title: Ras signaling inhibitors in in Adjuvant-induced Arthritis via targeting pathogenic antigen-specific Th17-type cells

status: Public on Aug 11 2017

first: jasmine

last: Jacob

summary: The Ras family of GTPases play an important role in signaling nodes downstream to T cell receptor and CD28 activation, potentially lowering the threshold for TCR activation by autoantigens. Somatic mutation in NRAS or KRAS may cause a rare autoimmune disorder coupled with abnormal expansion of lymphocytes. T cells from Rheumatoid Arthritis (RA) patients show excessive activation of Ras/MEK/ERK pathway. The small molecule farnesylthiosalicylic acid (FTS) interferes with the interaction between Ras GTPases and their prenyl-binding chaperones to inhibit   proper plasma membrane localization. In the present study, we tested the therapeutic and immunomodulatory effects of FTS and its derivative 5-fluoro-FTS (F-FTS) in the rat adjuvant-induced arthritis model (AIA). We show that AIA severity was significantly reduced by oral FTS and F-FTS treatment compared to vehicle control treatment. FTS was as effective as the mainstay anti-rheumatic drug methotrexate, and combining the two drugs significantly increased efficacy compared to each drug alone. We also discovered that FTS therapy inhibited both the CFA-driven in vivo induction of Th17 and IL-17/IFN-g producing double positive as well as the upregulation of serum levels of the Th17-associated cytokines IL-17A and IL-22. By gene microarray analysis of effector CD4+ T cells from CFA-immunized rats, re-stimulated in vitro with the mycobacterium tuberculosis heat-shock protein 65 (Bhsp65), we determined that FTS abrogated the Bhsp65-induced transcription of a large list of genes (e.g. Il17a/f, Il22, Ifng, Csf2, Lta, and Il1a). The functional enrichment bioinformatics analysis showed significant overlap with predefined gene sets related to inflammation, immune system processes and autoimmunity. In Conclusions, FTS and F-FTS display broad immunomodulatory effects in AIA with inhibition of the Th17-type response to a dominant arthritogenic antigen. Hence, targeting Ras signal-transduction cascade is a potential novel therapeutic approach for RA.

overall_design: Eight-week-old Lewis rats will be injected at the base of the tail with 100 μl CFA prepared by suspending heat-killed M. tuberculosis (Difco) in mineral oil at 10 mg/ml. For determining the clinical outcomes, we will measure starting day +9 the ankle diameter and score all paws on a scale of 0–4 for degree of swelling, redness, and deformity of the joints. For drug therapy, we will randomly divide the rats into two groups. Rats in the first group will be treated daily (starting on day +1 after AIA induction) with oral FTS (100 mg/kg). Rats in the second group of control Rats will receive only the oral vehicle CMC control (0.5% carboxymethyl cellulose).   At experiment end, the will be sacrificed and their spleens will be harvested for further testing. Single cell suspensions of spleen will be cultures with HSP65 (AG stimulation) or control media (Med group) for 72 hrs. Immediately thereafter, we will be process the cells for RNA isolation. Total RNA will be extracted and purified using the Direct-zol™ RNA MiniPrep w/ TRI-Reagent kits (Zymo Research Corp.)    N= 8 samples  ( 2 samples CMC Med, 2 samples CMC AG, 2 samples FTS Med, 2 samples FTS AG

first: Morad

last: Zayoud

first: Victoria

last: Marcu-Malina

first: Einav

last: Vax

first: Jasmine

last: Jacob-Hirsch

first: Galit

last: Elad-Sfadia

first: Iris

last: Barshack

first: Yoel

last: Kloog

first: Itamar

last: Goldstein


title: Chromatin-associated RNA-seq in MCF-7

status: Public on Oct 19 2017

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

type: Expression profiling by high throughput sequencing

summary: Deep sequencing of total RNA isolated from the chromatin fraction of MCF-7 cells.

overall_design: Stranded total RNA-seq (rRNA-minus) of chromatin-isolated RNA from estradiol starved and estradiol induced MCF-7 cells.

first: E

first: U

middle: A

last: Orom


title: Identification of differential expressed genes of JQ1 or JQ1+Bortezomib in colorectal cancer cells

status: Public on Oct 01 2017

city: Shanghai

first: Chen-Ying

last: Liu

address: 1665 Kong Jiang Road

country: China

institute: Xinhua Hospital, Shanghai Jiao Tong University

summary: The bromodomain and extra-terminal domain inhibitors (BETi) are promising epigenetic drugs for the treatment of various cancers through suppression of oncogenic transcription factors including MYC. However, only a subset of CRC cells response to BETi, suggesting an intrinsic resistance to BETi in CRC. We investigated the effect of JQ1 on cell proliferation, apoptosis, angiogenesis and MYC expression in a panel of 11 CRC cells in vitro and in vivo. JQ1-resistant CRC cells were used for the screening for the effective combination therapies with JQ1. RNA-seq of single drug or combined drugs treatment was performed to explore the mechanism of action.

overall_design: RKO cells were treated with  JQ1 (1 μM) for 6 h. HCT116 cells were treated with DMSO, JQ1 (1 μM) , Bortezomib (5nM), JQ1 (1 μM)+Bortezomib (5nM) for 6h. RNA was extracted for RNA-seq.

first: Long

last: Cui


title: Bisulfite sequencing coupled to target enrichment in MCF-7

type: Methylation profiling by high throughput sequencing

summary: Sequencing of bisulfite-converted MCF-7 genomic DNA captured on SureSelect Methyl-Seq (Agilent).

overall_design: Genomic DNA from estradiol starved and estradiol induced MCF-7 cells was processed according to the SureSelect MethylSeq Target Enrichment System (Agilent).


title: Evaluation of Invasive Breast Cancer Using a 12-Chemokine Gene Expression Score: Correlation With Clinical Outcomes

status: Public on Dec 31 2017

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

country: USA

institute: Moffitt Cancer Center

summary: Clinically annotated GEPs of 366 primary resected breast tumors ranked by a 12 gene chemokine score

overall_design: Gene expression profiles on banked samples from prospectively consented breast cancer stage 1-3 patients who underwent primary surgery, treatment, and follow up at the Moffitt Cancer Center.  Clinicopathologic and outcomes data (RFS,OS) were abstracted by chart review and registry data for each patient when available. Gene expression underwent normalization using the MAS5 method and the 12 gene signature was derived using the principal component method.

first: Hatem

middle: H

last: Soliman

first: Sangeetha

last: Prabhakaran


title: Genome-wide transcriptomic analysis of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (RNA-seq)

status: Public on Jul 10 2017

city: Clemson

first: Qing

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

summary: In this study, time-course transcriptome profiling of caidiomyocyte differentiation derived from human hESCs and hiPSCs was investigated. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes. The cells were collected for RNA-seq analysis at day0(undifferentiated cells) day2 (mesoderm), day4 (cardiac mesoderm) and day30 (cardiomyocytes) using Illumina HiSeq 2000 sequencer.

overall_design: Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were grown in 12-well plates with  Essential 8 medium (Thermo Fisher Scientific). The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific). At day 0, 2, 4 and 30 during the differentiation period (before the medium-change on that day), cells were collected using Accutase (Thermo Fisher Scientific), and then store in -80C till RNA isolation. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates. RNA-seq libriries were sequenced by a HiSeq 2000 sequencer (Illumina) with 2 X 101 cycles. RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser. Cuffdiff of the Cufflinks software (version 2.2.1) and GRCh39/hg19 Homo sapiens gtf file from UCSC Genome Browser were used to estimate abundances of transcripts and generate their FPKM values. Table of FPKM values of all samples were created using cummeRbund package in R.

first: Michael

last: Snyder


title: Genome-wide transcriptomic analysis and chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells

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

overall_design:
Refer to individual Series

Grant information: Michael Snyder, Stanford University, California Institute for Regenerative Medicine, CRIM GC1R-06673-A (MPS)


title: Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in a South Indian cohort

status: Public on Jan 24 2018

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

summary: We report the accuracy of various existing blood transcriptional signatures in distinguishing TB and LTBI individuals in a South Indian cohort

overall_design: Transcriptome profiles via RNAseq of TB and LTBI individuals in a South Indian cohort were used to assess the accuracy of established TB disease signatures

first: W

middle: E

last: Johnson


title: Overexpression of c-Myc antagonises transcriptional output of the androgen receptor in prostate cancer

status: Public on Apr 14 2017

city: Oslo

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

country: Norway

institute: Oslo University Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Preservation and Expansion of Blastomatous Cells in Stem-like Pleuropulmonary Blastoma Patient-derived Xenograft Affords Therapeutic Targets

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

summary: Pleuropulmonary blastoma (PPB) is a rare pediatric lung neoplasm that recapitulates developmental pathways of early embryonic lungs. As lung development proceeds with highly regulated mesenchymal-epithelial interactions, a DICER1 mutation in PPB generates a faulty lung differentiation program with resultant biphasic tumors composed of a primitive epithelial and mesenchymal stroma with early progenitor blastomatous cells. Deciphering of PPB progression has been hampered by the difficulty of culturing PPB cells, and specifically progenitor blastomatous cells. Here we show that in contrast with in-vitro culture, establishment of PPB patient-derived xenograft (PDX) in NOD-SCID mice selects for highly proliferating progenitor blastoma overexpressing critical regulators of lung development and multiple imprinted genes. These stem-like tumors were sequentially interrogated by gene profiling to show a FGF module that is activated alongside Neural cell adhesion molecule 1 (NCAM1). Targeting the progenitor blastoma and these transitions with an anti-NCAM1 immunoconjugate (Lorvotuzumab-mertansine) inhibited tumor growth and progression providing new paradigms for PPB therapeutics. Altogether, we successfully establish a novel in-vivo model of PPB and uncover anti-NCAM1 as a potential therapeutic strategy for this aggressive malignancy.

overall_design: We used Pleuropulmonary blastoma Xns, as well as, fetal and adult lung tissue originally obtained from patients, healthy adults or aborted fetus. This series includes three PPB xenograft samples. All three were derived from the same patient primary PPB sample (D492_PT).

first: Rachel

last: Shukrun

first: Hana

last: Golan

first: Revital

last: Caspi

first: Naomi

last: Pode-Shakked

first: Oren

last: Pleniceanu

first: Einav

last: Vax

first: Dekel

middle: D

last: Bar-Lev

first: Sara

last: Pri-Chen

first: Jasmine

first: Ginette

last: Schiby

first: Michal

last: Mark-Danieli

first: Orit

last: Harari-Steinberg

first: Benjamin

last: Dekel

first: Amos

last: Toren


title: Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells.

status: Public on May 31 2017

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

summary: Nuclear factor TDP-43 is known to play an important role in several neurodegenerative pathologies. In general, TDP-43 is an abundant protein within the eukaryotic nucleus that binds to many coding and non-coding RNAs and influence their processing. Using Drosophila, we have performed a functional screening to establish the ability of major hnRNP proteins to affect TDP-43 overexpression/depletion phenotypes. Interestingly, we observed that lowering hnRNP and TDP-43 expression has a generally harmful effect on flies locomotor abilities. In parallel, our study has also identified a distinct set of hnRNPs that is capable of powerfully rescuing TDP-43 toxicity in the fly eye (Hrb27c, CG42458, Glo and Syp). Most importantly, removing the human orthologs of Hrb27c (DAZAP1) in human neuronal cell lines can correct several pre-mRNA splicing events altered by TDP-43 depletion. Moreover, using RNA sequencing analysis we show that DAZAP1 and TDP-43 can co-regulate an extensive number of cellular pathways potentially important for the neuron biology. Our results suggest that changes in hnRNP expression levels can significantly modulate TDP-43 functions and affect pathological outcomes.

overall_design: SH-SY5Y cells were treated with siRNA anti-TDP-43 (n=3), or anti-DAZAP1  (n=3), or anti-Luciferase  (n=3)

first: Emanuele

last: Buratti


title: Overexpression of c-Myc antagonises transcriptional output of the androgen receptor in prostate cancer [expression]

first: Alfonso

last: Urbanucci

summary: Prostate cancer is the most common non-cutaneous cancer in men. The androgen receptor (AR) a ligand-activated transcription factor, constitutes the main drug target for advanced cases of the disease.  However, a variety of other transcription factors and signalling networks have been shown to be altered in patients and to influence AR activity. The oncogenic transcription factor c-Myc has been studied extensively in multiple malignancies, but its impact on AR activity in prostate cancer remains elusive. In this study we assessed the impact of clinically relevant levels of c-Myc overexpression on AR activity and transcriptional output. We found that c-Myc and the AR share a substantial amount of binding sites, which exhibit enhancer-like characteristics. Interestingly, c-Myc overexpression altered global AR chromatin occupancy and antagonised a subset of androgen-induced genes. Furthermore, c-Myc overexpression modified histone marks, most notably H3K4me1 and H3K27me3. Lastly, we validated the antagonistic relationship between c-Myc and two AR target genes, KLK3 and GNMT, in patient samples.

overall_design: Total RNA of three biological replicates for each condition was extracted using the RNeasy kit (Qiagen), conditions are: 5 h vehicle, 5h R1881, 5 h Doxycycline, 5h R17881+Dox, 12 h vehicle, 12h R1881, 12 h Doxycyline and 12h R1881+Dox

first: Stefan

middle: J

last: Barfeld

first: Ladan

last: Fazli

first: Paul

middle: S

last: Rennie

first: Vasan

last: Yegnasubramanian

first: Angelo

middle: M

last: de Marzo

first: Harri

last: Itkonen

first: Jessica

middle: L

last: Hicks

first: Bernd

last: Thiede

first: Ian

middle: G

last: Mills


title: Chromatin relaxation is a feature of advanced prostate cancer

status: Public on Jun 06 2017


title: PRMT1 and CSNK1a1 control epidermal progenitor maintenance

status: Public on Jan 25 2018

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

first: Xiaomin

last: Bao

first: Kun

last: Qu

last: Khavari


title: Overexpression of c-Myc antagonises transcriptional output of the androgen receptor in prostate cancer [ChIP-Seq]

summary:
c-Myc overexpression LNCaP cells were treated with R1881 or R1881+Doxycycline (to induce c-Myc overexpression) and ChIP-seq studies were performed using antibodies against c-Myc, AR, H3K4me1, H3K4me3, H3K27ac and H3K27m3
Prostate cancer is the most common non-cutaneous cancer in men. The androgen receptor (AR) a ligand-activated transcription factor, constitutes the main drug target for advanced cases of the disease.  However, a variety of other transcription factors and signalling networks have been shown to be altered in patients and to influence AR activity. The oncogenic transcription factor c-Myc has been studied extensively in multiple malignancies, but its impact on AR activity in prostate cancer remains elusive. In this study we assessed the impact of clinically relevant levels of c-Myc overexpression on AR activity and transcriptional output. We found that c-Myc and the AR share a substantial amount of binding sites, which exhibit enhancer-like characteristics. Interestingly, c-Myc overexpression altered global AR chromatin occupancy and antagonised a subset of androgen-induced genes. Furthermore, c-Myc overexpression modified histone marks, most notably H3K4me1 and H3K27me3. Lastly, we validated the antagonistic relationship between c-Myc and two AR target genes, KLK3 and GNMT, in patient samples.

overall_design: ChIP-seq study for c-Myc, AR, H3K4me1, H3K4me3, H3K27ac and H3K27m3 in a c-Myc overexpression LNCaP prostate cell line model (LNCaP MYC) treated with R1881 or R1881+Doxycycline

first: Itkonen

last: Harri


title: Chromatin relaxation is a feature of advanced prostate cancer [expression]

summary:
Altered patterns of transcription factor (TF) binding are now accepted as a hallmark of many aggressive cancers including prostate and breast cancers1,2. This implies that underlying global changes in chromatin accessibility may drive cancer progression, as previously hypothesized3-5. In addition there are epigenetic readers such as bromodomain containing protein 4 (BRD4), which have been shown to associate with these TFs6-8 and also to contribute to aggressive cancers of many types8,9 including prostate cancer (PC)6,10. Here we show for the first time that formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq) applied to human prostate tumors tissue can define castrate-resistant prostate cancer (CRPC) and can be used to inform the discovery of gene-level classifiers for therapy. In addition, we show that the androgen receptor (AR) overexpression alone is a primary driver for chromatin relaxation and that this effect can be reversed using bromodomain inhibitors. We also report that bromodomain-containing proteins (BRDs) are overexpressed in advanced CRPCs and that ATAD2 and BRD2 have prognostic value. In conclusion, this is the first study demonstrating a major impact of BRDs on chromatin accessibility in CRPC in patient samples. Consequently, targeting bromodomains provides a compelling rational for combination therapy in which BRD-mediated TF binding is enhanced or modified as cancer progresses.

Expression profile of LNCaP and VCaP prostate cancer cell lines treated with synthetic androgen R1881 with or without concomitant treatment with the pan-BET bromodomain inhibitor JQ1.

overall_design: Total RNA of three biological replicates for each condition was extracted using the RNeasy kit (Qiagen), conditions are: 5h R1881, 5h R1881+JQ1, 12h R1881, 12h R1881+JQ1, 24h R1881, and 24h R1881+JQ1

first: Ville

last: Kytölä

first: Ilsa

last: Coleman

first: Daniel

last: Vodák

first: Liisa

last: Sjöblom

first: Xia

last: Sheng

first: Teemu

last: Tolonen

first: Sarah

last: Minner

first: Christoph

last: Burdelski

first: Kati

middle: K

last: Kivinummi

first: Annika

last: Kohvakka

first: Steven

last: Kregel

first: Mandeep

last: Takhar

first: Mohammed

last: Alshalalfa

first: Elai

last: Davicioni

first: Nicholas

last: Erho

last: Lloyd

first: R

last: Karnes

first: Ashley

last: Ross

first: Edward

last: Schaeffer

first: Donald

last: Vander Griend

last: Knapp

first: Eva

last: Corey

first: Felix

middle: Y

last: Feng

first: Peter

last: Nelson

first: Fahri

last: Saatcioglu

first: Karen

last: Knudsen

first: Teuvo

last: Tammela

first: Guido

last: Sauter

first: Thorsten

last: Schlomm

first: Matti

last: Nykter

first: Tapio

last: Visakorpi


title: Chromatin relaxation is a feature of advanced prostate cancer  [FAIRE-Seq]

first: Alfonso

last: Urbanucci

summary:
Altered patterns of transcription factor (TF) binding are now accepted as a hallmark of many aggressive cancers including prostate and breast cancers1,2. This implies that underlying global changes in chromatin accessibility may drive cancer progression, as previously hypothesized3-5. In addition there are epigenetic readers such as bromodomain containing protein 4 (BRD4), which have been shown to associate with these TFs6-8 and also to contribute to aggressive cancers of many types8,9 including prostate cancer (PC)6,10. Here we show for the first time that formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq) applied to human prostate tumors tissue can define castrate-resistant prostate cancer (CRPC) and can be used to inform the discovery of gene-level classifiers for therapy. In addition, we show that the androgen receptor (AR) overexpression alone is a primary driver for chromatin relaxation and that this effect can be reversed using bromodomain inhibitors. We also report that bromodomain-containing proteins (BRDs) are overexpressed in advanced CRPCs and that ATAD2 and BRD2 have prognostic value. In conclusion, this is the first study demonstrating a major impact of BRDs on chromatin accessibility in CRPC in patient samples. Consequently, targeting bromodomains provides a compelling rational for combination therapy in which BRD-mediated TF binding is enhanced or modified as cancer progresses.
FAIRE-seq study for LNCaP and VCaP prostate cancer cell lines hormone starved or treated with R1881, and human prostate tissue samples from benign prostate hyperplasia (BPH), primary prostate cancer (PC), and castrate resistant prostate cancer (CRPC) patients.

overall_design: 2 biological replicates for prostate cancer cell lines hormone starved or treated with R1881, and 3 human prostate tissue samples from benign prostate hyperplasia (BPH), 3 primary prostate cancer (PCa), and 3 castrate resistant prostate cancer (CRPC) patients. Each sample was sequenced with an input control.

first: Stefan

last: Barfeld

first: Ville

last: Kytölä

first: Harri

last: Itkonen

first: Ilsa

last: Coleman

first: Daniel

last: Vodák

first: Liisa

last: Sjöblom

first: Xia

last: Sheng

first: Teemu

last: Tolonen

first: Sarah

last: Minner

first: Christoph

last: Burdelski

first: Kati

last: Kivinummi

first: Annika

last: Kohvakka

first: Steven

last: Kregel

first: Mandeep

last: Takhar

first: Mohammed

last: Alshalalfa

last: Davicioni

last: Erho

first: Paul

first: Ian

last: Mills


title: Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1

first: Evgenia

last: Ntini


title: Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]

status: Public on Mar 30 2017

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

summary:
Transcriptomic profiling of human breast tumors.

Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 53 invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Array-CGH results was validated by FISH using tumors showing 8p11-p12 DNA amplification and expression profiling was confirmed using qPCR for 11 transcripts. Low-level gain, high-level gain/amplification, heterozygous loss and homozygous deletion (henceforth referred to as gain, amplification, loss and deletion) were defined as log2 ratio thresholds set at +0.2, >= +0.5,  -0.2 and <=-1.0, respectively.

overall_design: Total RNA was isolated from fresh-frozen tissue samples

middle: Z

first: Elisabeth

middle: W

last: Rönnerman

first: Hanna

last: Engqvist

first: Jana

last: Biermann

first: Katarina

last: Truvé

first: Szilárd

last: Nemes

first: Eva

last: Forssell-Aronsson

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Lipid degradation promotes prostate cancer cell survival

status: Public on Mar 03 2017

first: Alfonso

last: Urbanucci

summary: Prostate cancer is the most common male cancer and androgen receptor (AR) is the major driver of the disease. Here we show that Enoyl-CoA delta isomerase 2 (ECI2) is a novel AR-target that promotes prostate cancer cell survival. Increased ECI2 expression predicts mortality in prostate cancer patients (p=0.0086). ECI2 encodes for an enzyme involved in lipid metabolism, and we use multiple metabolite profiling platforms and RNA-seq to show that inhibition of ECI2 expression leads to decreased glucose utilization, accumulation of fatty acids and down-regulation of cell cycle related genes. In normal cells, decrease in fatty acid degradation is compensated by increased consumption of glucose, and here we demonstrate that prostate cancer cells are not able to respond to decreased fatty acid degradation. Instead, prostate cancer cells activate incomplete autophagy, which is followed by activation of the cell death response. Finally, we identified a clinically approved compound, perhexiline, which inhibits fatty acid degradation, and replicates the major findings for ECI2 knockdown. This work shows that prostate cancer cells require lipid degradation for survival and identifies a small molecule inhibitor with therapeutic potential.

overall_design:
Two biological replicates for prostate cancer cell line (LNCaP) and cell line representing normal prostate epithelium (RWPE-1), transfected with scrambled siRNA or two different siRNAs targeting ECI2. RNA was extracted and used for RNA-sequencing.
The processed files provided are compressed folders containing multiple output files from CuffDiff runs estimating differentially expressed transcripts between the indicated ECI2 siRNA treated cells versus cells treated with Scrambled siRNAs.

first: Harri

last: Itkonen

first: Michael

last: Brown

first: Gregory

last: Tredwell

first: Chung

last: Lau

first: Stefan

last: Barfeld

first: Ingrid

last: Guldvik

first: Katarzyna

last: Bloch

last: Heemers

first: Nicholas

first: Elai

first: Etienne

last: Waelkens

first: Rita

last: Derua

first: Johan

middle: V

last: Swinnen

first: Hector

last: Keun

first: Ole-Petter

last: Rekvig

first: Claire

last: Hart

first: Hannelore

first: Jamew

last: Mohler

first: Noel

last: Clarke


title: The Transcription factor Zeb2 ia required to maintain tissue-specific identities of macrophages [microarray]

status: Public on Jul 14 2018

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

type:
Expression profiling by array
Third-party reanalysis

summary: Microarray, Bulk RNA Sequencing and Single cell RNA Sequencing of different murine tissue-resident macrophage populations to assess role of Zeb2 and LXRa

overall_design: Microarray = 4 replicates of alveolar Macrophages and 3 of Microglia. These were compared with previously published data (GSE75225, GSE76999 and GSE15907) to identify core macrophage profile. The file normalized_data_allsamples.txt available at the foot of this record contains the normalized values for the new samples included in this series and all re-analyzed samples.

first: Charlotte

last: Scott

first: Wouter

last: T'Jonck

first: Sofie

last: De Pricjk

first: Niels

last: Vandamme

first: Yvan

last: Saeys

first: Martin

last: Guilliams


title: Neisseria gonorrhoeae with knock-out of NgoAXP (ngo0545::km) and NgoAV (ngo406::cm) Restriction-modification system versus wild type

status: Public on Feb 13 2017

city: Warsaw

first: Monika

middle: Julita

last: Adamczyk-Poplawska

address: Miecznikowa 1

country: Poland

institute: University of Warsaw

summary: Transcriptional profiling of N. gonorrhoeae comparing wild type cells to cells with inactivated by kanamycin cassette (km) gene involved in restriction modification NgoAXP or with chloramphenicol cassette (cm) gene involved in restriction-modification NgoAV. The Goal was to study the role of M.NgoAXP and NgoAV methyltransferases in overall expression profile.

overall_design: Two-condition experiment, wild type cells vs. mutant cells . Biological replicates: 4 control replicates, 4 mutant replicates.

last: Adamczyk-Popławska

first: Agnieszka

last: Kwiatek


title: Global gene expression changes during human Angiomyolipoma xenograft propagation

status: Public on Feb 28 2017

first: jasmine

last: Jacob

summary: Angiomyolipoma (AML), the most common benign renal tumor, can result in severe morbidity from hemorrhage and renal failure. While mTORC1 activation is involved in its growth, mTORC1 inhibitors fail to eradicate AML, highlighting the need for new therapies. Moreover, the identity of the AML cell of origin is obscure. AML research, however, is hampered by the lack of in-vivo models. Here, we establish a human AML-xenograft (Xn) model in mice, recapitulating AML at the histological and molecular levels. Microarray analysis demonstrated tumor growth in-vivo to involve robust PPARG-pathway activation. Similarly, immunostaining revealed strong PPARG expression in human AML specimens. Accordingly, we demonstrate that while PPARG agonism accelerates AML growth, PPARG antagonism is inhibitory, strongly suppressing AML proliferation and tumor-initiating capacity, via an anti-TGFb mechanism. Finally, we show striking similarity between AML cell lines and multipotent mesenchymal stromal cells (MSCs) in terms of antigen and gene expression and differentiation potential. Altogether, we establishment the first in-vivo human AML model, provide evidence that AML may originate in a PPARG-activated renal MSC lineage that is skewed towards adipocytes and smooth muscle and away from osteoblasts, and uncover PPARG as a regulator of AML growth, which could serve as an attractive therapeutic target.

overall_design: In order to investigate the genetic changes accompanying AML Xn propagation, we compared the cell of origin of the Xn (i.e. the UMB cell line, derived from the AML of a human TSC patient), a first-generation Xn (T1), a fourth-generation Xn (T4) and primary human bone marrow-derived multipotent marrow stromal cells (MSCs), hypothesized to represent the AML cell of origin. The study was aimed at analyzing mainly the changes in gene expression accompanying the propagation of the AML Xn, by comparing T4- to T1-Xn. In addition, we were interested in studying the changes from MSCs (representing the presumptive cell of origin of the tumor) to UMB (representing a transformed equivalent of the former).

first: Oren

last: Pleniceanu

first: Racheli

last: Shukrun

first: Dorit

last: Omer

first: Einav

last: Vax

first: Klaudia

last: Dziedzic

first: Michal

last: Mark-Daniei

first: Sara

last: Pri-Chen

first: Nira

last: Varda-Bloom

first: Arnon

last: Nagler

first: Orit

last: Harari-Steinberg

first: Jack

last: Arbiser

first: Benjamin

last: Dekel


title: High depth sequencing of BrU-labeled nascent RNA.

status: Public on Aug 22 2017

first: Evgenia

last: Ntini

summary: BrU incorporation into nascent RNA followed by immunoprecipitation with a BrU specific antibody. The nascent RNA was subsequently eluted with BrU competition.

overall_design: HEK293T cells were incubated with 2mM bromouridine for 15min labeling time and chased with 20mM uridine for different time intervals (0min, 15min, 30min and 60min). Nascent RNA was purified during BrU-IP with anti-BrdU.

first: Annita

last: Louloupi

first: Ulf

last: Orom


title: Long Noncoding RNA Expression profiling of IMP1-expression and IMP1 nonexpression MDA231 Cells

status: Public on Dec 09 2016

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

summary: ZBP1/IMP1 is a RNA binding protein that post-transcriptionally regulates the expression of a handful mRNAs, implicated in maintaining cell polarity and adhesion.  We have previously shown that ZBP1 was able to inhibit proliferation and invasiveness of breast carcinoma cells in vitro.  To determine important LncRNA for breast tumor growth and metastasis in response to IMP1 expression, LncRNA expression data were obtained from, and compared between the breast cancer cell line MDA231-IMP1 and MDA231/GFP.

overall_design: Total RNA was extracted from IMP1-expression（MDA231-IMP）and IMP1-nonexpression MDA231 cells（MDA231-GFP）and used for hybridization on Agilent microarrays. LncRNA expression data from MDA231-IMP were collected and compared to LncRNA expression data from MDA231-GFP. The microarray experiments and data analysis were performed at the Shanghai Biotechnology Corporation in Shanghai, China.

first: Y

middle: C

last: Zhou

first: D

last: Li

first: W

last: Gu


title: Maternal methylmercury from a wild-caught walleye diet dysregulates gene expression in zebrafish offspring

status: Public on Sep 27 2016

first: Qing

last: Liu

summary: The goal of this project is to identify neural and molecular biomarkers as predictors of MeHg exposure and deficits in specific neurobehavioral endpoints. Specifically, we are investigating the effects of sublethal MeHg exposure (1, 2 and 3.5 ppm of wild-caught walleye diet) on developing zebrafish by analyzing early lifestage (ELS) toxicity, changes in global gene expression by microarray analysis and quantitative real-time PCR (QPCR), and neurobehavioral dysfunction. Gene expression analysis in exposed embryos was performed using an 8,000 element custom zebrafish cDNA microarray. Microarray results were validated using QPCR. A number of the early life stage zebrafish genes found to be dysregulated by maternal MeHg have functional annotations involving cell division, cell cycle progression, neurodevelopment, liver development, ion-binding, transcriptional regulation and endopeptidase activity.

overall_design: Female TL zebrafish were fed by wild-caught and lyophilized walleye fillets following Low and High MeHg (1 and 3.5 ppm), then bred with male GL fish which were fed normal food. Eggs were collected after 24 hpf. RNA was isolated from pooled 24 hpf embryos from each group (N=100) using Trizol reagent (Invitrogen) and further purified using an RNeasy MiniElute cleanup kit (Qiagen).cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen). Targets were labeled with Cy3 and Cy5 using the Array 50 Expression Array Detection kit (Genisphere).Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning. Arrays were scanned using an ScanArray Express (PerkinElmer) scanner. Raw data were extracted by Imagene version 6.0 software and analyzed by R version 2.9., Bioconductor 2.4, specifically limma 2.18.3. Graph 1.22.5 and Igraph 0.5.1 were used for network analysis which is visualized by Cytoscape 2.6.1.We used dual channel labeling system with Cy3 and Cy5, and did dye-swap. Duplicates were run for each comparison.

first: Michael

last: Carvan

first: Matthew

last: Rise

first: Daniel

middle: N

last: Weber

first: Giles

last: Goetz

first: Craig

last: Struble

first: Shawn

last: Gerstenberger

first: Tisha

last: King-Heiden

first: Martin

last: Hessner

first: Jessica

last: Grzybowski

last: Dellinger

first: John


title: p38 Mitogen-Activated Protein Kinase Signals the Immunoresolving Actions of Resolvin D1 in Inflamed Human Visceral Adipose Tissue

status: Public on Jul 28 2016

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Activation of the innate immune system leading to a persistent state of low-grade of tissue inflammation greatly influences the risk of developing metabolic complications associated with obesity. In this study, we characterized the inflammatory state in adipose tissue from obese patients and explored the potential of the specialized pro-resolving mediator (SPM) resolvin D1 (RvD1) to actively terminate inflammation and promote its resolution. By means of high-troughput transcritomic analysis we identified a  cytokine-related molecular signature in obese omental adipose tissue, characterized by a remarkable overexpression of interleukin (IL)-6, IL-1β and IL-10 associated with a concomitant increase in macrophage infiltration, which gradually increased in a body mass index-dependent manner.

overall_design: RNA profiling was conducted in 4 patients with morbid obesity and 4 control subjects using the Affymetrix Human Genome U219 expression array plate containing more than 36,000 transcripts and variants (Affymetrix, Inc., Santa Clara, CA).

first: E

last: Titos

first: B

last: Rius

first: C

last: López-Vicario

first: V

last: García-Alonso

first: J

last: Clària


title: Transcriptional signatures of sleep duration discordance in monozygotic twins

status: Public on Sep 09 2016

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

summary: Short sleep duration is associated with adverse metabolic, cardiovascular, and inflammatory effects. Co-twin study methodologies account for familial (e.g., genetics and shared environmental) confounding, allowing assessment of subtle environmental effects, such as the effect of short habitual sleep duration on gene expression. Therefore, we sought to investigate gene expression in monozygotic twins discordant for actigraphically phenotyped habitual sleep duration. Eleven healthy monozygotic twin pairs (82% female; mean age 42.7 years; SD=18.1), selected based on subjective sleep duration discordance, were objectively phenotyped for habitual sleep duration with two-weeks of wrist actigraphy. Peripheral blood leukocyte (PBL) RNA from fasting blood samples was obtained on the final day of actigraphic measurement and hybridized to Illumina humanHT-12 microarrays. Differential gene expression was determined between paired samples and mapped to functional categories using Gene Ontology. Next, a more comprehensive gene set enrichment analysis was performed based on the entire PBL transcriptome. The mean 24 hour sleep duration of the total sample was 439.2 minutes (SD=46.8 minutes; range 325.4 to 521.6 minutes). Mean within-pair sleep duration difference per 24 hours was 64.4 minutes (SD=21.2; range 45.9 to 114.6 minutes). The twin cohort displayed distinctive pathway enrichment based on sleep duration differences. Short sleep was associated with up-regulation of genes involved in transcription, ribosome, translation and oxidative phosphorylation. Unexpectedly, genes down-regulated in short sleep twins were highly enriched in immuno-inflammatory pathways such interleukin signaling and leukocyte activation, as well as developmental programs, coagulation cascade, and cell adhesion. Objectively assessed habitual sleep duration in monozygotic twin pairs appears to be associated with distinct patterns of differential gene expression and pathway enrichment. By accounting for familial confounding and measuring real life sleep duration, our study shows the transcriptomic effects of short sleep on dysregulated immune response and provides a potential link between sleep deprivation and adverse metabolic, cardiovascular and inflammatory outcomes.

overall_design: Total RNA from peripheral blood leukocytes (PBL) of 11 monozygotic twin pairs was isolated using PAXgene™ tubes. Samples were hybidized to 22 Illumina HumanHT-12 v4 Expression BeadChips.

middle: A


title: Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas

status: Public on Mar 31 2017

first: Toshima

last: Parris

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data that were specifically regulated by lncRNA-LFAR1 in livers of mice undergoing hepatic fibrosis.

status: Public on Oct 26 2016

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

summary:
Long noncoding RNAs (lncRNAs) play important roles in various biological processes; however, few have been identified that regulate hepatic stellate cells (HSCs) activation and the progression of liver fibrosis. Through a detailed analysis of the expression of lncRNAs in various tissues, we discovered the existence of a liver enriched lncRNA-LFAR1 (lncRNA-Liver Fibrosis Associated RNA1). To identify the roles of  lncRNA-LFAR1 in liver fiboris, we systematically analyzed the regulation of mRNAs in the livers of mice treated with oil in combination with injection of Lenti-NC (NC, n=3), CCl4 in combination with injection of Lenti-NC (NC+CCl4, n=3), oil in combination with injection of Lenti-shLFAR1 (shLFAR1, n=3) and CCl4 in combination with injection of Lenti-shLFAR1 (shLFAR1+CCl4, n=3) by mRNA microarrays, which revealed a panel of mRNAs that were specifically regulated by lncRNA-LFAR1 in livers of mice undergoing hepatic fibrosis.
To identify the roles of lncRNAs-LFAR1 in regulating liver fiboris and the potential targets of lncRNA-LFAR1 in liver fiboris,we determined the mRNA expression profiles in the livers of Balb/c mice treated with oil in combination with injection of Lenti-NC (NC, n=3), CCl4 in combination with injection of Lenti-NC (NC+CCl4, n=3), oil in combination with injection of Lenti-shLFAR1 (shLFAR1, n=3) and CCl4 in combination with injection of Lenti-shLFAR1 (shLFAR1+CCl4, n=3) by mRNA microarrays.

overall_design: The mRNA expression profile of twelve liver tissues from mice were treated with oil in combination with injection of Lenti-NC (NC, n=3), CCl4 in combination with injection of Lenti-NC (NC+CCl4, n=3), oil in combination with injection of Lenti-shLFAR1 (shLFAR1, n=3) and CCl4 in combination with injection of Lenti-shLFAR1 (shLFAR1+CCl4, n=3) were analyzed by Affymetrix GeneChip® Mouse Genome 430 2.0 Array.

first: Wei

last: Hong

first: Tao

last: Han


title: Transcriptional profle of bronchoalveolar cells in sarcoidosis

status: Public on Jul 22 2016

summary:
Introduction: Sarcoidosis is a multisystem immuno-inflammatory disorder of unknown etiology that most commonly involves the lungs. We hypothesized that an unbiased approach to identify pathways activated in alveolar macrophages—a key immuno-inflammatory cell in the lung—can shed light on the pathogenesis of this complex disease.
Methods: We recruited 15 patients with various stages of sarcoidosis and 12 healthy controls. All subjects underwent bronchoscopy with lavage. For each subject, total RNA was extracted from bronchoalveolar (BAL) cells  and hybridized to an Affymetrix GeneChip Human Genome U133A 2.0 microarray. Rigorous statistical methods were applied to identify differential gene expression between subjects with sarcoidosis vs. controls. To better elucidate pathways differentially activated between these groups, we applied gene set enrichment analysis (GSEA) to the transcriptional profiles of BAL cells. We used false discovery rate (FDR) < 0.01 to designate significant enrichment.
Results: Sarcoid patients were either non-smokers or ex-smokers, all had lung involvement and only 2 were on systemic prednisone.  Healthy controls were all non-smokers. Comparison of BAL cell gene expression between sarcoidosis and healthy subjects revealed over 1200 differentially expressed genes at an FDR cutoff < 0.01. Several previously described immune mediators, such as interferon gamma, were up-regulated in the sarcoidosis subjects. Since genes often exert their influence through functionally coherent modules, we performed GSEA based on global expression profiles of alveolar macrophages between the subject groups.  We identified more than 200 gene sets enriched in patients with sarcoidosis whereas very few pathways were over-represented in the healthy controls. Many of the sarcoidosis-associated pathways mapped to inflammatory and immune-related processes including T-cell signaling, graft vs. host disease, IL-12, IL-23, and IL-17 pathways, and oxidative phosphorylation. However, we also found and confirmed significant alteration in Proteasome-related pathways.
Conclusions: BAL cells in sarcoidosis are characterized by enrichment of distinct transcriptional networks involved in immuno-inflammatory and proteasomal processes. Our findings add to the growing evidence implicating airspace resident cells in the pathogenesis of sarcoidoisis and identify specific pathways whose activation may modulate disease progression.

overall_design: Total RNA from BAL cells of 15 subjects with sarcoidosis and 12 healthy controls was hybridized to 27 Affymetrix Genechip Human U133A 2.0 microarrays


title: Kinetics after JQ1 treatment in liver cancer cell

status: Public on Jul 20 2016

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

summary: Analysis of global gene expression after BRD4 inhibition by JQ1 in liver cancer cell lines SK-Hep1

overall_design: Total RNA obtained from human liver cancer cell line SK-Hep1 cells after treatment of JQ1

first: Seong

middle: H

first: Jueng

last: You

first: Jung

first: Suk

last: Nam


title: Identification of novel biomarkers for prediction of neurological prognosis following cardiac arrest

status: Public on Jan 01 2017

summary: We examined 22 comatose patients resuscitated after CA and obtained peripheral blood from the patients at 48 hours after CA. To identify novel blood biomarkers, we aimed to measure neurological outcomes according to the Cerebral Performance Category (CPC) score at 6 months after CA and to determine blood transcriptome-based molecular signature of poor neurological outcome group.

overall_design: 22 participants were dichotomized into good neurological outcome, CPC 1 (n=10), and poor neurological outcome CPC 4 (n=4) and CPC 5 (n=8) were analyzed on whole genome expression microarray to profile post-CA with its innate characteristic molecular signature.


title: Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [miRNA-Seq]

status: Public on Feb 10 2017

city: Beijing

first: Wen

last: Shi

state: Outside the US or Canada

address: Beijing, Haidian

department: Oral & Maxillofacial Surgery

institute: Peking University School and Hospital of  Stomatology

type: Non-coding RNA profiling by high throughput sequencing

summary: The purpose of this study was to systematically profile the expression of both mRNAs and miRNAs in OSCC and its premalignant disease to identify some novel potential biomarkers for the detection of malignant transformation.

overall_design: NGS was applied to investigate the differential transcriptome. The expression of mRNAs and miRNAs were analyzed in tumor tissues, premalignant tissues and adjacent normal tissues obtained from same OSCC patients with long history of oral mucosal disease.

first: Zhigang

last: Cai


title: Identification of lncRNA UCA1-associated microRNAs in breast cancer cell line MDA231 using miRNA-Seq

status: Public on Dec 14 2016

first: Zhou

last: Yanchun

summary: LncRNA urothelial carcinoma-associated 1 (UCA1) is an oncogene in breast cancer. Previous reports indicates that lncRNAs may function as competing endogenous RNAs (ceRNAs) to sponge miRNAs, thereby modulating the derepression of miRNA targets. To characterize microRNAs that associated with UCA1, the microRNAs associated with UCA1 were extracted from the UCA1-MS2 RNP complexes  and analyzed by miRNA-seq.

overall_design: Cell lysates were prepared from cultured MDA231-UCA1-MS2 cells and MDA231-Con cells and then incubated with Amylose-resin-attached MBP-MCP (MS2 coat protein) at 4°C for 5 h with gentle rotation. After incubation, the supernatant was removed by a short centrifugation and the Amylose beads were washed three times in lysis buffer，Bound UCA1-MS2 RNP complexes were eluted with 100 µl lysis buffer containing 20 mM maltose. miRNAs associated with UCA1 were extracted and analyzed by miRNA-seq.

first: Y

last: Zhou

first: S

last: Chen

first: W

last: Gu


title: An 18 gene expression-based score classifier predicts the clinical outcome in stage 4 neuroblastoma

status: Public on Apr 05 2016

city: Napoli

first: Mario

last: Capasso

address: Via Gaetano Salvatore, 486

department: Dept. of  Molecular Medicine and Medical Biotechnology

institute: University of Napoli "Federico II" - CEINGE Biotecnologie Avanzate Scarl

summary: The prognosis of children with metastatic stage 4 neuroblastoma (NB) has remained poor in the past decade. Using microarray analyses of 342 primary tumors, we here developed and validated an easy to use gene expression-based risk score including 18 genes, which can robustly predict the outcome of stage 4 patients. This classifier was a significant predictor of overall survival in two independent validation cohorts (cohort 1 (n=214): P=6.3x10-5; cohort 2 (n=27): P=3.1x10-2). The prognostic value of the risk score was validated by multivariate analysis including the established markers age and MYCN status (P=0.027). In the pooled validation cohorts (n=241), integration of the risk score with the age and/or MYCN status identified subgroups with significantly differing overall survival (ranging from 35% to 100%). Together, the 18-gene risk score classifier can identify patients with stage 4 NB with favorable outcome and may therefore improve risk assessment and treatment stratification of NB patients with disseminated disease.

overall_design: We analyzed expression profiling arrays of 27 Tumor samples from stage 4 neuroblastoma patients.

first: Daniela

last: Formicola

first: Giuseppe

last: Petrosino

first: Vito

last: Lasorsa

first: Piero

last: Pignataro

first: Flora

last: Cimmino

first: Simona

last: Vetrella

first: Luca

last: Longo

first: Gian

middle: P

last: Tonini

first: André

last: Oberthuer

first: Achille

last: Iolascon

first: Matthias

last: Fischer


title: Genome-wide chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (ATAC-seq)

status: Public on Jul 10 2017

first: Qing

last: Liu

summary: In this study, time-course genome-wide chromatin accessibility of caidiomyocyte differentiation derived from human hESCs and hiPSCs was profiled. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes by ATAC-seq. The cells were collected for ATAC-seq at day 0(undifferentiated cells) day 2 (mesoderm), day 4 (cardiac mesoderm) and day 30 (cardiomyocytes).

overall_design: Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific). The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific). At day 0, 2, 4 and 30 during the differentiation period (before the medium-change on that day), about 50,000 cells were collected for ATAC-seq. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates.

first: Michael

last: Snyder


title: Hierarchy within the mammary STAT5-driven Wap super-enhancer

status: Public on May 31 2016

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: Super-enhancers comprise of dense transcription factor platforms highly enriched for active chromatin marks. A paucity of functional data led us to investigate their role in the mammary gland, an organ characterized by exceptional gene regulatory dynamics during pregnancy. ChIP-Seq for the master regulator STAT5, the glucocorticoid receptor, H3K27ac and MED1, identified 440 mammary-specific super-enhancers, half of which were associated with genes activated during pregnancy. We interrogated the Wap super-enhancer, generating mice carrying mutations in STAT5 binding sites within its three constituent enhancers. Individually, only the most distal site displayed significant enhancer activity. However, combinatorial mutations showed that the 1,000-fold gene induction relied on all enhancers. Disabling the binding sites of STAT5, NFIB and ELF5 in the proximal enhancer incapacitated the entire super-enhancer, suggesting an enhancer hierarchy. The identification of mammary-specific super-enhancers and the mechanistic exploration of the Wap locus provide insight into the complexity of cell-specific and hormone-regulated genes.

overall_design: ChIP-Seq for STAT5A, GR, H3K27ac, MED1, NFIB, ELF5, RNA Pol II, and H3K4me3 in wild type (WT) mammary tissues at day one of lactation (L1), and ChIP-Seq for STAT5A, GR, H3K27ac, MED1, NFIB, ELF5, and H3K4me3 in WT mammary tissues at day 13 of pregnancy (p13). ChIP-Seq for STAT5A, GR, H3K27ac in Wap-delE1a, -delE1b, -delE1c, -delE2, -delE3, -delE1a_delE2, -delE2_delE3 and -delE1a_delE2_delE3  mutant mammary tissues at L1, and ChIP-Seq for NFIB and ELF5 in Wap-delE1b and -delE1c mutant mammary tissues at L1. ChIP-Seq for H3K4me3 in mammary-epthelial cells at p13 and L1. DNase-seq in WT mammary tissues at L1 and DNase-seq in Wap-delE1a, -delE1c, and -delE3 mutant mammary tissues at L1. ChIP-seq for STAT5A, H3K27ac in WT mammary tissues at p14, ChIP-seq for STAT5A, H3K27ac in WT mammary tissues at p16, and ChIP-seq for CTCF in in WT mammary tissues at L1.

first: HaYoun

last: Shin

first: KyungHyun

last: Yoo

first: Xianke

last: Zeng

first: Chaochen

last: Wang

first: Gil

last: Metser

first: Lothar

last: Hennighausen


title: Capacity of yolk sac macrophages, fetal liver and adult monocytes to colonize an empty niche and develop into functional tissue resident macrophages

status: Public on Mar 01 2016

first: Liesbet

last: Martens

summary: Tissue-resident macrophages can derive from yolk sac macrophages, fetal liver monocytes or adult bone marrow monocytes. Whether these precursors can give rise to transcriptionally identical alveolar macrophages is unknown. Here, we transferred traceable yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages as a control, into the empty alveolar macrophage niche of neonatal Csf2rb-/- mice. All precursors efficiently colonized the alveolar niche and generated alveolar macrophages that were transcriptionally almost identical, with only 22 genes that could be linked to their origin. Underlining the physiological relevance of our findings, all transfer-derived alveolar macrophages self-maintained within the lungs for up to 1 year and durably prevented alveolar proteinosis. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages.

overall_design: CD45.1+CD45.2+ yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages from the bronchoalveolar lavage were sorted from wild type CD45.1+CD45.2+ mice of indicated ages. From part of these samples RNA was isolated. The other part was transferred intranasally into the lungs of neonate Csf2rb-/- mice. 6 weeks post-transfer, transfer-derived CD45.1+CD45.2+ alveolar macrophages were sorted from the bronchoalveolar lavage. Wild type CD45.1+CD45.2 alveolar macrophages from the bronchoalveolar lavage of 6 week old mice were sorted as control. 36 samples (arrays) in total. RNA was isolated, amplified with Nugene pico kit, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

first: Lianne

last: van de Laar

first: Wouter

last: Saelens

first: Sofie

last: De Prijck

first: Charlotte

last: Scott

first: Gert

last: Van Isterdael

first: Eik

last: Hoffmann

first: Rudi

last: Beyaert

first: Yvan

last: Saeys

first: Bart

last: Lambrecht

first: Martin

last: Guilliams


title: Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation

first: Wen

last: Shi


title: Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [mRNA-Seq]

first: Zhigang

last: Cai


title: Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [aCGH]

first: Toshima

last: Parris

summary: DNA copy number alterations play an important role in cancer development and progression by changing the transcriptional levels of key cancer-related genes. However, gene expression patterns may also be affected by other mechanisms. To test these basic principles, we have applied genome-wide screening techniques to 53 invasive breast tumors with array comparative genomic hybridization and gene expression microarrays to assess the direct effect of gene dosage on gene expression levels and independently to test the effect of other mechanisms on transcriptional levels. Low-level gain, high-level gain/amplification, heterozygous loss and homozygous deletion (henceforth referred to as gain, amplification, loss and deletion) were defined as log2 ratio thresholds set at +0.2, ≥+0.5,  -0.2 and ≤-1.0, respectively.

overall_design: Genomic DNA was isolated from fresh-frozen tissue samples

first: Elisabeth

last: Rönnerman

first: Hanna

last: Engqvist

first: Jana

last: Biermann

first: Katarina

last: Truvé

first: Szilárd

last: Nemes

first: Eva

last: Forssell-Aronsson

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Circulating leukocyte transcriptional signatures in HIV patients with impaired gas exchange

status: Public on Apr 01 2016

first: Sina

last: Gharib

summary:
Background: HIV infection is associated with impaired gas transfer in the lung as indicated by a low diffusing capacity (DLCO). Mechanisms for reduced DLCO in the setting of HIV infection are not well understood. We hypothesized that HIV-associated gas exchange impairment is indicative of system-wide perturbations that could be reflected by alterations in peripheral blood gene expression.

Methods: A total of 40 HIV-infected (HIV+) and uninfected (HIV-) men with preserved versus reduced DLCO were selected from a larger cohort study of lung function. All subjects were current smokers and those with acute illness, lung diseases other than COPD or asthma were excluded. Total RNA was extracted from peripheral blood leukocytes (PBLs) and hybridized to whole-genome microarrays. Gene set enrichment analysis (GSEA) was performed between HIV+ vs. HIV- subjects with preserved DLCO and those with impaired DLCO to identify differentially activated pathways.

Results: Using pathway-based analyses we found that in subjects with preserved DLCO, HIV infection is associated with activation of processes involved in immunity, cell cycle, and apoptosis. When we applied a similar analysis to subjects with low DLCO, we identified a much broader repertoire of inflammatory and immune-related pathways in HIV+ patients relative to HIV- subjects, with up-regulation of multiple interleukin pathways, interferon signaling, Toll-like receptor signaling, and T cell/B cell receptor signaling. We confirmed elevated circulating levels of IL-6 in HIV+ patients with reduced DLCO relative to the other groups.

Conclusions: Our findings reveal that PBLs of subjects with HIV infection and low DLCO are distinguished by widespread enrichment of immuno-inflammatory programs. Activation of these pathways may alter the biology of circulating leukocytes and play a role in the pathogenesis of HIV-associated pulmonary gas exchange impairment.

overall_design: Total RNA was isolated from peripheral blood leukocytes in four subject groups: 1. HIV-, low DLCO (N = 11); 2. HIV+, low DLCO (N = 10); 3. HIV-, preserved DLCO (N = 9); 4. HIV+, preserved DLCO (N = 9). Each sample was hybridized to an Affymetrix PrimeView Human Gene Expression microarray for a total of 39 experiments.


title: The Wilms' tumor blastema propagating cell is a self-renewing committed epithelial stem cell

status: Public on Dec 31 2015

first: jasmine

last: Jacob

summary: Recently the cancer stem cell (CSC) model has been put forward to describe how a subset of cells within the tumor is responsible for tumor growth and heterogeneity. Wilms' tumor (WT), the most common pediatric renal malignancy, arises from developmentally arrested early renal progenitors. WT NCAM1+ALDH1+ CSCs have been recently isolated and shown to localize to tumor blastema. Herein by generating 'blastema'-only WT xenografts composed solely by cells expressing the SIX2 and NCAM1 embryonic renal stem cell markers, we surprisingly show that sorted ALDH1+ WT CSCs are phenotypically not the earliest renal stem cells. Rather, gene expression and proteomic comparative analysis disclose a more differentiated self-renewing epithelial cell type than bulk of the blastema. Thus, WT CSCs do not represent the transformed counterpart of the most primitive renal stem cell being more differentiated than the presumable WT cell of origin and are likely to de-differentiate to propagate the tumor blastema.

overall_design: We used Wilms tumor Xns, as well as, fetal renal tissue originally obtained from a patients or aborted fetus

first: Rachel

last: Shukrun

first: Naomi

last: Pode-Shakked

first: Oren

last: Pleniceanu

first: Einav

last: Vax

first: Dorit

last: Omer

first: Sara

last: Pri-Chen

first: Qianghua

last: Hu

first: Orit

last: Harari-Steinberg

first: Vicki

last: Huff

first: Benjamin

last: Dekel


title: Transcriptional effects of Pentraxin-2 in fibrotic disease of the kidney

status: Public on Aug 11 2016

summary: Pentraxin-2 (PTX-2) is a constitutive, anti-inflammatory, innate immune plasma protein whose circulating level is decreased in chronic human fibrotic diseases. Recent studies indicate that systemic delivery of recombinant PTX-2 inhibits inflammatory diseases associated with fibrosis by blocking pro-fibrotic macrophage activation and promoting anti-inflammatory and regulatory macrophages. Here we show that recombinant human PTX-2 (rhPTX-2) retards the progression of chronic kidney disease in Col4a3 mutant mice that develop Alport syndrome, reducing blood markers of kidney failure, enhancing lifespan by 20%, and improving histological signs of disease. Exogenously-delivered rhPTX-2 is detected in macrophages but is also found in tubular epithelial cells where it counteracts macrophage activation and is cytoprotective for the epithelium. We performed transcriptional profiling of whole kidney homogenates and human proximal tubule epithelial cells (PTECs) to identify pathways differentially activated or suppressed in response to treatment with PTX-2.  Computational analysis of genes regulated by rhPTX-2 identified the transcriptional regulator c-Jun and its binding partners, which form AP-1 complexes, as a central target for the function of rhPTX-2. Accordingly, PTX-2 attenuates c-Jun activation and reduces expression of AP-1 dependent inflammatory genes in both monocytes and epithelium. Our studies therefore identify rhPTX-2 as a potential therapy for chronic fibrotic disease of the kidney and an important inhibitor of pathological c-Jun signaling in this setting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1. Total RNA from whole kidney homogenates of wildtype (Col4a3+/+) and knockout (Col4a3-/-) mice treated with PTX-2 was isolated and hybidized to Illumina Mouse WG-6 v2 Expression BeadChips. 2. Total RNA from human proximal tubules treated with plasma and PTX-2 was isolated and hybidized to Illumina HumanHT-12 v4 Expression BeadChips.


title: Tristetraprolin disables prostate cancer maintenance by impairing proliferation and metabolic function

status: Public on Nov 08 2016

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Tristetraprolin (TTP) is an RNA-binding protein that post-transcriptionally suppresses gene expression by delivering mRNA cargo to processing bodies (P-bodies) where the mRNA is degraded. TTP functions as a tumor suppressor in a mouse model of B cell lymphoma, and in some human malignancies low TTP expression correlates with reduced survival. Here we report important prognostic and functional roles for TTP in human prostate cancer. First, gene expression analysis of prostate tumors revealed low TTP expression correlates with patients having high-risk Gleason scores and increased biochemical recurrence. Second, in prostate cancer cells with low levels of endogenous TTP, inducible TTP expression inhibits their growth and proliferation, as well as their clonogenic growth. Third, TTP functions as a tumor suppressor in prostate cancer, as forced TTP expression markedly impairs the tumorigenic potential of prostate cancer cells in a mouse xenograft model. Finally, pathway analysis of gene expression data suggested metabolism is altered by TTP expression in prostate tumor cells, and metabolic analyses revealed that such processes are impaired by TTP, including mitochondrial respiration. Collectively, these findings suggest that TTP is an important prognostic indicator for prostate cancer, and augmenting TTP function would effectively disable the metabolism and proliferation of aggressive prostate tumors.

overall_design: PC-3 cells were infected with a pRetroX-Tet-On-Advanced retrovirus and selected for by G418 resistance. Then the G418-resistant cells were secondarily infected with either a pRetroX-Tight-pPGK-tdTomato or a pRetroX-Tight-TTP-pPGK-tdTomato retrovirus and selected for by the expression of tdTomato. G418-resistant, tdTomato-positive cells were used for experiments, in triplicate for each cell type. Cells were treated with 300 ng/ml doxycycline (Dox) for 4h prior to collection. Cells infected with pRetroX-Tight-pPGK-tdTomato were used as controls.

first: Robert

middle: J

last: Rounbehler

first: Anders

middle: E

last: Berglund

first: John

last: Cleveland


title: ADAR1 regulates the resistance of melanoma cells to T cells via miR-222 and ICAM1

summary: The blossom of immunotherapy in melanoma highlights the need to delineate mechanisms of immune resistance. Recently, we have demonstrated that the RNA editing protein, adenosine deaminase acting on RNA-1 (ADAR1) is down-regulated during metastatic transition of melanoma, which enhances melanoma cell proliferation and tumorigenicity. Here we investigate the role of ADAR1 in melanoma immune resistance.   Importantly, knockdown of ADAR1 in human melanoma cells induces resistance to tumor infiltrating lymphocytes in a cell contact-dependent mechanism. We show that ADAR1, in an editing-independent manner, regulates the biogenesis of miR-222 at the transcription level and thereby Intercellular Adhesion Molecule 1 (ICAM1) expression, which consequently affects melanoma immune resistance. ADAR1 thus has a novel, pivotal, role in cancer immune resistance. Corroborating with these results, the expression of miR-222 in melanoma tissue specimens was significantly higher in patients who had no clinical benefit from treatment with ipilimumab as compared to patients that responded clinically, suggesting that miR-222 could function as a biomarker for the prediction of response to ipilimumab.   These results provide not only novel insights on melanoma immune resistance, but also pave the way to the development of innovative personalized tools to enable optimal drug selection and treatment.

overall_design: 13 formalin fixed paraffin embedded (FFPE) melanoma tissues were stained with hematoxilin and eosin for examination by an expert pathologist. Non-tumor tissue was removed. Total RNA was isolated using miRNeasy FFPE kit (Qiagen) according to the manufacture guidelines.

first: Gilli

last: Galore-Haskel

first: Yael

last: Nemlich

first: Eyal

last: Greenberg

first: Shira

last: Ashkenazi

first: Motti

last: Hakim

last: Itzhaki

first: Noa

last: Shoshani

first: Ronnie

last: Shapira-Fromer

first: Eytan

last: Ben-Ami

first: Efrat

last: Ofek

first: Liat

last: Anafi

first: Michal

last: Besser

first: Jacob

last: Schachter

first: Gal

last: Markel


title: Hepatic expression of Sonic Hedgehog induces liver fibrosis and promotes hepatocarcinogenesis in a transgenic mouse model

status: Public on Oct 30 2015

first: Jung Woo

last: Eun

summary: The causative role of activated Hedgehog signaling in liver fibrosis was investigated in vivo.

overall_design: Using hydrodynamics-based transfection, a transgenic mouse model has been developed that expresses Sonic Hedgehog (SHH), a ligand for Hedgehog signaling, in the liver. Levels of hepatic fibrosis and fibrosis-related gene expression were assessed in the model.

first: Sook

middle: I

last: Chung

first: Simon

last: Ro

first: J

first: S

last: Nam


title: High CDK6 protects cells from fulvestrant-mediated apoptosis and is a predictor of resistance to fulvestrant in estrogen receptor-positive metastatic breast cancer

status: Public on Feb 08 2017

city: Odense C

first: Daniel

last: Elias

address: J. B. Winsløwsvej 25

department: Cancer and Inflammation Research

country: Denmark

institute: University of Southern Denmark

summary:
Purpose: Resistance to endocrine therapy in estrogen receptor-positive (ER+) breast cancer remains a major clinical problem. Recently, the CDK4/6 inhibitor palbociclib combined with letrozole was approved for treatment of ER+ advanced breast cancer, and other CDK4/6 inhibitors are being investigated in combination with different endocrine treatments. However, the role of CDK4/6 in endocrine resistance and their potential as predictive biomarkers of endocrine treatment response remains undefined.
Experimental Design: We investigated the specific role of increased CDK6 expression in fulvestrant-resistant cells by gene knockdown and treatment with palbociclib, and evaluated the effect in cell proliferation, apoptosis and kinase activity. Furthermore, we evaluated CDK6 expression in metastatic samples from breast cancer patients treated or not with fulvestrant.
Results: We found increased expression of CDK6 in two fulvestrant-resistant cell models vs. sensitive cells. Reduction of CDK6 expression impaired fulvestrant-resistant cell growth and induced apoptosis by reducing p70 ribosomal S6 kinase 2 activity. Treatment with palbociclib re-sensitized fulvestrant-resistant cells to fulvestrant through alteration of retinoblastoma phosphorylation. High CDK6 levels in metastatic samples from breast cancer patients treated with fulvestrant (N=45) correlated significantly with shorter progression-free survival (PFS) (p=0.0006), while no association was observed in patients receiving other endocrine treatments (N=41, p=0.874).
Conclusions: Our results indicate that upregulation of CDK6 may be an important mechanism in overcoming fulvestrant-mediated growth inhibition in breast cancer cells. Patients with advanced ER+ breast cancer exhibiting high CDK6 expression in the metastatic lesions show shorter PFS upon fulvestrant treatment and thus may benefit from the addition of CDK4/6 inhibitors in their therapeutic regimens.

overall_design: The array included 20 fulvestrant resistant MCF7 cell lines named as ICI182 and ICI164 and 6 fulvestrant sensitive MCF7/S0.5. Ten biological replicates of each of ICI182 and ICI164 as well as 6biological replicates of parental fulvestrant sensitive cell lines were used in the study.

first: Carla

last: Alves

first: Maria

last: Lyng

first: Martin

last: Bak

first: Anne

last: Lykkesfeldt

first: Henrik

last: Ditzel


title: Massive LINE1 retrotransposon Invasion in Tuberous Sclerosis Astrocytomas

status: Public on Dec 31 2016

first: jasmine

last: Jacob

summary: Somatic retrotranspositions of various mobile genetic elements take place in tumors, and L1 retroelements physiologically transpose in neural progenitor cells during neurogenesis. We sequenced whole genomes of the neural progenitor cell-derived subependymal giant cell astrocytomas that typically affect patients suffering from the neurodevelopmental disease Tuberous Sclerosis. Here we show an unprecedented increased L1 retrotransposition in these tumors, with tens of thousands new genomic insertions, that preferentially invade genes involved in neural activity, synaptic transmission and cancer. The prevalent insertions are short, nested in preexisting L1 repeats in the same orientation, trimmed in both the 5’ and 3’ ends, representing unorthodox retrotransposition”. Most somatic L1 inserts in the genomically stable astrocytomas are nested in preexisting L1 elements. This preferred nested integration may act as a “lightning rod” mechanism dampening the effects of massive retrotransposition. In contrast, the enhanced transposition found in genomically unstable breast tumors includes regions of high-density clustered insertion, transposminos. These clustered insertions are expected to be more detrimental, as many of them are non-nested and frequently invade genic and exonic sequences.  Exaggerated L1 retrotransposition may be a common stochastic damaging pathway in neurological disorders and cancer.

overall_design: four subependymal giant cell astrocytomas (SEGAs). Three out of four showed a massive number of Mobile Element Insertions (MEI), mainly L1 retrotranspositions(Hil1 samples ) , those are compared to the fourth without this high MEI element number (Lol1 sample )

first: Jasmine

last: Jacob-Hirsch

first: Karen

last: Cesarkas

first: Chen

last: Gefen-Dor

first: Sarit

last: Farage-Barhom

first: Ortal

last: Barel

first: Eran

last: Eyal

first: Erez

last: Levanon

first: Ninette

last: Amariglio

first: Gideon

last: Rechavi


title: MMP28 is a key contributor to emphysema pathogenesis

status: Public on Feb 18 2017

first: Sina

last: Gharib

summary: Chronic Obstructive Pulmonary Disease, which is comprised of chronic bronchitis and emphysema, is a leading cause of morbidity and mortality. Because tissue destruction is the prominent characteristic of emphysema, extracellular proteinases, particularly those with elastolytic ability, are often considered to be key drivers in this disease. Several human and mouse studies have implicated roles for matrix metalloproteinases (MMPs), particularly macrophage-derived proteinases, in COPD pathogenesis. MMP28 is expressed by the pulmonary epithelium and macrophage, and we have found that it regulates macrophage recruitment and polarization. We hypothesized that MMP28 would have contributory roles in emphysema via alteration of macrophage numbers and activation. Because of the established association of emphysema pathogenesis to macrophage influx, we evaluated the inflammatory changes and lung histology of Mmp28-/- mice exposed to 3 and 6 months of cigarette smoke. At earlier time-points, we found altered macrophage polarization in the smoke-exposed Mmp28-/- lung consistent with other published findings that MMP28 regulates macrophage activation. At both 3 and 6 months, Mmp28-/- mice had blunted inflammatory responses more closely resembling non-smoked mice, with a reduction in neutrophil recruitment and CXCL1 chemokine expression. By 6 months, Mmp28-/- mice were protected from emphysema. These results highlight a previously unrecognized role for MMP28 in promoting chronic lung inflammation and tissue remodeling induced by cigarette smoke and highlight another potential target to modulate COPD.

overall_design: Total RNA from whole lungs homogenates of wildtype and knockout (Mmp28-/-) mice exposed to room air or 3 months of cigarette smoke was isolated and hybidized to Illumina Mouse Ref-8 v2 Expression BeadChips.


title: Advanced Study of Aortic Pathology (ASAP)

status: Public on Jan 15 2016

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

institute: National Genome Center

summary:
BACKGROUND: The vast majority of thoracic aortic aneurysms (TAAs) are observed either together with a bicuspid aortic valve (BAV), a common congenital disorder, or in idiopathic cases such as patients with a normal tricuspid aortic valve (TAV). The main objective of our study was to identify shared and unique gene expression properties underlying the aortic dilation of BAV and TAV patients.
METHODS AND RESULTS: Tissue biopsies for RNA and histological analyses were obtained from aorta of non-dilated (<40mm) and dilated (>45mm) aorta of BAV and TAV patients (in total 131 patients). Additional controls were from mammary artery of the same patients (n=88) and aorta from transplant donors (n=13). Gene expression profiles generated using Affymetrix Exon arrays were analyzed from controls and from aorta intima-media and adventitia of patients (in total 345 samples). 606 genes in aortic intima-media were found to be differentially expressed with dilation. Of these, only few (<4%) were differentially expressed in both BAV and TAV patients. Gene set enrichment analysis identified cell adhesion and extracellular region gene ontology sets as common features of TAA in BAV and TAV patients. The set of immune response genes was observed to be particularly overexpressed in aortic media of dilated TAV samples.
CONCLUSION: The divergent gene expression profiles indicate fundamental differences in TAA etiology of BAV and TAV patients. Immune response activation solely in the aorta media of TAV patients suggests that inflammation is a causal factor of TAA in this patient group.

overall_design: Biobank of patient material. Each tissue sample is from a different patient as indicated by patient ID.

first: Dick

last: Wågsäter

first: Valentina

last: Paloschi

first: Veronica

last: Jackson

first: Johan

last: Petrini

first: Sanela

last: Kurtovic

first: Shohreh

last: Maleki

last: Eriksson

first: Kenneth

last: Caidahl

first: Anders

last: Hamsten

first: Jean-Baptiste

last: Michel

first: Jan

last: Liska

last: Gabrielsen

last: Franco-Cereceda

first: Per


title: BAF controls genome accessibility

status: Public on Nov 12 2015

first: Douglas

last: Porter

summary: Somatic differentiation requires induction of lineage specific genes to fulfill specialized tissue functions yet the genomic control of this process is incompletely understood. Using the epidermis as a model, we show here that the BAF chromatin remodeling complex is essential to maintain a subset of open chromatin regions, which are strikingly enriched for the DNA binding motif of the stratified epithelial lineage-determining transcription factor p63 (p=1X10-1786). These p63 sites are intrinsically inaccessible. BAF is required to displace nucleosomes ~40 base pairs away from p63 motifs to enable p63 binding, to maintain active histone marks, and to recruit RNA polymerase II to promote gene expression. In this process, p63 was itself also essential for full BAF recruitment to p63 binding sites. Intrinsically, p63 binding sequences favor nucleosome occupancy. Our data therefore suggest a model where a lineage-specific transcription factor cooperates with the BAF complex to establish genome accessibility and engage tissue-specific gene expression.

overall_design: We examined chromatin accessibility controlled by the cooperation between BAF and p63 using ATAC-seq and ChIP-seq. ATAC-seq was performed in differentiating primary human keratinocytes in control and Brg1/Brm knock down conditions, two replicates each. We further compared the ChIP-seq signal of H3K27me3, H3K4me1, PolII, H3K27Ac, and p300 in keratinocytes between Brg1/Brm loss versus control. To test whether p63 recruits BAF to its binding sites, we also performed BAF ChIP-seq in keratinocytes between p63 loss versus control. In addition, we performed RNA-seq in BAF loss, p63 loss, and control conditions.

first: Xiaomin

last: Bao

first: Adam

last: Rubin

first: Qu

last: Kun

first: Howard

last: Chang

first: Paul

last: Khavari


title: Identification of Novel Serum Biomarkers for Early Decision of ST-elevation Myocardial Infarction

status: Public on May 23 2015

first: Jung Woo

last: Eun

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq of mouse hypothalamus

status: Public on Dec 01 2016

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: We sampled neurons populating the space encapsulated by the paraventricular and arcuate hypothalamic nuclei (rostrocaudal direction) and the ventromedial and dorsomedial hypothalamic nuclei marking its lateral extent. These neurons likely integrate metabolic and stress circuitries. Detailed clustering information on 898 neurons and the annotation of other cell types are presented.

overall_design:
Single cells were sampled randomly from a central column of the medial-ventral diencephalon, including in its rostrocaudal extent the posterior part of the preoptic area (posterior to the anterior commissure; from Bregma = -0.5 mm) and in the caudal direction the arcuate nucleus (Bregma = -2.1 mm). C57Bl6/N juvenile mice (postnatal day 14-28) of both sexes from either control (no treatment) or after acute formalin stress were used for cell collection. Formalin stress was induced by injection of 4% paraformaldehyde into the left paw 6 hours before sacrifice. The experiment aims at the unbiased identification of different cell types by clustering their mRNA expression profiles. Analysis relied on a divisive biclustering method using the BackSpinV2 algorithm (Tsafrir et al., 2005, Zeisel et al., 2015). Cells were sorted into major types (1001 oligodendrocytes, 267 astrocytes, 356 ependymal cells, 48 microglial cells, 240 endothelial cells, 71 vascular and smooth muscle lineage cells, and neurons). 2nd level analysis of 898 hypothalamic neurons classified these cells into 62 clusters with high-quality content.

The 'expressed_mols_with_classes.xlsx' contains mRNA molecule counts for each gene and cell as well as fine-grained two-level cell type classifications according to the associated publication.

first: Roman

last: Romanov

first: Amit

last: Zeisel

first: Tibor

last: Harkany


title: miR-495 regulates multiple epigenetic modifiers in gastric cancer

status: Public on Sep 18 2015

summary: Revealing Dominant Regulatory MicroRNA-495-3p that Governs Multiple Epigenetic Modifiers in Gastric Carcinogenesis

overall_design: In this study, we identified miR-495-3p targeting multiple epigenetic modifiers through comprehensive miRNA and mRNA profiling analysis with in silico target prediction in GC. Western blotting assay or quantitative real time PCR was performed to confirm the expression of miR-495-3p and targets of it. We applied miRNA mimics to ectopic overexpression in gastric cancer cells and observed tumor suppressive effects of miR-495-3p in the growth and metastasis of cancer. Also, we confirmed the status of CpG islands of miR-495-3p promoter using methylation specific PCR analysis.

first: Woo-Chan

last: Shin

first: Hyun-Jin

last: Bae

first: Jung-Woo

first: QingYu

last: Shen

first: Hyung-Seok

last: Kim

first: Hee-Doo

last: Yang

first: Hyung-Eun

last: Ahn

first: Hea-Young

first: Won-Sang

last: Park

first: Jung-Young

last: Lee

first: Suk-Woo

last: Nam


title: Expression data from blood samples of STEMI and Same STEMI patients after PIC

summary: We aim to determine blood transcriptome-based molecular signature of acute coronary syndrome (ACS), and to identify novel serum biomarkers for early stage ST-segment-elevation myocardial infarction (STEMI)

overall_design: We obtained peripheral blood from the patients with ACS who visited emergency department within 4 hours after the onset of chest pain: a set of blood samples of patients with STEMI (n=7) before and 7 days after the primary percutaneous coronary intervention (n=7) and normal control (n=10)

first: Jung

first: Suk


title: A human integrin-α3 mutation confers major renal developmental defects.

status: Public on Dec 15 2014

city: Shoham

first: jasmine

last: Jacob

address: haChevel 33

institute: Sheba Medical Center at Tel HaShomer

summary: Integrin-α3 plays a central role in the interplay of cells, morphogens and ECM, required for proper nephrogenesis, thus adding ITGA3 to the list of CAKUT (congenital anomalies of the kidney and urinary tract)-causing genes.

overall_design: we used renal tissue originally obtained from a patient with an ITGA3 mutation and assessed its gene expression profile as compared to controls

first: Rachel

last: Shukrun

first: Asaf

last: Vivante

first: Oren

last: Pleniceanu

first: Einav

last: Vax

first: Yair

last: Anikster

first: Benjamin

last: Dekel

first: Danny

last: Lotan


title: Assessment and Diagnostic Relevance of Novel Serum Biomarkers for Early Decision of ST-elevation Myocardial Infarction

first: Jung Woo

last: Eun

overall_design: We obtained peripheral blood from the patients with ACS who visited emergency department within 4 hours after the onset of chest pain: ST-elevation myocardial infarction (STEMI, n=7), Non-ST-elevation MI (NSTEMI, n=10) and unstable angina (UA, n=9), and normal control (n=7)


title: Differential regulation of aggressive features in melanoma cells by members of the miR-17-92 complex

status: Public on Dec 31 2014

summary: The various roles of microRNAs (miRNAs) in controlling the phenotype of cancer cells are the focus of contemporary research efforts. We have recently shown that miR-17 directly targets the ADAR1 gene and thereby enhances melanoma cell aggressiveness. miR-17 and miR-20a belong to the miR-17/92 complex, and their mature forms are identical except for two non-seed nucleotides. Nevertheless, here we show that these two miRNAs carry markedly different effects on melanoma cells. A strong positive correlation was observed between the expression of miR-17 and miR-20a among various melanoma cultures. Luciferase assays showed that miR-17 but not miR-20a directly targets the 3' untranslated region of the ADAR1 gene. Ectopic expression of these miRNAs in melanoma cells differentially alters the expression of five exemplar TargetScan-predicted target genes ADAR1, ITGB8, TGFBR2, MMP2 and VEGF-A. Whole genome expression microarrays confirm a markedly differential effect on the transcriptome. Functionally, over-expression of miR-20a but not of miR-17 in melanoma cells inhibits net proliferation in-vitro. The differential functional effect was observed following ectopic expression of the mature miRNA or of the pre-miRNA sequences. This suggests that the two non-seed nucleotides dictate target sequence recognition and overall functional relevance. These miRNAs are clearly not redundant in melanoma cell biology.

overall_design: miR-20a or miR-17 were cloned into pQCXIP and transduced into PAG (C81-61) cells.  The cells were subjected to RNA extraction and hybridization on Affymetrix  whole genome expression microarrays and compared with  control cells (mock transduction).

first: Eyal

last: Greenberg

first: Steven

last: Hajdu

first: Yael

last: Nemlich

first: Ronit

last: Cohen

first: Orit

last: Itzhaki

first: Jasmine

last: Jacob-Hirsch

first: Michal

last: Besser

first: Jacob

last: Schachter

first: Gal

last: Markel


title: Transcriptional Profiling  in Sepsis-induced Experimental Multiple Organ Dysfunction Syndrome

first: Sina

last: Gharib

summary: Sepsis-induced multiple organ dysfunction syndrome (MODS) is a major cause of morbidity and mortality in critically ill patients and remains impervious to most therapeutic interventions. We utilized a clinically relevant murine model of MODS induced by ventilator-associated pneumonia to systematically delineate pathways dysregulated in lung, liver, and kidney. We focused on processes commonly activated across injured organs and constructed a MODS-associated network based on connectivity among the gene members of these functionally coherent pathways. Our analyses led to the identification of several putative drivers of MODS whose expression was regulated by epidermal growth factor receptor. Our unbiased, integrative method is a promising approach to unravel mechanisms in system-wide disorders afflicting multiple compartments such as sepsis-induced MODS, and guide the discovery of novel putative therapeutic targets.

overall_design: A total of 27 independent microarray experiments were performed in lung, liver and kidneys of mice exposed to a combination of mechanical ventilation and S. aureus pneumonia  (MV+SA) or controls. The breakdown is as follows:(1) Lung: MV+SA, N=5; Control, N=4.(2) Liver: MV+SA, N=5; Control, N=3. (3) Kidney: MV+SA, N=5; Control, N=5.


title: Gene expression analysis of airway epithelial cells exposed to flagellin via microarray

status: Public on Dec 01 2014

summary: Airway epithelial cells (AEC) are critical components of the inflammatory and immune response during exposure to pathogens. AECs in monolayer culture and differentiated epithelial cells in air-liquid interface (ALI) represent two distinct and commonly used in vitro models, yet differences in their response to pathogens have not been investigated. In this study, we compared the transcriptional effects of flagellin on AECs in monolayer culture versus ALI culture using exon microarrays and RNAsequencing. We found that AECs cultured in monolayer and ALI have strikingly different transcriptional states at baseline. When challenged with flagellin, monolayer AEC cultures greatly increased transcription of numerous genes mapping to wounding response, immunity and inflammatory response. In contrast, AECs in ALI culture had an unexpectedly muted response to flagellin, both in number of genes expressed and relative enrichment of inflammatory and immune pathways. In conclusion, In vitro culturing methods have a dramatic effect on the transcriptional profile of AECs at baseline and after stimulation with flagellin. These differences suggest that epithelial responses to pathogen challenges are distinctly different in culture models of intact and injured epithelium.

overall_design: A total of ten independent microarray experiments were performed. Four micorarray experiments (n = 2 unstimulated, n = 2 stimulated with flagellin) were conducted using AECs grown in monolayer. Six microarray experiments (n =3 unstimulated, n = 3 stimulated with flagellin) were perfomerd using AECs grown in ALI cultures.

first: Kyong-Hee

last: Kim


title: Dose-dependent toxic effects of dietary TCDD on juvenile zebrafish

city: Clemson

first: Qing

last: Liu

address: Jordan Hall

institute: Clemson University

summary: Juvenile zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb. Fish were collected, sexed, weighed and length measured at 0, 7, 14, 28 or 42 d for TCDD assessment, histopathologic and microarray analysis. Microarray experiments were conducted in TCDD-treated (at 0, 0.1, 1, 10 and 100 ppb) for male and female sexed zebrafish at 28 d. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of TCDD-treated zebrafish. TCDD accumulated in a dose- and time-dependent manner and 100 ppb TCDD caused TCDD accumulation in female (15.49 ppb) and male (18.04 ppb) fish at 28 d post exposure. TCDD caused multiple lesions in liver, kidney, intestine and ovary of zebrafish and functional dysregulation such as depletion of glycogen in liver, retrobulbar edema, degeneration of neurosensory epithelium, underdevelopment of intestine, and diminution in the fraction of ovarian follicles containing vitellogenic oocytes. Microarray gene expression analysis comparing control to post TCDD diet revealed dysregulated genes located in pathways associated with cardiac necrosis/cell death, cardiac fibrosis, renal necrosis/cell death and liver necrosis/cell death. These baseline toxicological effects provide evidence for the potential biomarkers, mechanisms and pathology of TCDD induced dysregulation.

overall_design: Juvenile wild-type zebrafish (stock originally purchased from EkkWill Waterlife Resources, Ruskin, FL) (0.16 g, 2.10 cm) were were reared in 28 °C dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.  Zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb (nominal concentration, ethanol used as vehicle). Fish were collected, sexed, weighed and length measured at 0, 7, 14, 28 or 42 d for TCDD assessment and microarray analysis. Miicroarray experiments were conducted in TCDD-treated (at 0, 0.1, 1, 10 and 100 ppb) for male and female sexed zebrafish at 28 d. Zebrafish were were randomly selected from each group for the microarray experiments. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of TCDD-treated zebrafish. Differential expression analysis was performed with Bayesian Estimation of Temporal Regulation (BETR) method using Multiple Array Viewer (MeV, Dana-Farber Cancer Institute, MA) software, version 4.8.1.

first: Chun-Yuan

last: Huang

last: Jiang

first: Giles

last: Goetz

first: Reinhold

last: Hutz

first: Peter

last: Tonellato

first: Michael

last: Carvan


title: A LncRNA-MAF/MAFB transcription factor network regulates epidermal differentiation [expression]

status: Public on Nov 11 2014

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

institute: Stanford

summary: Using kinetic gene expression analysis of regenerated epidermis over a 7 day time-course, we identify a lncRNA-transription factor network with the MAF/MAFB transcription factors as central players in directing the epidermal differentiation program.

overall_design: Gene expression analysis: To establish a differentiation signature for regenerated epidermis over a 7 day time course and assess the effect of MAF/MAFB depletion in regenerated epidermis; total RNA was isolated in biologic duplicate from regenerated tissue in different conditions and hybridized to Affymetrix HGU133 2.0 arrays.

first: Vanessa

last: Lopez-Pajares

first: Kun

last: Qu

first: Jiajing

last: Zhang

first: Paul

last: Khavari


title: ZNF750 Interacts with KLF4 and Specific Chromatin Regulators to Control Epidermal Differentiation

status: Public on Sep 11 2014

summary: Here we find that ZNF750 activates epidermal differentiation genes and represses progenitor genes as part of two distinct protein complexes

overall_design: Identified genomic binding sites of ZNF750 and its interacting proteins

first: Lisa

middle: D

last: Boxer

first: Brook

last: Barajas


title: A LncRNA-MAF/MAFB transcription factor network regulates epidermal differentiation


title: A LncRNA-MAF/MAFB transcription factor network regulates epidermal differentiation [ChIP-seq]

summary: Here we reveal a lncRNA-transcription factor network with the MAF/MAFB transcription factors as central players in directing the epidermal differentiation program.

overall_design: Examination of global transcriptional changes and mapping genome-wide transcription factors occupancy during epidermal differentiation.


title: Genome-wide analysis of human mammary epithelial cells after kd of TRIM29

status: Public on Sep 30 2015

first: Jung Woo

last: Eun

summary: Analysis of global gene expression by TRIM29 level change in human mammary epithelial cells

overall_design: Total RNA obtained from human mammary epithelial cells after generating TRIM29 kd stable cell line

first: Sung

last: Choi

first: Jueng

middle: S

last: You

first: Jung

first: Suk

last: Nam


title: Toxic effects of dietary TCDD on juvenile zebrafish

first: Qing

last: Liu


title: Suppression of progenitor differentiation requires the long noncoding RNA ANCR

status: Public on Jun 02 2014


title: Pathways of ovarian cancer development

status: Public on Jun 22 2015

first: Chia-Ho

last: Cheng

summary: In order to evaluate pathways that drive the development of ovarian cancer, we compared Affymetrix expression profiles from normal ovarian surface epithelium to those from primary ovarian carcinomas.

overall_design: mRNA expression profiles for 57 ovarian carcinomas and 12 ovarian normal samples.

last: Marchion


title: HIF-1alpha and HIF-2alpha ChIP-chip profiling in intestinal epithelial cells

status: Public on Nov 05 2013

city: Aurora

first: Louise

last: Glover

state: CO

institute: University Colorado Anschutz Medical Campus

type: Genome binding/occupancy profiling by array

summary: Intestinal epithelia exist in a uniquely dynamic oxygen tension microenvironment. Adaptive responses to hypoxia in mammalian cells are regulated largely by hypoxia inducible factor (HIF) transcriptional complexes. Functional HIF exists as an obligate alpha/beta heterodimer, comprising both a constitutive subunit (HIF-1beta), and an oxygen-labile regulatory (alpha) component. To date, three regulatory subunits have been identified, namely HIF-1alpha, HIF-2alpha, and HIF-3alpha, with the highest level of sequence homology conserved between HIF-1alpha and HIF-2alpha. Despite their concurrent expression in intestinal epithelial cells, HIF-1 and HIF-2 play non-redundant roles in the regulation of an overlapping but distinct set of gene targets. In this study, we performed ChIP-on-chip analysis of chromatin isolated from hypoxic intestinal epithelia to delineate HIF-1 and HIF-2 specific loci.

overall_design: Comparison of HIF-1alpha ChIP-chip and HIF-2alpha ChIP-chip to map HIF-1- and HIF-2-specific gene targets across the genome.

first: Sean

last: Colgan