title: Immune landscape of viral- and carcinogen-drived head and neck cancer

status: Public on Nov 13 2019

first: Anthony

middle: Richard

last: Cillo

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

summary: Head and neck squamous cell carcinoma (HNSCC) arises through exposure to environmental carcinogens or malignant transformation by human papillomavirus (HPV). Here, we assessed the transcriptional profiles of 131,224 single cells from peripheral and intra-tumoral CD45+ immune populations from HPV– and HPV+ HNSCC and healthy donors. A spectrum of transcriptional signatures in immune lineages ranging from similar to highly divergent was present in the tumor microenvironments (TME) in HPV– and HPV+ HNSCC. CD8+ and regulatory CD4+ T cells were similar in HPV– and HPV+ HNSCC, compared to significant differences between helper CD4+ T cells, B cells and myeloid cells. Further dissection of the major immune lineages identified unique cell states and differentiation trajectories. We contextualized our results by performing multispectral immunofluorescence and evaluating putative cell-cell communication based on spatial proximity, and found longer progression free survival in patients with enrichment of a CD4+ T follicular helper cell signature.

overall_design: Total of 63 samples were analyzed by scRNAseq. Of these, 26 samples were paired peripheral blood mononuclear cells and tumor infiltrating immune cells from HNSCC patients (18 HPV- and 8 HPV+), 6 were peripheral blood mononuclear cells from healthy donors, and 5 were tissue resident immune cells from healthy donor tonsils.

middle: R

first: Tullia

middle: C

last: Bruno

last: Ferris

first: Dario

middle: A

last: Vignali


title: Tuberculosis-associated IFN-I induces Siglec-1 on microtubule-containing tunneling nanotubes and favors HIV-1 spread in macrophages

status: Public on Apr 04 2020

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

summary: To understand the susceptbility of human M(IL-10) macrophages to human immunodeficiency virus, we performed a genome-wide transcriptome analysis in these cells to identify a gene profile responsible for this phenomenon. A distinct 60 gene-transcript signature was defined in M(IL-10) macrophages, using a combination of the expression level, statistical filters and hierarchical clustering; 51 genes were up-regulated and 9 genes were down-regulated in M(IL-10) macrophages compared to control cells. Among the genes upregulated, we identified a interferon-stimulated gene (ISG) signature include SIGLEC-1. We confirmed SIGLEC-1 and other five ISG genes by qPCR, FACS and western blot.

overall_design: Human macrophages were diffentiated from freshly isolated monocytes treated with M-CSF and conditioned media. Conditioned media was generated from Mycobacterium tuberculosis-infected (coMtb) or non-infected (coCtrl) macrophages. Upon confirmation of the M(IL-10) macrophage phenotype induced by coMtb, and susceptbility to HIV-1 infectiion, the transcriptome analyses was performed in these conditioned cells from four independent donors.

first: Shanti

last: Souriant

first: Céline

last: Cougoule

first: Ingrid

last: Mercier

first: Maeva

last: Dupont

first: Christel

last: Vérollet

first: Geanncarlo

last: Lugo-Villarino


title: Dexamethasone inhibits respiratory syncytial virus-driven mucus production while increasing viral replication without altering antiviral interferon signaling

status: Public on Nov 19 2019

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

country: USA

institute: NIBR

type: Expression profiling by high throughput sequencing

summary:
Purpose: To understand how dexamethasone has beneficial effects on reducing mucus production but inhibits viral defense mechanisms
Methods: RSV-infected mouse lungs and various cell lines, plus and minus dexamethason, were examined by RNAseq, and pathway analysis of differentially-expressed genes were compared
Results:  Using RNA-seq we identified a subset of cytokines that were induced by RSV and repressed by dexamethasone.  Interestingly, while RSV induced interferons (IFNs) and IFN stimulated genes (ISGs), dexamethasone treatment did not affect the expression of these genes or antiviral IFN signaling pathways as has been observed with glucocorticoid treatment of other respiratory viruses [13].  Using an unbiased approach, we found that certain RSV-driven gene expression networks and genes were specifically modulated by dexamethasone treatment.  Importantly, dexamethasone also reduced RSV clearance in vivo, which correlated with a reduction in specific immune response markers.
Conclusion:  Our results support the possibility that the beneficial anti-inflammatory effects of dexamethasone treatment are counterbalanced by the increased viral load in patients, accounting for the lack of clinical benefit derived from treatment during RSV infection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Lungs from RSV-infected and dexamethasone treated or non-treated mice, or various cell lines infected and/or dexamethasone-treated were compared

first: Christopher

middle: S

last: McAllister

first: Dan

last: Ansaldi

first: Ellena

middle: J

last: Growcott

first: Yang

last: Zhong

first: Doug

last: Quackenbush

first: Karen

last: Wolff

first: Olga

last: Tanaseichuk

first: Gerald

last: Lelais

first: S

middle: W

last: Barnes

first: Glenn

last: Federe

first: Fabio

last: Luna

first: Yingyao

last: Zhou

first: Kelli

middle: L

last: Kuhen


title: Identification of miR-143 mRNA-targets by AGO-RIP in the myeloid cell line K562

status: Public on Jan 12 2020

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32A

department: Division of Hematology and Oncology

country: Germany

institute: Leipzig University Hospital

summary: MiR-143 is a miRNA commonly found to  be downregulated in a variety of cancers. The goal of this study is the identifacation of miR-143 target mRNAs by next generation sequencing (NGS) in myeloid cells after overxpression of miR-143.

overall_design: We lentiviraly overexpressed miR-143 in the myeloid cell line K562. After selection of positive cells we isolated RNAs associated with the RNA induced silencing complex (RISC) by immunoprecipitation of AGO2. Isolated RNA of 3 independent experiments was subjected to next generation sequencing.

first: J-U

last: Hartmann


title: 2-Methylcitrate cycle: a well-regulated controller in Bacillus sporulation

status: Public on Nov 14 2019

city: Wuhan

first: Xinfeng

last: Li

address: Shi zi shan street

country: China

institute: Huazhong Agricultural University

summary: To understand which gene(s) are affected by 2-methylcitrate to lead to the delayed sporulation in ∆prpD, we extracted the total RNA from BMB171 and ∆prpD at 12 h for whole genome transcription analysis by RNA sequencing (RNA-Seq). Our RNA-seq data showed that transcriptions of almost all of the SigF regulon genes, as concluded from the B. subtilis regulon, were significantly down-regulated in ∆prpD compared with the wild type BMB171. However, almost all the regulon genes of SigH, a sigma factor that functions upstream of SigF, were significantly up-regulated in ∆prpD. Those genes included spo0A, the early-expressed operon spoIIA and sigF itself. These results indicated that dysregulation of genes occurred on various levels. In particular, though, post-transcriptional inhibition of sigF functionality might subsequently lead to down-regulation of SigF regulon genes in the ∆prpD mutant.

overall_design: BMB171 and ΔprpD strains were cultured in GYS medium for 12 h, RNA samples were isolated and sequenced, each with two repetitions.

first: Cao

last: Zheng

first: Jin

last: He


title: Induction of a tumorigenic neural crest stem cell-like state in INK4A-expressing melanoma lines.

status: Public on May 22 2020

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

summary: We generated a live reporter for tumor-initiating cells in the 501MEL human melanoma line. We conducted mRNA sequencing of reporter high and reporter low expressing cells.

overall_design: Reporter high and low populations were sorted directly into trizol. RNA was harvested and sequenced.


title: Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

status: Public on Sep 20 2020

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

summary:
We report a new immunoprecipitation-coupled sequencing (DIP-Seq) application termed U-DNA-Seq, where a tailored and catalytically inactive uracil-DNA glycosylase (UNG) was used as uracil-DNA sensor to immunoprecipitate uracil containing genomic DNA fragments.
Genomic uracil was profiled in drug-treated (5-fluoro-2'-deoxyuridine (5FdUR) or raltitrexed (RTX)) or non-treated (NT) HCT116 cells expressing the UNG inhibitor (UGI). The same experiments were also performed in the mismatch repair proficient version of the HCT116 cells (HCT116MMR), where chromosome 3 is reinserted to restore functional MMR (PMID: 8044777). Moreover, wild-type HCT116 or K562 cells were also measured. We found that regions of uracil enrichment in this assay were rather broad as compared to the sharp peaks typical in ChIP-seq. Therefore, we applied an approach alternative to the conventional peak calling. Namely, we calculated genome scaled coverage tracks and log2 ratio tracks of the enriched versus the input samples using deepTools package (bamCoverage and bigwigCompare tools, respectively) to provide a more appropriate description of uracil-enriched genomic regions. Interval (bed) files were also derived from these log2 ratio tracks to be able to screen large datasets for colocalizing features with them. For wider context of the study, see the related publication.

overall_design:
Genomic uracil patterns were determined in drug-treated (5FdUR or RTX) HCT116 cells that are either deficient (HCT116) or proficient in mismatch repair (HCT116MMR) and stably express the UNG inhibitor protein, UGI (samples are as follows: 5FdUR_UGI_HCT116, RTX_UGI_HCT116, 5FdUR_UGI_HCT116MMR, RTX_UGI_HCT116MMR). These were compared to the non-treated UGI-expressing (NT_UGI_HCT116 and NT_UGI_HCT116MMR), as well as to the wild-type HCT116 (WT_HCT116) and K562 (WT_K562) cells. In case of both HCT116 and HCT116MMR samples two independent biological replicates were measured (rep1 and rep2), while in case of K562, only one experiment was done.
Genomic DNA was isolated from each sample and fragmented to approximately 300 bp fragments by sonication (“input” samples (son)). A part of the input sample was incubated with FLAG-tagged uracil-DNA sensor, which was finally precipitated by anti-FLAG beads, resulting in the “enriched U-DNA” sample (IP). Control U-DNA-IP experiments (ctr) were also done using sensor-free beads in 5FdUR treated and non-treated HCT116. Input, U-DNA enriched, and control samples were sequenced by Illumina paired-end reads (PE) 100 bp in a HiSeq 4000 or by PE 150 bp in a Novaseq 6000 platform. Reads were filtered and aligned to the reference human genome (GRCh38.d1.vd1, (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)). Here we provide the following processed files for each pair of samples: 1) log2 ratio (enriched versus input) tracks for individual replicates as well as for merged data (log2.bw); 2) interval files of uracil enriched regions derived from the log2 ratio tracks (region.bed). Regarding the control experiments, log2 ratio (enriched corrected with scaled control versus input) tracks are provided as processed data. For details see the Supplementary Material of the related publication.

first: Hajnalka

last: Pálinkás

first: Angéla

last: Békési

first: Lőrinc

last: Pongor

first: Eszter

last: Holub

first: Gábor

last: Papp

first: Carolina

last: Gemma

first: Simak

last: Ali

first: Balázs

last: Győrffy

first: Beáta

middle: G

last: Vértessy


title: ABCB5 is activated by MITF and b-catenin and is associated with melanoma differentiation

status: Public on Oct 16 2019

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: Defining markers of different phenotypic states in melanoma is important for understanding disease progression, determining the response to therapy, and defining the molecular mechanisms underpinning phenotype-switching driven by the changing intratumor microenvironment. The ABCB5 transporter is implicated in drug-resistance and has been identified as a marker of melanoma-initiating cells. Indeed, ongoing studies are using ABCB5 to define stem cell populations. However, we show here that the ABCB5 is a direct target for the Microphthalmia-associated transcription factor MITF and its expression can be induced by b-catenin, a key activator and co-factor for MITF. Consequently, ABCB5 mRNA expression is primarily associated with melanoma cells exhibiting differentiation markers. The results suggest first that ABCB5 is unlikely to represent a marker of dedifferentiated melanoma stem cells, and second that ABCB5 may contribute to the non-genetic drug-resistance associated with highly differentiated melanoma cells. To reconcile the apparently conflicting observations in the field we propose a model in which ABCB5 may mark a slow-cycling differentiated population of melanoma cells.

overall_design: Doxycycline inducible CTNNB1 cell line was generated using piggyBAC transposable system into IGR37 melanoma cell line. Positively integrated cells were selected using 1mg/ml G418. In order the assess the effect of ectopic Beta-catenin on transciptomics, the nuclear localisation signal derived from SV40 Large T-antigen was introduced to the N-terminus of CTNNB1 to confer constant nuclear localisation upon induction with doxycycline.

first: Colin

last: Goding


title: The majority of A-to-I RNA editing is not required for mammalian homeostasis

status: Public on Oct 27 2019

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

summary: RNAseq of Adult Brain in ADAR1 E861A, ADAR2 knock out,  ADAR1 E861A x ADAR2 knock out het, and ADAR1 E861A x ADAR2 knock out mice generated by deep sequencing.

overall_design: Whole brain from 3 replicates of each genotype were subjected to RNA sequencing.

middle: M

first: Jacki

middle: E

last: Heraud-Farlow

first: Scott

last: Taylor

first: Ankita

last: Gupte

first: Carl

last: Walkley


title: Effect of Bile Acids on C. difficile Growth

status: Public on Aug 28 2019

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

summary: Clostridium difficile epidemic strain R20291 was grown in presence of the two main bile acids, Deoxycholate and Cholate.

overall_design: Total RNA was extracted from 4 independent biological replicates of the R20291 C. difficile strain with 0.5 mM Deoxycholate or 5 mM Cholate or DMSO.

first: Joe

last: Sorg


title: RNA sequencing  in hepatocytes and DR-derived hepatocytes

status: Public on May 14 2019

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: During chronic liver injury, the ductular reaction generates hepatocytes. The aim of the analysis is to compare the phenotype of the DR-derived hepatocytes with that of native hepaotcytes in the same injured liver and control healthy hepatocytes.

overall_design:
We compared 5 biological replicates of each of the 3 populations. Due to technical constraints 10 samples were processed in a first experiment (Experiment 1) and 9 samples were processed in a second experiment (experiment 2). Log fold-change obtained from both experiment were highly correlated (r ~ 0.95).

Several of the same samples were processed in both Experiment 1 and Experiment 2: CTL 5, RED 2, RED 3, RED 4. For these samples, independent libraries were made for each Experiment following methods outlined in the Extraction protocol on the sample pages.

first: Jerome


title: Single-cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

status: Public on May 22 2019

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Single cell RNA sequencing using either an adapted Smart-seq2 protocol on Chx10-GFP (+) retinal progenitor cells; 10x Genomics Chromium Single Cell system across 10 timepoints of mouse retinal development to examine retinal progenitor cell heterogeneity across retinal development and global changes in gene expression from early retinal neuroepithelial cells through specification and differentiation of retinal cell types; 10X Genomics Chromium Single Cell on P14 Nfia/b/x het control or Nfia/b/x tCKO (Chx10-Cre-GFP) retinas

overall_design: Examination of transcript expression within 120,840 cells across 10 developmental time-points (14 experiments) via 10x Genomics and 864 cells via an adapted Smart-Seq2 protocol; Characterization of Nfia/b/x mutant phenotypes using single-cell RNA-seq

first: Seth

last: Blackshaw


title: Genome-wide maps in MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not

status: Public on Mar 10 2019

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

summary: Analysis of MCF-7 cells following  six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression. Overexpression of six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR positively regulates the abundance of embryonic stem cell function. Results provide insight into the role of six2 mediated-regulation on the ceRNA network between CYP4Z1 and pseudogene CYP4Z2P in breast cancer stemness.

overall_design: mRNA profiles of MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Tao

last: Xi


title: HEK293 TFAM Knockout Expression Study

status: Public on Jul 10 2019

city: Baltimore

first: Christina

last: Castellani

state: MD

address: 733 N Broadway

department: McKusick-Nathans Department of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: HEK293 cells with CRISPR KO were analyzed using RNA-Seq. Abstract: Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European Americans (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study using the Infinium Human Methylation 450K Beadchip (485,764 CpGs). Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5x10-8). To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1995). Meta-analysis across all cohorts identified 6 mtDNA-CN associated CpGs to be validated across cohorts at genome-wide significance (P<5x10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including CHD, CVD, and mortality. Experimental modification of mtDNA-CN through knockout via CRISPR-Cas9 of TFAM, a regulator of mtDNA replication, demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24x10-12), as well as the TFAM knockout methylation (P=4.41x10-4) and expression (P=4.30x10-4) studies. These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential gene expression of specific genes, including those acting in the ‘neuroactive ligand receptor interaction’ pathway that may impact human health and disease via altered cell signaling.

overall_design: 3 Biological Replicates of Negative Control Condition and 3 Biological Replicates of TFAM KO Condition

first: C

first: J

last: Sumpter

last: Newcomb

first: D

last: Arking


title: HEK293 TFAM Knockout Methylation Study

status: Public on Jul 09 2019

type: Methylation profiling by genome tiling array

summary: Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European Americans (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study using the Infinium Human Methylation 450K Beadchip (485,764 CpGs). Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5x10-8). To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1995). Meta-analysis across all cohorts identified 6 mtDNA-CN associated CpGs to be validated ac  ross cohorts at genome-wide significance (P<5x10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including CHD, CVD, and mortality. Experimental modification of mtDNA-CN through knockout via CRISPR-Cas9 of TFAM, a regulator of mtDNA replication, demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24x10-12), as well as the TFAM knockout methylation (P=4.41x10-4) and expression (P=4.30x10-4) studies. These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential gene expression of specific genes, including those acting in the ‘neuroactive ligand receptor interaction’ pathway that may impact human health and disease via altered cell signaling.

overall_design:
HEK293 cells with CRISPR KO were analyzed using Illumina EPIC Array
3 Biological Replicates of Negative Control Condition and 3 Biological Replicates of TFAM KO Condition


title: Deoxycholate induces biofilm formation by Clostridium difficile while repressing sporuation and toxin production

status: Public on Apr 05 2019

summary: The objective of our study was to characterize the response of C. difficle to deoxycholate. When C. difficile was grown in the presence of deoxycholate, we observed an increase in biofilm formation. We then analyzed the transcriptome of the DCA-induced biofilm and cells grown in the absence of deoxycholate. The transcriptome analysis was then confirmed using phenotypic assays and gene-deletion strains.

overall_design: Total RNA was extracted from 3 independent biological replicates of 630 C. difficile strains at 2 conditions with and without Deoxycholate 240 µM (6 samples).

first: Yannick

last: Tremblay


title: Pathogenomic study of Clostridium difficile strains

status: Public on Sep 09 2019

summary: In the present study we conducted a gene-wide analysis from nine couples of C. difficile strains. Each couple is composed of a high potential virulence (HPV) strain associated with its control (CON) strain. The HPV strains were chosen using two clinical criteria: prevalence and severity. The prevalent strains, defined in this study by an overrepresentation in European hospital, were associated with phylogenetically close control strain but rarely found in hospital. In other hand, the severe strains sampled on patient with very serious symptoms were associated with phylogenetically identical strain but that gave mild symptoms in another patient. The aim of this work was to determined if we could explain at least a part of the clinical criteria differences between these nine couples of strains in the light of their genomic and transcriptomic differences.

overall_design: Total RNA was extracted from one sample of each of the 17 C. difficile strains of the study.

first: Bruno

last: Dupuy


title: Augmented Pla2g4c/Ptgs2/Hpgds Axis in Bronchial Tissues of Experimental Asthma

status: Public on Jul 03 2018

city: Tokyo

first: Yoshihiko

last: Chiba

address: 2-4-41 Ebara, Shinagawa-ku

department: Department of Physiology and Molecular Sciences

country: Japan

institute: Hoshi University School of Pharmacy

summary: Rationale: Augmented smooth muscle contractility of the airways is one of the causes of airway hyperresponsiveness in asthmatics. However, the mechanism of the altered properties of airway smooth muscle cells is not well understood. Objectives: To identify differentially expressed genes (DEGs) related to the bronchial smooth muscle (BSM) hyper-contractility in a murine asthma model. Methods: The ovalbumin (OA)-sensitized mice were repeatedly challenged with aerosolized OA to induce asthmatic reaction. Transcriptomic profiles were generated by microarray analysis of BSMs from the OA-challenged and control animals, and KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway Analysis was applied. Measurements and Main Results: Tension study showed a BSM hyperresponsiveness to acetylcholine (ACh) in the OA-challenged mice. A total of 770 genes were differentially expressed between the OA-challenged and control animals. Pathway analysis showed a significant change in arachidonic acid (AA) metabolism pathway in BSMs of the OA-challenged mice. Validation of DEGs by quantitative RT-PCR showed a significant increase in PLA2 group 4c (Pla2g4c)/COX-2 (Ptgs2)/PGD2 synthase 2 (Hpgds) axis. PGD2 level in bronchoalveolar fluids of the OA-challenged mice was significantly increased. A 24-h incubation of BSMs with PGD2 caused a hyperresponsiveness to ACh in naive control mice. Conclusions: AA metabolism is shifted towards PGD2 production in BSMs of asthma. Increased PGD2 level in the airways might be a cause of the BSM hyperresponsiveness in asthma.

overall_design: A murine model of allergic bronchial asthma was prepared. In brief, male BALB/c mice (8 weeks of age) were actively sensitized by intraperitoneal injections of 8 µg ovalbumin (OA) with 2 mg Imject Alum on Day 0 and Day 5. The sensitized mice were challenged with aerosolized OA-saline solution (5 mg/mL) for 30 min on Days 12, 16 and 20. A control group of mice received the same immunization procedure but inhaled saline aerosol instead of OA challenge. Twenty-four hours after the last OA challenge, mice were sacrificed by exsanguination from abdominal aorta under urethane anesthesia (1.6 g/kg, i.p.) and both the left and right main bronchi were immediately isolated, and then total RNA was extracted using Trizol reagent according to the manufacturer’s protocol. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). To identify differentially expressed genes related to the disease, total RNAs of the OA-challenged (N=4) and control animals (N=4) were subjected to microarray analysis (Agilent One-Color Microarray-Based Gene Expression Analysis protocol (v6.5, Agilent Technologies)) and compared.

first: Wataru

last: Suto

first: Hiroyasu

last: Sakai


title: Loss of DNMT3A/B in human ES cells triggers increased cell-cell variability and transcriptional repression

status: Public on Aug 30 2019

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

summary: Maintenance of human pluripotent stem cells is dependent on extrinsic signals and cross talk between transcriptional and epigenetic regulators. Methylation of cytosines through the de novo methyltransferases DNMT3A and 3B plays an important role for exiting pluripotency and facilitating proper differentiation. Here, we generated and analyzed single cell expression data from wild-type and DNMT3A/B knockout human embryonic stem cells to better understand the precise effects on pluripotency and differentiation. Although DNA methylation is generally associated with gene silencing, we find unexpected and widespread transcriptional repression upon loss of DNMT3A or DNMT3A/3B. Furthermore, the transcriptional misregulation in DNMT3A knockout cells is largely propagated during differentiation towards mesoderm. Additionally, we observe increased cellular and transcriptional heterogeneity in undifferentiated cells upon deactivation of DNMTs as well as a notable change in cell cycle gene expression. Taken together, our single-cell RNA sequencing data provides several new insights into the role of DNA methylation in human pluripotent stem cells.

overall_design: Single-cell RNA-Sequencing of in vitro embryonic stem cells at different stages of differentiation and conditions

first: Marc

middle: H

last: Wadsworth II

last: Tsankov

middle: K

last: Meissner


title: Leptin and fractalkine: Novel subcutaneous cytokines in burn injury.

status: Public on Aug 31 2018

city: London

first: Istvan

last: Nagy

address: 369 Fulham Road

institute: Imperial College London

summary: Burn injury remains a major clinical challenge to both survival and to quality of life. Its progressive, aberrant inflammation underlies the lethal dysfunction of various organs and the pain it induces is excruciating and notoriously difficult to manage. While it is known that burn injury’s complex local and disseminating pathology is orchestrated from the burned tissue, few studies have sought to characterise the local signalling environment. An enhanced understanding of the local and acutely temporally-dynamic processes defining burn injury and its progression is required for the development of novel therapeutic interventions. Microdialysis was used as an interstitial sampling technique, conducted over three hours post-burn. Samples were analysed by metabolomics and a multiplex cytokine immunoassay. Next-Generation sequencing libraries of the burn and control microdialysis sites were prepared to measure transcriptional changes potentially underlying the interstitial profile characterising burn injury.

overall_design: All microdialysis sites in the study were excised for the extraction of RNA; 4 burn site and 4 control site samples were analysed.

first: Dominic

last: Friston

first: Sini

last: Junttila

first: Helen

last: Laycock

first: Jose

middle: V

last: Torres-Perez

first: Attila

last: Gyenesei


title: Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M

status: Public on Dec 01 2018

first: John

last: Walker

summary:
Regeneration of skeletal muscle is dependent on the function of tissue-resident muscle stem cells (MuSC), known as satellite cells. MuSC dysfunction is central to muscle pathophysiology, including in age-associated loss of muscle regenerative capacity and congenital disorders such as Duchenne muscular dystrophy. Despite the central role of satellite cells in muscle regeneration, the signals controlling the balance between muscle stem cell quiescence, proliferation, and differentiation remain incompletely understood. Knowledge of the signals that maintain a quiescent state is particularly lacking, yet such cues are crucial to maintaining a stem cell reservoir that can meet the needs of regeneration throughout life. Here we identify Oncostatin M (OSM), a member of the interleukin-6 family of cytokines, as a potent and essential trans-acting regulator of satellite cell quiescence. Key to this discovery is the development of a novel in vivo imaging-based screening strategy allowing identification of proteins that do not induce in vitro proliferation, but instead maintain MuSCs in a non-mitotic state, poised for rapid robust expansion upon transplantation.  We demonstrate that OSM induces reversible exit from the cell cycle and induction of a global transcriptional program significantly enriched within a newly established satellite cell “quiescence signature”.  Genetic ablation of the OSM receptor in mice demonstrates that signaling via OSM/R is essential for maintenance of satellite cell quiescence, and for proper skeletal muscle regeneration in vivo.  Given that aberrant activation and exhaustion of stem cells is seen in a variety of disorders, OSM constitutes an attractive therapeutic target in muscle disease states.
Microarray profiling was used to directly test the hypothesis that OSMR signaling in muscle stem cells promotes their engraftment by inducing a global transcriptional state equivalent to that of quiescent, freshly isolated, non-activated MuSC.

overall_design: Comparison of Oncostatin M-treated cultured muscle stem cells with either fresh or cultured but non-Oncostatin M-treated muscle stem cells

first: Srinath

last: Sampath

first: Srihari

first: Andrew

last: Ho

first: Stéphane

middle: Y

last: Corbel

first: Joshua

last: Millstone

last: Lamb

first: Bernd

last: Kinzel

first: Christian

last: Schmedt

last: Blau


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival

status: Public on Oct 04 2018

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

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

overall_design: Refer to individual Series


title: Global transcriptional control by the transcriptional regulator SinR in Clostridium difficile

status: Public on Dec 25 2018

last: Monot

overall_design: Two-conditions experiments, 630E strain vs SinR mutant grown in TY 7h, 4 biological replicates for each condition

first: Laure

last: Saujet

first: Monot

last: Marc


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [RNA-Seq]

summary: Ovarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (I, II) ovarian carcinomas (n=96) in relation to clinicopathological characteristics and clinical outcome, thereby identifying novel genetic features of ovarian carcinomas. Furthermore, mutation frequencies of specific genetic variants and/or their gene expression patterns were associated with histotype and overall survival, e.g. SLC28A2 (mucinous ovarian carcinoma histotype), ARCN1 (low expression in 0-2 year survival group), and tumor suppressor MTUS1 (mutation status and overall survival). The long non-coding RNA MALAT1 was identified as a highly promiscuous fusion transcript in ovarian carcinoma. Moreover, gene expression deregulation for 23 genes was associated with tumor aggressiveness. Taken together, the novel biomarkers identified here may improve ovarian carcinoma subclassification and patient stratification according to histotype and overall survival.

overall_design: Whole-transcriptome RNA sequencing (RNA-seq) was performed for 96 early-stage primary invasive ovarian carcinomas.

first: Toshima

middle: Z

last: Parris

first: Elisabeth

last: Werner Rönnerman

first: Elin

last: Söderberg

first: Jana

last: Biermann

first: Claudia

last: Mateoiu

first: Karin

last: Sundfeldt

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [ARRAY]

overall_design: Genome-wide SNP genotyping was performed for nine early-stage primary invasive ovarian carcinomas.


title: GPR68 senses flow and is essential for vascular physiology

status: Public on Apr 19 2018

first: John

last: Walker

summary: GPR68 is an essential flow sensor in arteriolar endothelium, and is a critical signaling component in cardiovascular pathophysiology

overall_design: RNAseq of cells from mesenteric endothelium of mice plus and minus GPR68

first: Jie

last: Xu

first: Jayanti

last: Mathur

first: Emilie

last: Vessières

first: Scott

last: Hammack

first: Keiko

last: Nonomura

first: Julie

last: Favre

first: Linda

last: Grimaud

first: Matt

last: Petrus

first: Allain

last: Francisco

first: Jingyuan

last: Li

first: Van

last: Lee

first: Fu-li

last: Xiang

first: James

last: Mainquist

first: Stuart

last: Cahalan

first: Anthony

middle: P

last: Orth

middle: R

first: Shang

last: Ma

first: Viktor

last: Lukacs

first: Laura

last: Bordone

first: Michael

last: Bandell

first: Bryan

last: Laffitte

first: Yan

first: Shu

last: Chien

first: Daniel

last: Henrion

first: Ardem

last: Patapoutian


title: Effect of PDGF-Ddstimulation on human tonsil ILC1

status: Public on Feb 01 2018

first: John

last: Walker

summary: The effect of PDGF-DD on the gene expression of human tonsil ILC1 is unknown. We used microarray to determine the transcriptional differences between unstimulated and PDGF-DD-stimulated human tonsil ILC1.

overall_design: Human ILC1 cells from tonsil were sorted to high purity for RNA extraction and hybridization on Affymetrix microarrays.

first: Cella

last: Marina

first: Barrow

last: Alexander


title: RNA seq from liver samples of C57BL/6 mice to study the gene expression synchrony of Plasmodium stages with host circadian cycle.

status: Public on Jun 01 2018

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

summary: The Plasmodium life cycle parasites differentiate and proliferate synchronously, paralleling the vertebrate host's circadian rhythm. Here we report that expression of carbohydrate metabolism and inflammatory genes in IFNγ-primed leukocytes and liver cells from infected mice are boosted in P. chabaudi-infected mice. In addition, a rhythmic gene expression of PPARG and TNFα, which are key regulators of glucose metabolism, parallel blood glucose levels across the circadian cycle in infected mice.

overall_design: Liver fragments from C57BL/6 mice were collected at different time points: 12 am; 6 am; 12 pm and 6 pm from mice at day 8 post-infection with P. chabaudi or uninfected control.


title: Transcriptional profiling of Primary Human Hepatocytes (PHH) depleted for CAR and treated with CITCO or Phenobarbital in -/+EGF medium

status: Public on Apr 27 2018

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: In primary human hepatocytes (PHH) the involvement of the Constitutive Androstane Receptor (CAR) in genes regulations has never been evaluated at the transcriptomic level. Here we investigated the impact of CAR depletion and epidermal growth factor on CAR dependent gene modulation in PHH. The xenosensor was activated by its direct (CITCO) or indirect (Phenobarbital/PB) agonists in presence or in absence of EGF.

overall_design: Primary Human Hepatocytes were isolated from 5 different human donors. Cells were cultured in presence or in absence of EGF for 6 days. Transfections with siRNA unspecific (siCT) or targeting CAR (siCAR) were performed at day 2 and 5. RNA was extracted at D6 after 24h treatment with DMSO, CITCO (1µM) or PB (0.5mM). Transcriptomic profiling was performed using Affymetrix HG-U133+PM arrays.

first: Hugues

last: de Boussac

last: Römer

first: Martine

last: Daujat-Chavanieu


title: Biological characterization of virulent therapeutic bacteriophage PAK_P4 infecting Pseudomonas aeruginosa

status: Public on Jul 07 2017

first: Marc

last: Monot

summary: We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P4 infecting PAK strain of P. aeruginosa.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas phage PAK_P4

overall_design: RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P4. Three biological replicates for each time point.

first: Bob

last: Blasel

first: Anne

last: Chevallereau


title: High Phosphate Diet Induces Exercise Intolerance and Impairs Fatty Acid Metabolism in Mice

status: Public on Jan 08 2019

city: Dallas

first: Wanpen

last: Vongpatanasin

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Inorganic phosphate (Pi) is used extensively as a preservative and a flavor enhancer in the Western diet. Physical inactivity, a common feature of Western societies, increases cardiovascular morbidity and mortality. We explore the relationship between dietary Pi excess and impaired exercise tolerance and physical inactivity. Analysis of the Dallas Heart Study shows association of higher serum Pi with reduced time spent in moderate to vigorous physical activity and increased sedentary time in humans. To test for causality, we investigated the impact of chronic exposure of high dietary Pi on exercise capacity in mice. Consumption of a high Pi diet for 3 months does not change the body weight but reduces maximal oxygen uptake, treadmill duration, and spontaneous locomotor activity, which is accompanied by substantial reduction in fat oxidation and fatty acid (FA) levels and downregulation of genes involved in FA synthesis, release, and oxidation, including Fabp4, Hsl, Fasn, and Ppar in muscle. Similar results are recapitulated in in vitro by incubating C2C12 myotubes with high Pi media. In conclusion, our findings indicate that dietary phosphotoxicity reduces skeletal muscle FA metabolism and impairs exercise capacity independent of obesity, and may represent a novel and modifiable risk factor for cardiovascular disease.

overall_design: To understand the mechanistic basis of high intake of dietary phosphate we profiled the transcriptomes (using RNA-seq), of gastrocnemius muscle tissue treated with high phosphate diet for 12 weeks compared to normal phosphate diet.

first: Kedryn

last: Baskin


title: Genome-wide comparison of gene expression between biofilm and planktonic growth

summary: In this study, we used an original system to produce C. difficile anaerobic biofilms consisting in continuous-flow microfermentors, that is compared to planktonic growth culture.

overall_design: Two-conditions experiments, 630E strain Biofilm in Bioreactor and Planktonic growth at 24h in TY, 4 biological replicates for each condition

first: Isabelle

last: Poquet

first: Monot

last: Marc


title: Global transcriptional control by the alternative sigma factor SigB in Clostridium difficile

summary: Genes encoding the alternative sigma factor SigmaB, involved in the general stress response in firmicutes, as well as its regulators are present in the genome of the enteropathogen Clostridium difficile. We inactivated the sigB gene using the ClosTron technology in order to identify the role of this sigma factor in the physiology of this bacterium. Transcriptomic experiments showed that SigB positively and negatively controlls several genes involved in different cellular processes such as metabolism, sporulation and stress response.

overall_design: Two-conditions experiments, 630E strain vs SigB mutant grown in TY 10h, 4 biological replicates for each condition

first: Nicolas

last: Kint


title: Patient-derived organoid cultures model human primary liver cancer in vitro

status: Public on Nov 13 2017

first: Charles

middle: Richard

last: Bradshaw

address: Tennis Court Road

institute: Gurdon Institute

summary: The study of human liver cancer has been hampered by the lack of reliable models that faithfully recapitulate the physiopathology of the patient’s original tumour ex vivo. Here, we describe the first culture system to allow the establishment and long-term expansion of human primary liver cancer (PLC) organoids (called tumoroids) from the three most common PLC subtypes: Hepatocellular carcinoma (HCC), Cholangiocarcinoma (CC) and mixed HCC/CC tumours (CHC). We evaluated whether tumoroid lines maintain the expression profile and the genomic landscape of the original tumor they derived from by performing genome-wide (RNAseq/WES) analyses before and after culture. These analyses reveal that the cultures closely recapitulate the gene expression and the mutational landscape of the original tumor, allowing discrimination between different tumor subtypes (HCC, CHC, CC).

overall_design: We generated RNAseq and WES data from healthy donor and 7 tumoral human PLC tissues and their derived organoid cultures maintained in our defined medium.

first: Laura

last: Broutier

first: Meritxell

last: Huch


title: Intragraft molecular pathways associated with tolerance induction in renal transplantation

status: Public on May 07 2018

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Complications associated with immunosuppression, specifically nephrotoxicity and infection risk, significantly affect graft and patient survival after kidney transplantation.
We previously showed that tolerance could be induced and full donor chimerism, as well as immunosuppression withdrawal, was obtained in highly mismatched allograft recipients using a bioengineered stem cell product (FCRx).

overall_design: Gene expression profiles in renal biopsy samples from tolerance-induced FCRx recipients, paired donor organs before implant, and subjects under standard immunosuppression (SIS) without rejection and with acute rejection were compared.

first: Valeria

last: Mas

first: Sai

last: Bontha

middle: I


title: ETV1 activates a rapid conduction transcriptional program in rodent and human cardiomyocytes

status: Public on Oct 15 2018

city: New York

first: Akshay

last: Shekhar

state: NY

address: 564 1st Ave Apt 11S

department: Medicine - Cardiology

institute: NYU School of Medicine

summary: ETV1 (ER81) was identified as a highly enriched transcription factor in rapidly conducting atrial and His-Purkinje cardiomyocytes. Previous work has shown that ETV1 is a critical factor in determining fast conduction physiology in the heart. This high-throughput sequencing project aims to uncover ETV1-dependent gene networks in cardiomyocytes. These results provide insight into the role of ETV1 in the establishment of rapid conduction zones in the heart.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
Neonatal rat ventricular myocytes were isolated and purified from postnatal day 1 Sprague-Dawley wild type male and female rats using Miltenyi Biotec rat neonatal cardiomyocyte isolation kit (Miltenyi Biotec, 130-105-420) according to the manufacture's protocol. The final myocyte cultures contained enriched cardiomyocytes at a density of 3X10^6 cells per 35-mm dish. Myocytes cultures were transduced with either Ad-ETV1-GFP or Ad-GFP 24 hours after plating. RNA was extracted at day 4 post-transduction to analyze transcriptional differences with the overexpression of ETV1 in cardiomyocytes.

Additional records discussed in the publication can be found in Series GSE322182.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE322182

first: Xianming

last: Lin

first: Bin

first: Fang-Yu

last: Liu

first: Jie

last: Zhang

first: Alireza

last: Khodadadi-Jamayran

first: Aristotelis

last: Tsirigos

first: Lei

last: Bu

first: Glenn

last: Fishman

first: David

middle: S

last: Park


title: Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

status: Public on Nov 14 2017

city: Bentley

first: Irina

last: Kuznetsova

state: Western Australia

address: Building 304, Kent Street

institute: Curtin University

summary: Differential gene expression in mouse models of mitochondrial dysfunction

overall_design: various mutants vs. wild type

first: Inge

last: Kuhl

first: Maria

last: Miranda

first: Ilian

last: Atanassov

first: Yvonne

last: Hinze

first: Arnaud

last: Mourier

first: Aleksandra

last: Filipovska

first: Nils-Goran

last: Larsson


title: Integrative analysis of behavioral, syaptic, and genomic plasticity in the hippocampus

status: Public on Jun 21 2017

city: Davis

first: Rayna

middle: Michelle

last: Harris

address: 1 Shields Ave

institute: University of California Davis

summary: We examined the the effects of cognitive training on behavior, synaptic physiology, and gene expression in the hippocampus.

overall_design: Homecage, Yoked Control, Consistently Trained, Conflict Trained

first: Hsin-Yu

last: Kao

first: Juan

last: Alarcon

first: Hans

last: Hofmann

first: Andre

last: Fenton


title: Gene expression of cardiac tissues in dietary obese mice administered with a dipeptidyl peptidase-4 inhibitor

status: Public on Apr 27 2017

city: Los Angeles

first: Masayoshi

last: Suda

address: 8700 Beverly Blvd.

institute: Cedars Sinai Medical Center

summary: Dipeptidyl peptidase-4 (Dpp4) inhibitors are used worldwide to combat diabetes, however, their roles in cardiovascular disorders are yet to be defined. Here we show that a DPP4 inhibitor, linagliptin, contributes for the suppression of capillary rarefaction in cardiac tissues of dietary obese mice model. Imposing a high fat diet into mice induced capillary rarefaction and cardiac dysfunction. These pathologies associated with high DPP4 level in circulation, and the administration of linagliptin into dietary obese mice suppressed the development of capillary rarefaction and ameliorated cardiac dysfunction. Early growth response protein 1 (EGR1), known as an angiogenic transcription factor, is significantly reduced in the cardiac tissue upon metabolic stress, and this suppression was inhibited by the administration of linagliptin.

overall_design: Total RNA of cardiac tissue was obtained from a normal chow- and  a high-fat diet-fed mice with or without a DPP-4 inhibitor. Mice were fed a high-fat diet or a normal chow for totally 8 weeks from 4 weeks age, and analyzed at 12 weeks of age.The DPP-4 inhibitor was administered within a water at the concentration of 10 mg/kg/day for 8 weeks since 4 weeks of age.

first: T

last: Minamino


title: Natural Killer cells control tumor growth by sensing a growth factor

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins Dr

institute: NIBR

summary: Many tumors produce platelet-derived growth factor (PDGF)-DD, which promotes cellular proliferation, epithelial-mesenchymal transition, stromal reaction, and angiogenesis through autocrine and paracrine PDGFRβ signaling. By screening a secretome library, we found that the human immunoreceptor NKp44 encoded by NCR2 and expressed on natural killer (NK) cells and innate lymphoid cells recognizes PDGF-DD. PDGF-DD engagement of NKp44 triggered NK cell secretion of IFN-γ and TNF-α that induced tumor cell growth arrest. A distinctive transcriptional signature of PDGF-DD-induced cytokines and the downregulation of tumor cell cycle genes correlated with NCR2 and greater survival in glioblastoma. NKp44 expression in mouse NK cells controlled the dissemination of tumors expressing PDGF-DD more effectively than control mice, an effect enhanced by blockade of the inhibitory receptor CD96 or CpG-oligonucleotide treatment. Thus, whilst cancer cell production of PDGF-DD supports tumor growth and stromal reaction, it concomitantly activates innate immune responses to tumor expansion.

overall_design: RNAseq of NK cell and tumor cell samples in reponse to various stimuli

first: Alexander

middle: D

last: Barrow

first: Melissa

middle: A

last: Edeling

first: Vladimir

last: Trifonov

first: Jingqin

last: Luo

first: Piyush

last: Goyal

first: Benjamin

last: Bohl

first: Jennifer

last: Bando

first: Albert

last: Kim

first: Mary

last: Andahazy

first: Mattia

last: Bugatti

first: Laura

last: Melocchi

first: William

last: Vermi

first: Daved

last: Fremont

first: Sarah

last: Cox

first: Marina

last: Cella

first: Christian

last: Schmedt

first: Marco

last: Colonna


title: NYGC ALS Consortium data

status: Public on Sep 20 2019

first: Hemali

last: Phatnani

address: 101 Avenue of the Americas

institute: New York Genome Center

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

Consortium contacts:
Maria Pedersen: mpedersen@nygenome.org
Hemali Phatnani: hphatnani@nygenome.org
NYGC ALS Consortium: cgndhelp@nygenome.org

overall_design: Refer to individual Series


title: Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-Seq]

status: Public on Apr 17 2017

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: RNA polymerase II (Pol II) pauses downstream of the transcription initiation site before beginning productive elongation. This pause is a key component of metazoan gene expression regulation. Some promoters have a strong disposition for Pol II pausing and often mediate faster, more synchronous changes in expression. This requires multiple rounds of transcription and thus cannot rely solely on pause release. But it is unclear how pausing affects the initiation of new transcripts during consecutive rounds of transcription. Using our recently developed ChIP-nexus method, we find that Pol II pausing inhibits new initiation. We propose that paused Pol II helps prevent new initiation between transcription bursts, which may reduce noise.

overall_design: ChIP-seq was performed against Pol II, TFIIA and TFIIB in Drosophila melanogaster Kc167 cells.

first: Wanqing

last: Shao


title: The microprotein Minion controls cell fusion and muscle formation

status: Public on May 19 2017

first: John

last: Walker

summary: These findings establish minion as a novel microprotein required for muscle development, and define a two-component program for the induction of mammalian cell fusion.

overall_design: RNAseq of muscle samples before and after cardiotoxin injury

first: Qiao

last: Zhang

first: Ajay

last: Vashisht

first: Jason

last: O’Rourke

first: Stéphane

last: Corbel

first: Rita

last: Moran

first: Angelica

last: Romero

first: Loren

last: Miraglia

first: Jia

first: Eric

last: Durrant

first: Srinath

middle: C

last: Sampath

first: Srihari


title: Paused RNA polymerase II inhibits new transcriptional initiation


title: PTCD1 is required for 16S rRNA maturation complex stability and mitochondrial ribosome assembly

status: Public on Apr 03 2018

first: Irina

last: Kuznetsova

summary: Differential gene expression as a consequence of PTCD1 loss

overall_design: We used RNA from control and PTCD1 knockout mice to investigate changes at the RNA level in response to PTCD1 loss

first: Kara

middle: L

last: Perks

first: Giulia

last: Rossetti

first: Laetitia

last: Hughes

first: Judith

last: Ermer

first: Nicola

last: Ferreira

first: Jakob

last: Busch

first: Danielle

last: Rudler

first: Henrik

last: Spahr

first: Thomas

last: Schöndorf

first: Ann-Marie

middle: J

last: Shearwood

first: Helena

middle: M

last: Viola

first: Stefan

last: Siira

first: Livia

last: Hool

first: Dusanka

last: Milenkovic

first: Nils-Göran

last: Larsson

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Effect of tcdR mutation in Clostridium difficile sporulation

status: Public on Mar 07 2017

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

summary: Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normal protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB are part of a pathogenicity locus, which also encodes the gene tcdR that codes for the toxin genes positive regulator. TcdR is an alternate sigma factor that initiates transcription of tcdA and tcdB at their promoters. Alternative sigma factors are known to regulate virulence and virulence associated genes in many pathogenic bacteria. We created a tcdR mutant in the epidemic-type C. difficile R20291 strain in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores derived from the tcdR mutant were found to be mildly temperature sensitive. Moreover, nearly two fold more taurocholate was needed to germinate spores from the tcdR mutant than the spores prepared from the wild-type parent strain. Comparison of the tcdR mutant transcriptome with the parent strain revealed many differentially expressed late sporulation genes in the tcdR mutant. These data suggests that gene regulatory networks of toxin production and sporulation in Clostridium difficile are linked with each other.

overall_design: Total RNA was extracted from 2 independent biological replicates of ∆tcdR and WT of the R20291 C. difficile strain.

first: Revathi

last: Govind


title: Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-nexus spike-in]

first: Julia

last: Zeitlinger

overall_design: ChIP-nexus was performed against Pol II in Drosophila melanogaster Kc167 cells. A fix amount of spike-in is added into each sample in order to control for the loss of Pol II ChIP signal after Triptolide treatment or NELF depletion.

first: Wanqing

last: Shao


title: Effects of vitamin A on ventricular myocardium gene expression

status: Public on Jul 25 2016

city: Scarborough

first: Douglas

last: Sawyer

state: ME

address: 81 Research Dr

department: Cardiovascular Institute

institute: Maine Medical Center

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


title: What’s a SNP between friends: the influence of single nucleotide polymorphisms on Clostridium difficile strain CD630 virulence

status: Public on Sep 28 2016

summary: Isogenic, toxin B (tcdB) mutants of two independently isolated erythromycin-sensitive derivatives (630E and 630Δerm) of the Clostridium difficile strain CD630 have previously been shown to behave differently in the hamster model of infection.  Those based on strain 630E failed to cause disease, whereas those based on 630Δerm did.  Here we show that whilst 630Δerm and its derivatives behave in a comparable way to the parental strain CD630 in terms of growth rate, motility, sporulation, toxin production and virulence, strain 630E and its derivatives do not.  They grow more slowly, achieve lower final cell densities, exhibit a reduced capacity for spore formation, express lower levels of toxin and are less virulent in the hamster model.  Using Next Generation Sequencing, a total of three SNPs were found that were in both CD630 and 630Δerm. In addition to these, 630Δerm had eight unique SNPs compared to CD630 and 630E, while 630E had 11 SNPs not found in the other two strains.  The strain-specific SNPs most likely arose during the repeated subculture experiments undertaken to isolate these ermB deletion strains.  The relatively large number of mutations present meant that the identification of those SNPs responsible for the altered properties of 630E was not possible.  Allelic exchange was used to correct three mutational changes in 630E, but with essentially no effect on phenotype.  These were a 150 bp inversion in the promoter region of a flagella operon, the truncation of CD630_12740 (topoisomerase I), and the correction of a SNP that results in the fusion of two components of a glucose phosphor-transferase-system.  To complete the analysis we performed RNAseq, comparing the transcriptome of the three strains at three different time points. The finding corroborated the many differences between the strains, but also highlighted that one SNP cannot necessarily be attributed to one particular expression pattern or even phenotype. In conclusion 630Δerm more accurately mirrors the behaviour of the parental strain CD630, hence if genetic-based studies with C. difficile strain CD630 are necessary, then the use of strain 630∆erm should be favoured over strain 630E.  At a fundamental level, our data underlines the importance of effective strain curation and the need to genome re-sequence master seed banks wherever possible.

overall_design: Total RNA was extracted from 2 independent biological replicates of 630, 630∆erm and 630E C. difficile strains at 3 time points (18 samples).

first: Bruno

last: Dupuy


title: Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource

status: Public on Jul 26 2016

city: Memphis

first: Robert

middle: W.

last: Williams

state: TN

address: 71 Manassas St.

department: Department of Genetics, Genomics and Informatics

institute: University of Tennessee

summary:
The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.

overall_design: Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.

middle: W

first: David

last: Airey

first: Dan

last: Goldowitz

first: Rupert

last: Overall

first: Gerd

last: Kempermann

first: Jeremy

last: Peirce

first: Lu

last: Lu

first: Fred

middle: H

last: Gage

first: Shirlean

last: Goodwin

first: August

middle: B

last: Smit

first: Glenn

last: Rosen

first: Leonard

last: Schalkwyk

last: Sutter

first: Richard

last: Nowakowski

first: Stephen

last: Whatley


title: Effects of vitamin A on Ventricular myocardium gene expression [right ventricle]

last: Sawyer

summary: LRAT knockout mice on vitamin A sufficient or deficient diets were compared to age-matched wildtype mice on a vitamin A sufficient diet

overall_design: RNA was isolated from right ventricle of the heart and one array was run for each sample.

first: Mary-Ann

last: Asson-Batres

first: Cristi

last: Galindo

first: Duarte

last: Christine


title: Next Generation Sequencing (RNAseq) of non-small cell lung cancer

status: Public on Jun 01 2016

city: Solna

first: Björn

last: Hallström

state: Stockholm

address: Tomtebodavägen 23A

department: Science for Life Laboratory

institute: Royal Institute of Technology, Stockholm

summary: Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small cell lung cancer (NSCLC), we compared RNAseq data of 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the CTdatabase, 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase. Cluster  analysis revealed that CTA expression is histology-dependent and concurrent expression is common. Immunohistochemistry confirmed tissue specific protein expression of selected genes. Furthermore, methylation was identified as a regulatory mechanism of CTA expression based on independent data from the Cancer Genome Atlas. The proposed prognostic impact of CTAs in lung cancer, was not confirmed, neither in our RNAseq-cohort nor in an independent meta-analysis of 1117 NSCLC cases.

overall_design:
Fresh frozen tumor tissue from 199 patients diagnosed with NSCLC and surgically treated 2006-2010 at the Uppsala University Hospital, Uppsala, Sweden and 19 paired normal lung tissues. Clinical data were retrieved from the regional lung cancer registry.
Several of the new CTAs are poorly characterized

Sample characteristics values represent;
pTNM: decided by Hans Brunnström, pathologist in Lund Spring 2013
Stage according to pTNM: 1=1a 2=1b 3=2a 4=2b 5=3a 6=3b 7=IV
Histology diagnosis spring 2013 HB:
1=squamous cell cancer 2=AC unspecified 3=Large cell/ NOS
Surgery date: the date when sample arrived at Patologen UAS
Age: age when surgery was performed
Vital date: day of death or latest contact
Dead: 0=no 1= yes
Smoking history : 1=current 2=ex >1year 3=never
WHO performance status: Performance status 0-4

Please note that the L608T_2122, L771T_1 data columns (in the processed data files) are associated with L608T and L771T samples, respectively.

first: Dijana

last: Djureinovic

first: Masafumi

last: Horie

first: Johanna

last: Mattsson

first: Linnea

last: La Fleur

first: Linn

last: Fagerberg

first: Hans

last: Brunnström

first: Cecilia

last: Lindskog

first: Katrin

last: Madjar

first: Jörg

last: Rahnenführer

first: Simon

last: Ekman

first: Elisabeth

last: Ståhle

first: Hirsh

last: Koyi

first: Eva

last: Brandén

first: Karolina

last: Edlund

first: Jan

middle: G

last: Hengstler

first: Mats

last: Lambe

first: Akira

last: Saito

first: Johan

last: Botling

first: Fredrik

last: Pontén

first: Mathias

last: Uhlén

first: Patrick

last: Micke


title: Effects of vitamin A on ventricular myocardium gene expression [left ventricle]

first: Douglas

last: Sawyer

summary: LRAT knockout mice on vitamin A sufficient or deficient diets were compared to age and gender matched wildtype mice on a vitamin A sufficient diet

overall_design: RNA was isolated  from the left ventricle of the heart and one array was run for each sample.

first: Mary-Ann

last: Asson-Batres

first: Cristi

last: Galindo

first: Duarte

last: Christine


title: Synchronized translation programs across cellular compartments

status: Public on May 11 2016

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Oxidative phosphorylation (OXPHOS) is fundamental for life. OXPHOS complexes pose a unique challenge for the cell, because their subunits are encoded on two different genomes, the nuclear genome and the mitochondrial genome. Genomic approaches designed to study nuclear/cytosolic and bacterial gene expression have not been broadly applied to the mitochondrial system, thus the co-regulation of OXPHOS genes remains largely unexplored. Here we globally monitored mitochondrial and nuclear gene expression processes during mitochondrial biogenesis when OXPHOS complexes are synthesized. Nuclear- and mitochondrial- encoded OXPHOS transcript levels do not increase concordantly. Instead, we observe that mitochondrial and cytosolic translation are rapidly and dynamically regulated in a strikingly synchronous fashion. Furthermore, the coordinated translation programs are controlled unidirectionally through the intricate and dynamic control of cytosolic translation. Thus the nuclear genome carefully directs the coordination of mitochondrial and cytosolic translation to orchestrate the timely synthesis of each OXPHOS complex, representing an unappreciated regulatory layer shaping the mitochondrial proteome. Our whole-cell genomic profiling approach establishes a foundation for global gene regulatory studies of mitochondrial biology.

overall_design: Examination of whole-cell RNA levels (rRNA-depleted RNA-seq) and both cytosolic and mitochondrial translation regulation (cytoribosome profiling and mitoribosome profiling) through mitochondrial biogenesis in S. cerevisiae

first: Iliana

last: Soto

first: Gergana

last: Shipkovenska

first: Stirling

last: Churchman


title: Clostridium difficile C630E: growth in TY with 30 mM proline vs. growth in TY alone

status: Public on Oct 01 2015

first: Marc

last: Monot

summary:
Clostridium difficile, a proteolytic Gram-positive anaerobe, has emerged as a significant nosocomial pathogen. Stickland fermentation reactions are thought to be important for growth of C. difficile. In Stickland reactions, pairs of amino acids donate and accept electrons, generating ATP and reducing power in the process. Reduction of the electron acceptors proline and glycine requires the D-proline reductase (PR) and the glycine reductase (GR) enzyme complexes, respectively. PrdR, a sigma54-dependent regulator, activates transcription of the PR-encoding genes in the presence of proline and negatively regulates the GR-encoding genes, suggesting that PrdR is a central metabolism regulator that controls preferential utilization of proline and glycine to produce energy via the Stickland reactions.

Here, transcriptional profiling of C. difficile comparing growth in TY medium supplemented with 30 mM L-proline to growth in TY medium alone is performed.

overall_design: Two-condition experiment: TY with excess of proline vs. TY alone. 2 biological replicates for each condition, including a dye-swap.

first: Laurent

last: Bouillaut

first: Thomas

last: Dubois


title: The Nicotinic alpha6 Subunit Gene Determines Variability in Chronic Pain Sensitivity and Nicotine Anti- allodynia via Cross-inhibition of P2X2/3 Receptors.

status: Public on Feb 18 2015

first: John

last: Walker

summary:
We used microarray-based expression genomics in 25 inbred mouse strains to identify dorsal root ganglion (DRG)-expressed genetic contributors to mechanical allodynia a prominent symptom of chronic pain.
Expression genetics identifies a role for the Chrna6 (alpha 6-nicotinic receptor) gene in pain in mice and humans.

overall_design: Dorsal root ganglion tissue across multiple inbred mouse strains, both male and female

first: Jeffrey

last: Wieskopf

first: Jayanti

last: Mathur

first: Walrati

last: Limapichat

first: Michael

middle: R

last: Post

first: Mona

last: Al-Qazzaz

first: Robert

middle: E

last: Sorge

first: Loren

last: Martin

first: Dmitri

middle: V

last: Zaykin

first: Shad

last: Smith

first: Kelen

last: Freitas

first: Jean-Sebastien

last: Austin

first: Feng

last: Dai

first: Jie

last: Zhang

first: Jaclyn

last: Marcovitz

first: Alexander

last: Tuttle

first: Peter

last: Slepian

first: Sarah

last: Clarke

first: Ryan

last: Drenan

first: Jeff

last: Janes

first: Shakir

last: Al Sharari

first: Samantha

middle: K

last: Segall

first: Eske

last: Aasvang

first: Weike

last: Lai

first: Reinhard

last: Bittner

first: Christopher

last: Richards

first: Gary

last: Slade

first: Henrik

last: Kehlet

first: Uwe

last: Maskos

first: Jean-Pierre

last: Changeux

first: Marshall

last: Devor

first: William

last: Maixner

first: Luda

last: Diatchenko

first: Inna

last: Belfer

first: Dennis

last: Dougherty

first: Andrew

last: Su

last: Lummis

first: M


title: Gene expression analysis of in vivo-grown tumors treated with compounds that either de-bulk the tumor or target cancer stem cells

status: Public on Jan 23 2015

first: John

last: Walker

summary:
A large body of evidence has demonstrated that many human tumors are maintained by a small cell population called cancer stem cells (CSCs) or tumor progenitors, which are responsible for tumor formation, therapy resistance and metastasis. We found that ionizing radiation treatment enriches for the CSC phenotype and properties by preferential survival and expansion of tumor progenitor cells. Our studies revealed that aldehyde dehydrogenase (ALDH) activity is indicative of prostate tumor progenitor cells with increased chemo- and radioresistance, enhanced migratory potential, improved DNA- double strand break repair and activation of the signaling pathways, which promote self-renewal and epithelial-mesenchymal transition. We found that X-ray irradiation can convert the bulk tumor cells to more clonogenic and radioresistant population positive for expression of CSC markers. For the first time we showed that irradiation increases histone H3K4 and H3K36 methylation in prostate cancer cells, thereby reactivating transcription of epigenetically silenced target genes. We showed that radioresistant tumor progenitor population undergoes a phenotypical switching during the course of irradiation, suggesting that controlling the phenotypical and functional properties of CSCs during radiation therapy is ultimative for the optimization of treatment strategies. Our studies have shown that CSC markers may be beneficial in prediction of tumor radiocurability, and combination of irradiation with therapies directed against CSCs can be a useful strategy to improve cancer treatment.
To identify potential biomarkers associated with CSC population in these xenograft tumors, we performed whole genome gene expression profiling of the xenograft tumors treated with NVP-BEZ235, which eliminates prostate cancer progenitor populations or with Taxotere, which targets the bulk tumor cells as compared with vehicle-treated control mice.

overall_design: Treatment with either vehicle, Taxotere, NVP-BEZ235, or a combination of these two.  There are no replicates

first: Monica

last: Cojoc

first: Claudia

last: Peitzsch

first: Ina

last: Kurth

first: Franziska

last: Trautmann

first: Leoni

last: Kunz-Schughart

first: Gennady

last: Telegeev

first: Eduard

last: Stakhovsky

first: Karl

last: Simin

first: Stephen

last: Lyle

first: Mechthild

last: Krause

first: Michael

last: Baumann

first: Anna

last: Dubrovska


title: Comparison of the expression profiles of R20291 strain and a R20291 strain after 4h, 6h, 8h, 14h, 38h of growth in vivo

status: Public on Jan 31 2016

first: Marc

last: Monot

summary: Transcriptionnal profiling of C. difficile R20291 strain vs a R20291 strain after4h 6h 8h 14h 38h of growth in Vivo

overall_design: two-conditions experiments, WT strain after 4h, 6h, 8h, 14h, 38h, of growth in vivo, 4 biological replicates for each condition except 3 biological replicates for 14h, in an indirect design using a DNA preparation as Reference.

first: Amira

last: Barketi


title: Spatiotemporal characterization of the cellular and molecular contributors to liver fibrosis in a murine hepatotoxic-injury model

status: Public on Dec 01 2015

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: The interplay between the inflammatory infiltrate and tissue resident cell populations (e.g. epithelial cells, fibroblasts and macrophages) invokes fibrogenesis. However, the temporal and mechanistic contributions of these cell populations to fibrosis remain poorly defined. To address this issue, liver inflammation, ductular reaction (DR) and fibrosis were induced in C57BL/6 mice by thioacetamide (TAA) administration for up to 12 weeks. TAA treatment induced two phases of liver fibrosis.  A rapid peri-central inflammatory infiltrate enriched in F4/80+ monocytes co-localized with SMA+ myofibroblasts resulted in early collagen deposition, marking the start of an initial fibrotic phase (1-6 weeks).  An expansion of bone marrow derived macrophages proceeded a second phase, characterized by accelerated progression of fibrosis (> 6 weeks) followed the migration of the DR from the portal tracts to the centrilobular site of injury, in association an increase in DR/macrophage interactions. Although CCL2 mRNA was rapidly induced in response to TAA, CCL2 deficiency only partially abrogated fibrosis. In contrast, CSF-1R blockade diminished CCR2neg (Ly6Clo) monocytes, attenuated the DR and significantly reduced fibrosis, illustrating the critical role of CSF-1 dependent monocyte/macrophage differentiation and linking the two phases of injury. We demonstrate that in response to liver injury, CSF-1 drives early monocyte mediated myofibroblast activation and collagen deposition, subsequent macrophage differentiation and their association with the advancing DR, the formation of fibrotic septa and the progression of liver fibrosis to cirrhosis.

overall_design: Single colour, Illumina MouseRef-8 v2.0 Beadarrays.

first: Michelle

last: Melino

first: Victoria

last: Gadd

first: Kylie

last: Alexander

first: Lynette

last: Beattie

first: Katie

last: Lineburg

last: Martinez

first: Bianca

last: Teal

first: Laetitia

last: LeTexier

first: Katharine

last: Irvine

first: Gregory

last: Miller

first: Geoffrey

last: Hill

first: Andrew

last: Clouston

first: Elizabeth

last: Powell

first: Kelli

middle: P

last: MacDonald


title: Comparison of the expression profiles of the 630E (JIR8094) strain and a prdR mutant (LB-CD8) after 4h growth in TY supplemented with L-proline

last: Monot

summary:
Clostridium difficile, a proteolytic Gram-positive anaerobe, has emerged as a significant nosocomial pathogen. Stickland fermentation reactions are thought to be important for growth of C. difficile. In Stickland reactions, pairs of amino acids donate and accept electrons, generating ATP and reducing power in the process. Reduction of the electron acceptors proline and glycine requires the D-proline reductase (PR) and the glycine reductase (GR) enzyme complexes, respectively. PrdR, a sigma54-dependent regulator, activates transcription of the PR-encoding genes in the presence of proline and negatively regulates the GR-encoding genes, suggesting that PrdR is a central metabolism regulator that controls preferential utilization of proline and glycine to produce energy via the Stickland reactions.

Here, transcriptional profiling of the C. difficile 630E strain vs. a prdR mutant (LB-CD8) after 4h of growth in the presence of proline is performed.

overall_design: Two-condition experiment: 630E (JIR8094) strain vs. prdR mutant (LB-CD8) grown in TY supplemented with 30 mM L-proline. 2 biological replicates for each condition, including a dye-swap.

first: Laurent

last: Bouillaut

first: Thomas

last: Dubois


title: Expression of cytokine-sensitive genes in islets from diabetes-prone mice

status: Public on Jun 01 2015

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Genome-wide association studies in human type 2 diabetes (T2D) have renewed interest in the pancreatic islet as a major site of T2D risk. In this study, microarray data collected from mouse islets were used to identify genes that are regulated by cytokines at levels consistent with the chronic low-grade inflammation observed in T2D.  The most cytokine-sensitive genes were then examined for association of single nucleotide polymorphisms (SNPs) with acute insulin response to glucose (AIRg) measured in the Genetics UndeRlying DIAbetes in HispaNics (GUARDIAN) study. In GUARDIAN, there was evidence of association of AIRg with SNPs in ARAP3 (5q31.3), F13A1 (6p25.3), KLHL6 (3q27.1), NID1 (1q42.3), PAMR1 (11p13), RIPK2 (8q21.3), and STEAP4 (7q21.12). These data support the mouse islet microarray data in detection of seven novel genes with potential importance to islet dysfunction in T2D. To further assess each gene, murine islets were exposed for 48-hrs to the following stressors representing models of beta-cell failure: 20nM rotenone (oxidative stress), 100nM thapsigargin (ER stress), 10pg/ml IL-1B + 20pg/ml IL-6 (cytokines/low-grade inflammation), 28mM glucose (hyperglycemia), or 50uM palmitate + 100uM oleate + 50uM linoleate (lipotoxicity). RT-PCR revealed that F13a1 was downregulated 3.3-fold by cytokines (P<0.05) and 2.6-fold by rotenone (P<0.05), Klhl6 was upregulated 4.3-fold by thapsigargin (P<0.01), Ripk2 was mildly (1.5-3-fold) but significantly upregulated by all stressors (P<0.05), and STEAP4 was profoundly cytokine-sensitive (167-fold upregulation, P<0.01). These findings reveal promising leads in elucidating islet dysfunction during the development of T2D.

overall_design: Islets were isolated from prediabetic male BKS.Cg-m+/+Leprdb/J (db/db) mice and non-diabetic heterozygous controls. Islets were treated with proinflammatory cytokines overnight or left untreated and then collected for mRNA. Microarray analysis of Affymetrix chips was performed by the UVA Biomolecular Research Facility.

first: Craig

middle: S

last: Nunemaker


title: Human beta cell proliferation induced by inhibition of Dyrk1a and GSK3b

status: Public on Oct 22 2015

first: John

last: Walker

state: CA

summary:
Purpose: Single-cell whole transcriptome sequencing was used to better understand the mechanism of action of our Dyrk1a inhibitor's proliferation of pancreatic islets.
Methods: primary pancreatic islets were isolated, cultured, and stimulated with either 0.1% DMSO or 3 µM GNF4877.  Single cells were captured and cDNA isolated on a Fluidigm C1 instrument.  Sequencing libraries were made with Nextera XT reagents (Illumina) and single-end 50 bp reads were generated on an Illumina HiSeq 1000.  Reads were mapped to the rat transcriptome.
Results:  Consistent with GNF4877 eliciting beta cell proliferation, we observed an increase in the number of beta cells co-expressing insulin 1 and genes involved in cell cycle including the M phase marker Cyclin B1. Comparison of Cyclin B1 expressing cells from GNF4877-treated islets to beta cells from DMSO-treated islets further revealed a significant increase expression of genes associated with full cell cycle progression and enrichment of Gene Ontology (GO) categories for proliferation.
Conclusions:  Since only a small subset of islet cells proliferate when stimulated with GNF4877, single-cell transcriptome sequencing allowed us to examine expression of genes co-regulated with known proliferation markers and will hopefully allow us to characterize beta cell subsets which are responsive to proliferation-associated therapies.

overall_design: 84 GNF4877-treated and 86 DMSO-treated rat islet cells containing greater than 100,000 mapped sequencing reads per cell and having a single verified cell per port were compared

first: Weijun

last: Shen

middle: F

last: Powers

first: Ann

last: Herman

first: Anwesh

last: Kamireddy

first: Austin

last: Swafford

first: Badry

last: Bursalaya

first: Bernhard

last: Hering

first: Brandon

last: Taylor

first: Carolina

middle: N

last: Turk

first: Christophe

last: Filippi

first: George

last: Harb

first: Jing

last: Li

last: Lamb

first: Lisa

last: Deaton

first: Martin

last: Seidel

first: Minhua

last: Qiu

first: Peter

last: McNamara

first: Qihui

last: Jin

first: Richard

last: Glynne

first: Bryan

last: Laffitte

first: Shanshan

last: Yan

first: Shelly

last: Meeusen

first: Tingting

last: Mo

first: Tom

last: Wu

first: Van

last: Nguyen-Tran

first: Wilma

last: Suarez-Pinzon

first: Xueshi

last: Hao

first: Yahu

last: Liu

first: You-Qing

last: Zhang


title: Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-nexus]

first: Julia

last: Zeitlinger

summary: RNA polymerase II (Pol II) pauses downstream of the transcription initiation site before beginning productive elongation. This pause is a key component of metazoan gene expression regulation. Some promoters have a strong disposition for Pol II pausing and often mediate faster, more synchronous changes in expression. This requires multiple rounds of transcription and thus cannot rely solely on pause release. But it is unclear how pausing affects the initiation of new transcripts during consecutive rounds of transcription. Using our recently developed ChIP-nexus method, we find that Pol II pausing inhibits new initiation. We propose that paused Pol II helps prevent new initiation between transcription bursts, which may reduce noise.

overall_design: ChIP-nexus was performed against Pol II, TBP, TFIIA, TFIIB, TFIIF, TAF2, XPB and NELF-E in Drosophila melanogaster Kc167 cells.

first: Wanqing

last: Shao


title: The Microbial Metabolite Deoxycholic Acid Modulates Cholesterol Metabolism in the Germ-Free Mouse

status: Public on Jan 08 2015

first: John

last: Walker

summary: Deoxycholic acid (DCA) is a secondary bile acid produced by a small number of commensal species of bacteria present in the mammalian gut.  Elevated DCA concentration correlates with disease states including colon cancer and cholesterol gallstones, but the associated mechanisms are not fully understood. Both primary and secondary bile acids are also capable of affecting gene expression through nuclear receptors such as FXR.  To better understand the impact of a commensal-derived secondary bile acid on host metabolism we fed DCA to germ-free (GF) mice, which normally lack DCA, and compared the hepatic transcriptomes of bile acid fed GF mice to GF mice receiving a control diet, as well as to those of conventionally housed control animals.  Interestingly, the feeding of DCA to GF mice, but not the feeding of cholic acid (CA) from which DCA is derived, results in an up-regulation of genes of cholesterol biosynthetic pathways.  GF mice normally have elevated hepatic cholesterol compared to conventionally housed mice. Despite increase in the expression of cholesterol biosynthetic genes, the DCA fed GF mice showed a markedly decreased level of hepatic cholesterol equivalent to the hepatic cholesterol concentration of conventionally colonized animals.  Total cholesterol in the serum was unaffected by DCA, but there was a decrease in the HDL lipoprotein fraction as well as an increase in the non-HDL lipoprotein fraction of the serum cholesterol.  DCA, but not CA, is sufficient to modulate host lipoprotein metabolism.  Taken together, these results suggests that a minor component of the gut microbiome has a significant impact on cholesterol homeostasis through secondary metabolism of bile acids and suggests a possible therapeutic intervention route through  the microbial metabolic pathways.

overall_design: two mouse strains, three diets, one time point

first: Thomas

last: Hollenbeck

first: Andrew

last: Anfora

first: Ganes

last: Bhat

first: Eric

middle: C

last: Peters

first: Sanjay

last: Agarwalla

first: Scott

middle: A

last: Lesley


title: Comparison of the expression profiles of the 630E JIR8094 strain and a prdR mutant in the presence of proline in TY

first: Marc

last: Monot

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

overall_design: Refer to individual Series


title: Comparison of the expression profiles of 630E strain and hfQ mutants

status: Public on Jul 15 2014


title: Biological characterization of virulent therapeutic bacteriophage PAK_P3 infecting Pseudomonas aeruginosa.

status: Public on Jul 20 2016

summary: We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas phage PAK_P3

overall_design: RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.

first: Anne

last: Chevallereau

first: Bob

last: Blasel


title: Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?

status: Public on May 05 2014

summary: The alternative subunit of RNA polymerase RpoS/σS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of σS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by σS is mainly a passive phenomenon, due to competition between σS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). Genome expression profiling and physiological characterization of mutants of Salmonella ser. Typhimurium deleted for rpoS or producing a σS protein efficient for binding to RNAP, but not to the -10 promoter element, revealed that gene repression by σS requires its binding to DNA. Therefore, gene repression by σS is an active phenomenon rather than the sole cause of σS competing with other sigma factors for RNAP binding.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA profiles of the wild type strain and two rpoS mutants of Salmonella enterica serotype Typhimurium were generated by RNA sequencing, using three biological replicates. One rpoS mutant is deleted for rpoS (delta-rpoS), while the other (rpoSdb) contains two point mutations in rpoS (C421A and G469A) and produces an σS protein inefficient for binding to the -10 promoter element.

first: Françoise

last: Norel

first: Corinne

last: Lévi-Meyrueis

first: Bernd

last: Jagla

first: Odile

last: Sismeiro

first: Marie

last: Dillies


title: Comparison of the expression profiles of the Clostridium difficile 630E strain and a spoIIID mutant after 15h of growth

status: Public on Feb 20 2014

summary: Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. We also performed a transcriptome experiment of the spoIIID mutant compared to the 630E strain and showed that SpoIIID represses the expression of SigE target genes and activates the expression of sigK.

overall_design: Transcriptional profiling of the C. difficile 630E strain vs. a spoIIID mutant after 15h of growth in MS. Two-condition experiment: 630E strain 15h vs. spoIIID mutant 15h. 2 biological replicates for each condition.

first: Laure

last: Saujet


title: Comparison of the expression profiles of 630E strain and a hfQ mutant after 7.5h of growth in Tyt

summary: Clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent deep-sequencing data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. The RNA chaperon protein Hfq is a key component of post-transcriptional regulatory network in various bacterial systems. In an effort to understand the function of Hfq in C. difficile, we have constructed and characterized an Hfq-depleted strain in this bacterium. We present evidence that Hfq is necessary for the normal cell growth, for the establishment of bacillary form and might be involved in metabolic adaptations, stress response and sporulation, important during C. difficile infection cycle. In accordance to these phenotypic changes, our transcriptome analysis revealed pleiotropic effects of Hfq on gene expression in C. difficile. This microarray analysis showed altered expression of genes encoding cell wall and membrane transport components, sporulation proteins, as well as stress response, transcriptional regulator genes and genes of unknown function. Remarkably, a great number of genes belonging to the regulon dependent on sporulation-specific sigma K factor were generally up-regulated in the strain depleted for Hfq. Many important metabolic pathways were also affected by Hfq depletion. Finally, the altered accumulation of several previously identified sRNAs suggests potential involvement of Hfq in these regulatory RNA function. Altogether, these results provide evidence for the pleiotropic role of Hfq protein in C. difficile physiology expanding our knowledge of Hfq-dependent regulation in Gram-positive bacteria.

overall_design: Two-conditions experiments, 630E strain vs. hfQ mutant grown in TYt, 4 biological replicates for each condition.

first: Pierre

last: Boudry


title: Immunotherapy Targets in Tumors

status: Public on Mar 14 2014

first: John

last: Walker

summary: Recent work has shown that cytotoxic T cells play a central role in immune-mediated control of cancers1-3, and monoclonal antibodies that target inhibitory receptors on T cells can induce significant clinical benefit in patients despite advanced disease4-6. However, many of the regulatory pathways that result in loss of T cell function within immunosuppressive tumors remain unknown. Here we show that such regulatory mechanisms can be systematically discovered in vivo in the tumor microenvironment. We devised a pool shRNA screening approach aimed at identifying genes that block the function of tumor-infiltrating CD8 T cells. We postulated that shRNAs targeting key inhibitors would enable robust T cell infiltration and proliferation in tumors, despite multiple inhibitory signals. Candidate shRNAs were discovered by transfer of shRNA-transduced T cells into tumor-bearing mice, followed by deep sequencing to quantify the representation of all hairpins in tumors and lymphoid organs. A subset of shRNAs induced T cell accumulation in tumors but not the spleen, demonstrating feasibility of discovering shRNAs with differential action across tissues. One of the targets was Ppp2r2d, a regulatory subunit of the family of PP2A phosphatases7. Control shRNA-transduced T cells underwent apoptosis upon recognition of melanoma cells, while Ppp2r2d shRNA-transduced T cells accumulated in tumors due to enhanced proliferation and reduced apoptosis. Ppp2r2d shRNAexpressing T cells also significantly delayed tumor growth. This in vivo approach has wide applications to dissect complex immune functions in relevant tissue microenvironments.

overall_design: OT-I derived T cells were transduced with shRNA's and adoptively transferred to B16 tumor bearing mice. Following incubation the T cells were purified from either tumors or spleens. The shRNA's targeted either a control gene (LacZ) or one of 5 selected genes found to regulate the presence of T cells in tumors vs in spleen

first: Penghui

last: Zhou

first: Donald

last: Shaffer

first: Diana

last: Alvarez Arias

first: Yukoh

last: Nakazaki

first: Wouter

last: Pos

first: Alexis

middle: J

last: Torres

first: Viviana

last: Cremasco

first: Stephanie

last: Dougan

first: Glenn

last: Cowley

first: Kutlu

last: Elpek

first: Jennifer

last: Brogdon

last: Lamb

first: Shannon

last: Turley

first: Hidde

middle: L

last: Ploegh

first: David

last: Root

first: J

last: Love

last: Dranoff

first: Nir

last: Hacohen

first: Harvey

last: Cantor

first: Kai

last: Wucherpfennig