title: Transcriptional repression of IRF7 by MYC is critical for antiviral immune response in human pDC [GEN2.2]

status: Public on Nov 30 2016

overall_design: 21 total GEN2.2 samples assayed at 3 time points post CpGB stimulation. 12 of those 21 GEN2.2 samples were treated with negative CONTROL siRNA and were assayed at 3 time points post CpGB stimulation (4 replicates of 0hrs; 4 replicates of 2 hrs; 4 replicates of 4 hrs). The remaining 9 of those 21 GEN2.2 samples were MYC-ablated by treatment with MYC siRNA and were assayed at 3 time points post CpGB stimulation (3 replicates of 0hrs; 3 replicates of 2 hrs; 3 replicates of 4 hrs)

first: Tae

last: Kim

first: Seunghee

last: Hong

first: Yin

last: Lin

first: HyeMee

last: Joo

first: Taeil

first: Yong-Jun

last: Liu


title: Influenza Vaccines Differentially Regulate the Interferon Response in Human Dendritic Cell Subsets

status: Public on Dec 25 2016

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

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

overall_design: Refer to individual Series


title: Transcriptional repression of IRF7 by MYC is critical for antiviral immune response in human pDC

type: Genome binding/occupancy profiling by high throughput sequencing


title: Histone modification and RNA changes in macrophages exposed to Beta-glucan and Fumarate

status: Public on Nov 01 2016

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

type: Expression profiling by high throughput sequencing

summary: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as Beta glucan. We apply an epigenomic approach to characterize the molecular events involved in fumarate or BG induced trained innate immunity. ChIP-seq and RNA-seq data were generated. This analysis identified epigenetic programs in trained macrophages, with fumarate exposure inducing a small subset of BG-induced histone acetylation and methylation changes.

overall_design: Primary human monocytes were exposed to BG or fumarate for 24 hours in culture. The stimulus was then removed and cells were allowed to differentiate to macrophages for an additional 5 days. Macrophages were collected at day 6.

first: Arts

last: Rob

first: Mihai

last: Netea


title: Nasopharyngeal microbiota, host transcriptome and disease severity in children with respiratory syncytial virus infection

status: Public on May 09 2016

summary: Rationale: Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and hospitalizations in infants worldwide. Known risk factors, however, incompletely explain the variability of RSV disease severity among children. We postulate that severity of RSV infection is influenced in part by modulation of the host immune response by the local microbial ecosystem at the time of infection.  Objectives: To define whether different nasopharyngeal microbiota profiles are associated with distinct host transcriptome profiles and severity in children with RSV infection.  Methods:  We analyzed the nasopharyngeal microbiota profiles of young children with mild and severe RSV disease and healthy matched controls by 16S-rRNA sequencing. In parallel, we analyzed  whole blood gene expression profiles to study the relationship between microbial community composition, the RSV-induced host transcriptional response and clinical disease severity.  Measurements and Main results: We identified five nasopharyngeal microbiota profiles characterized by enrichment of H. influenzae, Streptococcus, Corynebacterium, Moraxella or S. aureus. RSV infection and RSV hospitalization were positively associated with H. influenzae and Streptococcus, and negatively associated with S. aureus abundance, independent of age. The host response to RSV was defined by overexpression  of interferon-related genes, and this was independent of the microbiota composition. On the other hand, transcriptome profiles of RSV infected children with H. influenzae and Streptococcus-dominated microbiota were characterized by greater overexpression of genes linked to toll-like receptor-signaling and neutrophil activation and were more frequently hospitalized   Conclusions: Our data suggest an immunomodulatory role for the resident nasopharyngeal microbial community early in RSV infection, potentially affecting RSV disease severity.

overall_design: 104 total samples; 81 are RSV, of which 20 are outpatient and 61 are inpatient; 23 healthy age-matched controls. No technical replicates. 41 of the samples are from a batch run in 2015, the remaining 63 were run in a batch in 2011.

first: Wouter

middle: A

last: de Steenhuijsen Piters

first: Santtu

last: Heinonen

first: Raiza

last: Hasrat

first: Eleonora

last: Bunsow

first: Bennett

last: Smith

first: Maria-Carmen

last: Suarrez-Arrabel

first: Damien

last: Chaussabel

first: Daniel

last: Cohen

first: Elisabeth

last: Sanders

first: Octavio

last: Ramilo

first: Debby

last: Bogaert

first: Asuncion

last: Mejias


title: Defining RNA Transcriptional Biosignatures to Distinguish Febrile Infants 60 Days of Age and Younger with Bacterial vs Non-Bacterial Infections

status: Public on Jul 27 2016

summary: The use of microbiological cultures for diagnosing bacterial infections in young febrile infants have substantial limitations, including false positive and false negative cultures, and non-ideal turn-around times. Analysis of host genomic expression patterns (“RNA biosignatures”) in response to the presence of specific pathogens, however,  may provide an alternate and potentially improved diagnostic approach. This study was designed to define bacterial and non-bacterial RNA biosignatures to distinguish these infections in young febrile infants.

overall_design:
A total of 279 febrile infants and 19 healthy afebrile control infants aged 0-6 months (for a total of 298 samples) for microarray analysis.  For analytic purposes, we classified patients into two groups, those with bacterial infections (n=89) and those with non-bacterial infections (n=190).
144 of the samples were run on Illumina HT12 V4 R1 chips. Of these, there were 34 bacterial infections, 105 non-bacterial infections, and 5 healthy afebrile controls.
154 of the samples were run on Illumina HT12 V4 R2 chips. Of these, there were 55 bacterial infections, 85 non-bacterial infections, and 14 healthy afebrile controls.

first: Prashant

last: Mahajan

first: Nathan

last: Kuppermann

last: Meijas

first: Nicolas

last: Suarez

first: T

middle: C

last: Casper

first: J

middle: M

last: Dean


title: Genome-wide mRNA expression profiling for Wild Type and Itch-/- colonic mucosa Transcriptomes by RNA sequencing

status: Public on Jun 20 2016

first: Nicole

last: Baldwin

summary: To test the hypothesis that defects in the termination of inflammatory signaling led to colon inflammation, we isolated RNA from the colonic mucosa of Itch-/- mice and from the colonic mucosa of wild-type mice treated with DSS and performed genome-wide mRNA expression profiling by RNA sequencing.

overall_design: mRNA profiles comparison between wild type (WT) colon and Itch-/- mice inflammed colon

first: Poojary

last: Venuprasad


title: Transcriptional profiles of human blood dendritic cell (DC) subsets at steady state

status: Public on May 22 2017

summary: Innate sensing of viruses by dendritic cells (DCs) is critical for the initiation of anti-viral adaptive immune responses. Virus, however, have evolved to suppress immune activation in infected cells. We now analyze the susceptibility of different populations of dendritic cells to viral infections. We find that circulating human CD1c+ DCs support infection by HIV and influenza virus. Viral infection of CD1c+ DCs is essential for virus-specific CD8+ T cell activation and cytosolic sensing of the virus. In contrast, circulating human CD141+ DCs and pDCs constitutively limit viral fusion. The small GTPase RAB15 mediates this differential viral resistance in DC subsets through selective expression in CD141+ DCs and pDCs. Therefore, dendritic cell sub-populations evolved constitutive resistance mechanisms to mitigate viral infection during induction of antiviral immune response.

overall_design: Examination of transcriptional profiles in 4 DC subsets purified from 3 donors using RNASeq

first: Aymeric

last: Silvin

first: Chun

middle: I

last: Yu

first: Xavier

last: Lahaye

first: Francesco

last: Imperatore

first: Sylvain

last: Cardinaud

first: Christian

last: Becker

first: Wing-Hong

last: Kwan

first: Cécile

last: Conrad

first: Mathieu

last: Maurin

first: Santy

last: Marques-Ladeira

first: Christel

last: Goudot

first: Yuanyuan

last: Wang

first: Virginia

last: Pascual

first: Esperanza

last: Anguiano

first: Adolfo

last: Garcia-Sastre

first: Marc

last: Dalod

first: Randy

last: Albrecht

first: Arnaud

last: Moris

first: Miriam

last: Merad

first: A

middle: K

last: Palucka

last: Mane


title: Transcriptional repression of IRF7 by MYC is critical for antiviral immune response in human pDC [ChIP-seq]

first: Nicole

last: Baldwin

summary: Type I interferons (IFN) are crucial mediators of human innate and adaptive immunity and are massively produced from plasmacytoid dendritic cells (pDC). IRF7 is a critical regulator of type I IFN production when pathogens are detected by TLR7/9 in pDC. However, hyperactivation of pDC can cause life-threatening autoimmune diseases. To avoid the deleterious effects of aberrant pDC activation, tight regulation of IRF7 is required. Nonetheless, the detailed mechanisms of how IRF7 transcription is regulated in pDC are still elusive. To this end, we identified the global gene expression changes after stimulation of human primary pDC with the TLR9 agonist CpGB. We identified that the transcription factor MYC is prominently upregulated upon CpGB engagement in pDC. Moreover, when we knocked down MYC in the pDC-like cell line GEN2.2, production of interferon-stimulated genes (ISGs) was dramatically increased and was further enhanced by CpGB.  Interestingly, MYC is shown to be recruited to the IRF7 promoter region through interaction with NCOR2/HDAC3 for its repression, and HDAC3 inhibition enhanced IRF7 expression and IFNβ production. Interestingly, activation of TLR9-mediated NF-kB and MAPK and nuclear translocation of IRF7 were greatly enhanced by MYC depletion. Pharmaceutical inhibition of MYC recovered IRF7 expression, further confirming the negative role of MYC in the antiviral response by pDC. Furthermore, the inverse correlation of MYC and IRF7 was validated in psoriasis skin sample datasets. Therefore, our results identify the novel immunomodulatory role of MYC in human pDC and may add to our understanding of aberrant pDC function in autoimmune diseases.

overall_design: 1 sample unstimulated GEN2.2 cells with 2 μg of anti-MYC antibody; 1 sample unstimulated GEN2.2 cells with 2 μg of rabbit IgG control antibody.

first: Tae

middle: W

last: Kim

first: Seunghee

last: Hong

first: Yin

last: Lin

first: HyeMee

last: Joo

first: Taeil

first: Yong-Jun

last: Liu


title: Longitudinal transcriptional pediatric SLE study with clinical parameters

status: Public on Mar 31 2016

summary: The goal of the study was to identify transcriptional correlates of SLE disease activity both at the cohort and at the individual levels. To do so, we longitudinally profiled the whole blood transcriptomes of 158 SLE patients by microarray for up to 4 years, yielding 924 SLE samples and 48 matched pediatric healthy samples. The transcriptional data are complemented by demographic, laboratory and clinical data.

overall_design: 996 samples analyzed of which 72 are Healthy controls and 924 are SLE; 24 technical replicates of healthy samples are included and were used for batch correction purposes.

first: Romain

last: Banchereau

first: Brandi

last: Cantarel

first: Jeanine

last: Baisch

first: Michelle

last: Edens

first: Alma-Martina

last: Cepika

first: Peter

last: Acs

first: Jacob

last: Turner

first: Parvathi

last: Vinod

first: Shaheen

last: Kahn

first: Gerlinde

last: Obermoser

first: Derek

last: Blankenship

first: Edward

last: Wakeland

first: Lorien

last: Nassi

first: Alisa

last: Gotte

first: Marilynn

last: Punaro

first: Jacques

first: Jose

last: Rossello-Urgell

first: Tracey

last: Wright


title: Muscle-specific gene expression changes in normal and high-fat diet in spinal and bulbar muscular atrophy (SBMA)

status: Public on Apr 11 2016

city: Trento

first: maria

last: pennuto

state: --Choose--

address: Centre for Integrative Biology

department: CIBIO

country: Italy

institute: University of Trento

summary: The pattern of gene expression changes were analyzed in the skeletal muscle of knock-in mouse models of SBMA fed either a normal chow diet (NCD) or a high-fat diet (HFD).

overall_design: Microarray analysis was performed in 180-day-old mice (wild type-NCD, wild type-HFD, AR113Q-NCD, and AR113Q-HFD).

first: Maria

last: Pennuto

first: Pamela

last: Gatto

first: Valentina

last: Adami

first: Michael

last: Pancher

first: Anna

last: Rocchi


title: Whole blood Transcriptional Profiles as a Prognostic and Diagnostic Tool in Complete and Incomplete Kawasaki Disease

status: Public on Apr 14 2016

first: Nicole

last: Baldwin

summary: The diagnosis of Kawasaki disease (KD) is often difficult to distinguish from adenovirus (HAdV) and Group A streptococcal disease (GAS). We sought to: 1) to define the KD transcriptional signature that can aid in the diagnosis of complete and incomplete KD in children; 2) to identify specific biomarkers that objectively discriminate between KD and other mimicking conditions, including HAdV and 3) to test the prognostic utility of GEP to determine response to IVIG therapy and development of coronary artery lesions (CAL). Methods: Blood RNA samples were analyzed from 76 pediatric patients with complete KD, 13 with incomplete KD, 19 patients with HAdV, 17 patients with GAS disease, and  age- and sex-matched healthy controls (HC). We used class comparisons (MW p< 0.01, Benjamini-Hochberg, and 1.25 fold change filter), class prediction, modular analysis and MDTH analyses to define the specificity of the KD profiles and identify markers of severity. Results: Statistical group comparisons identified 7,899 genes differentially expressed in 39 complete KD patients versus HC (KD biosignature). This signature was validated in another 37 patients with complete KD and in 13 patients with incomplete KD. Modular analysis in children with complete KD demonstrated overexpression of inflammation, neutrophils, myeloid cell, coagulation cascade, and cell cycle genes. The KNN class prediction algorithm identified 25-classifier genes that differentiated children with KD vs HAdV infection in two independent cohorts of patients with 96% (95% CI [80%-99%]) sensitivity and 95% [74%-99%] specificity. MDTH scores in KD patients significantly correlated with the baseline c-reactive protein (R=0.29, p=0.008) and was four fold higher than in children with HAdV (p<0.01). In addition, KD patients that remained febrile 36 hours after treatment with IVIG (non-responders) demonstrated higher baseline, pre-treatment MDTH values compared with responders [12,290 vs. 5,572 respectively; p=0.009]. Conclusion: Transcriptional signatures can be used as a tool to discriminate between KD and HAdV infection, and may also provide prognostic information.

overall_design: 113 samples, no replicates, 9 HAdV, 57 cKD, 12 FUO, 13 GAS, 3 GAS/SF, 5 inKD, 14 healthy control

first: Preeti

last: Jaggi

first: Asuncion

last: Mejias

first: Zhaohui

last: Xu

first: Han

last: Yin

first: Nicolas

last: Suarez

first: Jane

last: Burns

first: Adriana

last: Tremoulet

first: Alejandro

last: Jordan-Villegas

first: Monica

last: Ardura

first: Damien

last: Chaussabel

first: Virginia

last: Pascual

first: Octavio

last: Ramilo


title: Whole Blood Transcriptional Profiling Differentiates Between Asymptomatic and Symptomatic Human Rhinovirus Detection in Children

status: Public on Jan 14 2016

summary: Human rhinoviruses (HRV) are among the most common causes of respiratory infections in humans but can be frequently detected also in asymptomatic subjects. We evaluated the value of gene expression profiles to differentiate asymptomatic detection from symptomatic HRV infection in children.

overall_design: Previously healthy children <2 years old (n=151) were enrolled at four study sites (Columbus, OH; Dallas, TX; Turku, Finland; and Malaga, Spain). Children were classified into: HRV- healthy controls (HC; n=37); HRV+ asymptomatic (n=14); HRV+ outpatients (n=30); and HRV+ inpatients (n=70). Whole blood RNA samples were hybridized into Illumina arrays.

first: Santtu

last: Heinonen

first: Blerta

last: Dimo

first: Tuomas

last: Jartti

first: Silvia

last: Oliva

first: Carla

last: Garcia


title: Transcriptome of human ILC2s; primary vs IL-1b-primed

status: Public on Apr 25 2016

first: Nicole

last: Baldwin

summary: ILC2s regulate type2 immune responses and protect against helminth infection. We found that ILC2s can be expanded in the presence of a combination of cytokines IL-2 and IL-1b. To better understand the functional and phenotypic consequence of IL-1β activation of ILC2s, we utilized whole transcriptome sequencing (RNA-seq) of freshly isolated ILC2s and IL-1β-primed ILC2s. Differential expression analysis revealed a substantial number of genes underwent significant change between the two conditions (total 4,744 gene, FDR<0.01, Fold change >2), among which 3,871 genes were upregulated in IL-1β –primed ILC2s.

overall_design: Six samples were analyzed, three biological replicates of isolated ILC2s and three biological replicates of isolated ILC2s cultured with IL-1b

first: Yoichiro

last: Ohne

first: LuAnn

last: Thompson-Snipes


title: Oxidized mitochondrial nucleoids released by neutrophils drive  type I Interferon production in human lupus

status: Public on Apr 07 2016

summary: Autoantibodies against nucleic acids and excessive type I Interferon (IFN) are hallmarks  of human Systemic Lupus Erythematosus (SLE). We previously reported that SLE  neutrophils, exposed to TLR7-agonist autoantibodies, release interferogenic DNA, which  we now demonstrate to be of mitochondrial origin. We further show that healthy human  neutrophils do not complete mitophagy upon induction of mitochondrial damage. Rather,  they extrude mitochondrial components, including DNA (mtDNA), devoid of oxidized  residues. When MtDNA undergoes oxidation, it is directly routed to lysosomes for  degradation. This rerouting requires dissociation from the transcription factor TFAM, a  dual high mobility group (HMG) protein involved in maintenance and compaction of the  mitochondrial genome into nucleoids. Exposure of SLE neutrophils, or healthy IFNprimed  neutrophils, to anti-RNP autoantibodies blocks TFAM phosphorylation, a  necessary step for nucleoid dissociation. Consequently, oxidized nucleoids accumulate  within mitochondria and are eventually extruded as potent interferogenic complexes. In  support of the in vivo relevance of this phenomenon, mitochondrial retention of oxidized  nucleoids is a feature of SLE blood neutrophils, and autoantibodies against oxidized  mtDNA are present in a fraction of patients. This pathway represents a novel therapeutic  target in human SLE.

overall_design: 4 samples, no replicates, 2 controls. 2 samples are Neutrophils cultured with and without CCCP (control). 2 samples are Monocytes cultured with and without CCCP (control).

first: Simone

last: Caielli

first: Shruti

last: Athale

first: Bojana

last: Domic

first: Elise

last: Murat

first: Manjari

last: Chandra

first: Romain

last: Banchereau

first: Jeanine

last: Baisch

first: Kate

last: Phelps

first: Sandra

last: Clayton

first: Mei

last: Gong

first: Tracey

last: Wright

first: Marilynn

last: Punaro

first: Karolina

last: Palucka

first: Cristiana

last: Guiducci

first: Jacques


title: human Ino80 chromatin remodeling complex downstream gene

status: Public on Sep 26 2015

city: Changchun

first: Yong

last: Cai

address: Qianjin Street

country: China

institute: JiLin University

summary: HeLa cells were cultured in 6-well tissue culture plates (~2x105 cells/well) in DMEM medium containing 10% fetal bovine serum. Arp8 siRNA (sc-60072) was obtained from Santa Cruz, while all specific siRNAs including non-targeting siRNA (D-001206), Ino80 siRNA (D-004176), Ies6 siRNA (D-019327) and Ies2 siRNA (D-009848) SMART pool were from Dharmacon (U.S.A.). The cells were transiently transfected with 10~20 pmol specific siRNAs using Lipofetamine RNAMAX transfection kit (Invitrogen, Cat.No-864425) following the manufacture’s instruction. 24 hours after transfection, cells were divided into new 6-well plates for western blot, RT-PCR, and DNA microarray analysis. 48 hours after siRNAs transfection, cells were harvested and lysed. Whole-cell extract (WCE) were prepared by adding 4 x SDS sample buffer, and total RNA was isolated using TRIzol® LS Reagent (Invitrogen). In addition, cells from 1 well of a 6-well plate were rinsed twice with warm PBS and harvested. Cells were then stored in an RNA hold solution (ER501-01, Beijing Transgen Biotech Co., Ltd.). After the knockdown efficiency was confirmed, cells in RNA hold solution were sent to EMTD Science and Technology Development Co., Ltd. (Beijing, China) for DNA microarray analysis.

overall_design: RNA obtained from knock down four subunits of human INO80 complex in Hela cells and control sample

first: Cai

last: Yong

first: Jin

last: Jingji

first: Cao

last: Lingling


title: FinHER trial : Patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer

status: Public on Feb 02 2016

city: Brussels

first: Christos

last: Sotiriou

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

summary: The FinHER trial is a multicentre phase 3 randomised adjuvant breast cancer trial that enrolled 1010 patients. The women were randomly assigned to receive three cycles of docetaxel or vinorelbine, followed by three cycles of fluorouracil, epirubicin, and cyclophosphamide.

overall_design: Of the available Finher HER2 samples, gene mRNA expression data was produced from 202 samples. All samples were re-evaluated to ensure tumour was present in the specimen. RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) primary breast tumour tissue.

first: Debora

last: Fumagalli

first: Amir

last: Sonnenblick

first: Sylvain

last: Brohée

first: Sherene

last: Loi

first: Christine

last: Desmedt

first: Michail

last: Ignatiadis

first: Martine

last: Piccart

first: Heikki

last: Jensu

first: Patrick

last: Neven

first: Sybile

last: Loible

first: Carsten

last: Denker

first: Diether

last: Lambrecht


title: Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana

status: Public on Sep 18 2015

city: Umeå

first: Edouard

last: Pesquet

address: Umeå University

department: Department of Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

summary: Transcriptomic analysis of gene expression during the differentiation of cell suspension cultures into tracheary elements using the biological system published by Pesquet et al., Current Biology (2010): tracheary element differentiation was triggered by externally supplying hormone-free habituated cell suspension cultures of Arabidopsis thaliana Col-0 with auxin, cytokinin and epibrassinolides; RNA samples extracted from 3 independent time-courses every 12h from 0h to 4 days were analyzed using ATH1 Arabidopsis Affymetrix micro-array

overall_design: Time-course design during tracheary element differentiation (3 independepent time-course were harvested from initiation 0h to 4 days every 12h) - total of 27 samples corresponding to the 3 replicates of 9 time point time-courses - gene expression was monitored along the time-course compared to 0h


title: Folic acid induces cell type-specific changes in the transcriptomes of breast cancer cell lines

status: Public on May 08 2015

city: Southampton

first: Graham

last: Burdge

address: IDS Building (Mailpoint 887), Southampton General Hospital, Tremona Road

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

summary: The effect of folic acid (FA) on breast cancer (BC) risk is uncertain. We hypothesised that this uncertainty may be due, in part, to differential effects of FA between BC cells with different phenotype. To test this we investigated the effect of treatment with FA concentrations within the range of unmetabolised FA reported in humans on the expression of the transcriptomes of non-transformed (MCF10a) and cancerous (MCF7 and Hs578T) BC cells.

overall_design: Total RNA obtained from three breast cancer cell lines (MCF10a, MCF7, Hs578T) treated with 100nmoles/l folic acid untreated control cells. Six replicates per treatment group.

first: R

middle: J

last: Price

first: Karen

last: Lillycrop


title: Genome-wide mRNA expression profiling for Wild Type and Itch-/- Skin Transcriptomes by RNA sequencing

status: Public on Mar 04 2015

first: Nicole

last: Baldwin

summary: To test the hypothesis that defects in the termination of inflammatory signaling led to skin inflammation that results in the “Itchy” phenotype, we isolated RNA from the lesional skin of Itch-/- mice and from the skin of wild-type mice and performed genome-wide mRNA expression profiling by RNA sequencing. We ranked genes based on the fold change in their expression (increased or decreased) in Itch-/- skin relative to that in wild-type skin. The expression of several TNF–induced genes were increased in Itch-/- skin, including, IL-1β, IL-6, IL-11, IL-19, IL-1RL1, CCL4, CXCL3, CXCL2, CCL3, and CD14.

overall_design: mRNA profiles comparison between wild type (WT) skin and Itch-/- mice lesional skin

first: Poojary

last: Venuprasad


title: BDCA1+ mDCs and BDCA3+ mDCs stimulated with vaccines for 6 hr

status: Public on Oct 22 2014

summary: The mechanisms by which vaccines interact with human APCs remain elusive. We applied systems biology to define the transcriptional programs induced in human DCs by pathogens, innate receptor ligands and vaccines. Upon exposing DCs to influenza, Salmonella enterica and Staphylococcus aureus, we built a modular framework containing 204 pathogen-induced transcript clusters. Module fingerprints were then analyzed in DCs activated with 16 innate receptor ligands. This framework was then used to characterize human monocytes, IL-4 DC and blood DC subsets responses to 13 vaccines. Different vaccines induced distinct signatures based on pathogen type, adjuvant formulation and APC targeted. Fluzone broadly activated IL-4 DC whereas pneumovax only activated monocytes and gardasil (HPV) only activated CD1c+ mDC. This highlights that different antigen-presenting cells respond to different vaccines. Finally, the blood signatures from individuals vaccinated with fluzone or infected with influenza were interpreted using these modules. We identified a signature of adaptive immunity activation following vaccination and symptomatic infections, but not asymptomatic infections. These data, offered with a web interface, might guide the development of improved vaccines.

overall_design: 5 donors; 88 samples; duplicate technical replicates for the medium control for each donor for the BDCA1+ mDC population; single medium control for each donor for the BDCA3+ mDC population (15 total medium controls).

last: Banchereau

first: N

first: A

last: Cepika

first: S

last: Athale

first: Y

last: Xue

first: G

last: Obermoser

first: L

last: Snipes

first: H

last: Xu

last: Cheruku

first: I

last: Berthier

last: Gayet

first: C

last: Yu

first: P

last: Metang

first: M

last: Ohouo

middle: Y

last: Wang

last: Walters

last: Harrod

last: Oh

first: O

last: Ramilo

first: D

last: Chaussabel

first: J

first: K

last: Palucka

first: V

last: Pascual


title: IL4 DCs and monocytes stimulated by 13 human vaccines and LPS for 6hr

first: Nicole

last: Baldwin

summary: While dendritic cells (DCs) are known to play a major role in the process of vaccination, the mechanisms by which vaccines induce protective immunity in humans remain elusive. Herein, we used gene microarrays to characterize the transcriptional programs induced over time in human monocyte-derived DCs (moDCs) in vitro in response to influenza H1N1 Brisbane, Salmonella enterica and Staphylococcus aureus. We built a data-driven modular analytical framework focused on 204 pathogen-induced gene clusters. The expression of these modules was analyzed in response to 16 well-defined ligands, targeting TLRs, cytoplasmic PAMP receptors and cytokine receptors. This multi-dimensional framework covers the major biological functions of APC, including the IFN response, inflammation, DC maturation, T cell activation, antigen processing, cell motility and histone regulation. This framework was used to characterize the response of monocytes and moDCs to 14 commercially available vaccines. These vaccines displayed quantitatively and qualitatively distinct modular signatures in monocytes and DCs, in particular Fluzone and Pneumovax, highlighting the functional and phenotypic differences between APC subsets. This modular framework allows the application of systems immunology approaches to study early transcriptional changes in human APC subsets in response to pathogens and vaccines, which might guide the development of improved vaccines.

overall_design: 64 samples of IL4 DC, and 64 samples of monocytes stimulated by media (controls, designated 1 and 2 to indicate biological replicates), Menomune (Neisseiria meningitis vaccine, MGL), Fluzone 09-10 (Influenza vaccine, FZ), Havrix (Hepatitis A vaccine, HEPA), Ixiaro (Japanese encephalitis vaccine, JPE), ActHib (Haemophilus influenza vaccine, HIB) and Pneumovax (Pneumococcus vaccine, PVX), Engerix-B (Hepatitis B vaccine, HEPB), Zostavax (Herpes Zoster vaccine, HER), and Gardasil (Human Papilloma virus vaccine, HPV), LPS, Ipol (Polio vaccine, POL), Rabies vaccine (RAB), toxoid-based vaccine (TDAP), Varivax (Varicella vaccine, VAR)

first: Romain

last: Banchereau

first: Shruti

last: Athale

first: Alma

last: Cepika

first: Gerlinde

last: Obermoser

first: Hui

first: Marina

first: Isabelle

first: LuAnn

first: Yuanyuan

first: Carson

first: Sangkon

first: Octavio

first: Jacques

first: Damien

first: Karolina

last: Paluka

first: Virginia


title: IFNa DCs and IL4 DCs exposed to H1N1, heat killed S. aureus, or heat killed S. enterica (HKSE) for 1h, 2h, 6h, 12h, or 24h

first: Nicole

overall_design: 60 samples of IFNa DC and 60 samples of IL4 DC grown in Media and exposed to either H1N1 Brisbane virus, heat killed Staphylococcus aureus (HKSA), heat killed Salmonella enterica (HKSE), or nothing (media control) for 1h, 2h, 6h, 12h, or 24h

last: Xu

last: Berthier

last: Snipes


title: Genomic Fingerprints of DC Subsets in the Human Vaginal Mucosa, Skin, and Blood

status: Public on Dec 17 2014

summary: Dendritic cells (DC) localize throughout the body, where they sense and capture invading pathogens to induce protective immune responses. Hence, harnessing the biology of tissue-resident DC is crucial for the rational design of vaccines against pathogens. Herein, we characterized the transcriptomes of four antigen presenting cell (APC) subsets from the human vagina (vLC, vCD14- DC, vCD14+ DC, vMΦ) and compared them to those of three skin DC (sDC) subsets and blood myeloid DC. We find that APC genomic fingerprints are significantly influenced by the tissue of origin as well as by individual APC subsets. Nonetheless, CD14+ APC from both vagina and skin are geared towards innate immunity and pro-inflammatory responses, whereas CD14- DC, particularly sLC, vLC, and vCD14- DC, display both Th2-inducing and regulatory phenotypes. We also identified vAPC subset-specific cellular and functional biomarkers that will guide the design of mucosal vaccines against sexually transmitted pathogens.    Vaginal and skin tissues were obtained from female patients who underwent pelvic or cosmetic surgeries under protocols approved by the Institutional Review Board (IRB) of Baylor Research Institute (BRI). Patients were not infected with HIV, HCV or TB and did not display inflammation in the tissues. No other diagnosis information was available. Blood from healthy female volunteers was obtained under a protocol approved by the IRB of BRI.

overall_design: 87 total samples. 6 Blood mDC; 16 Dermal CD1c+CD14-; 10 Epidermal LC; 12 Vaginal CD1c+CD14-; 13 Vaginal CD1c+CD14+; 7 Vaginal HLADR- w/ 2 replicates (Vaginal HLADR-_VM610 and Vaginal HLADR-_VM611); 9Vaginal LC; 14 Vaginal Macrophage.

first: Dorothee

last: Duluc

first: Romain

first: Julien

last: Gannevat

last: Thompson-Snipes

first: Jean-Philippe

last: Blanck

first: Seunghee

last: Hong

first: Sandy

last: Zurawski

first: Jose

last: Rossello-Urgell

first: Jack

last: Stecher

first: Michael

last: Carley

first: Muriel

last: Boreham

first: SangKon


title: SLE serum induced transcripts regulated by IFNa2b

status: Public on Jun 03 2014

last: Baldwin

summary: To explore the full extent of IFN-regulated transcriptional changes, we exposed monocytes from two healthy donors to recombinant type I IFN (IFN-α2b) in vitro. RNA was extracted at 6 hrs and the expression data was normalized to that of monocytes cultured with medium.

overall_design: Blood monocytes isolated from healthy volunteers were incubated with 20% autologous serum alone or in the presence of 1000 U/ml of IFNα2b (Schering Plough, Kenilworth, NJ) in 6-well plates at a concentration of 106 monocytes per well in 3 ml of media. After incubation for six hours at 37 ⁰C, cells were harvested and RNA was extracted.

first: Alicia

last: Rodriquez-Pla

first: Pinakeen

last: Patel

first: Holden

last: Maecker

first: Lynda

last: Bennett

first: Victoria

last: Cantrell

first: Marilynn

last: Punaro

first: Alisa

last: Gotte

first: Lorien

last: Nassi

last: Palucka

last: Banchereau

last: Pascual


title: Transcripts induced by exposure to SLE serum in healthy blood monocytes

first: Nicole

summary: Monocytes from 3 healthy donors were cultured for 6 hours in the presence of 20% serum from three newly diagnosed, untreated SLE patients. Microarray analysis was then performed upon normalizing the gene expression levels of samples incubated with SLE sera to those incubated with autologous serum.

first: Karolina

first: Jacques

first: Virginia


title: Expression data from Arabidopsis suspension cells overexpressing LHW and T5L1-GFP

status: Public on Aug 18 2014

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

country: Japan

institute: the university of tokyo

summary: Plant vascular tissues are essential for the existence of land plants. Many studies have revealed the process underlying the development of vascular tissues. However, the initiation of vascular development is still a mystery. LONESOME HIGHWAY (LHW), which encodes a bHLH transcription factor, is expressed in the initial step of vascular development in roots. LHW and TMO5 LIKE1 (T5L1) interact each other and function as a heterodimer. Here, we identified specific genes downstream of  LHW-T5L1 with transformed suspension culture cells in microarray experiments.

overall_design: To identify genes downstream of LHW-T5L1, we collected three samples at 0h and 12h with or without estrogen with triplicates.

first: Kuninori

last: Iwamoto

first: Hiroo

last: Fukuda


title: Systemic lupus erythematosus

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

overall_design: Refer to individual Series


title: IFNa and IL4 DCs stimulated with microbial components for 6hr

overall_design: 38 samples of IFNa DC and 39 samples of IL4 DC stimulated by CL097, CpG 2006, CpG 2216, Flagellin, IFNa, IL10, IL15, IL1b, LPS, MDP, PAM3, Poly I:C, Poly I:C-LMW-Lyovec, R837 or TNFa

first: Romain

first: Shruti

last: Athale

first: Alma

last: Cepika

first: Gerlinde

last: Obermoser

first: Hui

last: Xu

first: Marina

last: Ohouo

first: Isabelle

last: Berthier

first: LuAnn

last: Snipes

first: Yuanyuan

last: Wang

first: Carson

last: Harrod

first: Sangkon

last: Oh

first: Octavio

last: Ramilo

first: Damien

last: Chaussabel

last: Paluka


title: Differentially expressed transcripts in SLE blood monocytes according to their capacity to induce mixed lymphocytic reaction

first: Nicole

last: Baldwin

summary: We screened SLE monocytes from 19 SLE patients and selected 4 that induced CD4+ T cell proliferation in vitro and 4 that did not. CFSE labeled CD4-T cells (105) were incubated with SLE monocytes (2 x 104). Cells were harvested at 6 hours for RNA extraction.

first: Alicia

last: Rodriquez-Pla

first: Pinakeen

last: Patel

first: Holden

last: Maecker

first: Jose

last: Rossello-Urgell

first: Lynda

last: Bennett

first: Victoria

last: Cantrell

first: Marilynn

last: Punaro

first: Alisa

last: Gotte

first: Lorien

last: Nassi

first: Karolina

last: Palucka

first: Jacques

last: Banchereau

first: Virginia

last: Pascual


title: Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines

first: Romain

first: Shruti

last: Athale

first: Alma

last: Cepika

first: Gerlinde

last: Obermoser

first: Hui

last: Xu

first: Marina

last: Ohouo

first: Isabelle

last: Berthier

first: LuAnn

last: Snipes

first: Yuanyuan

last: Wang

first: Carson

last: Harrod

last: Oh


title: Transcripts differentially expressed in healthy blood mDCs compared to healthy monocytes

first: Nicole

last: Baldwin

summary: To directly compare the SLE monocyte transcriptional program with that of blood mDC precursors, we purified lineage HLA-DRhighCD11chigh mDCs and CD14+ monocytes from the blood of five healthy donors. Their gene expression profiles were then compared to those of blood SLE monocytes. An unsupervised clustering analysis of transcripts present in >20% of the samples classified healthy monocytes, SLE monocytes and healthy mDCs into three well defined groups. A supervised analysis was then performed to find genes: 1) differentially expressed in healthy mDCs compared to monocytes; 2) shared by healthy blood mDCs and SLE blood monocytes.

first: Alicia

last: Rodriquez-Pla

first: Pinakeen

last: Patel

first: Holden

last: Maecker

first: Jose

last: Rossello-Urgell

first: Lynda

last: Bennett

first: Victoria

last: Cantrell


title: Transcripts induced by recombinant IFNa in healthy blood monocytes at different time points

summary: To explore the full extent of IFN-regulated transcriptional changes, we exposed monocytes from two healthy donors to recombinant type I IFN (IFN-α2b) in vitro. RNA was extracted at different incubation times (1, 6, 24, 48 and 72 hrs) and the expression data was normalized to that of monocytes cultured with medium.

overall_design: Blood monocytes isolated from healthy volunteers were incubated with 20% autologous serum alone or in the presence of 1000 U/ml of IFNα2b (Schering Plough, Kenilworth, NJ) in 6-well plates at a concentration of 106 monocytes per well in 3 ml of media. After incubation for one hour at 37 ⁰C, cells were harvested and RNA was extracted. Identical experiments were done after the following incubation time points: six hours, twenty four hours, two days, and three days.

first: Marilynn

last: Punaro

first: Alisa

last: Gotte

first: Lorien

last: Nassi

first: Karolina

last: Palucka

first: Jacques

last: Banchereau

first: Virginia

last: Pascual


title: Dominant Th1 and Minimal Th17 Skewing in Discoid Lupus Revealed by Transcriptomic Comparison with Psoriasis

status: Public on Nov 18 2013

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Discoid lupus erythematosus (DLE) is the most common skin manifestation of lupus. Despite its high frequency in systemic lupus in addition to cases without extracutaneous manifestations, targeted treatments for DLE are lacking, likely because of a dearth of knowledge of the molecular landscape of DLE skin. Here, we profiled the transcriptome of DLE skin in order to identify signaling pathways and cellular signatures that may be targeted for treatment purposes. Further comparison of the DLE transcriptome with that of psoriasis, a useful reference given our extensive knowledge of molecular pathways in this disease, provided a framework to identify potential therapeutic targets. Although a growing body of data support a role for IL-17 and T helper type 17 (Th17) cells in systemic lupus, we show a relative enrichment of IFN-γ-associated genes without that for IL-17-associated genes in DLE. Extraction of T cells from the skin of DLE patients identified a predominance of IFN-γ-producing Th1 cells and an absence of IL-17-producing Th17 cells, complementing the results from whole-skin transcriptomic analyses. These data therefore support investigations into treatments for DLE that target Th1 cells or the IFN-γ signaling pathway.

overall_design: Comparison of transcriptomes between skin conditions

first: Ali

last: Jabbari

last: Suárez-Fariñas

first: James

middle: G

last: Krueger


title: Genome-wide analysis of whole blood transcriptional response to Respiratory Syncytial Virus, Influenza and Rhinovirus lower respiratory tract infection (LRTI) in children

status: Public on Nov 12 2013

last: Baldwin

summary: Analysis of transcriptional profiles in whole blood from children < 2 years of age (and healthy matched controls) with RSV, rhinovirus and influenza infection. The hypothesis tested is that transcriptional profile heterogeneity will reflect patient clinical heterogeneity and that RSV infection induces a distinct host response compared with influenza and rhinovirus infection

overall_design:
Total RNA extracted from whole blood (lysed in Tempus tubes) drawn from individual pediatric patients with acute RSV, influenza and Rhinovirus lower respiratory tract infection. A total of 241 samples are analyzed: 135 with acute RSV LRTI, 30 with Rhinovirus LRTI, 16 with influenza LRTI, 39 age-sex matched healthy controls and 21 samples obtained one month after the acute hospitalization in children with RSV.

Samples GSM1226237-GSM1226272, which were hybridized to Platform GPL10558, were normalized separately from the other Samples in this Series, which were hybridized to Platform GPL6884.
'GSE38900_non-normalized_GSM1226237-GSM1226272.txt.gz' includes the non-normalized data for Samples GSM1226237-GSM1226272; 'GSE38900_non-normalized.txt.gz' includes the non-normalized data for the other Samples.

first: Asuncion

last: Meijas

first: Blerta

last: Dimo

first: Nicholas

last: Suarez

first: Carla

last: Garcia

first: M.

last: Suarez-Arrabal

first: Tuomas

last: Jartti

first: Derek

last: Blankenship

first: Alejandro

last: Jordan-Villegas

first: Monica

last: Ardura

first: Zhaohui

last: Xu

first: Damien

last: Chaussabel

first: Octavio

last: Ramilo


title: Trivalent Inactivated Influenza Vaccine (TIV) and Live Attenuated Influenza Vaccine (LAIV) Induce Different B cell and Transcriptional Responses in Children

status: Public on Mar 31 2014

first: Nicole

summary: LAIV and TIV are effective for prevention of influenza infection in children, but the mechanisms associated with protection are still not well defined. We analyzed the differences in B cell responses and transcriptional profiles. Compared to baseline, LAIV elicited a significant increase in naïve, memory and transitional B cells on day 30, while vaccination with TIV elicited an increase in number of plasmablasts on day 7. Antibody titers against the three vaccine strains (H1N1, H3N2 and B) were significantly higher in the TIV group and correlated with number of antibody-secreting cells. Regarding transcriptional profiles, both vaccines induced expression of interferon signaling, but at different time points, TIV on 1 day, and LAIV on day 7 day post-vaccination, the last only in children younger than 5 years old. Interferon-related genes over expressed in both vaccinated groups correlated with antibody titers of H3N2 vaccines strain. These results suggest that LAIV and TIV induced significant different B cell responses in vaccinated children. Early induction on interferon genes appears important for development of effective antibody responses.

overall_design: Longitudinal study with time points at baseline (day 0), 24hr, day 7 and day 30. 136 total samples analyzed. This was a prospective cohort of previously healthy children 6 months to 14 years of age enrolled between October 2011 and February 2012. Thirty seven subjects were randomized to receive one dose of either LAIV (FluMist®, MedImmune) (n= 20) or TIV (Fluzone®, Sanofi Pasteur) (n= 17). Two exceptions were applied to the randomization: four children with ages between 6 months and 2 years old received TIV, since LAIV is not licensed on this age group, and four children with controlled asthma also received TIV following CDC’s recommendations. One child aged 6 months at the time of enrollment received two doses of the vaccine with one month interval apart, since it was his first influenza vaccination. Exclusion criteria included any medical comorbidities or chronic conditions (lung, kidney or heart disease), use of systemic steroids in the previous 2 weeks, and congenital or acquired immunodeficiencies. The 2011-2012 LAIV and TIV vaccines contained A/California/7/2009 (H1N1)-like, A/Perth/16/2009 (H3N2)-like and B/Brisbane/60/2008-like antigens, the same strains used on the 2010-2011 influenza vaccine. TIV recipients aged 6 to 35 months old received 0.25 mL intramuscularly and recipients aged 36 months and older received 0.5 mL. LAIV recipients received 0.2 mL by intranasal route, 0.1 mL per nostril. Blood samples were collected at four time points, on day zero prior to vaccination, and day 1, day 7 (range 6-8) and day 30 (range 27-33) post-vaccination.

first: Raquel

last: Cao

first: Gerlinde

last: Obermoser

first: Nicolas

first: Santiago

last: Lopez

first: Emilio

last: Flano

first: Sara

middle: E

last: Mertz

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre

last: Mejias

first: Karolina

last: Palucka

last: Pascual


title: Transcriptional Profiling is Superior to Procalcitonin to Discriminate Bacterial vs. Viral Lower Respiratory Tract Infections in Hospitalized Adults

status: Public on Sep 14 2015

last: Baldwin

summary: Background: Distinguishing between bacterial and viral lower respiratory tract infections (LRTI) in hospitalized patients remains challenging. Transcriptional profiling is a promising tool for improving diagnosis in LRTI.     Methods: We performed whole blood transcriptional analysis in a cohort of 118 adult patients (median [IQR] age, 61 [50-76] years) hospitalized with bacterial, viral or viral-bacterial LRTI, and 40 age-matched healthy controls (60 [46-70] years). We applied class comparisons, modular analysis and class prediction algorithms to identify distinct biosignatures for bacterial and viral LRTI, which were validated in an independent group of patients.     Results: Patients were classified as bacterial (B, n=22), viral (V, n=71) and bacterial-viral LRTI (BV, n=25) based on comprehensive microbiologic testing. Compared with healthy controls statistical group comparisons (p<0.01; with multiple test corrections) identified 3,376 differentially expressed genes in patients with B-LRTI; 2,391 in V-LRTI, and 2,628 in BV-LRTI. Independent of etiologic pathogen, patients with LRTI demonstrated overexpression of innate immunity and underexpression of adaptive immunity genes. Patients with B-LRTI showed significant overexpression of inflammation (B>BV>V) and neutrophils (B>BV>V) while those with V-LRTI displayed significantly greater overexpression of interferon genes (V>BV>B). The K-Nearest Neighbors (K-NN) algorithm identified 10 classifier genes that discriminated patients with bacterial vs viral LRTI with 97% [95%CI: 84-100] sensitivity and 92% [77-98] specificity. In comparison, procalcitonin classified bacterial vs viral LRTI with 38% [18-62] sensitivity and 91% [76-98] specificity.      Conclusions: Transcriptional profiling can be used as a helpful tool for the diagnosis of adults hospitalized with LRTI.

overall_design: 158 samples, no replicates; bacterial LRTI n=22, viral LRTI n=71, bacterial-viral coinfections n=25, and healthy controls n=40

last: Suarez

first: Eleonora

last: Bunsow

first: Ann

middle: R

last: Falsey

first: Edward

last: Walsh

first: Asuncion


title: Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 4)

status: Public on Jul 15 2013

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

summary: When adapting to environmental stress, cells attenuate and reprogram their translational output.  In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs.  The Ago2/microRNA machinery has been shown to participate in stress-induced translational upregulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking.  Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by CLIP-seq.  Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3` UTR and CDS sites exhibiting stronger interaction.  Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction.  To compare the changes in Ago2 binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA-seq.  Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated.  Taken together, these data point to a role for Ago2 and the mammalian microRNAs in mediating the translational component of the stress response.

overall_design: In this sub-series, RNAseq data from sucrose gradient fractions with arsenite treatment are presented.

middle: V

first: Gregory

last: Hannon


title: Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 3)

overall_design: In this sub-series, CLIP and RNAseq data from the hippuristanol treatment experiment are presented.  Experiments on 293S cells +/- hippuristanol treatment, in 2 biological replicates.  Here, for each treatment/replicate sample, an aliquot was used for RNA-seq, and the rest was split into three aliquots to perform 3 parallel CLIP-seq protocols with different antibodies.  So, each RNA-seq dataset here corresponds to 3 CLIP-seq datasets.


title: SHARP1 suppresses breast cancer metastasis by promoting degradation of hypoxia-inducible factors

status: Public on Jul 19 2012

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
Triple Negative Breast cancer accounts for some of the most aggressive types of breast cancer. By interrogating clinical datasets, we found that the activities of p63 and Hypoxia-Inducible-Factors (HIFs), two master regulators of the invasive and metastatic cancer cell phenotype are  linked in TNBC through the p63-target Sharp1. Mechanistically, Sharp1 promotes HIF-1α/HIF-2α proteasomal degradation by serving as HIFs presenting factor to the proteasome independently from oxygen levels and prior ubiquitination.
To investigate unbiasedly if Sharp1 is a general inhibitor of HIF induced transcriptional program, we compared the transcriptomic profile of cells either overexpressing Sharp1 or depleted of HIF1a and HIF2a.

overall_design: We collected RNA from control MDA-MB-231 cells (shGFP) or MDA-MB-231 cells overexpressing Sharp1 or MDA-MB-231 cells depleted of HIF1a and HIF2a (shHIF). Cells were left untreated in normal culturing conditions before harvesting. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each of the 4 conditions (1: shGFP, control cells; 2: shHIF cells; 3: Sharp1-overexpressing cells) for a total of 12 samples.

first: Marco

last: Montagner

first: Elena

last: Enzo

first: Zanconato

last: Francesca

first: Anna

last: Parenti

first: Antonio

last: Rosato

last: Rampazzo

first: Genesio

last: Leo

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates

type: Non-coding RNA profiling by high throughput sequencing


title: Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors.

status: Public on Sep 01 2011

first: Boris

last: Novakovic

summary: Background: the human placenta facilitates the exchange of nutrients, gas and waste between the fetal and maternal circulations. It also protects the fetus from the maternal immune response. Due to its role at the feto-maternal interface, the placenta is subject to many environmental exposures that can potentially alter its epigenetic profile. Previous studies have reported gene expression differences in placenta over gestation, as well as inter-individual variation in expression of some genes. However, the factors contributing to this variation in gene expression remain poorly understood. Results: in this study, we performed a genome-wide DNA methylation analysis of gene promoters in placenta tissue from three pregnancy trimesters. We identified large-scale differences in global DNA methylation levels between first, second and third trimesters, with an overall progressive increase in average methylation from first to third trimester. The most differentially methylated genes included many immune regulators, reflecting the change in placental immuno-modulation as pregnancy progresses. We also detected increased inter-individual variation in the third trimester relative to first and second, supporting an accumulation of environmentally induced (or stochastic) changes in DNA methylation pattern. These highly variable genes were enriched for those involved in amino acid and other metabolic pathways, potentially reflecting the adaptation of the human placenta to different environments. Conclusions : the identification of cellular pathways subject to drift in response to environmental influences provide a basis for future studies examining the role of specific environmental factors on DNA methylation pattern and placenta-associated adverse pregnancy outcomes.

overall_design: A total of 42 samples, with 18 first trimester, 10 second trimester, 14 full term placenta

first: Ryan

last: Yuen

first: Lavinia

last: Gordon

first: Maria

middle: S

last: Panaherrera

first: Andrew

last: Sharkey

first: Ashley

last: Moffett

first: Jeffrey

last: Craig

first: Wendy

last: PRobinson

first: Richard

last: Saffery


title: Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

status: Public on Jun 04 2015

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary:
Neuronal activity causes the rapid expression of immediate early genes that are crucial for experience driven changes to synapses, learning, and memory.
Here, using both molecular and genome-wide next generation sequencing methods, we report that neuronal activity stimulation triggers the formation of DNA double strand breaks (DSBs) in the promoters of a subset of early-response genes, including Fos, Npas4, and Egr1. Generation of targeted DNA DSBs within Fos and Npas4 promoters is sufficient to induce their expression even in the absence of an
external stimulus. Activity-dependent DSB formation is likely mediated by the type II topoisomerase, Topoisomerase IIb (Topo IIb), and knockdown of Topo IIb attenuates both DSB formation and early response gene expression following neuronal stimulation.
Our results suggest that DSB formation is a physiological event that rapidly resolves topological constraints to early-response gene expression in neurons.

overall_design: Generation of sequencing data from ChIP-seq with antibodies against γH2AX and Topo IIβ after neuronal activity stimulation, and RNA-seq after etoposide treatment

first: Ram

last: Madabhushi

first: Fan

last: Gao


status: Public on Feb 01 2011

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

summary:
The aim of this study was to determine the effects of unprotected dietary unsaturated fatty acids (UFA) from different plant oils on gene expression in the mammary gland of grazing dairy cows.
Milk composition and gene expression in the mammary gland tissue were evaluated in grazing dairy cows supplemented with different unsaturated fatty acids (UFA). The UFA supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health.

SUBMITTER_CITATION: Mach, N., A. A. A. Jacobs, L. Kruijt, J. Van Baal, and M. A. Smits. 2011. Alteration of gene expression in mammary gland tissue of dairy cows in response to dietary unsaturated fatty acids. Animal.DOI:10.1017/S1751731111000103

overall_design: A total of 28 Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), days in milk (DIM; 153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to four UFA-sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days (Period I) after which, all 28 cows were switched to a control diet for an additional 28 days (Period II). On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in lipid metabolism gene expression.

first: Anton

last: Jacobs

first: Leo

last: Kruijt

first: Jurgen

last: van Baal

first: Mari

last: Smits


title: Histone Modifications by ChIP-seq from ENCODE/Broad Institute

status: Public on Jun 02 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (mailto:nshoresh@broad.mit.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track displays maps of chromatin state generated by the Broad/MGH ENCODE group using ChIP-seq. Chemical modifications (methylation, acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription.
The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
ChIP-seq: Cells were grown according to the approved ENCODE cell culture protocols. Cells were fixed in 1% formaldehyde and resuspended in lysis buffer. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibodies against each of the histone antibodies listed above. Antibody-chromatin complexes were pulled-down using protein A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, treated with RNAse and purified. One to ten nanograms of DNA were end-repaired, adapter-ligated and sequenced by Illumina Genome Analyzers as recommended by the manufacturer.
Alignment: Sequence reads from each IP experiment were aligned to the human reference genome (GRCh37/hg19) using MAQ with default parameters, except '-C 11' and '-H output_file', which outputs up to 11 additional best matches for each read (if any are found) to a file. This information was used to filter out any read that had more than 10 best matches on the genome. Note: It is likely that instances where multiple reads align to the same position and with the same orientation are due to enhanced PCR amplification of a single DNA fragment. No attempt has been made, however, to remove such artifacts from the data, following ENCODE practices.
Signal: Fragment densities were computed by counting the number of reads overlapping each 25 bp bin along the genome. Densities were computed using igvtools count with default parameters (in particular, '-w 25' to set window size of 25 bp and '-f mean' to report the mean value across the window), except for '-e' set to extend the reads to 200 bp, and the .wig output was converted to bigWig using wigToBigWig from the UCSC Kent software package.
Peaks: Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal. All data sets where processed with '-task chip', and with '-windows 100,200,500,1000,5000,10000,100000'. (No mask file nor the '-trim' option have been used.) The resulting called segments were then further filtered to remove intervals that are significantly enriched only because they contain smaller enriched intervals within them. This post-processing step has been implemented using Matlab. The use of the post-processing step allowed very large enriched intervals (of the order of Mbps for H3K27me3, for instance) to be detected, as well as much smaller intervals, without the need to tailor the parameters of Scripture based on prior expectations.

first: Noam

last: Shoresh


title: Differentially expressed transcripts in SLE blood monocytes

first: Nicole

last: Baldwin

summary: To better characterize the molecules that could potentially confer antigen presenting capacity to SLE monocytes, we assessed their gene expression profile.

overall_design: Blood monocytes from five healthy controls and five pediatric SLE patients were isolated using CD14+ selection. Because drugs used to treat SLE could induce considerable transcriptional changes, we selected active, newly diagnosed patients who had never received oral or intravenous (IV) medications.

first: Alicia

last: Rodriquez-Pla

first: Pinakeen

last: Patel

first: Holden

last: Maecker

first: Jose

last: Rossello-Urgell

first: Lynda

last: Bennett

first: Victoria

last: Cantrell

first: Marilynn

last: Punaro

first: Alisa

last: Gotte

first: Lorien

last: Nassi

first: Karolina

last: Palucka

first: Jacques

last: Banchereau

first: Virginia

last: Pascual


title: Deinococcus radiodurans R1: wildtype strains vs. DR1790-deletion strains

status: Public on Sep 10 2010

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

institute: Zhejiang University

summary:
Transcriptional profiling of comparing wildtype strains with DR1790-deletion strains under normal growth contidions.

Keywords: Genetic modification

overall_design: One-condition experiment, wild type strains vs. DR1790-deletion strains. Two biological replicates were carried out.

first: Hu

last: Wang


title: HIRA null vs parental mES cell line

status: Public on Dec 19 2009

city: London

first: Ariane

last: Chapgier

address: 30 guilford street

department: Institute of Child Health

institute: University College London

summary:
Hira has been implicated in replication-independent chromatin assembly.
To determine the role of Hira in the regulation of embryonic stem (ES) cell gene expression, we used microarrays to analyze the global program of gene expression in Hira null versus WT undifferentiated ES cells.

overall_design: Undifferentiated Mus musculus ES cells were harvested at different confluent stages, and assessed for gene expression

first: Nipurna

last: Jina

first: Pete

last: Scambler

first: Simon

last: Elsässer

first: Aaron

middle: D

last: Goldberg

first: C

last: Allis


title: Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

status: Public on Jun 25 2010

first: Fedor

last: Karginov

summary: Messenger RNAs are regulated by a variety of degradation mechanisms in mammalian cells.  In the canonical animal microRNA pathway, microRNAs in complex with Argonaute proteins bind to many mRNA targets with imperfect complementarity, leading to degradation of the mRNA through the regular decay machinery.  The ancestral “slicer” endonuclease activity of Argonaute2 itself, which requires more extensive complementarity with the target RNA, is not used in this pathway, and has only been observed in two microRNA-guided cases.  Nevertheless, the cleavage capacity of mammalian Ago2 is conserved and essential for viability.  Here, we assess the endonucleolytic function of Ago2 and other nucleases by identifying cleavage products retaining 5`-phosphate groups in mouse ES cells on a transcriptome-wide scale.  We detect a significant signature of Ago2-dependent cleavage events and validate several targets.  Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in this mode of mRNA regulation.  Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events, including one in the Dgcr8 mRNA, that functionally regulate mRNA levels in mES cells.  Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Global 5`-phosphate-dependent RACE in WT, Ago2-KO and Drosha-excised mouse ES cells and human 293S cells

first: Gregory

last: Hannon


title: Whole Genome Segregation of light and nitrate effect in rice plants

status: Public on Dec 31 2009

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

summary: The current study aimed at segregating the light and nitrate effect in rice plants (Oryza sativa indica). The primary aim of the study was to demarcate the genes that were purely regulated by light and nitrate. A separate list of genes that were co-regulated by these two signals would provide insights into the exact mode of regulation of primary metabolic pathways.

overall_design:
Rice plants (Oryza sativa indica) were grown in light with  12 hour diurnals in the absence of nutrients at 25 °C for 8-10 days before being treated with 120 mM nitrate prior to RNA isolation. In case of dark experiments the plants were grown in total darkness and treated with 120mM nitrate in dark prior to RNA isolation.
Total RNA was isolated from 2 separate biological replicates for each treatment.Two-color arrays were performed for each treatment. Flip dye replicates were performed with biological replicates being flip dye labeled i.e. The biological replicates for individual treatments were labeled with opposite dyes.

first: Ravi

last: Pathak


title: Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 1)

overall_design: In this sub-series, CLIP and RNAseq data from the arsenite treatment experiment are presented.  Experiments on 293S cells +/- arsenite treatment, in 4 biological replicates.  On each treatment/replicate biological sample, both a CLIP-seq protocol and an RNA-seq protocol were performed, so these datasets are “paired” in addition to the treatment pairing.


title: Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 2)

overall_design: In this sub-series, CLIP and RNAseq data from the emetine treatment experiment are presented.  Experiments on 293S cells +/- emetine treatment, in 1 biological replicate.  Here, for each treatment/replicate sample, an aliquot was used for RNA-seq, and the rest was split into three aliquots to perform 3 parallel CLIP-seq protocols with different antibodies.  So, each RNA-seq dataset here corresponds to 3 CLIP-seq datasets.


title: Intertwining threshold settings, biological data and database knowledge to optimize the selection of differentially expressed genes

status: Public on Jun 19 2011

city: MONTPELLIER

first: Paul

last: Chuchana

address: 80 avenue Augustin Fliche

institute: INSERM

summary: Background: Many tools used to analyze microarrays in different conditions have been described. However, the integration of the deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion, based on biological functions exists, to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings: To improve transcriptomic analysis of microarrays, we propose a new statistical approach, which takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed gene in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter, which is associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us select the optimal threshold required for the most pertinent selection of differently expressed genes. Conclusions/significance: We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. For example, we thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes, which are truly differentially expressed.

overall_design: Macrophages isolated from six heathy donnor was/or not stimulated. Paired data, i.e. LPS stimulated macrophages versus unstimulated macrophages from the same donor have been compared (eg, Donor1_LPS vs Donor1_NT; see processed data file linked below). The six comparaisons have been globaly analyse using two parameters, i.e. threshod and occurency, associated with a request of a database knowledge. Both parameters has been tune to define the best setting allowing to optimize the selection of differentially expressed genes

last: CHUCHANA

first: Philippe

last: HOLZMULLER

first: Frederic

last: VEZILIER

first: David

last: BERTHIER

first: Isabelle

last: CHANTAL

first: Jean

middle: L

last: LEMESRE

first: Gerard

last: CUNY

last: NIRDE

first: Bruno

last: BUCHETON


title: Genome-wide effect of cholera toxin and nitrate treatment in etiolated rice plants

status: Public on Dec 01 2010

summary: The present study used microarray approach to identify the genomewide response to cholera toxin in the presence of nitrate. Considering that fact that the possibility of the existence of multiple Gα genes/proteins in plants has not been conclusively ruled out, analysis of the genomewide impact of RGA1 mutation in rice and GPA1 mutation in Arabidopsis reveal only those genes that are under their direct control. On the other hand, assuming that all those different Gα subunits in any given plant are regulated by cholera toxin, analysis of the genomwide response to cholera toxin could capture the entire G-protein responsive transcriptome, beyond what can be revealed by the mutant approach. This could reveal even those genes that respond to other, as yet unidentified Gα subunits, as well as reveal some genes that are non-specifically regulated by cholera toxin, independent of any G-proteins.

overall_design: Total RNA was isolated from 10 day old excised rice leaves treated with or without cholera toxin in the presence of nitrate.Total RNA was first converted into cDNA and then into cRNA labeled with Cy3 and Cy5 dyes. These were hybridized on the 44K 60-mer whole genome arrays on glass slides. The slides were washed and scanned on an Agilent scanner (G2565B) at 100 %  laser power. Data extraction was carried out with Agilent Feature Exiraction software (version 9.1). The experiment was repeated with a biological-cum-technical replicate where total RNA samples were isolated from a fresh batch of rice plants and the cRNAs were labeled with opposite dyes (dye-swap).


title: MicroRNA profiling in mouse medulloblastomas and normal cerebellar tissues

status: Public on Jan 17 2009

summary: Medulloblastomas (MBs) are the most common brain tumors in children.  Some are thought to originate from cerebellar granule neuron progenitors (GNPs) that fail to undergo normal cell cycle exit and differentiation.  Since microRNAs regulate numerous aspects of cellular physiology and development, we reasoned that alterations in miRNA expression might contribute to MB.  We tested this hypothesis using two spontaneous mouse MB models with specific initiating mutations, Ink4c-/-; Ptch1+/- and Ink4c-/-; p53-/-.  We found that 26 miRNAs showed increased expression and 24 miRNAs showed decreased expression in proliferating mouse GNPs and MBs relative to mature mouse cerebellum, regardless of genotype.  Among the 26 overexpressed miRNAs, nine were encoded by the miR-17~92 cluster family, a group of microRNAs implicated as oncogenes in several tumor types.  Analysis of human MBs demonstrated that three miR-17~92 cluster miRNAs (miR-92, miR-19a and miR-20) were also overexpressed in human MBs with a constitutively activated SHH signaling pathway, but not in other forms of the disease.  To test whether the miR-17~92 cluster could promote MB formation, we enforced expression of these miRNAs in GNPs isolated from cerebella of postnatal (P) day P6 Ink4c-/-; Ptch1+/- mice.  These, but not similarly engineered cells from Ink4c-/-; p53-/- mice, formed MBs in orthotopic transplants with complete penetrance.  Interestingly, orthotopic mouse tumors ectopically expressing miR-17~92 lost expression of the wild-type Ptch1 allele.  Our findings suggest a functional collaboration between the miR-17~92 cluster and the SHH signaling pathway in the development of MBs in mouse and man.

overall_design: Samples: purified CGNP-like mouse medulloblastoma cells; purified CGNPs from age day 6 (P6) mice; whole cerebellum from P6 mice; whole cerebellum from 1 month old mice.  Each from three backgrounds (except tumors)  - wt; Ptc+/-,Ink4c-/-; p53-/-,Ink4c-/-.  Two to five biological replicates each.

first: Martine

middle: F

last: Roussel


title: CESTA transcript analysis

status: Public on Jul 12 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: Brassinosteroids (BRs) are steroid hormones that are essential for the development of plants. A tight control of BR homeostasis is vital for modulating their impact on various growth responses. However, whilst it is recognized that the rapid adaptation of de novo synthesis plays a key role in adjusting required BR levels, our knowledge of the mechanisms governing feedback control is limited. We identified the transcription factor CESTA as a novel regulator of BR biosynthesis. ces-D was isolated in a screen of Arabidopsis mutants by BR over-accumulation phenotypes. Loss-of-function analysis and the use of a dominant repressor version revealed functional overlap among CESTA and its homologues and confirmed the role of these basic helix-loop-helix proteins in the positive control of BR biosynthetic gene expression. In this experiment we compare the transcriptome of the CESTA mutant to wild-type plants using the Affymetrix ATH1 array.

overall_design: 4 samples were used in this experiment.

first: Mamoona

last: Khan