title: Transcriptome sequencing of K-562 cells

status: Public on Apr 24 2017

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

institute: BC Cancer

summary: We analyzed the global effect of c-Myb knockdown by sequencing the transcriptomes of K-562 cells transfected with control siRNA and si2992 (MYB knockdown), as well as K-562 cells stably expressing TY-tagged wild type c-Myb and c-Myb D152V transfected with si2992

overall_design: Cells were tranfected with siRNA and 24 hours after total RNA was extracted. Three individual experiments were performed. Libraries were prepared and 125-bp paired-end reads were obtained using an Illumina HiSeq 2500 sequencer

first: Odd

last: Gabrielsen

middle: M

first: Arvind

last: Sundaram


title: Dynamics of gene expression changes in the spinal cord during FUS-mediated proteinopathy

status: Public on Apr 04 2018

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

type: Expression profiling by high throughput sequencing

summary: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder leading to the eventual death of motor neurons. Described cases of familial ALS have emerged the significance of protein misfolding and aggregation of two functionally related proteins, FUS and TDP-43, implicated in RNA metabolism. Herein, using the in vivo model of FUS-mediated proteinopathy (FUS1-359 mice) we performed the comprehensive analysis encompassing the onset of the first clinical symptoms, inclusions formations as well as changes in gene expression profile in motor neurons and surrounding microglia. The obtained data show that FUS-mediated proteinopathy is predominantly asymptomatic in terms of both the clinical symptoms and molecular aspects of neurodegeneration until it reaches the terminal stage of disease progression (120 days from birth). From this time point the pathological process develops very rapidly resulting in massive FUS-positive inclusions formation which is accompanying by the transcriptional “burst” in the spinal cord cells. Specifically it manifests in activation of pro-inflammatory phenotype of microglial cells and malfunction of acetylcholine synapse transmission in motor neurons. We conclude that a stable course of the pathological process, as well as described accompanying features, make FUS1-359 mice a convenient model for testing potential therapeutics against proteinopathy-induced decay of motor neurons.

overall_design: RNA-sequencing of transgenic and non-transgenic mice cervical region of spinal cord

middle: P


title: The effect of upper-respiratory infection on transcriptomic changes in the CNS

status: Public on Jun 14 2017

city: Urbana

first: Andrew

middle: J

last: Steelman

state: IL

address: 1201 West Gregory

country: USA

institute: University of Illinois

summary:
Purpose:  The goal of this study was to determine the effect of an upper-respiratory infection on changes in RNA transcription occuring in the cerebellum and spinal cord. post infection.
Methods:  Gender matched eight week old C57BL/6 mice were inoculated saline or with Influenza A (Puerto Rico/8/34; PR8, 1.0 HAU) by intranasal route and transcriptomic changes in the cerebellum and spinal cord tissues were evaluated by RNA-seq (100bp paired end reads) at days 0 (non-infected), 4 and 8
Results:  After trimming and excluding multi-mappeing reads an average of 92.07% (cerebellum) and 91.71% (spinal cord) of genes were uniquely mapped to a gene.  The average number of single end reads per sample was 36.42 and 37 million for the spinal cord and cerebellum respectively. Infection caused significant changes to the transcriptome of each tissue, which was most prominent at day 8 post infection.
Conclusion:  This study represents the first to use RNA-seq tecnology to evaluate the effect of peripheral influenza a infection on changes in gene expression of the cerebellum and spinal cord.


title: Comparison of wildtype and agrB-null mutant Type A Clostridium perfringens strain CP1

status: Public on Apr 18 2017

city: Guelph

first: Dion

last: Lepp

address: 93 Stone Rd W

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Clostridium perfringens encodes at least two different quorum sensing (QS) systems, the Agr-like and LuxS, and recent studies have highlighted their importance in the regulation of toxin production and virulence.  The role of QS in the pathogenesis of necrotic enteritis (NE) in poultry and the regulation of NetB, the key toxin involved, has not yet been investigated. We have generated isogenic agrB-null and complemented strains from parent CP1, and demonstrated that the virulence of the agrB-null mutant was strongly attenuated in a chicken NE model system, and restored by complementation. The production of NetB, a key NE-associated toxin, was dramatically reduced in the agrB mutant at both the transcriptional and protein level, though not in a luxS mutant.  Transwell assays confirmed that the Agr-like QS system controls NetB production through a diffusible signal. Global gene expression analysis of the agrB mutant identified additional genes modulated by Agr-like QS, including operons related to phospholipid metabolism and adherence, which may also play a role in NE pathogenesis. This study provides the first evidence that the Agr-like QS system is critical for NE pathogenesis, and identifies a number of Agr-regulated genes, most notably the NetB toxin, that are potentially involved in mediating its effects.  The Agr-like QS system thus may serve as a target for developing novel interventions to prevent NE in chickens.

overall_design: three replicate arrays were performed, each hybridized with Cy3 or Cy5-labelled cDNA from wildtype and mutant.  For one of the arrays, the dyes were swapped.

first: Qiang

last: Yu

first: Joshua

last: Gong


title: Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages (single cell RT-PCR)

status: Public on Mar 27 2017

city: New Haven

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

summary: Cell-to-cell expression variation is a prevalent feature of cell populations, but the environmental, cellular and biochemical conditions under which variability in the level of one gene can or cannot be propagated to affect that of other genes in the underlying network within cells remain poorly understood.  Here we explore this issue using single-cell qPCR and bulk-level RNAseq, CAGE, and ChIPseq analysis of human macrophages exposed to different cytokine environments. Our analyses reveal that cellular adaptation to different environments could involve tuning the extent of such variability (or information) propagation (IP) in the network, thereby shaping environment-dependent patterns of gene-gene correlations and phenotypic heterogeneity across single cells. We find that IP can be regulated through modification  of multiple network and signaling parameters, such as the degree of transcription factor-chromatin interactions. Our findings thus suggest that adaptive IP may be a widespread, yet underexplored, aspect of cellular adaptation to distinct environments.

overall_design: single cells

first: Manikandan

last: Narayanan

first: John

middle: S

last: Tsang


title: Microarray analysis of microRNAs expression in A549 cells during influenza A virus infection

status: Public on May 09 2018

city: Beijing

first: Sen

last: Zhang

address: East Street of Fengtai

country: China

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: To investigate whether influenza A virus (IAV) infection alters cellular miRNA profiles, A549 cells were either mock-infected or infected with two different subtypes of IAV, A/Beijing/501/2009 (H1N1; MOI=5) and A/Vietnam/1194/2004 (H5N1; MOI=2), for 24 or 48 h. Total RNA was purified from cell samples, and microarray analysis of miRNAs was performed. The expression of selected miRNAs was further confirmed by quantitative real-time PCR.

overall_design: A549 cells were mock-infected or infected with two different subtypes of IAV, A/Beijing/501/2009 (H1N1; MOI=5) and A/Vietnam/1194/2004 (H5N1; MOI=2), for 24 or 48 h. Then total RNA was purified from cell samples to measure the microRNAs expression.

first: Yi

last: Hu


title: Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages (10 cell RT-PCR)

overall_design: 10 cells


title: Activation of DAF-16/FOXO by reactive oxygen species promotes longevity in long- lived mitochondrial mutants in C. elegans

status: Public on Feb 26 2018

city: Montreal

first: Jeremy

middle: Michael

last: Van Raamsdonk

state: QC

address: 1001 Decarie Boulevard

department: Neurology and Neurosurgery

institute: McGill University

summary: Mild deficits in mitochondrial function have been shown to increase lifespan in multiple species including worms, flies and mice. Here, we study three C. elegans mitochondrial mutants (clk-1, isp-1 and nuo-6) to identify overlapping genetic pathways that contribute to their longevity. We find that genes regulated by the FOXO transcription factor DAF-16 are upregulated in all three strains, and that the transcriptional changes present in these worms overlap significantly with the long-lived insulin-IGF1 signaling pathway mutant daf-2. We show that DAF-16 and multiple DAF-16 interacting proteins (MATH-33, IMB-2, CST-1/2, BAR-1) are required for the longevity of all three mitochondrial mutants. Our results suggest that the activation of DAF-16 in these mutants results from elevated levels of reactive oxygen species. Overall, this work reveals an overlapping genetic pathway required for longevity in three mitochondrial mutants, and, combined with previous work, demonstrates that DAF-16 is a downstream mediator of lifespan extension in multiple pathways of longevity.

overall_design: Six biological replicates per genotype (WT, sod-2, clk-1, nuo-6, isp-1, daf-2) or three biological replicates per genotype (sod-1, ctl-1, prdx-2); mRNA was isolated individually from each replicate; Six WT and sod-2 were sequenced individually in a different experiment though were analyzed in the same way as other samples

first: Benjamin

middle: K

last: Johnson

first: Megan

last: Bowman


title: Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum

status: Public on May 10 2017

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

institute: University of California, Riverside

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.

overall_design: Analysis of transcriptional activity of P. falciparum during erythrocytic stages using newly synthesized RNA, nascent RNA. In addition, RNA polymerase II occupancy was explored and used to verify findings discovered using nascent RNA data set.

first: Gayani

last: Batugedara

first: Michael

last: Lee

first: Jacques

last: Prudhomme

first: Evelien

last: Bunnik

first: Karine

middle: G

last: Le Roch


title: Methylation of miRNA encoding genes in NSCLCs

status: Public on Mar 01 2017

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

type: Methylation profiling by genome tiling array

summary: DNA methylation is an important mechanism for gene silencing in lung cancer. In this study we identified several tumor specifically methylated miRNA encoding genes in NSCLC patients by methylome profiling.

overall_design: Genomic DNA was extracted from tumor and matching non-malignant lung tissue samples from 50 NSCLC patients and genome wide DNA methylation was analyzed using the MeDIP-chip technology as described previously (Weber et al., 2005).

first: Sabine

last: Zöchbauer-Müller


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation

status: Public on Jan 31 2018

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to identify key transcription factors governing differentiation through comparing thel transcriptome profilings in hESC samples collected from day 0 to day 4 after hematopoietic differentiation.
Conclusions: 68 transcriptional factors were found up-regulated gradually and steadily during early hematopoietic differentiation of H1 hESCs. After 4 days of differentiation, the mRNA levels of all these factors increased by more than 10 folds.

overall_design: Methods: mRNA profiles of hESC samples collected from day 0 to day 4 after hematopoiesis differentiation were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Hongtao

last: Wang


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and MEIS1 deleted H1 drived cells at day3 of hematopoietic differentiation

summary:
Purpose: The goals of this study are to investigate the molecular mechanism by which MEIS1 controls HEP specification through compareing the mRNA profiling of Wild Type and MEIS1 deleted H1 drived cells at day3 of hematopoietic differentiation.
Conclusions:a large number of genes were down-regulated in MEIS1-deleted H1 hESCs when compared with the wild-type cells. Among those, a number of mammalian hematopoiesis-associated genes such as FLI1, APLN, TAL1 and MYB were significantly down-regulated.

overall_design: Methods: mRNA profiles of Wild Type and MEIS1 deleted H1 drived cells at day3 of hematopoietic differentiation. were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays


title: Transcriptional identity and function of human dendritic cells is dictated by origin not tissue microenvironment

status: Public on Dec 24 2016

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: It has been well established that murine myeloid and plasmacytoid dendritic cells (DCs) derive from a separate hematopoietic precursor before they migrate via the blood stream to peripheral tissues. Moreover, two classes of murine conventional DCs (cDC1 and cDC2 DCs) and one class of plasmacytoid DCs (pDCs) were shown to be transcriptionally and functionally distinct entities. In humans, these DC subtypes have also been identified based on the cell surface markers CD1c (cDC2), CD141 (cDC1), and CD303 (pDCs), albeit it still remains elusive whether DC functionality is mainly determined by ontogeny or the tissue microenvironment. Moreover, an in-depth analysis of their transcriptome in different human tissues has not been established. By phenotypic and transcriptional profiling of these three DC subtypes in different human tissues derived from a larger number of human individuals, we here demonstrate that DC subpopulations – in contrast to macrophages – are more strongly defined by ontogeny rather than their localization. We provide a compendium of novel markers distinguishing DCs in different human tissues. Furthermore, bioinformatical modeling revealed a network of DC subtype-specific transcriptional regulators (TRs). Particularly CD141+ DCs were underrepresented in previous data as determined by gene set enrichment analysis using ImmuneSigDB signatures. Collectively, the data provided in this study should serve the community as a rich resource guiding further studies into human DC biology during homeostasis and inflammation.

overall_design: Single cell suspensions were generated from freshly isolated human tissues, namely blood, spleen and thymus; subpopulations of each 10.000 cells CD1c+ DCs, CD141+ DCs, pDCs, CD3+CD4+ T cells, CD3+CD8+ T cells, CD19+CD20+ B cells, and CD14+CD11b+ monocytes were FACS sorted and cells were directly snap frozen upon sorting. RNA preparation, super amplification and RNA quality control, and hybridization onto Whole Human Genome Oligo Microarray Agilent 8X60K was performed by Miltenyi Biotech (Bergisch-Gladbach, Germany)

first: Gordon

middle: F

last: Heidkamp

first: Jil

last: Sander

first: Christian

last: Lehmann

middle: L

first: Diana

last: Dudziak


title: MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition

status: Public on Jan 12 2017

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

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

overall_design: Refer to individual Series


title: Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages (RNA-Seq, CAGE and ChIP-Seq)

first: Andrew

last: Martins

summary: Through analysis of gene expression and chromatin state, this study examines human monocyte-derived macrophages activated in vitro by various stimuli such as cytokines or microbial products

overall_design: Macrophages, differentiated for 6 days from human blood monocytes using M-CSF (100ng/mL) cultured in X-vivo 15, were treated with stimuli for 18 or 24 hours and RNA and Chromatin collected for RNAseq (Illumina Truseq Ribo Zero stranded and mRNA unstranded protocols), ChIPseq (H3K27ac), and ATACseq.

first: Manikandan

last: Narayanan

first: John

last: Tsang


title: Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages


title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia

status: Public on Nov 22 2016

city: Heidelberg

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and MEIS1 deleted H1 drived cells at day6 of megakaryocytic differentiation

summary: Purpose: The goals of this study are to investigate the molecular mechanism by which MEIS1 controls megakaryocytic maturation and thrombopoiesis through compareing the mRNA profiling of Wild Type and MEIS1 deleted H1 drived cells at  day6 of megakaryocytic differentiation.

overall_design: Methods: mRNA profiles of Wild Type and MEIS1 deleted H1 drived cells at day6 of megakaryocytic differentiation. were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays


title: Drosophila melanogaster midgut transcriptome analysis after an oral infection by the entomopathogen bacteria Serratia marcescens

city: Strasbourg

first: Dominique

last: Ferrandon

address: 15, rue René Descartes

country: France

institute: UPR9022 CNRS

summary: Drosophila melanogaster oral infection by the entomopathogen bacteria Serratia marcescens trigger, at the midgut level, a drastic phenotype during the early phase of the exposure. In response to Serratia marcescens virulence factors the enterocytes present a rapid formation of megamitochondria and a subsequent controlled extrusion of the cytoplasm along with damaged organelles, which may constitute a repair mechanism. This results in a thin intestinal epithelium that then recovers its original shape in just a few hours. In order to identify, at the midgut level, the transcriptional modifications induced by Serratia marcescens during this early phase of the infection, we performed a RNAseq transcriptomics analysis of the  flies intestine three hours after  bacteria ingestion. We found that 144 genes were significantly induced and that 34 genes were repressed at this time point in comparison to the non infected midguts.

overall_design: RNAseq triplicate analysis of the transcriptomes of 3h Serratia marcescens infected Drosophila midguts (crop and Malpighian tubules are not included) compared to midguts of flies fed on sucrose for 3h.

first: Matthieu

last: Lestradet

first: Kwang-Zin

last: Lee

first: Céline

last: Keime


title: Identification of differentially expressed key-lncRNAs in lung adenocarcinoma

status: Public on Feb 01 2017

city: Changsha

first: Zhen

middle: zi

last: Peng

state: Hunan

address: Xiangya Road 87th

institute: Xiangya hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Lung cancer is a heterogeneous disease with high mortality rate globally. Lung adenocarcinoma (ADC) is the most common histological subtype of lung cancer. Multiple studies indicate that lncRNAs emerge as a novel class of critical regulators of cancer. However, the expression of lncRNAs has not been comprehensively surveyed in ADC at a genome-wide scale. Herein we examined landscapes of the lncRNAs and their potential target genes in an integrative fashion in ADC. The differences expression level of lncRNAs and mRNA were determined by microarray. qRT-PCR was performed to validate the lncRNAs expression level in a cohort of 42 tumor tissues and adjacent normal lung tissues. R and Bioconductor were used for data analysis. TF-lncRNAs-gene networks were generated by Cytoscape software. A total of 3045 lncRNAs were differentially expressed between tumor and normal tissues (1048 up and 1997 down). The qRT-PCR of 9 lncRNAs results showed that the expression patterns of these lncRNAs were consistent with the microarray data. Meanwhile, we find NONHSAT077036 expression was associated with N classification and clinical stage. Further, we analyzed the potential co-regulatory relationship between the lncRNAs and target genes using the ‘cis’ and ‘trans’ model. In the 25 related transcription factors (TFs), our analysis in TCGA database found that patients with lower expression of POU2F2 and higher expression of TRIM28 had a shorter overall survival time, suggesting that POU2F2 and TRIM28 could be biomarkers for poor prognosis of ADC. Hence, “POU2F2-lncRNAs” “TRIM28-lncRNAs” two element networks and “POU2F2-lncRNAs-mRNAs” “TRIM28-lncRNAs-mRNAs” there element relationship tables were generated.

overall_design: Overall, 12 adenocarcinoma and non-tumor tissue samples were selected for the analyses. The experiment was repeated 6 times. Samples were assayed using OE Human lncRNAs Microarray V4.0 with 78243 probe-sets of lncRNAs and 32776 probe-sets of mRNAs.

first: Chaojun

last: Duan

first: Zhenzi


title: Comparison of gene expression patterns of two SCLC genetically-engineered mouse models; Rb1 floxed, Trp53 floxed, LSL-Myc T58A-IRES-Luc vs. Rb1 floxed, Trp53 floxed, Rbl2 (p130) floxed

summary: Myc expression cooperates with Rb1 and Trp53 loss in mouse lungs to generate rapid, aggressive, highly metastatic and neuroendocrine-low tumors that are similar to human variant subset of SCLC with high NEUROD1 expression. Targeted drug screening reveals that mouse and human MYC-driven SCLC are vulnerable to Aurora kinase inhibition in combination with chemotherapy in vivo.

overall_design: Tumor formation is induced by infecting the conditional Rb1 fl/fl; Trp53 fl/fl, LSL-Myc (T58A) and Rb1 fl/fl; Trp53 fl/fl, p130 fl/fl GEMMs with adenoviruses with  Cgrp promoter driving Cre recombinase. The tumors were macro-dissected from lungs. RNA was extracted from fresh or flash frozen tumors and subjected to single end RNA sequencing.

first: Martin

last: Sos


title: A time series of autumn senescence leaves from populus tremula

status: Public on Dec 11 2016

city: Umeå

first: Erik

last: Edlund

address: Bärnstensvägen 24

department: Plant physiology

country: Sweden

institute: UPSC

summary:
A gene expression analysis of the changes in in popolulus tremula during the autumn sensencece. Leaves were analyzed from late summer and late into autumn.
Cytokinins are plant hormones that typically block or delay leaf senescence. We profiled 34 different cytokinins/cytokinin metabolites (including precursors, conjugates and degradation products) in leaves of a free-growing mature aspen (Populus tremula) before and after the initiation of autumnal senescence over three consecutive years. The levels and profiles of individual cytokinin species, or classes/groups, varied greatly between years, despite the fact that the onset of autumn senescence was at the same time each year, and senescence was not associated with depletion of either active or total cytokinin levels. Levels of aromatic cytokinins (topolins) were low and changed little over the autumn period. Diurnal variations and weather-dependent variations in cytokinin content were relatively limited. We also followed the expression patterns of all aspen genes implicated as having roles in cytokinin metabolism or signaling, but neither the pattern of regulation of any group of genes nor the expression of any particular gene supported the notion that decreased cytokinin signaling could explain the onset of senescence. Based on the results from this tree, we therefore suggest that cytokinin depletion is unlikely to explain the onset of autumn leaf senescence in aspen.

overall_design: 16 time points were analyzed from leaf samples gathered during the autumn.

first: Stefan

last: Jansson


title: CD36 deficiency causes intestinal extracellular matrix disruption and chronic neutrophil

status: Public on Oct 01 2016

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

summary:
BACKGROUND & AIMS: The scavenger receptor CD36 has versatile immuno-metabolic actions. CD36 is abundantly expressed in the small intestinal epithelium but its impact on gut homeostasis is unknown.
METHODS: Wild type (WT) and CD36-null (CD36KO) mice were fed a chow diet and small intestinal morphology assessed by immunohistochemistry and electron microscopy (EM). Inflammation was evaluated from neutrophil infiltration, expression of cytokines and toll-like receptors. Barrier integrity was determined using FITC-dextran and circulating lipopolysaccharide (LPS). Enterocyte (Ent-CD36KO) and endothelial (EC-CD36KO) CD36 null mice were generated to test contribution of epithelial versus endothelial CD36 to the intestinal phenotype.
RESULTS: The small intestine of CD36KO mice fed a chow diet showed abnormal remodeling of the extracellular matrix (ECM) with altered expression of ECM and junction proteins. Hypertrophy of cell junctions and basement membranes was observed by EM. The CD36KO intestines displayed neutrophil infiltration, inflammation and compromised barrier function. Systemic leukocytosis and neutrophilia were present in CD36KO mice and there was 80% reduction of anti-inflammatory Ly6Clow monocytes important for ECM regulation and tissue repair. Bone marrow transplants supported primary contribution of tissue injury in initiation of inflammation. Studies with Ent-CD36KO mice did not support a major contribution of enterocyte CD36 while endothelial CD36 deficiency associated with neutrophil infiltration, aberrant expression of tight junctions and inflammation in the small intestine.
CONCLUSION: CD36 is important for maintenance of barrier function in the small intestine. CD36 deletion causes ECM remodeling with collagen accumulation, depletion of the Ly6Clow monocyte subset and chronic inflammation. Endothelial but not enterocyte CD36 loss is a significant contributor to the spontaneous inflammation.

overall_design: 2 samples

first: Vincenza

last: Cifarelli

first: Nada

middle: A

last: Abumrad


title: Long-term administration of nicotinamide mononucleotide mitigates age-associated physiological decline in mice

status: Public on Dec 01 2016

summary: NAD+ availability decreases with age and in certain disease conditions.  Nicotinamide mononucleotide (NMN), a key NAD+ intermediate, has been shown to enhance NAD+ biosynthesis and ameliorate various pathologies in mouse disease models.  In this study, we conducted a 12 month-long NMN administration to regular chow-fed wild-type C57BL/6N mice during their normal aging.  Orally administered NMN was quickly utilized to synthesize NAD+ in tissues.  Remarkably, NMN effectively mitigates age-associated physiological decline in mice.  Without any obvious toxicity or deleterious effects, NMN suppressed age-associated body weight gain, enhanced energy metabolism, promoted physical activity, improved insulin sensitivity and plasma lipid profile, and ameliorated eye function and other pathophysiologies.  Consistent with these phenotypes, NMN prevented age-associated gene expression changes in key metabolic organs and enhanced mitochondrial oxidative metabolism and mitonuclear protein imbalance in skeletal muscle.  These effects of NMN highlight the preventive and therapeutic potential of NAD+ intermediates as effective anti-aging interventions in humans.

overall_design: To evaluate anti-aging effects of NMN on molecular events, we conducted microarray analyses and compared global gene expression profiles in key metabolic organs including skeletal muscle, WAT, and the liver between 6- and 12-month time points in each group of control and 300 mg/kg/day NMN-administered mice.

first: Kathryn

last: Mills

first: Shohei

last: Yoshida

first: Liana

middle: R

last: Stein

first: Alessia

last: Grozio

first: Shunsuke

last: Kubota

first: Yo

last: Sasaki

first: Philip

last: Redpath

first: Marie

last: Migaud

first: Rajendra

last: Apte

first: Koji

last: Uchida

first: Shin-ichiro

last: Imai


title: Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons (ChIP-Seq)

status: Public on Sep 21 2016

city: Davis

first: Alex

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

institute: University of California Davis

summary: The embryonic basal ganglia generates multiple projection neurons and interneuron subtypes from distinct progenitor domains. Combinatorial interactions of transcription factors (TFs), regulatory elements (REs), and chromatin are thought to precisely regulate gene expression. In the medial ganglionic eminence (MGE), the NKX2-1 TF controls regional identity and, with LHX6, is necessary to specify pallidal projection neurons and forebrain interneurons. We dissected the molecular functions of NKX2-1 by defining its chromosomal binding regions, regulation of gene expression and epigenetic state. NKX2-1 binding at distal REs led to a repressed epigenetic state and transcriptional repression in the ventricular zone. Conversely, Nkx2-1 is required to establish a permissive chromatin state and transcriptional activation in the sub- ventricular and mantle zones. Moreover, combinatorial binding of NKX2-1 and LHX6 promotes transcriptionally permissive chromatin and activates genes expressed in cortical migrating interneurons. Our integrated approach provides a foundation for elucidating transcriptional networks guiding the development of the MGE and its descendants.

overall_design: We examined RNA expression (microarray), genome-wide modified histone marks (ChIP-seq), and NKX2-1 and LHX6 binding (TF ChIP-seq) from medial ganglionic eminence (MGE) in WT and conditional Nkx2-1 null mutant mice.

first: Magnus

last: Sandberg

first: Pierre

last: Flandin

first: Shanni

last: Silberberg

first: Linda

last: Su-Feher

first: James

middle: D

last: Price

first: Jia

last: Hu

first: Carol

last: Kim

first: Axel

last: Visel

first: John

last: Rubenstein


title: The effect of n-3 PUFA therapy on skeletal muscle gene expression profile

status: Public on Jul 01 2016

first: Jun

last: Yoshino

summary: The purpose of this study was to evaluate the effect of fish oil-derived n-3 PUFA therapy, which had statistically and clinically significant beneficial effects on muscle mass and strength, on skeletal muscle gene expression profile.

overall_design: We selected 10 subjects with the largest hypertrophy response (change in thigh muscle volume) from the treatment group.

first: Gordon

last: Smith

first: Bettina

last: Mittendorfer


title: Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons


title: Direct in vivo evidence for B-cell receptor and NF-KB activation in mantle cell lymphoma: role of the lymph node microenvironment and activating mutations. [RNA-Seq]

status: Public on Jul 15 2016

city: Bethesda

first: Delong

last: Liu

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

summary: We provide direct in vivo evidence for activation of the BCR and canonical NF-KB pathways in MCL that, in the absence of activating mutations, is dependent on the lymph node microenvironment. This finding provides a mechanistic explanation for the surprising efficacy of ibrutinib for the treatment of this type of lymphoma. Mutations in components of the BCR and NF-KB pathways are associated with cell-autonomous signaling and resistance to ibrutinib.

overall_design: Lymph node biopsies and peripheral blood samples were obtained from patients with previously untreated MCL.

first: Nakhle

last: Saba


first: Christian

last: Rohde

summary: Poor outcome of AML patients is closely related with therapy failure or relapse after initial response. The underlying mechanisms remain largely unknown. In this study we discovered the histone methyltransferase EZH2 as a novel marker for response to chemotherapy and patients` survival. Protein levels of EZH2 and subsequently H3K27 trimethylation (H3K27me3) are reduced in chemoresistant AML cells. To analyze which genomic regions were affected by the loss of EZH2 and reduced H3K27me3 mark we performed Chromatin Immunoprecipitation followed by high-throughput DNA sequencing (ChIP-Seq). ChIP-Seq for the H3K27me3 repressive mark revealed genome-wide differences between sensitive (MV4-11) and resistant (MV4-11R) cells. Overall, 4699 genomic regions showed a more than 1.5 fold reduction of H3K27me3 around TSS ±5kb in MV4-11R compared to MV4-11cells. Promoter regions of HOX genes, classical targets of PRC2, revealed drastically reduced H3K27me3 enrichment in the MV4-11R cells. The H3K27me3 level at the transcriptional start site (TSS) of the ABCC1 promoter was decreased in resistant compared to sensitive cells (Fig. 6D) with increased levels of H3K4me3 and H3K27ac. As expected, we found H3K27me3 enrichments to be inversely correlated with gene expression whereas histone modifications H3K4me3 and H3K27ac, known as markers for active genes, positively correlated with gene expression in our analysis. Differentially regulated genes were characterized to be involved in protein modification/phosphorylation pathways and signaling and apoptosis.

overall_design: Examination of histone modifiactions H3K27me3, H3K27ac and H3K4me3 in a sensitive (MV4-11) and a drug resistant (MV4-11R) AML cell line

first: Stefanie

last: Göllner

first: Carsten

last: Müller-Tidow


title: Gene expression profiling of early-activated targets of antidepressants in glia cells

status: Public on Nov 16 2016

city: Regensburg

first: Barbara

last: Di Benedetto

address: Franz-Joseph-Strauß Allee 11

institute: University of Regensburg

summary: The identification of cell-type-specific and early-activated pharmacological targets of antidepressants might help to implement the search for alternative targets to develop drugs with safer side-effect profiles and faster onset of actions. Glia cells are active partners of neurons and blood vessels in supporting a variety of functions such as synaptic communication and blood-brain barrier permeability. Impaired glia cells (astrocytes and microglia cells) characterize postmortem brains of major depressive disorder patients, suggesting that they might be specifically modulated by pharmacological treatments to reverse disease phenotypes. Here, we have treated rat C6 glioma cells, used as a model of astrocytes, with two different classes of antidepressants (desipramine and fluoxetine) and two drugs without antidepressant properties (haloperidol and diazepam) to compare transcriptomes of glia cells after treatment with antidepressants versus drugs without antidepressant properties. To this aim, we used microarrays to detail the global early-activated cell-type-specific gene expression program and identified multiple classes of genes selectively modulated by antidepressants in astrocytes.

overall_design: Rat C6 glioma cells were chosen as they are considered a model of astrocytes. They were treated with antidepressants from two different classes (desipramine, a norepinephrine and serotonine reuptake inhibitor, and fluoxetine, a selective serotonin reuptake inhibitor) and drugs without antidepressant properties (haloperidol, a typical antipsychotic, and diazepam, a benzodiazepine). RNA extraction and hybridization on Illumina microarrays followed after 2 hours of drug treatment. Six replicates each treatment. Two diazepam-treated samples did not meet quality control, and were not included in this submission. We used C6 glioma cells instead of primary astrocytes to obtain a homogeneous populations of cells in order to increase the consistency and reproducibility of data analysis after expression profiling.

first: Benno

last: Pütz

first: Peter

last: Weber

first: Claudia

last: Kühne

first: Jan

last: Deussing


title: Genome-wide analysis of hepatic gene expression in patients with non-alcoholic fatty liver disease  and in healthy donors in relation to hepatic fatty acid composition and other nutritional factors

status: Public on Nov 08 2016

city: Toronto

first: Johane

middle: P.

last: Allard

state: Ontario

address: 585 University Ave, 9-NU-973

department: Medicine

institute: University Health Network

summary:
In nonalcoholic fatty liver disease (NAFLD), hepatic gene expression and fatty acid (FA) composition have been reported independently but a comprehensive gene expression profiling in relation to FA composition is lacking. The aim was to assess this relationship.
In a cross-sectional study, hepatic gene expression (Illumina Microarray) was first compared among 20 patients with simple steatosis (SS), 19 with nonalcoholic steatohepatitis (NASH), and 24 healthy controls (HC). FA composition in hepatic total lipids was compared between SS and NASH, and associations between gene expression and FA were examined. Gene expression differed mainly between HC and patients (SS and NASH), including genes related to unsaturated FA metabolism. Twenty-two genes were differentially expressed between NASH and SS; most of them correlated with disease severity and related more to cancer progression than to lipid metabolism. Biologically long-chain polyunsaturated FA (PUFA) (eicosapentaenoic acid + docosahexaenoic acid, arachidonic acid) in hepatic total lipids were lower in NASH than in SS. This may be related to overexpression of FADS1, FADS2, and PNPLA3. The degree and direction of correlations between PUFA and gene expression were different among SS and NASH which may suggest that low PUFA content in NASH modulates gene expression in a different way compared with SS or, alternatively, gene expression influences PUFA content differently depending on disease severity (SS versus NASH). Conclusion: Well-defined subjects with either healthy liver, SS or NASH showed distinct hepatic gene expression profiles including genes involved in unsaturated FA metabolism. In NASH, hepatic PUFA were lower and associations with gene expression were different than in SS.

overall_design: Cross-sectional study, including patients with non-alcoholic fatty liver disease (25 SS, 23 NASH) and 24 healthy living liver donors as HC. Nine samples (5 SS, 4 NASH) were excluded during quality control. The final analysis inclulded 63 participants (20 SS, 19 NASH, 24 HC).

first: Bianca

last: Arendt

first: Elena

last: Comelli

first: David

middle: W

last: Ma

first: Wendy

last: Lou

first: Anastasia

last: Teterina

first: TaeHyung

first: Scott

last: Fung

last: Wong

first: Ian

last: McGilvray

first: Sandra

middle: E

last: Fischer


title: Low and high dose TLR4 stimulation in bone-marrow derived mouse macrophages

status: Public on Apr 12 2016

city: New Haven

first: Andrew

last: Martins

address: 100 College Street Rm 1155

institute: Yale School of Medicine

summary: The goal of this study was to compare gene expression in mouse bone marrow-derived macrophages stimulated with high or low doses of the TLR4 ligand Kdo2-Lipid A.

overall_design: Mouse bone marrow derived marcophages were exposed to 0.03 nM or 10 nM does of the TLR4 ligand KDO Lipid A, and RNA was harvested at 1 and 2 hours post-stimulation. Two independent experimental replicates were performed.

first: Rachel

last: Gottschalk

first: John

last: Tsang

first: Ronald

middle: N

last: Germain


title: caArray_meyer-00114: TCGA Analysis of Gene Expression for Ovarian Serous Cystadenocarcinoma Using Affymetrix HT_HG-U133A

status: Public on Jun 04 2016

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: TCGA Analysis of RNA Expression for Ovarian Serous Cystadenocarcinoma Using Affymetrix HT_HG-U133A

overall_design:
meyer-00114
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HT_HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Ovary
Material Types: organism_part, organism_part, solid_tumor, cell, solid_tumor, normal_tissue
Disease States: Serous cystadenocarcinoma


status: Public on Oct 20 2016

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary:
Impaired post-ischemic angiogenesis in rats with chronic kidney disease: underlying changes in ischemia-induced early regulation of gene expression
We investigated potential molecular mechanisms underlying impaired angiogenesis by a systematic comparison of early gene expression in response to ischemia in rats with or without CKD

overall_design: CKD was induced in male rats by 5/6 nephrectomy (SNX); control rats were sham operated (sham). Eight weeks later, ischemia of the right limb was induced by ligation and resection of the femoral artery. Rats were sacrificed 24 hours after the onset of ischemia, and RNA was extracted from the musculus soleus of the ischemic and the nonischemic hindlimb. RNA was isolated and subjected to Affymetrix gene chip analysis

first: Rafael

last: Heiss

first: Fabian

middle: B

last: Fahlbusch

first: Andrea

last: Hartner

first: Karl

last: Hilgers


title: Transcriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons (microarray)

first: Alex

last: Nord

first: Magnus

last: Sandberg

first: Pierre

last: Flandin

first: Shanni

last: Silberberg

first: Linda

last: Su-Feher

first: James

last: Price

first: Jia

last: Hu

first: Carol

last: Kim

first: Axel

last: Visel

last: Rubenstein


title: High-protein intake eliminates the weight loss-induced improvement in insulin sensitivity

first: Jun

last: Yoshino

summary: The purpose of this study was to conduct a randomized-controlled trial to evaluate the effect of a high-protein (HP) diet weight loss (WL) on changes in body composition, insulin sensitivity and skeletal muscle gene expression profile in postmenopausal women who were obese and randomized to one of three dietary intervention groups: 1) a weight maitenance group, 2) a weight loss group (normal protein intake, 0.8 g protein/kg body weight per day) and 3) a weight loss group (high protein intake, 1.2 g protein/kg body weight per day) and studies before and after they lost 10% of their body weight (WL groups) or a time-matched weight maintenacne period.

overall_design: We examined skeletal muscle samples obtained from two groups; 1) 9 subjects in a WL-HP group and 2) 6 subjects in a WL-NP group before and after 10% weight loss (i.e. the weight maitenance group was not included in the current microarray study).

first: Gordon

middle: I

last: Smith

first: Bettina

last: Mittendorfer


title: Systems biology of immunity to MF59-adjuvanted versus non-adjuvanted trivalent seasonal influenza vaccines in early childhood

status: Public on Jan 31 2016

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: Here we applied systems approaches to investigate the innate and adaptive responses to trivalent inactivated influenza vaccine (TIV) and MF59-adjuvanted TIV (ATIV) in ninety 14-24 month old healthy children.

overall_design: This study was a phase II, open labeled randomized control trial to describe immune & transcriptomic responses to trivalent inactivated vaccine (TIV, Imuvac®, Abbott Healthcare Products Ltd) and MF59-adjuvanted trivalent influenza vaccine (ATIV, Fluad®, Novartis Vaccines) in 14-26 month old, healthy children (n=90). Subjects within each vaccine arm were randomized to three cohorts: A, B and C. All subjects received two vaccinations at D0 and D28. Blood samples were obtained from all subjects at D0 (pre-vacciantion baseline) and D56. Additionally, blood samples were obtained at D29 (cohort A), D31 (Cohort B) and D35 (Cohort C) (D1, 3, and 7 post boost respectively). Staggered cohort design allowed to obtain 5 blood samples while liniting the number of blood draws for each subject to 3.

first: Helder

last: Nakaya

first: Bali

last: Pulendran


title: Robust inference of cell-to-cell expression variations from single- and k-cell profiling (RNA-Seq)

status: Public on Jun 17 2016

first: Andrew

last: Martins

summary: Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population measurements. However, the levels of many transcripts in single cells fall below the detection limit of even the most sensitive technologies currently available. One proposed approach to overcome this challenge is to measure random pools of k cells (e.g., 10) to increase sensitivity, followed by computational deconvolution of cellular heterogeneity parameters (CHPs), such as the biological variance of single-cell expression levels. Existing approaches infer CHPs using either single-cell or k-cell data alone, and typically within a single population of cells. However, quantifying differences in CHPs across cell populations or conditions could reveal novel biological information, and integrating both single- and k-cell data may reap additional benefits. Here we present a Bayesian approach that can utilize single-cell, k-cell, or both simultaneously to infer CHPs within a single condition or their differences across two conditions. Using simulated as well as experimentally generated single- and k-cell data, we found situations where each data type would offer advantages, but using both together can improve precision and better reconcile CHP information contained in single- and k-cell data. We illustrate the utility of our approach by applying it to jointly generated single- and k-cell data to reveal CHP differences in several key inflammatory genes between resting and inflammatory cytokine-activated human macrophages, delineating differences in the distribution of 'ON' versus 'OFF' cells and in continuous variation of expression level among cells. Our approach thus offers a practical and robust framework to assess and compare cellular heterogeneity within and across biological conditions using modern multiplexed technologies.

overall_design: Macrophages, differentiated for 6 days from human blood monocytes using M-CSF (100ng/mL) cultured in X-vivo 15, were treated with stimuli for 18 hours and RNA collected for RNAseq (Illumina Truseq Ribo Zero stranded  protocol).

middle: J

first: Manikandan

last: Narayanan

first: John

middle: S

last: Tsang


title: EVI1 promotes tumor growth via transcriptional repression of MS4A3

status: Public on Aug 30 2015

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

institute: Medical University of Vienna

summary: Background: The transcription factor EVI1 regulates cellular proliferation, differentiation, and apoptosis, and contributes to an aggressive course of disease in myeloid leukemias and other malignancies. Notwithstanding, knowledge about the target genes mediating its biological and pathological functions remains limited. We therefore aimed to identify and characterize novel EVI1 target genes in human myeloid cells.  Methods: U937T_EVI1, a previously established human myeloid cell line expressing EVI1 in a tetracycline regulable manner, was subjected to genome wide gene expression microarray analysis. qRT-PCR was used to confirm the regulation of MS4A3 by EVI1. Reporter constructs containing various parts of the MS4A3 upstream region were employed in luciferase assays, and direct binding of EVI1 to the MS4A3 promoter was investigated by chromatin immunoprecipitation. U937 derivative cell lines experimentally expressing EVI1 and/or MS4A3 were generated by retroviral transduction, and tested for their tumorigenicity by subcutaneous injection into severe combined immunodeficient mice. Experimental results were tested for statistical significance using ANOVA and Student's t-test (two-tailed).  Results: Gene expression microarray analysis identified 27 unique genes that were up-regulated and 29 that were down-regulated in response to EVI1 induction in the human myeloid cell line, U937. The most strongly repressed gene was membrane-spanning-4-domains subfamily-A member-3 (MS4A3), and its down-regulation by EVI1 was confirmed by qRT-PCR in additional, independent experimental model systems. Reporter gene assays and chromatin immunoprecipitation showed that EVI1 regulated MS4A3 via direct binding to a promoter proximal region. Experimental re-expression of MS4A3 in an EVI1 overexpressing cell line counteracted the tumor promoting effect of EVI1 in a murine xenograft model.  Conclusions: Our data reveal MS4A3 as a novel direct target of EVI1 in human myeloid cells, and show that its repression plays a role in EVI1 mediated tumor aggressiveness.

overall_design: Time course of 2 biological replicates, plus 2 control samples; 20 arrays in total

first: Petra

last: Heffeter

first: Hubert

last: Hackl

first: Anna

last: Rommer

first: Katarina

last: Steinleitner

first: Julia

last: Etzler

first: Thais

last: Topakian

first: Birgit

last: Steinmetz

first: Martin

last: Filipits

first: Simone

last: Klingenbrunner

first: Sabine

last: Zöchbauer-Müller

first: Rotraud

last: Wieser


title: Citrullination of Histone H3 drives IL-6 production by bone marrow mesenchymal stem cells in MGUS and multiple myeloma

status: Public on Aug 03 2016

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: Multiple myeloma (MM), an incurable plasma cell malignancy, requires localisation within the bone marrow in order to survive and proliferate. Interactions between the malignant plasma cell and bone marrow mesenchymal stem cell (BMMSC) are thought to be a critical determinant of this requirement, and include both physical and chemical components. There is increasing evidence that the phenotype of the BMMSC is stably altered in patients with MM. More recently, it has been suggested that this phenotypic transformation is also observed in patients with the benign condition known as monoclonal gammopathy of undetermined significance (MGUS), which almost always precedes MM. In this study, we describe a mechanism by which the peptidyl arginine deiminase 2 (PADI2) enzyme plays an key role in the control of malignant plasma cell phenotype by BMMSCs. PADI enzymes deiminate (citrullinate) peptidyl arginine residues, changing the function or interactions made by the target protein. We identified PADI2 as one of the most highly upregulated transcripts in BMMSCs from both MGUS and MM patients, and that through citrullination of arginine residue 26 of histone H3, it induces the upregulation of interleukin-6 (IL-6) expression. This directly leads to the acquisition of resistance to the chemotherapeutic agent, bortezomib, by malignant plasma cells. We therefore describe a novel mechanism by which BMMSC dysfunction in patients with MGUS and MM directly leads to pro-malignancy signalling through the citrullination of histone H3R26.

overall_design: 30 samples, 10 from each of three categories (control, MGUS, MM)

first: Gavin

last: McNee

first: Deborah

last: Williams

first: Angelique

last: Barkhuisen

first: David

last: Bartlett

first: Sarah

last: Essex

first: Seetharam

last: Anandram

last: Filer

first: Paul

last: Moss

first: Guy

last: Pratt

first: Supratik

last: Basu

first: Clare

middle: C

last: Davies

first: Daniel

last: Tennant


title: Robust inference of cell-to-cell expression variations from single- and k-cell profiling (10 cell RT-PCR)

first: Andrew

last: Martins

overall_design: ten cells

first: Manikandan

last: Narayanan

first: John

last: Tsang


title: Robust inference of cell-to-cell expression variations from single- and k-cell profiling (single cell RT-PCR)

overall_design: single cells


title: Robust inference of cell-to-cell expression variations from single- and k-cell profiling

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

relation:
SuperSeries of: GSE83446
SuperSeries of: GSE83447
SuperSeries of: GSE83450

overall_design: Refer to individual Series


title: Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups.

status: Public on May 21 2015

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary: Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.

overall_design: We investigated a set of 562 ependymal tumors using the Illumina 450k methylation array.

first: Kristian

last: Pajtler

first: Hendrik

last: Witt

middle: T

last: Jones

first: Volker

last: Hovestadt

first: Fabian

last: Kratochwill

first: Ruth

last: Tatevossian

first: Chandanamali

last: Punchihewa

first: Steve

last: Mack

first: Vijay

last: Ramaswamy

first: Pascal

last: Johann

first: Marina

last: Rhyzova

last: Capper

first: Hans

last: Warnatz

first: Jüri

last: Reimand

first: Laura

last: Sieber

first: Andrea

last: Wittmann

first: Peter

last: van Sluis

first: Richard

last: Volckmann

first: Jan

last: Koster

first: Rogier

last: Versteeg

last: Fults

first: Smadar

last: Avigad

first: Lindsey

middle: M

last: Hoffman

last: Donson

first: Mark

last: Gilbert

first: Terry

last: Armstrong

first: Andreas

last: Kulozik

first: Olaf

first: V

middle: P

last: Collins

first: Katja

last: von Hoff

first: Torsten

last: Pietsch

first: Gary

last: Bader

first: Marie

last: Yaspo

last: von Deimling

last: Lichter

first: Michael

last: Taylor

last: Gilbertson

last: Ellison

first: Kenneth

last: Aldape

first: Andrey

last: Korshunov

first: Marcel


title: Inhibiting Monoacylglycerol Acyltransferase 1 Ameliorates Hepatic Metabolic Abnormalities, but not Inflammation and Injury in Mice

status: Public on Nov 05 2014

first: Jun

last: Yoshino

summary: Abnormalities in hepatic lipid metabolism are believed to play a critical role in the etiology of nonalcoholic steatohepatitis (NASH). Monoacylglycerol acyltransferase (MGAT) enzymes convert monoacylglycerol to diacylglycerol, which is the penultimate step in one pathway for triacylglycerol (TAG) synthesis. Hepatic expression of Mogat1, which encodes an MGAT enzyme, is increased in the livers of mice with hepatic steatosis and knocking down Mogat1 improves insulin sensitivity, but whether increased MGAT activity plays a role in the etiology of NASH is unclear. To examine the effects of knocking down Mogat1 in the liver on the development of NASH, C57BL/6 mice were placed on a diet containing high levels of trans fatty acids, fructose, and cholesterol (HTF-C diet) or a low fat control diet for 4 weeks. Mice were then injected with antisense oligonucleotides (ASO) to knockdown Mogat1 or a scrambled ASO control for 12 weeks while remaining on diet. HTF-C diet caused glucose intolerance, hepatic steatosis, and induced hepatic gene expression markers of inflammation, macrophage infiltration, and stellate cell activation. Mogat1 ASO treatment, which suppressed Mogat1 expression in liver, attenuated weight gain, improved glucose tolerance, and decreased hepatic TAG content compared to control ASO-treated mice on HTF-C chow. However, Mogat1 ASO treatment did not reduce hepatic DAG, cholesterol, or free fatty acid content, improve histologic measures of liver injury, or reduce expression of markers of stellate cell activation, liver inflammation, and injury. In conclusion, inhibition of hepatic Mogat1 in HTF-C diet-fed mice improves glucose tolerance and hepatic TAG accumulation without attenuating liver inflammation and injury.

overall_design: Total RNA obtained from liver of 4 control vs. 4 Mogat1 ASO treated higf-fat diet (HFD) fed mice.

first: Nisreen

last: Soufi

first: Angela

last: Hall

first: Sara

middle: L

last: Collier

first: James

last: Mathews

first: Elizabeth

last: Brunt

first: Carolyn

last: Albert

last: Graham

first: David

last: Ford

first: Brian

last: Finck


title: The effects of moderate weight gain in adipose tissue gene expression in metabolically-normal (MNO) and metabolically-abnormal (MAO) subjects

status: Public on Jan 09 2015

summary: Obesity is associated with insulin resistance and increased intrahepatic triglyceride (IHTG) content, which are key risk factors for diabetes and cardiovascular disease. However, a subset of obese people does not develop these metabolic complications. We tested the hypothesis that MNO, but not MAO, people are protected from the adverse metabolic effects of weight gain. To this end, global transcriptional profile in adipose tissue before and after weight gain was evaluated by microarray analyses.

overall_design: We collected subcutaneous adipose tissue samples from MNO (n=11) and MAO (n=7) subjects before and after moderate (~6%) weight gain (total 36 samples). We evaluated the effects of weight gain on adipose tissue gene expression in both MNO and MNO subjects.We used the GeneChip Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA, USA).

first: Samuel

last: Klein


title: Genome-wide DNA methylation profiling of 68 GBM (primary & recurrent), 4 glioma spheres and 5 non-tumor brain samples

status: Public on Jan 06 2015

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

country: Australia

institute: Australian National University

summary: DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients  Keywords: Disease state comparison

overall_design: Bisulphite converted genomic DNA from the 77 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip

first: Pierre

last: Bady

first: Marie-France

last: Hamou

first: Annie-Claire

last: Diserens

first: Roger

last: Stupp

first: Mauro

last: Delorenzi

first: Monika

last: Hegi


title: Direct in vivo evidence for B-cell receptor and NF-KB activation in mantle cell lymphoma: role of the lymph node microenvironment and activating mutations.

first: Delong

last: Liu

type:
Expression profiling by array
Other


title: Genome-wide analysis of the Integrator complex (BeadChip)

status: Public on Sep 09 2014

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: We investigated the genomic occupancy of INTS11, in normal condition and after stimulation of EGF. Total RNAPII was profiled in the presence or absence of INTS11, along with the Super Elongation Complex proteins AFF4 and ELL2. Additionally, we extensively examined the transcriptional response to EGF, before and after depletion of INTS11, using RNA-seq on ribosome-depleted total RNA and Global Run-on sequencing (GRO-seq).

overall_design: EGF stimulation of Hela cells, trasnfected with a control shRNA, INTS1 shRNA or INTS11 shRNA

last: Baillat

first: Ramin

last: Shiekhattar


title: Nautilus and muscle development

status: Public on Apr 01 2015

first: Anandarao

last: Ravulapalli

state: maryland

address: 9000 Rockville Pike

department: LBMB


title: Genome-wide analysis of the Integrator complex


title: DNA Methylation Changes in Whole Blood and CD16+ Neutrophils in Response to Chronic Folic Acid Supplementation in Women of Childbearing Age

status: Public on Nov 21 2014

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

summary:
Folate, a water-soluble vitamin, is a key source of one-carbon groups for DNA methylation, but studies of the DNA methylation response to supplemental folic acid yield inconsistent results.  The aim of this study was to determine if DNA methylation patterns in the dominant white blood cell type, neutrophils, would respond differently than whole blood in response to chronic folic acid supplementation.
Saliva and blood methylation was clearly distinguishable though there was positive correlation overall. There was little correlation in CpG sites within relevant candidate genes.  Correlated CpG sites were more likely to occur in areas of low CpG density (i.e. CpG shores and open seas). There was more variability in CpG sites from saliva than blood, which may reflect its heterogeneity. Thus, this study provides a framework for using DNA methylation from saliva and suggests that DNA methylation of saliva may offer distinct opportunities for epidemiological and longitudinal studies of psychiatric traits.

overall_design: DNA methylation was assessed in whole blood and CD16+ neutrophils from obese and normal weight adult women undergoing 8 weeks of folate supplementation.  Blood was collected in EDTA vacuum tubes, and CD16+ nutrophils were isolated by positive selection with Dynabeads.  DNA was extracted using the DNeasy Kit (Qiagen). DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).

first: Deanna

last: Shade

first: Hea

last: Park

first: Dorothy

last: Hausman

first: Natalie

last: Hohos

first: Richard

last: Meagher

first: Gail

last: Kauwell

last: Lewis

middle: K

first: Lynn

last: Bailey


title: Comparison of gene expression profiles of Pten, Keap1 and Nrf2 knockout mouse livers.

status: Public on Dec 31 2013

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

institute: Tohoku University

summary: Whole livers were collected from mice at the age of day 15 (P15).  Total RNA was purified using Isogen.

overall_design: Gene expression was measured in livers at the age of 15 days (P15).

first: Hozumi

last: Motohashi


title: postnatal fluoxetine evoked gene expression changes in the rat hippocampus

status: Public on Dec 01 2013

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: to understand the consequences of chronic exposure to fluoxetine during postnatal life on global transcriptional changes withing the rat hippocamps

overall_design: Agilent one-color experiment,Organism: Rattus Norvegicus, Agilent-016352  Genotypic designed Custom Rattus Norvegicus  8x15k, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Ambalika

last: Sarkar

first: Vidita

middle: A

last: Vaidya


title: GENOME-WIDE CpG ISLAND METHYLATION ANALYSIS IN NON-SMALL CELL LUNG CANCER PATIENTS

status: Public on Nov 26 2012

first: Gerwin

last: Heller


title: Genes and Pathways Underlying Regional and Cell Type Changes in Alzheimer's Disease

status: Public on Jun 07 2013

city: Seattle

first: Jeremy

last: Miller

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: Along with the two hallmark pathologies—intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques—transcriptional studies suggest that Alzheimer's disease (AD) results from dysfunction of many cellular pathways including synaptic transmission, cytoskeletal dynamics, and apoptosis.  While these studies consistently point to the same pathways involved in AD, there is no consensus on which genes in each pathway are disease-relevant, much less on whether these genes play causative roles or are downstream effects of disease progression.  To address these issues, we have performed a large-scale transcriptional analysis in brain of individuals with advanced AD and non-demented controls, focusing specifically on CA1 and the relatively less affected CA3.  For comparisons between regions and across disease status, we find consistency in both pathway enrichment as well as specific differentially expressed genes across several studies.  Furthermore, genes that show decreased expression with AD progression also tend to show enrichment in CA3 (and vice versa), suggesting that transcription levels in a region may reflect that region's vulnerability to disease.  In particular, we find several strong candidate vulnerability (ABCA1, MT1H, PDK4, RHOBTB3) and protection (FAM13A1, LINGO2, UNC13C) genes based on expression patterns.  We have also applied weighted gene coexpression network analysis (WGCNA) to explore the pathophysiology of AD from a systems perspective, finding modules for major cell types, which each show distinct disease-relevant expression patterns. In particular, a microglial module shows increased expression in the brain of non-demented controls harboring early NFT pathology, suggesting that microglial activation is an early event in AD progression.

overall_design: Total RNA obtained from 60um sections of frozen human hippocampus was collected using scalpel dissection.  Control and AD brains were matched for all non-disease characteristics as closely as possible.  CA1 and CA3 dissections for a given individual were taken from the same section.  Several region- and disease-related comparisons were performed.

first: Randall

last: Woltjer

first: Jeff

last: Goodenbour

first: Steve

last: Horvath

first: Daniel

middle: H

last: Geschwind


title: IRF8-induced monocyte differentiation

status: Public on Jan 24 2013

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University


title: Genome-wide analysis of the Integrator complex (HTS)

first: Alessandro

last: Gardini

overall_design: Comparison of the genome-wide profiles of INTS11 and RNAPII in HeLa cells.

first: David

last: Baillat

first: Matteo

last: Cesaroni

first: Deqing

last: Hu

first: Ramin

last: Shiekhattar


title: GENOME-WIDE CpG ISLAND METHYLATION ANALYSIS IN NON-SMALL CELL LUNG CANCER PATIENTS [Affymetrix expression data]

summary: Epigenetic changes largely contribute to the regulation of gene expression in cancer cells. DNA methylation is part of the epigenetic gene regulation complex which is relevant for the pathogenesis of cancer. We performed a genome-wide search for methylated CpG islands in tumors and corresponding non-malignant lung tissue samples of 101 stage I-III non-small cell lung cancer (NSCLC) patients by combining methylated DNA immunoprecipitation and microarray analysis using NimbleGen´s 385K Human CpG Island plus Promoter arrays. By testing for differences in methylation between tumors and corresponding non-malignant lung tissues, we identified 298 tumor-specifically methylated genes. From many of these genes epigenetic regulation was unknown so far. Gene Ontology analysis revealed an over-representation of genes involved in regulation of gene expression and cell adhesion. Expression of 182 of 298 genes was found to be upregulated after 5-aza-2´-deoxycytidine (Aza-dC) and/or trichostatin A (TSA) treatment of 3 NSCLC cell lines by Affymetrix microarray analysis. In addition, methylation of selected genes in primary NSCLCs and corresponding non-malignant lung tissue samples were analyzed by methylation-sensitive high resolution melting analysis (MS-HRM). Our results obtained by MS-HRM analysis confirmed our data obtained by MeDIP-chip analysis. Moreover, by comparing methylation results from MeDIP-chip analysis with clinico-pathological parameters of the patients we observed methylation of HOXA2 as potential parameter for shorter disease-free survival of NSCLC patients. In conclusion, using a genome-wide approach we identified a large number of tumor-specifically methylated genes in NSCLC patients. Our results stress the importance of DNA methylation for the pathogenesis of NSCLCs.

overall_design: Overall, samples of 3 untreated, with Aza-dC treated and with Aza-dC/TSA treated NSCLC cell lines were hybridized to Affymetrix HG-U133_plus_2.0 microarrays (18 in total).

first: Sabine

last: Zöchbauer-Müller


title: Somatic Mutation Screen of Clear Cell RCC II

status: Public on Jan 05 2010

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/.

overall_design:
Correlating gene expression profiling with mutational status
To access mutation information in these samples please query the COSMIC database with the IDs listed in GSE17895_Cancer_Genome_Project_ID.txt.gz. (http://www.sanger.ac.uk/genetics/CGP/cosmic/)


title: Genome-wide microRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers

status: Public on Mar 13 2012

summary:
Purpose: The major aim of this study was to investigate the role of DNA methylation (referred to as methylation) on microRNA (miRNA) silencing in non-small cell lung cancers (NSCLC).
Experimental Design: We performed microarray expression analyses of 856 miRNAs in NSCLC A549 cells before and after treatment with the DNA methyltransferase inhibitor   5-aza-2´-deoxycytidine (Aza-dC) and with a combination of Aza-dC and the histone deacetylase inhibitor trichostatin A. MiRNA methylation was determined in 11 NSCLC cell lines and in primary tumors and corresponding non-malignant lung tissue samples of 101 stage I-III NSCLC patients.
Results: By comparing microarray data of untreated and drug treated A549 cells, we identified 33 miRNAs whose expression was upregulated after drug treatment and which are associated with a CpG island. Thirty (91%) of these miRNAs were found to be methylated in at least 1 of 11 NSCLC cell lines analysed. Moreover, miR-9-3 and miR-193a were found to be tumor-specifically methylated in NSCLC patients. We observed a shorter disease-free survival of miR-9-3 methylated lung squamous cell carcinoma (LSCC) patients compared to miR-9-3 unmethylated LSCC patients by multivariate analysis (HR = 3.8, 95% CI = 1.3 to 11.2, p = 0.017) and a shorter overall survival of miR-9-3 methylated LSCC patients compared to miR-9-3 unmethylated LSCC patients by univariate analysis (p = 0.013).
Conclusions: Overall, our results suggest that methylation is an important mechanism for inactivation of certain miRNAs in NSCLCs and that miR-9-3 methylation may serve as a prognostic parameter in LSCC patients.

overall_design: MiRNA expression (LC Sciences, mirBASE12) was analyzed before and after treatment of A549 cells with 5-aza-2´-deoxycytidine (Aza-dC) and a combination of Aza-dC and trichostatin A (TSA). Experiments were performed in duplicates.


title: C-JUN promotes BCR-ABL induced lymphoid leukemia by inhibiting methylation of the 5´ region of Cdk6

status: Public on Feb 04 2011

summary: The transcription factor c-JUN and its upstream kinase JNK1 have been implicated in BCR-ABL induced leukemogenesis. JNK1 has been shown to regulate BCL2 expression thereby altering leukemogenesis, but the impact of c-JUN remained unclear. In this study we show that JNK1 and c-JUN promote leukemogenesis via separate pathways, since lack of c-JUN impairs proliferation of p185BCR-ABL transformed cells without affecting viability. The decreased proliferation of c-JunD/D cells is associated with the loss of cyclin dependent kinase 6 (CDK6) expression. In c-JunD/D cells CDK6 expression becomes down-regulated upon BCR-ABL induced transformation which correlates with CpG island methylation within the 5´ region of Cdk6. We verified the impact of Cdk6 deficiency by using Cdk6-/- mice that developed BCR-ABL induced B-lymphoid leukemia with significantly increased latency and an attenuated disease phenotype. In addition we show that re-expression of CDK6 in BCR-ABL transformed c-JunD/D cells reconstitutes proliferation and tumor formation in Nu/Nu mice. In summary, our study reveals a novel function for the AP-1 transcription factor c-JUN in leukemogenesis by antagonizing promoter methylation. Moreover, we identify CDK6 as relevant and critical target of AP-1 regulated DNA methylation upon BCR-ABL induced transformation, thereby accelerating leukemogenesis.

overall_design: Overall, 8 samples consisting of 4 wild type and 4 c-jun knock out samples were hybridized to MoGene-1_0-st-v1 microarrays.

first: Veronika

last: Sexl

first: Karoline

last: Kollmann


title: Nicotinamide mononucleotide, a key NAD+ precursor, treats the pathophysiology of diet- and age-induced diabetes

status: Public on Dec 05 2011

city: Izumo

first: Jun

last: Yoshino

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: Type 2 diabetes (T2D) has become an epidemic in our modern lifestyle, likely due to calorie-rich diets overwhelming our adaptive metabolic pathways.  One such pathway is mediated by nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in mammalian NAD+ biosynthesis, and the NAD+-dependent protein deacetylase SIRT1.  Here we show that NAMPT-mediated NAD+ biosynthesis is severely compromised in metabolic organs by high-fat diet (HFD).  Strikingly, nicotinamide mononucleotide (NMN), a product of the NAMPT reaction and a key NAD+ intermediate, ameliorates glucose intolerance by restoring NAD+ levels in HFD-induced T2D mice.  NMN also enhances hepatic insulin sensitivity and restores gene expression related to oxidative stress, inflammatory response, and circadian rhythm, partly through SIRT1 activation.  Furthermore, NAD+ and NAMPT levels show significant decreases in multiple organs during aging, and NMN improves glucose intolerance and lipid profiles in age-induced T2D mice.  These findings provide critical insights into a novel intervention against diet- and age-induced T2D.

overall_design: 4 regular chow fed mice (RC1-4) vs 4 high-fat diet fed (HFD) (HFD1a-4a) mice were analyzed on one chip (Chip-A). 4 HFD mice (HFD1b-4b) vs 4 HFD-NMN treated mice (NMN1-4) were examined on the other chip (Chip-B).

first: Shin-ichiro

last: Imai

first: Kathryn

middle: F

last: Mills

first: Myeong

last: Yoon


title: Glioblastoma from a homogenous cohort of patients treated within clinical trial

status: Public on Jun 20 2008

city: Lausanne

first: Monika

last: Hegi

state: Vaud

address: Bugnon 46

department: Neurosurgery

country: Switzerland

institute: CHUV

summary:
Analysis of 80 glioblastoma specimen of patients treated within clinical trials and 4 samples of  "normal"  brain tissue (non-tumoral). The data was used to identify factors of resistance to a chemoradiation therapy  protocol of radiotherapy and concomitant and adjuvant temozolomide (alkylating agent).
Keywords: Disease state comparison

overall_design: 80 glioblastoma specimen and 4 non-tumoral brain samples

first: Anastasia

last: Murat

first: Eugenia

last: Migliavacca

first: Thierry

last: Gorlia

first: Wanyu

last: Lambiv

first: Tal

last: Shay

first: Marie-France

last: Hamou

first: Luca

last: Regli

first: Wolfgang

last: Wick

first: Mathilde

last: Kouwenhoven

first: Johannes

last: Hainfellner

first: Frank

last: Heppner

first: Pierre-Yves

last: Dietrich

first: Yitzhak

last: Zimmer

middle: R

last: Macdonald

first: Abijihit

last: Guha

first: Adrian

last: Merlo

first: Nicolas

last: de Tribolet

first: Robert

last: Janzer

first: Eytan

last: Domany

first: Mauro

last: Delorenzi

first: Roger

last: Stupp


title: Age-dependent aorta transcriptomes in wild-type and apoE-deficient C57BL/6J mice

status: Public on Dec 16 2008

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

institute: Ludwig Maximilians Universität München

summary:
We previously observed that formation of aorta and innominate artery atherosclerotic lesions in the intima of hyperlipidemic apoE-deficient mice but not wild-type mice was accompanied by a marked age-dependent adventitial T cell infiltration. As the mice aged, adventitial T cells formed T/T cell-, T/B cell-, and T/B/dendritic cell aggregates adjacent to atherosclerotic lesions. Some of the adventitial infiltrates formed large clusters of various immune cells including T cells, B cells (centrocytes, follicular mantle cells), dendritic cells, follicular dendritic cells, and plasma cells with preferential formation in the suprarenal portion of the abdominal aorta. These data demonstrated that the immune lineage cell composition of atherosclerotic lesions and adventitia were distinct: The macrophage-foam cell-, T cell-, and SMC-dominated cell composition of atherosclerosis lesions versus the presence of immune cells capable of carrying out antigen-dependent T cell-driven humoral immune responses in the adventitia also indicated that immune reactions carried out in lesions or the adventitia are fundamentaly different. To distinguish between immunity-regulating genes in atherosclerosis lesions versus the adventitia, a combination of microarray profiling and laser capture microdissection was used. Stringent filters revealed 1163 differentially up-regulated probesets in apoE-/- mouse aortae at 78 weeks (w) versus 6 w. A fuzzy c-means cluster algorythm identified 2 clusters that significantly differed in their slope angles between time points: An apparent atherosclerosis cluster consisted of 771 probesets and an apparent adventitia cluster consisted of 392 probesets. Up-regulated genes at 32 w mirrored the influx of monocyte/macrophages into intima lesions whereas genes up-regulated between 32-78 w mirrored adventitial inflammation. To segregate both clusters into separate gene ontology (GO) molecular function groups, we determined statistically significant up-regulation (unpaired Student t-test; p < 0.05) between 6-32 w for the atherosclerosis cluster and between 32-78 w for the adventitia cluster. Among others, GO molecular function terms cytokine activity, cytokine binding, and immunoglobulin binding in the atherosclerosis cluster and cytokine activity, chemokine receptor activity, and antigen binding in the ATLO cluster suggested candidate genes in relation to inflammation triggered by macrophages or adventitia infiltration, respectively. Among other prototype atherosclerosis genes such as Itgax (complement receptor 4), Cd68, Lysz (lysozyme), Vcam1, and Icam1, the atherosclerosis cluster showed markedly overrepresented prototype macrophage/foam cell genes regulating inflammation in cytokine activity (GO: 0005125): Spp1 (osteopontin) and Il6; in cytokine binding (GO: 0019955) Cd74, Il10rb, Ccr2, and Ccr5; and in immunoglobulin binding (GO: 00119865) the proinflammatory galactose-binding lectin Lgals3, as well as genes in scavenger receptor activity and lipid transporter activity. By contrast, the adventitia cluster showed overrepresented genes regulating B cell recruitment, B cell maturation, germinal center formation, and autoimmunity in cytokine activity including Cxcl13, Ccl21, and Ltb, in CXC chemokine receptor activity the secondary lymphoid organ counterreceptor of CXCL13 Blr1 (also known as Cxcr5), Cxcr3, and Cxcr6; and in antigen binding several histocompatibility-2 loci and various markedly expressed immunoglobulin genes. As embryonic lymph node development and tertiary lymphoid organ neogenesis share common features signal intensities of genes specifying the GO molecular function term lymph node development (GO: 0048535) were examined in arrays prepared from wild-type and apoE-/- aortae. These results showed that Id2, Nfkb1, and Ltbr were constitutively expressed at significant levels in aortae of both mouse genotypes whereas other genes including Lta, Ltb, Glycam1, and the two lymphorganogenic genes Cxcl13 and Ccl21 were induced at 78 w in apoE-deficient aortae only. Thus, genes expressed by macrophage-foam cells and genes regulating ATLO neogenesis, embryonic lymph node development, or B cell maturation were constitutively expressed in the arterial wall in both genotypes or emerged in a stepwise fashion at 32 w and 78 w. To verify microarray signal intensity data, separate aortae extracts were examined by quantitative RT-PCR (QRT-PCR) analyses of wild-type and apoE-deficient mice at 32 and 78 w. These data showed that array signal values accurately reflected gene transcripts. Cell lineage analyses of the adventitial infiltrate and kinetic aorta microarray- and QRT-PCR analyses thus provided circumstantial evidence that immune responses in atherosclerosis intima lesions and the adventitia were distinct. To examine this possibility further, we selected areas of the abdominal aorta burdened with advanced lesions and separated lesions and corresponding adventitial infiltrates of 78 w old apoE-deficient mice by laser dissection microscopy. In addition, adventitiae of aorta segments that were not associated with adjacent lesions and adventitiae of wild-type mice were prepared. Consistent with the lack of a major adventitial leukocyte infiltration, wild-type adventitiae showed gene expression levels that were similar to lesion-free adventitiae of apoE-deficient mice indicating that atherosclerotic lesions directly affected adventitial inflammation in a segmental fashion. Stringent filter criteria identified genes that were differentially expressed in adventitiae and atherosclerotic lesions. Statistical analyses of overrepresented genes in GO molecular function or biological process groups were particularly instructive in cytokine activity, cytokine binding, antigen processing and presentation as well as in lymph node development. Thus, adventitiae in aorta segments with associated atherosclerotic lesions in cytokine activity showed overrepresentation of genes known to be associated with tertiary lymphoid organ formation including Cxcl13, Ccl21, and Ltb, whereas atherosclerotic lesions showed overrepresentation of prototype atherosclerosis-associated genes Ssp1 (osteopontin), Bmp4 (bone morphogenic protein 4), and Cxc3cl1 (fractalkine); in cytokine binding adventitiae showed overrepresentation of receptors implicated in B cell immunity and autoimmunity including Brl1 (counterreceptor for CXCL13), Ccr7, Tnfrsf4, and Cxcr3 whereas lesions showed overrepresentation of inflammatory mediator receptors including Tnfrs1b, Tgfbr1, and Il7r; moreover, in antigen processing and presentation, adventitiae showed overrepresentation of several histocompatibility loci; additional adventitial gene expression overrepresentations were observed in lymph node development (Fas, SpiB, Ltb, Flt3) whereas lesions showed expression of prototype macrophage genes including Tlr4, Tgfb1, and Tgfb2.  These data provide comprehensive topographical transcriptome information in adventitial tissue adjacent to atherosclerotic lesions versus lesions and are expected to form the basis for future cell lineage expression analyses using single cell detection methodology including ISH.
Keywords: Atherosclerosis, aorta transcriptomes, adventitia, lymphocytes, dendritic cells, immune response, tertiary lymphoid organogenesis

overall_design: Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 6 (n=3), 32 (n=3), or 78 (n=3) w and microarrays were prepared from total RNA extracts or extracts of atherosclerotic lesions and adventitiae obtained by the use of a laser dissection microscope.

first: Rolf

last: Graebner

first: Sandra

last: Doepping

first: Markus

last: Hildner

first: Michael

last: Beer

first: Beatrix

last: Lippert


title: The effect of progressive weight loss on metabolic function

status: Public on Feb 26 2016

first: Jun

last: Yoshino

summary: The purpose of this study was to evaluate the effect of progressive weight loss (5, 10, 15% weight loss) on metabolic function such as multi-organ insulin sensitivity and beta-cell function in obese people. We conducted microarray analysis to determine the effect of progressive weight loss on adipose tissue gene expression profile.

overall_design: We examined subcuntaneous adipose tissue samples obtained from 9 obese subjects before (A) and after 5% (B), 10% (C) and 15% (D) weight loss (total 36 samples).

first: Samuel

last: Klein

first: Faidon

last: Magkos


title: Gene expression in RAW264.7 cells infected with VSV and HSV-1

status: Public on Apr 05 2016

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: The purpose of this study was to determine which genes are differentially regulated virus infection in RAW264.7 cells. Cells were infected with Vesicular Stomatitis Virus (VSV) or herpes simplex virus 1 (HSV-1) for 6h. Then the differentially regulated genes were analyzed, focusing on F-box proteins and E3 ubiquitin ligases.

overall_design: RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

first: Zhou

last: Yu

first: Xuetao

last: Cao