall_design: Adult zebrafish were injected with vehicle or alfacalcidol daily for three days. Hearts were extracted 24 hours after the last injection. Total RNA were harvested using TRIzol reagent, digested with DNaseI, and purified with Zymo Quick-RNA MiniPrep kit. Libraries were prepared and sequenced using an Illumina HiSeq2000 at the Duke Center for Genomic and Computational Biology.

first: Kenneth

last: Poss


title: IL-23 producing IL-10Rα-deficient gut macrophages elicit an IL-22-driven pro-inflammatory epithelial cell response

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

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

overall_design: Refer to individual Series


title: Gene expression in pulmonary non-tuberculous mycobacterial infection

status: Public on Apr 04 2019

city: London

first: Steven

last: Cowman

address: Dovehouse Lane

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: The factors predisposing towards the development of pulmonary non-tuberculous mycobacterial disease (pNTM) and influencing disease progression remain unclear. Impaired immune responses have been reported in individuals with pNTM but data are limited and inconsistent. This study aimed to use gene expression profiling to examine the host response to pNTM.    Microarray analysis of whole blood gene expression was performed on 25 subjects with pNTM and 27 uninfected controls with respiratory disease. Gene expression results were compared to phenotypic variables and survival data.    Compared with uninfected controls, pNTM was associated with down-regulation of 213 transcripts enriched for terms related to T cell signalling including IFNG. Reduced IFNG expression was associated with more severe CT changes and impaired lung function. Mortality was associated with  the expression of transcripts related to the innate immune response and inflammation, whereas transcripts related to T and B cell function were associated with improved survival.    These findings suggest that pNTM is associated with an aberrant immune response which may reflect an underlying propensity to infection, or result from NTM infection itself. There were important differences in the immune response associated with survival and mortality in pNTM.

overall_design: Gene expression was performed on a total 89 samples taken from 69 subjects recruited as part of a larger study. The current analysis was performed on a subset of 52 subjects (25 pNTM cases and 27 controls) indicated in the metadata. However as background correction, normalisation and summarisation was performed using all 89 samples, data on the additional samples is provided to allow for reproducibility.    FEV1 = forced expiratory volume in 1 second, percent predicted; FVC = forced vital capacity, percent predicted; TLC = total lung capacity, percent predicted; TLCO = transfer factor for carbon monoxide, percent predicted; KCO = transfer factor for carbon monoxide, corrected for alveolar volume, percent predicted; CTscore = composite NTM CT score; CT_extent = CT score for bronchiectasis extent; CT_severity = CT score for bronchiectasis severity; CT_TIB = CT score for tree-in-bud opacification; CT_nodules = CT score for nodules; CT_nod_cav = CT score for cavitating nodules; CT_severe_cav = CT score for severe cavitation; CT_aspergilloma = CT score for aspergilloma; CT_consolidation = CT score for consolidation; Albumin = serum albumin g/L; CRP = serum c-reactive protein mg/L; Neutrophils = blood neutrophil count, cells x 10E9/L; Disease_duration = duration from diagnosis to recruitment, years; Death = death during study (1 = yes, 0 = no); Survival_time = survival from study enrolment, weeks.

first: S

middle: A

first: W

middle: O

last: Cookson

first: M

middle: F

last: Moffatt

last: Loebinger


title: The microbiota regulates white adipose tissue inflammation and progression of obesity through a highly conserved family of microRNAs.

first: Jonathan

last: Kotzin

address: 421 Curie Boulevard, Biomedical Research Building II/III, Room 312

institute: UPenn

summary: The gut microbiota is a key environmental determinant of mammalian metabolism. Regulation of white adipose tissue (WAT) by the gut microbiota is a critical process that maintains metabolic fitness, while dysbiosis contributes to the development of obesity and insulin resistance (IR). However, how the gut microbiota controls WAT functions remain largely unknown. Herein, we show that tryptophan-derived metabolites produced by the microbiota control the expression of the miR-181 family in white adipocytes to regulate energy expenditure and insulin sensitivity. Moreover, we show that dysregulation of the microbiota-miR-181 axis is required for the development of obesity, IR, and WAT inflammation. Thus, our results indicate that regulation of miRNA levels in WAT by microbiota-derived cues is a central mechanism by which host metabolism is tuned in response to dietary and environmental changes. As MIR-181 is dysregulated in WAT from obese human individuals, the MIR-181 family may represent a potential therapeutic target to modulate WAT function in the context of obesity.

overall_design: Epididymal white adipose tissue (eWAT) mRNA profiles of wild type (WT) and miR-181-double knockout mice following 12 weeks on high fat diet.

first: Anthony

middle: T

last: Virtue

first: Sam

last: McCright

first: Jorge

last: Henao-Mejia


title: Effects of CADM1 expression in human melanoma

summary:
CADM1 expression in non-adherent conditions was found to potently induce caspase-independent cell death.
We sought to use microarray analysis to glean insights to the mechanism associated with CADM1 induced non-adherent cell death.

overall_design: WM793TR LacZ or CADM1 cells were seeded in 10cm dishes with or without bacto-agar coating.  Transgene was then induced for 24 hours then cells were harvested, RNA isolated and analyzed.


title: Field application of a new low density stress response microarray STREM

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary:
Development of a new low density stress response microarray to evaluate biological effects of contaminants in Mytilus sp: laboratory validation.
In this work, we investigated the health status of mussels caged in three sites of the Sardinian coastlines characterized by different levels of contamination (Fornelli “F” considered as reference site, Cala-Real “CR” and PortoTores “PT”). A new low density oligonucleotide microarray platform was used to investigate the gene expression regulation in the studied sites. The new platform consists of 465 probes covering the same number of genes. Target genes were selected to cover most of the well-known biological processes in the stress response documented over the last decade in bivalve species at the cellular and tissue levels. Moreover, a battery of well-established biomarkers (comprising biomarkers of stress, genotoxicity and exposure) was employed.  Chemical analysis revealed relatively higher loads of heavy metals (Pb and Cu) as well as total polyaromatic hydrocarbons in “PT”. In animals caged in site “CR”, functional genomics analysis of the microarray data rendered 78 DEGs involved in 11 biological processes. Animals exposed in PT showed 105 DEGs that were characterized by the regulation of 14 biological process among them Mitochondrial activity, adhesion to substrate, DNA metabolism, Translation, metal resistance and Cytoskeleton. Biomarker data termed as lysosomal membrane stability, Lysosomal/cytoplasm ratio, lipofuscine accumulation and metallothionein protein content were in trend with transcriptomic output. Moreover immunhistochemical analysis on digestive gland sections revealed higher tubulin accumulation in mussels from PT confirming the gene expression pattern of the gene. Our data should be carefully considered in view of the use of the new platform in monitoring programs .

platform_organism:
Mytilus californianus
Mytilus edulis
Mytilus galloprovincialis
Magallana gigas

overall_design: Digestive gland tissue from individual animals in different experimental conditions were analyzed in a complete  design. Dual color competitive hybridizations (Fornelli vs CR/Fornelli Vs PT) including label swap. polls of 2 animals . Four biological replicates. three replicates per array.

first: Caterina

last: MILLINO

first: Beniamina

last: PACCHIONI

first: Mohamed

last: BANNI

last: OLIVERI

first: Aldo

last: VIARENGO


title: Connective Tissue Growth Factor Inhibition Enhances Cardiac Repair and Limits Fibrosis After Myocardial Infarction

status: Public on Apr 02 2019

city: San Francisco

first: Todd

last: Seeley

state: CA

address: 409 Illinois St

department: Molecular Biology

institute: FibroGen, Inc.

summary:
Background. Accumulation of extracellular matrix in the myocardium attenuates cardiac contractile function, and predisposes to arrhythmias and sudden cardiac death. Connective tissue growth factor (CTGF) is a matricellular protein that has been shown to promote development of cardiac fibrosis.
Objectives. To investigate for the potential of CTGF monoclonal antibody (CTGF mAb) in protecting from development of cardiac fibrosis following myocardial infarction (MI), and to evaluate its effect during infarct repair and acute cardiac ischemia-reperfusion (I/R) injury.
Methods. Mice were subjected to MI or to I/R injury and treated with either control IgG or CTGF mAb. Cultured human cardiac fibroblasts were used to investigate the signalling mechanisms modulated by CTGF mAb.
Results. Treatment with CTGF mAb for four days from day three after MI improved survival, attenuated infarct expansion, and resulted in better preserved left ventricular (LV) systolic function. CTGF mAb therapy for six weeks from day seven after MI reduced the MI-induced increase in cardiomyocyte size, heart weight to body weight ratio and remote LV fibrosis. RNA sequencing analysis of LV samples showed that CTGF mAb induced expression of cardiac repair/developmental genes and normalized the MI-induced increase in expression of inflammatory/profibrotic genes. CTGF mAb induced c-Jun N-terminal kinase (JNK) phosphorylation in vivo and in vitro, and inhibition of JNK abrogated the reduced collagen production in CTGF mAb treated fibroblasts.
Conclusions. Treatment with CTGF mAb induces expression of cardiac repair/developmental genes and inhibits expression of inflammatory/pro-fibrotic genes in MI hearts providing benefit during post-MI cardiac repair and reducing post-MI cardiac fibrosis.

overall_design: Comparison of gene expression between Sham (n=3), MI;IgG(n=5) or MI+FG-3149 (n=5) treated animals

first: Shaun

middle: D

last: Fouse

middle: W

last: Lipson

first: Risto

last: Kerkela


title: Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding

city: Haifa

first: Oz

last: Solomon

address: Technion

institute: Technion

summary: The construction of complex gene regulatory networks requires both inhibitory and up-regulatory modules. However, the vast majority of RNA-based regulatory “parts” are inhibitory. Using a synthetic biology approach combined with SHAPE-Seq, we explored the regulatory effect of RBP-RNA interactions in bacterial 5’-UTRs. By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational stimulation, translational repression, and cooperative behavior. Our combined approach revealed three distinct states in-vivo: in the absence of RBPs, the RNA molecules can be found either in a molten state that is amenable to translation, or a structured phase that inhibits translation. In the presence of RBPs, the RNA molecules are in a semi-structured phase with partial translational capacity. Our work provides new insight into RBP-based regulation and a blueprint for designing complete gene regulatory circuits at the post-transcriptional level.

sample_organism:
Escherichia coli
Pseudomonas phage PP7

platform_organism:
Escherichia coli
Pseudomonas phage PP7

overall_design: Constructs containing a single hairpin, based on the binding sites of the coat RBPs of bacteriophages PP7  where tested using in-vivo (in-cell) and in-vitro SHAPE-seq experiment  in duplicactes (2 replicates for in-vivo and in-vitro for each PP7-wt and PP7-USs modified or non-modified by the SHAPE reagent (NAI)= 16 samples, total)

first: Noa

last: Katz

first: Roni

last: Cohen

first: Beate

last: Kaufmann

first: Orna

last: Atar

first: Zohar

last: Yakhini

first: Sarah

last: Goldberg

first: Roee

last: Amit


title: Gene expression profiles of maresin 1-treated Kupffer cells

city: Seoul

first: Yong-Hyun

last: Han

state: Seoul

address: Daehak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: To reveal the transcriptomes associated with Maresin 1-treated Kupffer cells, the primary Kupffer cells isolated from mouse liver were treated with maresin 1 and the gene expression patterns were analyzed by microarray.

overall_design: Gene expression profiles were obtained from Vehicle (Veh) or Maresin 1 (MaR1)-treated, and compared.

first: Mi-Ock

last: Lee


title: GEF-H1-IRF5 mediated gene expression changes in BMDM by MDP recognition

city: Dallas

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

department: Medicine

institute: University of Texas Southwestern Medical Center

summary: The transcription factor IRF5 is essential for immune defense against pathogens. Here, the authors show that the microtubule-associated factor GEF-H1 plays a critical role in host defense against Listeria monocytogenes in macrophages via activation of the IRF5 kinase IKKe

overall_design: Examination of MDP stimulated BMDM from WT, Arhgef2 and Irf5 KO mice


title: Optimizing genome editing strategy by primer-extension-mediated sequencing

city: Beijing

first: Mengzhu

last: Liu

address: Yiheyuan Road No.5

country: China

institute: Peking University

summary: High specificity of e\ngineered nucleases ensures precise genome editing. Couple methods were developed to identify off-target sites of CRISPR/Cas9, but hardly any high-throughput sequencing method can unequivocally determine their targeting efficiencies. Here we describe a comprehensive method, primer-extension-mediated sequencing (PEM-seq), which could sensitively detect CRISPR/Cas9 off-target sites as well as assess their editing efficiency by quantifying DNA interference events at on-target sites. Demonstrated by PEM-seq, we generated a high-fidelity Cas9 variant FeCas9 that possesses similar targeting ability as the wild-type while with extremely low off-target activities. Moreover, we provided further evidences for the broader range of xCas9 protospacer adjacent sequence. We also found the AcrIIA4 inhibitor could inhibit both on- and off-target activities of SpCas9, but it suppressed SpCas9 cleavage at the off-target loci not so efficiently as at the on-target sites. Finally, we believe PEM-seq is applicable to optimizing genome editing strategy for clinical purpose or creating animal model.

overall_design: Detecting editing efficiency and off-targets of engineered nucleases. 3  biological replicates were operated for each sample and  Illumina Hiseq was used for sequencing.

first: Jianhang

last: Yin

first: Yang

first: Jiazhi

last: Hu


title: Mesenchymal niche-specific expression of Cxcl12 controls quiescence of treatment-resistant leukemia stem cells

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

summary: In this study, we show that targeted deletion of CXCL12 from mesenchymal stromal cells (MSC) reduces normal HSC numbers, but in contrast expands murine LSC numbers by increasing self-renewing cell divisions, related to enhanced EZH2 activity. CML development leads to emergence of abnormal niches of MSC and LSC clusters that are lost upon CXCL12 deletion. Importantly, CXCL12 deletion from MSC also increases LSC elimination by TKI treatment. These studies reveal a critical role for CXCL12-expressing MSC niches in maintaining a population of quiescent, TKI-resistant LSC, and support targeting of these niche interactions to enhance LSC elimination.

overall_design: LTHSC were sorted from the bone marrow of Cre-negative (No Cre), Tek-Cre, and Prx1-Cre mice directly into RLT buffer and RNA prepared, with four biological replicates from each group.

first: Puneet

last: Agarwal


title: Adaptive plasticity of IL10 + and IL35 + regulatory T cells

city: Pittsburgh

first: Maria

last: Chikina

address: 3501 5th ave

institute: University of Pittsburgh

summary: Regulatory T cells (T regs) maintain host self-tolerance but are a major barrier to effective cancer immunotherapy. T regs subvert beneficial anti-tumor immunity by modulating inhibitory receptor (IR) expression on tumor infiltrating lymphocytes (TILs); however, the underlying mediators and mechanisms remain elusive. Here we show that interleukin-10 (IL10) and interleukin-35 (IL35; Ebi3/IL12α heterodimer) are divergently expressed by T reg subpopulations in the tumor microenvironment (TME) and cooperatively promote intratumoral T cell exhaustion. T reg -restricted deletion of Il10 and/or Ebi3 resulted in delayed tumor growth, loss of multi-IR expression, and reduced intratumoral CD8 + T cell exhaustion signature. While Il10 or Ebi3 loss was associated with reduced expression of B lymphocyte-induced maturation protein-1 (BLIMP1; Prdm1), IL10 and IL35 differentially impacted effector versus memory T cell fates, respectively, highlighting their differential, partially overlapping but non-redundant regulation of anti-tumor immunity. Our results reveal previously unappreciated cooperative roles for IL10 and IL35, produced by limits effective anti-tumor immunity

overall_design: TIL CD8 cells from Treg specific IL10, IL35 and double knockouts, sorted into populations based on exhaustion markers. TIL Tregs sorted based on IL10 and IL35 expression.


title: Generation and persistence of human tissue-resident memory T cells in lung transplantation

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Tissue resident memory T cells (TRM) maintain immunity in diverse sites as determined in mouse models, while their establishment and role in human tissues has been difficult to assess.  Here, we investigated human lung TRM generation, maintenance and function in airway samples obtained longitudinally from HLA-disparate lung transplant recipients, where donor and recipient T cells could be localized and tracked over time. Donor T cells persist specifically in the lungs (and not blood) of transplant recipients and express high levels of TRM signature markers including CD69, CD103, and CD49a, while lung-infiltrating recipient T cells gradually acquire TRM phenotypes over months in vivo. Single cell transcriptome profiling of airway T cells reveals that donor T cells comprise two TRM-like subsets with varying levels of expression of TRM-associated genes while recipient T cells comprised non-TRM and similar TRM-like subpopulations, suggesting de novo TRM generation. Transplant recipients exhibiting higher frequencies of persisting donor TRM experienced fewer adverse clinical events such as primary graft dysfunction and acute cellular rejection compared to recipients with low donor TRM persistence, suggesting that monitoring TRM dynamics could be clinically informative. Together, our results provide novel spatial and temporal insights into how human TRM develop, function, persist, and impact tissue integrity within the complexities of lung transplantation.

overall_design: Pooled Single-cell RNA-seq of FAC-sorted T cells in 96-well plates

first: Mark

last: Snyder

first: Erin

middle: C

last: Bush

first: Michael

last: Finlayson

first: Donna

middle: L

last: Farber


title: Dysfunction and stemness of tumor-infiltrating T cells are triggered by a common mechanism

city: Bethesda

first: Suman Kumar

last: Vodnala

state: MD

address: 10 Center Drive

department: Surgery Branch

institute: NCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The paradox of tumor immunology is that tumor infiltrating lymphocytes (TILs) are dysfunctional in situ and yet are capable of stem cell-like behavior with self-renewal, massive expansion, multipotency, and eradication of large metastatic tumors. Here we report that the overabundance of potassium in the tumor microenvironment (TME) can explain both phenomena.

overall_design: Ctrl (or Samples labelled V- Vehicle) and elevated potassium (or Samples labelled K) were used to perfrom ChiP assays. CD8+ T cells from pmel mice were stimulated in vitro with 1 μM human gp100 peptide (10 μg/ml) in Ctrl (V) or elevated potassium (K) for 5 days and secondary re-stimulation was done for 48hrs with plate-bound anti-CD3 (1 μg/ml; BD Biosciences) and soluble anti-CD28 (1 μg/ml; BD Biosciences) and expanded in culture medium (Ctrl /K) containing 60 IU/mL of IL-2 for a total of 10 days.

first: Suman

middle: K


title: Loss of hydroxymethylcytosine is an independent adverse prognostic factor in clear cell Renal Cell Carcinoma (ccRCC) and can be abrogated by ascorbic acid mediated TET activation

city: Bronx

first: Amit

last: Verma

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: The experiment was performed to study high resolution gene specific changes induced by Ascorbic acid tretament in clear cell RCC cells (786-0 cell line)

overall_design: 786-O ccRCC cells were treated either with control (catalase) or with catalase+ ascorbic acid. BS and OxBS were performed in both.

first: Kith

last: Pradhan

first: Tushar

last: Bhagat


title: Apoptosis-associated transcriptome changes in peripheral blood leukocytes during HHV-6 antiviral therapy

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

summary: refer to the SuperSeries

overall_design: Each microarray encompasses 4 identical probe-containing areas. Blood samples obtained from 7 HHV-6 patients during acute mononucleosis and after convalescence were included in the experiment. The present design/platform covers significantly larger number of apoptosis and survival genes (450) than the former (221). Another advantage of this new platform is the presence of several different probes targeted to a single mRNA isoform. Also, the design covers 12 Epstein-Barr virus genes.

first: Nikolay

last: Sakharnov

first: Elena

last: Filatova

first: Leonid

last: Solntsev

first: Oleg

last: Utkin


title: Transcriptional profile of Mouse liver after MitoCDNB application

city: Cambridge

first: Filip

last: Cvetko

state: Cambridgeshire

address: Cambridge Biomedical Campus Hill Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

summary: To assess the effect of MitoCDNB on transcriptional profile of mouse liver tissue we injected mice with either vehicle (0.1 % ethanol) or 5 mg/kg of MitoCDNB. Liver was taken from both vehicle or MitoCDNB injected mice after 1 or 4 hours and the transcriptome assessed using Illumina RNASeq.

overall_design: Purified mRNA profiles from the medial liver lobe after 1 or 4 hours of Vehicle or MitoCDNB injections generated using Illumina based RNASeq

middle: P

last: Murphy

first: John

last: Ferdinand


title: Identification of m6dA in genomic DNA and transcriptional patterns in human genomes by DIP-Seq and RNAseq

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

summary: We identify m6dA in human genomic DNA by DNA immunoprecipitation and subsequent Hi-Throughput Illumina sequencing (DIP-Seq). We use a dA6m specific antibody for DNA pulldown, and input as control. In addition, we performed RNA High Throughput Illumina Sequencing on biologically matched samples. This data supplements our analysis of already published data.

overall_design: We identify m6dA in human genomic DNA by DNA immunoprecipitation and subsequent High Throughput Illumina sequencing (DIP-Seq). We use a dA6m specific antibody for DNA pulldown, and input as control. In addition, we performed RNA High Throughput Illumina Sequencing on biologically matched samples.

first: Clare

last: Pacini

first: Nigel

last: Garrett

first: Magdalena

last: Koziol


title: Whole transcriptome array in female virgin and pregnant C57BL6 mouse liver

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Affymetrix whole genome microarray in female livers from virgins and 14.5dpc pregnant mice

overall_design: Mice were time mated and livers collected. Virgins were used as controls. RNA isolated with Trizol and Qiagen RNeasy RNA isolation kit.

first: Matthew

last: Quinn

last: Cidlowski


title: Murine cells: MSC+LLC-serum-exosome vs LLC-serum-exosome

city: ChangSha

first: xina

last: zhang

state: HuNan

address: 110 XiangYa Road

department: Cancer Research Institute

institute: Central South University

summary: Exosomal miRNAs including 86 exosomal miRNAs were significantly increased and 354 exosomal miRNAs were significantly decreased in the co-injection group compared to LLC injection alone  through expression profiling of a total of 1903 genes.

overall_design: Two-condition experiment, MSC+LLC-serum-exosome vs LLC-serum-exosome.There is no biological repetition of this experiment.

first: Xina

last: Zhang


title: A transcriptional-level gene regulation strategy in Chinese fir seedlings under nitrogen deficiency

city: hangzhou

first: bohui

last: wu

address: No. 666 Wusu Street, Lin‘an City

institute: Zhejiang A&F University

summary: To screen the genes related to nitrogen use efficiency, a Chinese fir clone named X6 was subjected to low nitrogen (LN) stress and was used along with control (CK) plants for de novo RNA sequencing of root transcriptomes. The differences in the expression of genes under both conditions were determined. A total of 4,300 significant differentially expressed genes (SDEGs) were obtained by comparing the transcriptomes of the plants in the LN and CK groups. Among these genes, 2,970 were upregulated, and 1,330 were downregulated. All the SDEGs obtained from the LN and CK samples were subjected to KEGG annotation and classification. Using classification and statistical analysis with WEGO software, KEGG pathway annotations were obtained for 980 SDEGs, which were related to 222 metabolic pathways, and the pathway for nitrogen metabolism was determined. Twenty-four unigenes related to nitrogen metabolism in the Chinese fir were screened. They were found to encode seven enzymes: nitrate reductase (NADH, NR1), ferredoxin-nitrite reductase (NIR1), glutamine synthetase (GS), glutamate synthase (ferredoxin; Fd-GOGAT), glutamate synthase (NADPH/NADH, NADH-GOGAT), glutamate dehydrogenase (NADP+, GDH1), and glutamate dehydrogenase (NAD(P)+,GDH2), as well as two transporters, namely, ammonium transporter (AMT) and nitrate transporter (NRT). Under nitrogen-deficient conditions, AMT, NRT, NR1, and GS were significantly upregulated, whereas NIR1, NADH-GOGAT, and GDH2 were significantly downregulated; the other genes showed no significant changes. This is the first report on the global transcriptome response of the Chinese fir to nitrogen deficiency. Our results might help illustrate the preference of the Chinese fir for NH4+ rather than for NO3−. Our data provide insights into the coordinated system of nitrogen metabolism in this valuable tree species.

overall_design: Low nitrogen (LN, the nitrogen present in distilled water, which was determined to be less than 0.01mM) and nitrogen sufficient (CK, nitrogen concentration of 5.03 mM) treated Chinese fir root were generated by deep sequencing.

first: Yongquan

last: Lu

first: Dingwei

last: Luo

first: Guifang

last: Ma

first: Jianhui

last: Li

first: Bohui

last: Wu


title: RNA sequencing in LLCs from  co-injected mice or LLC injection alone.

summary: we analyzed transcriptomic profiles in LLC cells isolated from primary cancer sites. C57BL/6 mice were subcutaneously injected with LLC-RFP with or without BMSCs.

overall_design: Two-condition experiment, LLCs from co-injected mice or LLC injection alone.Gene expression profiling was performed on LLCs collected from 3 samples for each group.


title: Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 2215-B Garland Ave, 1075 MRB4

institute: Vanderbilt University Medical Center

summary: The myeloid translocation gene family member MTG16 is a transcriptional corepressor that relies on the DNA-binding ability of other proteins to determine specificity. One such protein is the ZBTB family member Kaiso, and the MTG16:Kaiso interaction is necessary for repression of Kaiso target genes such as matrix metalloproteinase-7. Using the azoxymethane and dextran sodium sulfate (AOM/DSS) murine model of colitis-associated carcinoma, we previously determined that MTG16 loss accelerates tumorigenesis and inflammation. However, it was unknown whether this effect was modified by Kaiso-dependent transcriptional repression. To test for a genetic interaction between MTG16 and Kaiso in inflammatory carcinogenesis, we subjected single and double knockout (DKO) mice to the AOM/DSS protocol. Mtg16-/- mice demonstrated increased colitis and tumor burden; in contrast, disease severity in Kaiso-/- mice was equivalent to wild type controls. Surprisingly, Kaiso deficiency in the context of MTG16 loss reversed injury and pro-tumorigenic responses in the intestinal epithelium following AOM/DSS treatment, and tumor numbers were returned to near to wild type levels. Transcriptomic analysis of non-tumor colon tissue demonstrated that changes induced by MTG16 loss were widely mitigated by concurrent Kaiso loss, and DKO mice demonstrated downregulation of metabolism and cytokine-associated gene sets with concurrent activation of DNA damage checkpoint pathways as compared with Mtg16-/-. Further, Kaiso knockdown in intestinal enteroids reduced stem- and WNT-associated phenotypes, thus abrogating the induction of these pathways observed in Mtg16-/- samples. Together, these data suggest that Kaiso modifies MTG16-driven inflammation and tumorigenesis and suggests that Kaiso deregulation contributes to MTG16-dependent colitis and CAC phenotypes.

overall_design: Adjacent normal colon tissue was harvested from WT, Kaiso-/-, Mtgt16-/-, and double knockout mice after conclusion of the AOM/DSS treatment protocol. 3 samples were used per genotype

first: Sarah

last: Short

middle: S


title: Variability in the Analgesic Response to Ibuprofen Following Third Molar Extraction is Associated with Differences in Activation of the Cyclooxygenase Pathway

city: Philadelphia

first: Katherine

middle: N

last: Theken

address: 3400 Civic Center Blvd, Bldg 421

department: Systems Pharmacology and Translational Therapeutics

institute: University of Pennsylvania

summary: It has long been recognized that there is substantial inter-individual variability in the analgesic efficacy of non-steroidal anti-inflammatory drugs (NSAIDs), but the mechanisms underlying this variability are not well understood.  In order to characterize the factors associated with heterogeneity in response to ibuprofen, we performed functional neuroimaging, pharmacokinetic/pharmacodynamic assessments, biochemical assays, and gene expression analysis in twenty-nine healthy subjects who underwent third molar extraction. Subjects were treated with rapid-acting ibuprofen (400 mg; N=19) or placebo (N=10) in a randomized, double-blind design.  Compared to placebo, ibuprofen-treated subjects exhibited greater reduction in pain scores, alterations in CBF in brain regions associated with pain processing, and inhibition of ex vivo COX-1 and COX-2 activity and urinary prostaglandin metabolites (p<0.05). Ibuprofen-treated subjects could be stratified into partial responders (N=9, required rescue medication) and complete responders (N=10, no rescue medication). This variability in analgesic efficacy was not associated with demographic/clinical characteristics, markers of systemic inflammation, or ibuprofen pharmacokinetics. Complete responders exhibited less suppression of urinary prostaglandin metabolites and greater induction of serum tumor necrosis factor-α and interleukin 8, compared to partial responders (p<0.05).  Partial responders exhibited more alterations in gene expression in peripheral blood mononuclear cells after surgery, with an enrichment in inflammatory pathways.  These findings suggest that activation of the prostanoid biosynthetic pathway and regulation of the inflammatory response to surgery differs between partial and complete responders.  Future studies are necessary to elucidate the molecular mechanisms underlying this variability and identify biomarkers that are predictive of ibuprofen response.

overall_design:
Human subjects were given Ibuprofen (400 mg; n=19) or placebo (n=10) following surgical extraction of their third molars. Subjects given Ibuprofen were retrospectively classified as partial responders (n=9) if they required rescue medication (hydrocodone 5 mg/acetaminophen 325 mg), or full responders (n=10) if they did not. All subjects in the placebo group received rescue medication.  Blood was collected from subjects before surgery (baseline) and at two time points following surgery (post-surgery 1, post-surgery 2). Both post-surgery samples were collected after subjects were given drug/placebo. Peripheral blood mononuclear cell (PBMCs) were isolated from blood samples and their RNA content was assayed via RNA-seq.

The following samples were dropped from normalization and final analyses due to low read depths: GSM3405457 (1004_post-surgery_1), GSM3405459 (1005_post-surgery_1), GSM3405462 (1007_baseline), GSM3405463 (1007_post-surgery_1), GSM3405464 (1008_baseline), GSM3405465 (1008_post-surgery_1), GSM3405466 (1008_post-surgery_2), GSM3405468 (1011_post-surgery_1), GSM3405469 (1011_post-surgery_2), GSM3405472 (1012_post-surgery_2), GSM3405491 (1020_baseline).

first: Elliot

middle: V

last: Hersh

first: Nicholas

last: Lahens

first: Hyo

last: Lee

first: Eric

last: Granquist

first: Helen

last: Giannakopoulos

first: Lawrence

middle: M

last: Levin

first: Stacey

last: Secreto-Dankanich

first: Gregory

last: Grant

first: John

last: Detre

first: Garret

last: FitzGerald

first: Tilo

last: Grosser

last: Farrar


title: TRAIL receptor activation overcomes resistance to trastuzumab in HER2 positive breast cancer cells

city: Salamanca

first: Javier

last: Pérez Peña

address: C/Richard Ford Nº39, 2ºB

department: Centro Regional de Investigaciones Biomédicas

country: Spain

institute: Universidad de Castilla La Mancha

summary:
During the last few years and thanks to the development of new targeted therapies, the prognosis of patients diagnosed with breast cancer overexpressing HER2 has clearly improved. Nonetheless, it is frequent to find patients in which after a time of response to these therapies, tumors progress due to the development of resistances. Identifying the mechanisms leading to those resistances as well as new therapeutic strategies in that context represents nowadays an important challenge in the oncology clinic.
With this purpose a new model of in vitro resistance to trastuzumab was generated in the laboratory based on the continuous culture with this drug.

overall_design: The prototypical BT474 HER2+ breast cancer cell line was plated at low density and grown in the presence of 50 nM trastuzumab (7.5 mg/ml) for 6 months. Trastuzumab-resistant cells were pooled, generating a cell population that was named BT-RH (for “Resistant to Herceptin™”). BT-RH cells were maintained in the presence (BT-RH+) or absence (BT-RH-) for an additional 6 months period. BT-RH- cells grew similarly in the presence or absence of trastuzumab. The acquired resistance obtained in BT-RH- cells was stable and quantitatively analogous to the resistance of BT-RH+ cells.

first: Elena

last: Díaz-Rodríguez

last: Pérez-Peña

first: Atanasio

last: Pandiella


title: RNA-Sequencing, Physiological and RNAi Analyses Provide Insights into the Response Mechanism of the ABC-Mediated Resistance to Verticillium Dahliae Infection In cotton

city: Anyang

first: Dong

middle: Odongo

last: Qi

state: Henan

address: HUANGHE ROAD, No 38.

department: Cotton research Institute

institute: Chinese Academy of Agricultural Sciences

summary: Verticillium wilt which is caused by Verticillium dahliae causes massive annual losses of cotton yield. Control by conventional mechanisms is not possible due to wide host range and longevity of dormant fungi in the soil in case of absence of a suitable host. Plants have developed various mechanisms to boost their immunity against various diseases, and one of which is through the induction of various genes. In this research work, carried out of RNA sequencing and identified the members of the ABC genes are critical in enhancing resistance to V. dahliae infection. A total of 166 ABC genes were identified in Gossypium raimondii with varying physiochemical properties. A novel ABC gene, Gorai.007G244600 was found to be highly upregulated, its homolog in the tetraploid cotton Gh_D11G3432, was then silenced through virus induced gene silencing (VIGS) in tetraploid cotton, the mutant cotton seedlings that have the ability to tolerate V. dahliae infection were significantly reduced. Evaluation of oxidant, hydrogen peroxide (H2O2) and malondialdehyde (MDA) were found to have increased levels in the leaves of the mutant compared to the wild types. In addition, antioxidant enzymes, peroxidase (POD), catalase (CAT) and superoxide dismutase (SOD) concentration levels were significantly reduced in the mutant cotton compared to the wild types. Moreover, expression levels of the biotic stress genes, cotton polyamine oxidase (GhPAO), cotton ribosomal protein L18(GhRPL18) and cotton polygalacturonase-inhibiting protein-1 (GhPGIP1) were all downregulated in the mutant but highly upregulated in the wild cotton tissues. The outcome of this research has shown that ABC genes could be playing an important role in enhancing immunity of cotton to V. dahliae infection and can be explored in developing more resilient cotton genotypes with improved resistance to V. dahliae infection.

sample_organism:
Gossypium raimondii
Gossypium thurberi
Gossypium trilobum

overall_design: Examination of three tissues leaf, stem and root of three cotton species in three time points 0h, 12h and 48h with 81 samples which contain three biological duplication.

first: Fang

last: Liu

first: Qi

last: Dong

first: Richard

last: Magwanga

first: Pu

last: Lu


title: An investigation of the effect of anti-apoptosis mutations on human pluripotent stem cells transcriptome when apoptosis stress was applied

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary: We performed RNA-sequencing on hPSCs treated with mitosis poison nocodazol (NOC) or MCL1 inhibitor A1210477 (A121). Our data revealed that NOC and A121 treatment lead to significant upregulation of apoptosis related genes as well as NIK/NF kappa B pathway gene. To investigate effects of anti-apoptotic mutations on hPSCs under stress, we also preformed RNA-seq on BCL-XL overexpression cells and NOXA-/- cells with NOC or A121 treatment. Results showed that anti-apoptotic mutations can promote hPSCs survival by inhibiting both apoptosis pathway and NIK/NF kappa B pathway. Furthermore, SNP analysis showed that cells with anti-apoptotic mutation gained more SNP under NOC or A121 treatment.

overall_design: RNA-seq of wild type, BCL-XL overexpression, NOXA-/- knockout and p53 knock-down H9 cells and iPS cells treated with mitosis poison nocodazol or MCL1 inhibitor A1210477. RNA-seq of inducible HA-BCLXL overexpression H9 recovered from repeated NOC or AZD treatment.

first: Jing

last: Zhang


title: miRNA Characterization in Antarctic fish

city: Rohnert Park

first: Sean

last: Place

address: 1801 E. Cotati Ave.

department: Biology

institute: Sonoma State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Using RNAseq of small RNA libraries isolated from the gill tissue of the Antarctic fish Trematomus bernacchii we have characterized the termal sensitivity of miRNA homologues in these highly stenothermic fish.

overall_design: Small RNA libraries were sequenced from the gill tissue of four biological replicates per experimental treatment (-1.5 C or +4 C) per acclimation time point (7d, 28d, 56d).


title: PI3K inhibition activates SGK1 via a feedback loop to promote chromatin-based regulation of ER-dependent gene expression

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: The phosphoinositide 3-kinase (PI3K) pathway integrates extracellular stimuli to phosphorylate and activate key downstream effectors such as AKT and serum-and glucocorticoid-inducible kinase (SGK1). We have previously reported that the PI3K pathway regulates ER-dependent transcription in breast cancer through the phosphorylation of the epigenetic regulator KMT2D by AKT. Here, we provide new insights into how the PI3K pathway propagates its effects to control KMT2D and ER function via SGK1, another PI3K downstream effector. Specifically, we show that PI3K inhibition, via a negative feedback loop, activates SGK1 to promote chromatin-based regulation of ER-dependent gene expression. PI3K/AKT inhibitors activate ER, which subsequently promotes SGK1 transcription through direct binding to its promoter. Elevated SGK1, in turn, phosphorylates KMT2D, suppressing its function and altering the chromatin landscape to attenuate ER-dependent expression. Thus, we have determined that SGK1 regulates the chromatin landscape and ER-dependent transcription via the direct phosphorylation of KMT2D. These findings reveal an ER-SGK1-KMT2D signaling circuit aimed to attenuate ER response through a previously unknown role for SGK1 to program chromatin and ER transcriptional output.

overall_design: Genome-wide analysis of chromatin accessibility upon overexpression of catalytically active SGK1 S422D

first: Eneda

last: Toska


title: Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression

first: Michael

middle: M.

last: Gottesman

address: 37 Convent Dr. Bldg. 37 RM 2112

department: National Cancer Institute

institute: National Institutes of Health

summary: Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant environment for cell culture in terms of cell-cell architecture, extracellular matrix composition, and spatiotemporal delivery of key growth factors and small molecules, such as oxygen. Here, we describe a three-dimensional (3D) approach to cell culture in vitro, utilizing a bioreactor system designed to control oxygenation of 3D cancer cell cultures, in order to better mimic tumor microenvironments observed in vivo. We found transcriptomic differences in breast and ovarian cancer cell cultures grown in traditional monolayer cultures as compared to cultures grown in a Matrigel three-dimensional matrix. We also investigated the transcriptomes of 3D cultures grown in 21% O2, 3% O2, and a gradient of 3% O2 to 0% O2 using our bioreactor system. By controlling oxygen delivery, we observed differences in cell growth morphology and transcriptome regulation under the three conditions.

overall_design: Examination of the effects of oxygenation gradients on 3D cancer cell cultures grown in a bioreactor. 3D cell cultures grown in 3% oxygen, 21% oxygen, and gradient oxygen are examined and compared to cells grown in 2D 21% oxygen. MCF-7 and OVCAR-8 cell lines are investigated.

first: William

last: Wulftange

first: Michelle

last: Rose

first: Marcial

last: Garmendia-Cedillos

first: Davi

last: da Silva

first: Joanna

middle: E

last: Poprawski

first: Dhruv

last: Srinivasachar

first: Taylor

last: Sullivan

first: Langston

last: Lim

first: Valery

last: Bliskovsky

first: Matthew

last: Hall

first: Thomas

last: Pohida

first: Robert

last: Robey

first: Nicole

middle: Y

last: Morgan


title: To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Reads were aligned to the mm10 genome with annotations provided by Ensembl.  Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition. To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

overall_design: Single-end RNA sequencing of total RNA extracted from colon crypts obtained from Stat5 knockout, wildtype, and overexpressing mice.

first: Xiaonan

last: Han


title: human HCC cell MHCCLM3: HOXB7-siRNA transfected vs. control

city: Shanghai

first: weimin

last: wang

address: 136 Yi Xue Yuan Road

institute: Zhongshan Hospital, Fudan University

summary: We found that HOXB7 promotes HCC cell proliferation, migration, and invasion. To further explore the mechanism, we performed a cDNA microarray assay to compare the differential gene expression profiles of HOXB7 depletion (HOXB7-siRNA-treated) and negative control siRNA-treated in MHCCLM3 cells.

overall_design: Biological sample: HOXB7-siRNA-treated MHCCLM3 cells vs. negative control siRNA-treated MHCCLM3 cells. Replicates: One replicate per array, the cells independently transfected, grown and harvested. Comparisons were made between HOXB7-siRNA group and control group.

first: Weimin

last: Wang


title: Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos

city: Fukuoka

first: Wan Kin

last: Au Yeung

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

country: Japan

institute: Kyushu University

summary: We report the first genome-wide landscape of H3K9me2 ChIP-seq profile in mouse oocytes. We also performed whole-genome bisulfite sequencing and RNA-seq analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos. Our findings illuminate the functional importance of G9a in preimplantation development and, in addition, pose a question on the proposed role for H3K9me2 in protection of the maternal genome from active CG demethylation.

overall_design: ChIP-seq H3K9me2 profile was generated from wildtype fully-grown oocytes (FGOs). Whole-genome bisulfite sequencing anlaysis was performed on G9a conditional KO oocytes (growing oocytes, FGOs and MII oocytes) and maternal KO preimplantation embryos (early 2-cell embryos and blastocysts).

first: Julie

last: Brind'Amour

first: Yu

last: Hatano

first: Kazuo

last: Yamagata

first: Roert

last: Feil

last: Lorincz

first: Makoto

last: Tachibana

first: Yoichi

last: Shinkai

first: Hiroyuki

last: Sasaki


title: Adaptive plasticity of IL10+ and IL35+ regulatory T cells cooperatively promote intratumoral T cell exhaustion

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

summary:
Abstract: Regulatory T cells (Tregs) maintain host self-tolerance but are a major barrier to effective cancer immunotherapy. Tregs subvert beneficial anti-tumor immunity by modulating inhibitory receptor (IR) expression on tumor infiltrating lymphocytes (TILs); however, the underlying mediators and mechanisms remain elusive. Here we show that interleukin-10 (IL10) and interleukin-35 (IL35; a heterodimer of Ebi3 and IL12) are reciprocally expressed by Treg-subpopulations in the tumor microenvironment (TME) and cooperatively promote intratumoral T cell exhaustion. Treg-restricted deletion of either Il10/Ebi3 or dual deletion resulted in delayed tumor growth and significant reduction of transcriptomic exhaustion signature associated with reduced expression of B lymphocyte-induced maturation protein-1 (BLIMP1; Prdm1). While the two cytokines share the BLIMP1 axis to drive multi-IR expression; they differentially impact effector vs. memory fate, highlighting their overlapping and non-redundant regulation of anti-tumor immunity. Our results reveal previously unappreciated adaptive plasticity in inhibitory cytokine expression pattern by Tregs in TME for maximal immunosuppression.
Data purpose: to understand the segregated cytokine expression pattern and the preferential generation of single cytokine positive Treg subpopulations, we performed single cell RNASeq (scRNAseq) contrasting Tregs isolated from naïve, unchallenged LNs or day 14 B16 tumor from Foxp3Cre-YFP WT mice

first: Deepali

last: Sawant

first: Hiroshi

last: Yano


title: Intraductal Adaptation of the 4T1 Mouse Model of Breast Cancer Reveals Effects of the Epithelial Microenvironment on Tumor Progression and Metastasis

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

summary: Tumors were harvested at day 24 post tumor cell engraftment and dissociated into single-cell suspensions. RFP-positive 4T1 cells were isolated by fluorescence-activated cell sorting (FACS). RNA was extracted using the RNeasy Mini Kit. Three independent RNA preparations from cultured 4T1-Luc2-RFP cells and FACS-isolated 4T1-Luc2-RFP cells were submitted for RNA sequencing analysis.

overall_design: Primary tumor 4T1-Luc-RFP (n=3) and non-injected 4T1-Luc-RFP (n=3)

first: Huda

last: Atiya

first: Anna

last: Dvorkin-Gheva

first: John

last: Hassel

first: Shrusti

last: Patel

first: Rachel

last: Parker

first: Adam

last: Hartstone-Rose

first: Johnie

last: Hodge

first: Daping

last: Fan

first: Ann

last: Ramsdell


title: Comparative gene expression analysis between wild-type (WT) and Cables2-deficient epiblast-like cells (EpiLCs).

status: Public on Apr 01 2019

city: Tsukuba

first: Hiroyoshi

last: Iseki

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: We found that Cables2 physically interacts with Smad2 and beta-catenin, and enhances their transcriptional activities. To identify the target genes that are regulated by Cables2 together with Smad2 and/or beta-catenin, we conducted a comparatvie RNA-seq experiment between WT- and Cables2-deficient EpiLCs.

overall_design: mRNA expression profiles of WT- and Cables2-deficient EpiLCs were generated by RNA sequencing using the NextSeq 500 (Illumina)

first: Tra

middle: H

last: Dinh

first: Masafumi

last: Muratani

first: Fumihiro

last: Sugiyama


title: The consequences of trehalose intake on brain metabolism in mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: In the present study, we investigated the consequences of trehalose intake on brain metabolism in mice drinking for 0, 1, and 10 days. Microarray analyses were performed to identify the molecular targets involved in the brain metabolism of trehalose intake.

overall_design: Male C57Bl/6J mice (9 weeks old) were housed in groups of three mice per cage at 22°C in a 12h light/dark cycle and given free access to diet and water. After an acclimatization period of 1 week, the mice were given water (0 day) or trehalose for 1, 10 days. At the end of the study period, mice (0 day, n=2; trehalose for 1 day, n=3; trehalose for 10 day) were anesthetized after a 6h period of fasting. Mice were transcardially perfused with 0.1M PB plus heparin, brain was taken, left hemispheare was  immedeately frozen at -80°C for arrey analysis, right hemispheare was used for histological analysis. All mice experiments were approved by the local animal ethics committee.

first: Kunikazu

last: Tanji

first: Tomoh

last: Matsumiya

first: Fumiaki

last: Mori

first: Koichi

last: Wakabayashi


title: NOTCH signaling is activated in and contributes to resistance in enzalutamide-resistant prostate cancer cells

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Prostate cancer is the second leading cause of cancer death among men in the United States. The Androgen receptor (AR) antagonist Enzalutamide is a FDA approved therapy for treatment of late stage prostate cancer patients and is currently under clinical study for early stage prostate cancer treatment. After a short positive response period, patients will develop drug resistance. In this study we used RNA-sequencing and bioinformatics analysis to identify Notch signaling pathway as a deregulated pathway in Enzalutamide-resistant cells. NOTCH2 and c-MYC positively correlated with AR expression in patients' samples mimicking cells with Enzalutamide-resistance. In Enzalutamide-resistant cells, MR49F and C4-2R, we found that cleaved-NOTCH1, HES1 and c-MYC protein expression are significantly elevated indicating an activated NOTCH1 pathway in those cells. In addition, ADAM10 and ADAM17 had a higher expression in Enzalutamide-resistant cells, suggesting a role for S2 cleavage in the increased cleaved NOTCH1 expression. Furthermore, treatment of Enzalutamide-resistant cells with PF-03084014 in combination with Enzalutamide increased cell death, decreased colony formation ability and re-sensitized Enzalutamide-resistant cells to Enzalutamide. Knockdown of NOTCH1 in C4-2R increases Enzalutamide sensitivity by decreasing cell proliferation and increasing cell death. In a 22RV1 xenograft model, PF-03084014 and Enzalutamide induced a decrease in tumor growth through a reduced cell proliferation and increased apoptosis. These results indicate that Notch1 signaling can contribute to Enzalutamide-resistance in Prostate cancer and inhibition of this pathway can re-sensitize resistant cells to Enzalutamide.

overall_design: Method: polyA selection of mRNA from enzalutamide sensitive and resistant cells (n=3 biological replicates) and sequenced on a HiSeq2500

first: Elia

last: Farah

middle: A

last: Lanman

first: Vhaohao

last: Li

first: Lijun

last: Cheng

first: Yifan

last: Kong

first: Yanquan

last: Zhang

first: Gabrielle

middle: R

last: Lorenz

first: Nihal

last: Ahmad

first: Lang

first: Xiaoqi

last: Liu

first: Pete

last: Pascuzzi


title: Murine MSCs: MSC-exosome-hypoxia vs MSC-exosome-normoxia

first: xina

last: zhang

address: 110 XiangYa Road

institute: Central South University

summary: MiRNA microarray analysis was performed on exosomes secreted by mouse MSC cells under two different conditions of normal oxygen and hypoxia, in order to find out the different miRNAs in exosomes secreted by MSC under two different conditions.

overall_design: Two-condition experiment, MSC-exosome-hypoxia vs MSC-exosome-normoxia.There is no biological repetition of this experiment.

first: Xina


title: RNA-seq data of alveolar type 2 epithelial cell derived from organoids treated with IL-1b or TNFa

city: Durham

first: Hiroaki

last: Katsura

state: NC

address: 353 Nanaline Duke Bldg

institute: Duke University

summary: Treatment with IL-1b or TNFa enhance the proliferation of alveolar type 2 cells in organoid culture. Here, we examine the downstream mechanisms that enhance AEC2 proliferation after IL-1b and TNFa treatments, we performed RNA-seq analysis of AEC2s isolated from organoids 6 hrs after exposure to either cytokine. We identified 165 differentially expressed genes that were common in both IL-1b and TNFa treated AEC2s compared to saline treated controls.

overall_design: mRNA was isolated from FACS-sorted cells and sequenced using Illumina HiSeq X

first: Yoshihiko

last: Kobayashi

first: Purushothama

last: Rao Tata

first: Brigid

last: Hogan


title: Plasma circulating extracellular RNAs in left ventricular remodeling post-myocardial infarction

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

institute: MGH

summary: Despite substantial declines in mortality following myocardial infarction (MI), subsequent left ventricular remodelling (LVRm) remains a significant long-term complication. Extracellular small non-coding RNAs (exRNAs) have been associated with cardiac inflammation and fibrosis and we hypothesized that they are associated with post-MI LVRm phenotypes. RNA sequencing of exRNAs was performed on plasma samples from patients with “beneficial” (decrease LVESVI ≥20%, n=11) and “adverse” (increase LVESVI ≥15%, n=11) LVRm. Selected differentially expressed exRNAs were validated by RT-qPCR (n=331) and analyzed for their association with LVRm determined by cardiac MRI. Principal components of exRNAs were associated with LVRm phenotypes post-MI; specifically, LV mass, LV ejection fraction, LV end systolic volume index, and fibrosis.  We then investigated the temporal regulation and cellular origin of exRNAs in murine and cell models and found that: 1) plasma and tissue miRNA expression was temporally regulated; 2) the majority of the miRNAs were increased acutely in tissue and at sub-acute or chronic time-points in plasma; 3) miRNA expression was cell-specific; and 4) cardiomyocytes release a subset of the identified miRNAs packaged in exosomes into culture media in response to hypoxia/reoxygenation. In conclusion, we find that plasma exRNAs are temporally regulated and are associated with measures of post-MI LVRm.

overall_design: qPCR gene expression profiling from plasma of patients who underwent a myocardial infarction.  Equal amount total RNA from each donor was extracted prior to gene expression analysis.

first: Ashish

last: Yeri


title: Effects of inhibiting sphingolipid synthesis and TOR signaling on the Candida albicans transcriptome

city: Würzburg

first: Valentina

last: del Olmo Toledo

state: Bayern

address: Josef-Schneider-Str. 2/D15

country: Germany

institute: Institute of Molecular Infection Biology

summary: Goal: We employed RNA-seq to detect changes in the transcriptome of the yeast Candida albicans in response to the addition of myriocin, a sphingolipid synthesis inhibitor, or caffeine, a drug that blocks the TOR kinase. The effects of the drugs were studied in wild-type cells and in the rtg3 mutant strain.

overall_design: Comparison of the transcriptome of two Candida albicans strains: wild-type and rtg3 deletion mutant. RNA was prepared from each strain grown under three different conditions: no drug added, addition of myriocin or addition of caffeine. Two biological replicates per strain per condition. RNA-seq data generated with Illumina HiSeq2500.

first: J

last: Pérez

first: Sergio

last: Moreno-Velasquez


title: Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma (RNA-Seq)

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary:
Purpose: Identification of core transcriptional regulatory programs and bromodomain and extraterminal (BET) protein dependency in liposarcoma (LPS)

Methods: ChIP-seq and RNA-seq were performed on LPS cells. Antibodies against H3K27ac, H3K4me1, H3K4me3, RNA-Pol2, BRD2, BRD3, BRD4, FOSL2, pan-RUNX, and DDIT3 (FUS-DDIT3) were used for ChIP-seq assays. The transcriptome responses of LPS141 and MLS402 cells to OTX015 and ARV-825 were compared.

Result: We generated genome-wide chromatin-state maps of LPS cells. By charting the super-enhancer structures, we identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS. This study also provides a framework for discovering and targeting of core oncogenic transcriptional programs.

first: Liang

last: Xu

first: Ye

last: Chen

first: H

last: Koeffler


title: BRU1 is required for Heat Stress Memory in Arabidopsis

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary:
Abiotic stress is a major factor for crop productivity, a problem likely to be exacerbated by climate change. Improving the tolerance to environmental stress is one of the most important goals of crop breeding programmes. While the early responses to abiotic stress in plants are well studied, plant adaptation to enduring or recurring stress conditions has received little attention. This project investigates the molecular mechanism of the maintenance of acquired thermotolerance as a model case of stress memory in Arabidopsis. Arabidopsis seedlings acquire thermotolerance through a heat treatment at sublethal temperatures. To investigate the underlying mechanisms, we are investigating changes in the transcriptome at two timepoints after a heat acclimation treatment using Arabidopsis thaliana seedlings.
Microarrays were used to compare gene expression at two timepoints after a heat acclimation treatment.

overall_design: RNA from three biological replicates per genotype and treatment (4 h after acclimation 52 h after acclimation, and 4 h non-treated control) was purified over an RNeasy Plant RNA extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips (NASC microarray facility). The times were chosen to harvest all samples at the same time of day.

first: Anna

last: Stief

first: Simone

last: Altmann

first: Karen

last: Hoffmann


title: Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness

first: Blake

middle: W.

last: Tye

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

summary: To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although ribosomes are essential in all cells, natural disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we model these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result in acute loss of proteostasis. Imbalances in the synthesis of r-proteins and rRNAs lead to the rapid aggregation of newly synthesized orphan r-proteins and compromise essential cellular processes, which cells alleviate by activating proteostasis genes. Exogenously bolstering the proteostasis network increases cellular fitness in the face of challenges to ribosome assembly, demonstrating the direct contribution of orphan r-proteins to cellular phenotypes. We propose that ribosome assembly is a key vulnerability of proteostasis maintenance in proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic perturbations that generate orphan r-proteins.

overall_design: RNA-seq from yeast cells treated in the indicated condition

middle: W

first: L

last: Churchman


title: Osmotic stress response in Mtb

city: London

first: larrouy-maumus

last: gerald

address: exhibition road

department: life sciences

institute: Imperial college london

summary: determine the wide transcriptionnal response of Mtb to osmotic stress and hyperosmotic stress

overall_design: Mtb stressed for 2, 8 or 24 hours with sodium chloride at 250 mM and 1,000 mM or 2000 mM sucrose

first: Gerald

last: Larrouy-maumus


title: Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma (ChIP-Seq)

overall_design: ChIP-seq and RNA-seq were performed on LPS cells.


title: Combinatorial Ixazomib and Belinostat Therapy Induce Nuclear Factor Erythroid 2-Related Factor 2 (NRF2)-Dependent Apoptosis in Hodgkin and T-cell Lymphoma

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

summary: Ixazomib has documented pre-clinical activity in T cell (TCL) and Hodgkin (HL) lymphoma models with transcriptomic analyses predicting synergistic activity in combination with histone deacetylase (HDAC) inhibition. In the present study, we determined the mechanistic basis for synergism with ixazomib in combination with the HDAC inhibitor, belinostat, in HL and TCL cells lines (ixazomib-sensitive and -resistant clones) and primary tumor cells. In ixazomib-treated TCL and HL cells, we observed induction of proteasomal gene expression and NRF2 as a prominent upstream regulator. Ixazomib treatment in TCL and HL cells resulted in transient inhibition followed by full recovery of proteasomal activity within 72 hours. Furthermore, transcriptomic analysis following belinostat treatment resulted in downregulation of both NRF2 and proteasomal gene expression (validated by qPCR) without direct impact on proteasomal activity in Jurkat and L428. In addition, CRISPR/Cas9 mediated knockdown of NRF2 in Jurkat cells resulted in a significant decrease in cell viability with ixazomib compared with untreated control cells. Using transcriptomic and proteosomal activity evaluation of ixazomib, belinostat or ixazomib+belinostat treated cells, we observed that NRF-2, proteasome gene expression and functional recovery were abrogated by the combination. We also confirmed that ixazomib/belinostat resulted in synergistic activity in ixazomib-sensitive and -resistant cell lines and primary cells.  Altogether, these results suggest that the synergistic activity of ixazomib and belinostat is mediated via inhibition NRF2-dependent proteasomal recovery and extended proteasomal inhibition culminating in increased cell death.  Further investigation is warranted to determine the full biological role for NRF2 as a response modifier in proteasomal targeted therapies.

overall_design: Jurkat, HH, L428, L540 cells were authenticated (by ATCC STR profiling) and maintained under 5% CO2 and at 37OC in culture medium RPMI1640 (Corning, Manassas, VA) with 10% heat inactivated Fetal Bovine Serum (FBS) and antibiotic-antimycotic (200 I.U. Penicillin/Streptomycin, 25µg Amphotericin; Corning, Manassas, VA). Primary lymphoma cells were obtained from cells isolated from ascites fluid of a patient with enteropathy-associated T-cell lymphoma (EATL) refractory to standard chemotherapy, via Institutional Review Board approved consent process and made available for research through Tufts tumor biorepository. The obtained de-identified specimen labeled as EL-8, were cultured using RPMI1640 complete medium through successive passages. Ixazomib resistant cell lines (Jurkat-R and L428-R) were established by culturing in increasing concentrations of ixazomib, 5-50 nM for several months. Ixazomib resistance was determined by comparing IC50 in parental and resistant cells using MTT based cell viability assay. Total RNA was isolated from Jurkat cells treated with ixazomib, belinostat or ixazomib+belinostat for 24 hours, using RNeasy Mini Kit (Qiagen, Valencia, CA). Transcriptomic analysis was performed using Human HT 12 Genechip Illumina (Yale Center for Genomic Analysis). Data normalization (using R), statistical analysis, Gene set enrichment analysis (GSEA) as defined by Subramanian et al. and Ingenuity Pathway Analysis (IPA) were performed as described previously.

first: Frank

middle: C

last: Passero

first: Dashnamoorthy

last: Ravi

middle: T

last: McDonald

first: Andrew

last: Evens


title: Genome-wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

institute: Stanford University

type: Genome binding/occupancy profiling by array

summary: We have used chromatin immunoprecipitation followed by microarray analysis (chIP-chip) to identify DNA regions bound by the ChvI protein in Sinorhizobium meliloti cells.  We then used quantitative PCR with chvI mutant strains to test the ChvI-dependent expression of genes downstream of the ChvI-bound DNA regions.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Chromatin immunoprecipitation followed by custom Affymetrix GeneChip analysis (chIP-chip) to identify DNA regions enriched for binding of ChvI

first: Esther

first: Erich

last: Sabio

first: Sharon

last: Long


title: Gene expression data from rhesus macaque postnatal testis development

city: Ankara

first: Babür

last: Erdem

state: Çankaya

address: ODTÜ, Biyoloji Böl., Lab 205

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

summary: We measured the timing of gene expression changes in the testises of rhesus macaques throughout postnatal development.

overall_design: Post-mortem testis samples from 12 rhesus macaques of different ages (16 days to 26 years) were collected. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST® arrays.

first: Zheng

last: Yan

first: Haiyang

last: Hu

first: Mehmet

last: Somel

first: Babur

first: Philipp

last: Khaitovich


title: Transcript data affected by natural variation or PME17 mutation in Arabidopsis thaliana, infested or not with the aphid Myzus persicae

city: Amiens

first: Christopher

last: Wattier

state: Somme

address: 33 rue Saint Leu

department: Faculté des Sciences

country: France

institute: Université de Picardie Jules Verne

summary: Investigation of the ecotype difference between Columbia-0 (Col)  and Wassilewskija-0 (WS) on whole gene expression level, of PME17 mutation effect (compared to background WS) and of the aphid infestation effect on Col, WS and pme17 (infested plants compared to non-infested plants).

overall_design: 12plex high density chips using total RNA extracted from three independent biological replicates and one or two technical replicates.


title: Differential expression of Hdc-GFP+/hiCD11b+Gr1lo vs Hdc-GFP+/hiCD11b+Gr1hi myeloid cells from mouse bone marrow

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary:
Bone marrow Hdc-GFP+/hiCD11b+Gr1lo vs Hdc-GFP+/hiCD11b+Gr1hi myeloid cells were isolated from bones from histidine decarboxylase (Hdc) green fluorescent protein (Hdc-GFP) mice.
Hdc-GFP+/hiCD11b+Gr1hi cells and Hdc-GFP+/hiCD11b+Gr1/lo cells were sorted by combinations of GFP and myeloid cell surface markers CD11b and Gr1 and their differential mRNA expression compared with Affymetrix microarrays.

overall_design:
a. Hdc-GFP+/hiCD11b+Gr1lo (n=3)
b. Hdc-GFP+/hiCD11b+Gr1hi cells (n=3)

first: Xiaowei

last: Chen

first: Richard

last: Friedman


title: Transcriptional response of Pseudomonas aeruginosa PA3 to its phage gene product gp68

status: Public on Mar 31 2019

city: Chongqing

first: zichen

last: yang

address: Gaotanyan

institute: Army Medical University (Third Military Medical University)

summary: Explore the genome-scale influence of PA3 phage gene product gp68 on Pseudomonas aeruginosa PA3

overall_design: Samples were taken from the PA3 strains transformed with pHerdB20T-gp68. Three independent experiments were performed

first: Zichen

last: Yang


title: Ikaros tumor suppression and epigenetic regulation [gene expression]

city: Hershey

first: Sinisa

last: Dovat

state: PA

address: 500 University Dr

institute: Penn State University

summary: Ikaros encodes a transcription factor that functions as a tumor suppressor in T-ALL. The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells results in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic global epigenomic and gene expression analyses to determine the role of Ikaros in tumor suppression during this process. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, as well as de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effect of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Ikaros induces profound, global re-distribution of HDAC1 via recruitment of HDAC1 to promoter and enhancer regions of different target genes. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.

overall_design: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days. Microarrays were performed for cells from these four time points.

first: Yali

last: Ding

first: Bo

last: Zhang


title: Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

institute: University of Manchester

summary: Networks of interacting co-regulated genes distinguish the inner cell mass (ICM) from the differentiated trophectoderm (TE) in the preimplantation blastocyst, in a species specific manner. In mouse the ground state pluripotency of the ICM appears to be maintained in murine embryonic stem cells (ESCs) derived from the ICM. This is not the case for human ESCs. In order to gain insight into this phenomenon, we have used network analysis to quantify how similar human (h)ESCs are to the human ICM.  Using the hESC lines MAN1, HUES3 and HUES7 we have shown that all have only a limited overlap with ICM specific gene expression, but that this overlap is enriched for network properties that correspond to key aspects of function including transcription factor activity and the hierarchy of network modules. These analyses provide an important framework which highlights the developmental origins of hESCs.

overall_design: We used a genebarcode on microarray transcriptomic data to identify genes expressed. This was used as a basis to compare inner cell mass, trophectoderm and human embryonic stem cells.

first: Susan

last: Kimber


title: Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma

first: Tuan Zea

last: Tan

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

overall_design: Refer to individual Series


title: Amygdala NPY circuits are critical for the development of accelerated obesity under chronic stress

city: Darlinghurst

first: CHI KIN

last: IP

state: NSW

address: 384 Victoria Street, Garvan Institute of Medical Research

department: Neuroscience division

country: Australia

institute: Garvan Institute of Medical Research

summary: Neuropeptide Y (NPY) exerts powerful feeding related functions in the hypothalamus. However, NPY is also present in extra-hypothalamic nuclei, however their influence on energy homeostasis is unclear. Here we uncover a previously unknown feeding stimulatory pathway that is activated under conditions of stress in combination with calorie dense food with NPY neurons in the central amygdala (CeA) being responsible for an exacerbated response to a combined stress and high fat diet intervention. CeA NPY neuron specific Npy overexpression mimics the obese phenotype seen in a stress/HFD model, which is prevented by the selective ablation of Npy. Using food intake and energy expenditure (EE) as readout we demonstrate that selective activation of CeA NPY neurons results in increased food intake and a decrease in EE, which requires the presence of NPY. Mechanistically it is the diminished insulin signalling capacity on CeA NPY neurons under stress combined with HFD conditions that leads to the exaggerated development of obesity.

overall_design: RNA from both sides of the amygdala of NpyCre/+;TRAPlox/lox mice were immunoprecipitated by using the TRAP protocol described above. Input RNA and immunoprecipitated (IP) RNA from three mice were pooled together to give enough material for RNA-sequencing. Two replicates were included for both IP and input samples. A total of 200 ng of the IP RNA and its corresponding input control was used for RNA-sequencing experiment. Illumina HiSeq HT chemistry sequencing with 100 base pair single-end read was employed. RNA quality and quantity were determined by Bioanalyzer Nanokit (Agilent). The same amount of RNA from both the immunoprecipitated samples and the input samples were used for library preparation (Illumina) in the Australian Genome Research Facility. Sequencing quality check of the raw sequencing reads was performed using the FastQC tool (Andrew S. 2010) through the Galaxy Project platform. No over-represented sequences were detected, indicating that adapter sequences did not affect the overall dataset. Read alignment was performed using TopHat (Trapnell et al., 2012) with default parameter, and iGenome (http://cole-trapnell-lab.github.io/cufflinks//igenome_table/ index.html) mm10 UCSC transcriptome annotation. Differential expression was determined by Cufflinks and Cuffdiff analysis, and a false discovery rate of <0.05 were considered to be statistically significant.

first: Chi

middle: K

last: Ip

first: Herbert

last: Herzog


title: Genome-wide mapping of UPF1 and Pol II [ChIP-seq]

city: Birmingham

first: Anand

middle: Kumar

last: Singh

state: West Midlands

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary:
ChIP with NMD core componenet UPF1 antibody in normal S2 cells and ChIP with Pol II Ser2 antibodies in S2 cells.
UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm.

overall_design: To examine the presence of UPF1 RNA helicase on chromosomes, replicates of  UPF1 ChIP DNA were sequenced by using Illumina HiSeq4000. Input was sequenced as ChIP control. Role of UPF1 in transcription regulation was examined by Pol II Ser2 or Pol II ChIP in control and UPF1 depleted cells. All the experiments were done using Drosophila embryonic S2 cells.

first: Saverio

last: Brogna


title: LiCl and Bax Antagonist Peptide (BAP) treated KG1a cells, irradiated at 4Gy and 8Gy, incubated for 48hr

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

country: India

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

summary: Gene expression following ionizing radiation exposure to LiCl and BAP treated cells

overall_design: 2mM LiCl pre-treated KG1a cells were irradiated at 4Gy and 8Gy in triplicate. Subsequently, novel BAP was added to cells to study cell survival.

first: Yogesh

last: Verma

middle: U


title: Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [Modifications - validation]

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Base Editing has been touted the most intelligent and precise application of the CRISPR platform so far, merging the simplicity of RNA-guided nucleases with deaminases that allow for the programmable generation of single base substitutions - without introduction of double-strand breaks. Even though the two-component system has been expected to cause off-target substitutions, studies involving cytosine base editors (CBEs) showed that in most cases, relatively few single base off-targets could be detected on DNA. We introduce the concept of multi-dimensional off-targeting, presenting an extensive amount of RNA cytidines being edited by DNA base editors. Epitranscriptomic off-target effects affected different cell lines and were independent of the guide RNAs used, suggesting Cas9-independent activity of the cytidine deaminase rAPOBEC1 on single-stranded RNA. With the help of protein engineering, we developed CBE variants with massively reduced inadvertent mutation of RNA that preserve and enhance DNA base editing capabilities.

overall_design: HEK293T and HepG2 cells were transfected with regular and modified pCAG-BE3-P2A-EGFP or control pCAG-nCas9(D10A)-UGI-NLS-P2A-EGFP or control pCAG-P2A-EGFP constructs with various gRNAs as described below. Cells were sorted for top 5% GFP or all GFP + cells based on FITC signal. RNA-seq was performed to measure transcriptional changes associated with different constructs and guides.

first: Julian

last: Grunewald


title: WNT signalling activity on epiblast cells (RNA-seq analysis)

city: WESTMEAD

first: PIERRE

last: OSTEIL

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

summary: The impact of WNT signalling activity on the acquisition and restriction of lineage propensity of germ layer progenitors and the gene network activity for cell fate decision during the development of the embryonic head was modelled in the epiblast stem cells derived and maintained under different signalling conditions. Our findings showed that the modulation of WNT activity is critical for the specification of the anterior (head) tissue progenitors in the multipotent early epiblast and the repression of WNT activity enhances the ectoderm lineage potency of the epiblast cells and poises the activation of endogenous WNT activity that drives neurogenesis during head morphogenesis.

overall_design: 4 different lines with 2 or 3 replicates each.

first: Pierre

last: Osteil

first: Patrick

middle: P

last: Tam


title: Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [BaseEditors - RNA]

overall_design: HEK293T and HepG2 cells were transfected with pCAG-BE3-P2A-EGFP or control pCAG-nCas9(D10A)-UGI-NLS-P2A-EGFP or control pCAG-P2A-EGFP constructs with various gRNAs as described below. Cells were sorted for top 5% GFP or all GFP + cells based on FITC signal. RNA-seq was performed to measure transcriptional changes associated with different constructs and guides.


title: RNA-seq data from double positive thymocyte and CD4 or CD8 single positive spleen T cell

city: Yokohama

first: kiyokazu

last: kakugawa

address: 1-7-22 Suehiro-cho

department: IMS

institute: Riken

summary: Control RNA-seq data for thymocyte and spleen T cell.

overall_design: two sets of wild type double positive thymocyte, CD4 single positive spleen T cell and CD8 single positive spleen T cell

first: Hilde

last: Cheroutre

first: Kiyokazu

last: Kakugawa


title: microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR


title: Transcriptome analysis of SH-SY5Y cells after knockdown of circSLC45A4

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Str. 10

department: Systems Biology of Gene Regulatory Elements

institute: Max-Delbrück Center for Molecular Medicine / Berlin Institute for Medical Systems Biology

summary: We perturbed the expression levels of circSLC45A4 in the human neuroblastoma cell line (SH-SY5Y) by RNAi/siRNAs. 96 h post-knockdown the cells were harvested, RNA extracted with Trizol and polyA+ libraries were generated with Illumina's TruSeq RNA Library Prep Kit v2. We find many significant changes in the transcriptomic profile after knockdown of circSLC45A4 and the induction of many genes connected to nervous system development, neuron projection development, synapse organization and cell adhesion.

overall_design: Examination of 3 different siRNAs against circSLC45A4 vs. 1 scrambled siRNAs, 2 biological replicates per siRNA.

first: Christin

last: Suenkel


title: Human Endothelial cell microRNA expression in high and low stiffness

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

summary: Purpose: mechanical homeostasis is a crucial process for Humen dermal fibroblast cell (HDFs) survival and functionality. Cell can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study we observed change in microRNA levels linked with mechanical response. HDFs were seeded for 48 our on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then sRNA-seq was performed.

overall_design: Human Dermal fibroblastcells (HDFs) were seeded for 48h on substrate at 3 and 30 kPa to approximate “soft” and “rigid” tissue respectively. SRNA-seq was performed to establish the microRNA profile in the two condition

first: Moro

last: Albertomaria

first: Tristn

last: Driscoll

first: Liana

last: Boraas

first: Nicoli

last: Stefania


title: Gene expression data from mouse postnatal brain development

first: Babür

last: Erdem

summary: We measured the timing of gene expression changes in the brains of mouses throughout postnatal development.

overall_design: Mouse brain samples from the cortex region were collected after sacrifice. The age ranges of the individuals covered the postnatal maturation period from infancy to late adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Mouse Gene 1.0 ST® arrays.

first: Zheng

last: Yan

first: Haiyang

last: Hu

first: Mehmet

last: Somel

first: Babur

first: Philipp

last: Khaitovich


title: Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

status: Public on Mar 29 2019

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: The replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We now report a sequencing method for the measurement of replication fork movement on single molecules by Detecting Nucleotide Analogue signal currents on extremely long nanopore traces (D‑NAscent). Using this method, we detect BrdU incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse labelling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kb, to generate the first whole genome single-molecule map of DNA replication dynamics and discover a new class of low frequency stochastic origins in budding yeast.

sample_organism:
Saccharomyces cerevisiae
synthetic construct

overall_design: Direct detection of BrdU by Nanopore (ONT) sequencing

first: Carolin

last: Müller

first: Michael

last: Boemo

first: Paolo

last: Spingardi

first: Benedikt

middle: M

last: Kessler

first: Skirmantas

last: Kriaucionis

first: Jared

last: Simpson


title: Role of cytokines in cardiac fibrosis and exercise

status: Public on Mar 30 2019

city: Beijing

first: Cao

last: Ning

address: 49 Huayuan North Road

institute: Peking university

summary: During acute sympathetic stress, the overeactivation of β-adrenergic receptors (β-ARs) caused cardiac fibrosis, by triggering inflammation and cytokine expression. It is unknown whether exercise training inhibited acute β-AR overactivation-induced cytokine expression and cardiac injury. Here, we reported that running exercise inhibited cardiac fibrosis and improved cardiac function in mice treated by isoproterenol, a β-AR agonist. Cytokine antibody array revealed that exercise prevented the expression changes of most cytokines induced by isoproterenol. Specifically, 18 ISO-upregulated and 3 ISO-downregulated cytokines belonged to six families (eg. chemokine) were prevented. A further KEGG analysis of these cytokines revealed that Hedgehog and Rap1 signaling pathways were involved in the regulation of cytokine expression by exercise. The expression changes of some cytokines that were prevented by exercise were verified by ELISA and real-time PCR. In conclusion, running exercise prevented the cytokine changes following acute β-AR overactivation and therefore attenuated cardiac fibrosis.

overall_design: 10-weeks male C57BL/6 mice were divided into 4 groups (n=4/group), untreated group (Ctrl goup), Running exercise for 6 weeks  (Run goup), sedentary group with acute sympathetic stress induced by isoproterenol  (Sed+ISO group), and ISO group with running exercise pretreatment (Run+ISO group). 144 cytokines expression were detected by Cytokine Antibody Array.

first: Ning

last: Cao

first: Alemasi

last: Akehu

first: Han

last: Xiao

first: Wei

last: Gao


title: Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Interleukin (IL)-2 is a pleiotropic cytokine that is necessary to prevent chronic inflammation in the gastrointestinal tract.  The protective effects of IL-2 involve the generation, maintenance and function of regulatory T cells (Tregs), and low-dose IL-2 has emerged as a potential therapeutic strategy in inflammatory bowel disease (IBD) patients.  However, the cellular and molecular pathways that control the production of IL-2 in the context of intestinal health are undefined.  Here we identify that IL-2 is acutely required to maintain Tregs and immunologic homeostasis throughout the gastrointestinal tract.  Strikingly, lineage-specific deletion of IL-2 in T cells could recapitulate these phenotypes in the large intestine, but not in the small intestine.  Unbiased analyses revealed that group 3 innate lymphoid cells (ILC3) are the dominant cellular source of IL-2 in the small intestine, which is selectively induced by IL-1β.  Macrophages produce IL-1β in the small intestine and activation of this pathway involves MyD88- and Nod2-dependent sensing of the microbiota.  Loss-of-function studies defined that ILC3-derived IL-2 is essential to maintain Tregs, immunologic homeostasis and oral tolerance to dietary antigens uniquely in the small intestine.  Furthermore, ILC3 production of IL-2 was significantly reduced in the small intestine of Crohn’s disease patients, and this correlated with diminished Tregs.  Collectively, these results reveal a previously unappreciated pathway whereby a microbiota- and IL-1β-dependent axis promotes ILC3 production of IL-2 to orchestrate immune regulation in the small intestine.

overall_design: RNAs of ILC3s or CD4+ T cells were respectively sorted as CD45+CD3-RORγtGFP+CD127+ or CD45+CD3+CD4+ from 3 wild type mice.

first: Lei

last: Zhou

last: Sonnenberg


title: ATACseq from FACS sorted HopX positive cells from mouse brain

status: Public on Mar 28 2019

city: Philadelphia

first: Yijing

last: Su

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Analysis of FACS sorted HopX positive cells from mouse brain on open chromatin regions

overall_design: ATACseq was performed on  FACS sorted HopX positive cells from mouse brain at E15, P3 and adult.

first: Hongjun

last: Song