title: DNA methylation profile of PBMC following decitabine therapy

city: bei jing

first: Jing

last: Nie

state: bei jing

address: 28 fuxing road

institute: PLA General Hospital

summary:
The epigenetic regulation, for example, DNA methylation, controls the development and differentiation of both tumor cells and immunocytes. Treatment with DNA demethylating agent (such as decitabine) has shown a dramatic clinical benefit in hematological malignancies and solid tumors.
However, the influence of epigenetic therapy on host immune system remains unclear.

overall_design: To investigate the effects of low-dose decitabine therapy on T cells, we collected whole blood samples from two solid tumor patients pre and post low-dose decitabine therapy, and detected the DNA methylation profiles of PBMCs.

first: Weidong

last: Han


title: Expression data from iPS cell derived hepatocyte-like cells sorted with antibody against cell surface protein SLC10A1

status: Public on Dec 22 2016

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

country: USA

institute: Medical University South Carolina

summary:
Most differentiation protocols for generation of hepatocyte-like cells from iPS cells generate cells with heterogenous expression of hepatic markers, which confounds results from liver disease models involving complex traits and subtle phenotypes
We utilized proteomics to identify heptocyte-restricted cell surface proteins that mark a subpopulation of iPS cell derived hepatocytes. By performing microarray on FACS sorted cells, we demonstrate that subpopulation of hepatocyte-like cells expressing SLC10A1 are enriched for hepatic markers

overall_design: Hepatocyte-like cells generated from iPS cells were FACS sorted using antibody against cell surface protein SLC10A1. Microarray was performed on pre-sort, SLC10A1 positive sort, and SLC10A1 negative sort cell population. Microarray on FACS sorted cells from four independent differentiations are presented.

first: Sunil

middle: K

last: Mallanna


title: Dynamic responses by lymph node stromal cells to primary and secondary infection.

status: Public on Dec 21 2016

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

summary: Lymph nodes (LN) are constructed of intricate networks of endothelial and mesenchymal stromal cells. These include the fibroblastic reticular cells (FRC), lymphatic endothelial cells (LEC) and blood endothelial cells (BEC). We performed a comprehensive analysis of LSC responses to skin viral infection and found that LSC subsets responded robustly. Infection induced rapid transcriptional regulation of large numbers of both shared and unique genes in FRC, LEC and BEC to support LN remodeling and the immune response. This transcriptional program was transient, returning to homeostasis within one month of infection. Yet, expanded FRC networks persisted for greater than three months after infection. Our results reveal the complexity of LN stromal cell responses during infection and suggest that LN remodeling to acute infection supports successive immune responses.

overall_design: 46 samples were analyzed. 5 replicates of fibroblastic reticular cells (FRC; gp38+ CD31-), 3 replicates of lymphatic endothelial cells (LEC; gp38+ CD31+) and 4 replicates of blood endothelial cells (BEC; gp38- CD31+) were isolated from the brachial lymph nodes (bLN) of naive C57BL/6 mice. 4 replicates of FRC, 4 replicates of LEC and 4 replicates of BEC from the bLN of C57BL/6 infected on the skin with HSV KOS 3 days p.i. 4 replicates of FRC, 4 replicates of LEC and 4 replicates of BEC from the bLN of C57BL/6 infected on the skin with HSV KOS 6 days p.i. 4 replicates of FRC, 3 replicates of LEC and 3 replicates of BEC from the bLN of C57BL/6 infected on the skin with HSV KOS 30 days p.i.

first: Julia

middle: L

last: Gregory

first: Anne

last: Walter

first: Yannick

middle: I

last: Alexandre

first: Jyh

last: Hor

first: Ruijie

last: Liu

middle: Z

first: Sapna

last: Devi

first: Nobuko

last: Tokuda

first: Yuji

last: Owada

first: Laura

last: Mackay

first: Gordon

last: Smyth

first: William

middle: R

last: Health

first: Scott

middle: N

last: Mueller


title: Migrating glioma cells express stem cell markers and give rise to new tumors upon xenografting

city: Odense

first: Sune

last: Munthe

address: Sdr. Boulevard 29

country: Denmark

institute: Odense University Hospital

summary: Glioblastoma (GBM) is the most frequent and malignant brain tumor with an overall survival of only 14.6 months. Although these tumors are treated with surgery, radiation and chemotherapy recurrence is inevitable. A critical population of tumor cells in terms of therapy, the so-called cancer stem cells (CSCs), has been identified in gliomas and many other cancers. These tumor cells have a stem cell-like phenotype and are suggested to be responsible for tumor growth,  chemo- and radio-resistance as well as recurrence. However, functional evidence for migrating glioma cells having a stem cell-like phenotype is currently lacking.

overall_design: We used microarray to evaluate gene expression in five different patient derived glioblastoma cell cultures. From these five patient we investigated the gene expression in migrating and non-migrating tumor cells. The isolation of migrating and non-migrating tumorcells was done in a novel in vitro migration assay.

first: Bjarne

middle: W

last: Kristensen


title: Human parthenogenetic embryonic strem cell-derived neural stem cells express HLA-G.

status: Public on Dec 01 2016

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary: To evaluate differences between human PG and N ESCs and NSCs, we performed global gene expression analysis. PG NSCs have unique immunological properties due to elevated HLA-G expression suggesting that parent-of-origin effects influence HLA-G.

overall_design: Global expression profiling of PG and N hESCs and hESC-derived NSCs.

first: Jessica

last: Schmitt

middle: J

first: Albrecht

middle: M

last: Müller


title: Genome-wide analysis of gene expression during adipogenesis in human adipose-derived mesenchymal stromal cells reveals novel patterns of gene expression during adipocyte differentiation

city: Pretoria

first: Melvin

middle: Anyasi

last: Ambele

state: Gauteng

address: 5 Bophelo Road

department: Immunology

country: South Africa

institute: University of Pretoria

summary:
To better understand the scale of gene expression changes that occur during the formation of mature adipocytes from preadipocytes, we compared and characterised the transcriptome profile of mesenchymal stromal cells derived from human adipose tissue, otherwise known as adipose-derived stromal cells (ASCs), undergoing adipocyte differentiation on day 1, 7, 14 and 21 (representing the early to late stage process of adipogenesis).  Microarray technique was systematically employed to study gene expression in adipose-derived stromal cells during adipogenic differentiation over a 21 day period to identify genes that are important in driving adipogenesis in humans.
We have undertaken an in-depth transcriptome analysis of adipogenesis in human adipose-derived stromal cells (ASCs) induced to differentiate into adipocytes in vitro. Genes were differentially expressed on days 1, 7, 14 and 21 post-induction and numbered 128, 218, 253 and 240 respectively. Up-regulated genes were associated with neural and blood vessel development, leukocyte migration, and tumor growth, invasion and metastasis. They also shared common pathways with certain obesity-related pathophysiological conditions.  Down-regulated genes were associated with osteogenesis and the immune response. KLF15, LMO3, FOXO1 and ZBTB16 transcription factors were up-regulated throughout the differentiation process. CEBPA, PPARG, ZNF117, MLXIPL, MMP3 and RORB were up-regulated only on days 14 - 21, which coincides with the maturation of adipocytes and could possibly serve as candidates for controlling fat accumulation and the size of mature adipocytes. We identified genes that were up-regulated only on day 1 - 7 and day 14 - 21 that could serve as potential early and late-stage differentiation markers. This study reveals potential markers for the different stages in ASC adipogenic differentiation which could serve as good candidates to combat obesity and further link the biology of fat cell formation to the co-morbidities of obesity.

overall_design: RNA was extracted from both adipogenic induced adipose-derived stromal cell cultures and their respective controls (non-induced) on day 1, 7, 14 and 21. The RNA were hybridized to Affymetrix HuGene 2.0 ST arrays

first: Carla

last: Dessels

first: Chrisna

last: Durandt

first: Michael

middle: S

last: Pepper


title: Gene array analysis of anaplastic thyroid carcinoma cell lines versus normal thyroid cell lines

status: Public on Nov 30 2016

city: Jacksonville

first: John

last: Copland

state: FL

address: 4500 San Pablo Road

department: Biochemistry & Molecular Biology

institute: Mayo Clinic College of Medicine

summary:
Currently there is a lack of effective therapies which result in long-term durable response for patients presenting with anaplastic thyroid carcinoma (ATC), a very rare and lethal variant of thyroid cancer. ATC is resistant to chemotherapy, radiation, and targeted therapies currently available.
In an effort to identify novel tumor-specific therapeutic targets, we performed high throughput gene array analysis screening numerous ATC cell lines, and compared their gene expression levels to normal thyroid cell lines.

overall_design: RNA was extracted from Anaplastic Thyroid Cancer cell lines and Normal Thyroid cell lines. Gene array analysis was performed, and resulting expression levels were compared between Normal and ATC samples

first: Paul

last: Weinberger

first: Ashok

last: Sharma


title: Expression data from human choroidal melanocyte cultures

city: Copenhagen

first: Tina

last: Jehs

address: Blegdamsvej 3

institute: University of Copenhagen

summary:
Purpose: To determine to which extend inflammatory cytokines affect chemokine secretion by primary human choroidal melanocytes (HCMs), their capacity to attract monocytes and if HCMs are able to influence the proliferation of activated T cells.
Methods: Primary cultures of HCMs were established from eyes of thirteen donors. HCMs were stimulated with IFN-γ and TNF-α or with supernatant from activated T-cells (T-cell conditioned media (TCM)). Gene expression analysis was performed using microarrays. Protein levels were quantified with ELISA or cytometric bead array. Supernatants of HCMs were assessed for the capability to attract monocytes in a trans-well plate. Proliferation of activated T-cells was assessed in a direct co-culture with HCMs by a [3H]-thymidine incorporation assay.
Results: Stimulation of HCMs with TCM or IFN-γ and TNF-α resulted in increased expression and secretion of CXCL8, CXCL9, CXCL10, CXCL11, CCL2, CCL5 and intercellular adhesion molecule 1. Vascular endothelial growth factor and monocyte migration inhibitory factor were constitutively expressed without changes in response to pro-inflammatory cytokines. Supernatants derived from unstimulated cultures of ten HCM donors induced a high initial level of monocyte migration, which decreased upon stimulation with either TCM or IFN-γ and TNF-α. The supernatants from three HCM donors initially showed a low level of monocyte attraction which increased following exposure to pro-inflammatory cytokines. Direct co-culture of HCMs with T-cells resulted in inhibition of T-cell proliferation.
Conclusion: These results show that normal and activated HCMs are immunologically active by secreting chemokines, and that HCMs are able to attract monocytes in addition to inhibit T-cell proliferation.

overall_design: Choroidal melanocyte cultures from thirteen donors were analyzed before and after exposure to supernatants from activated T-cells and to 27 ng/ml recombinant IFN-γ and 10 ng/ml recombinant TNF-α.

first: Carsten

last: Faber

first: Maja

last: Udsen

first: Martina

last: Jager

first: Simon

last: Clark

first: Mogens

middle: H

last: Nissen


title: Expression data from NT and PHB siRNA treated hESCs

city: Shanghai

first: Zhexin

last: Zhu

address: 320 Yue Yang Road

country: China

institute: Chinese Academy of Sciences

summary:
Embryonic stem cells (ESCs) are useful resources for clinical cell therapy as its unlimited self- renewal and pluripotecy properties, so it is critical to understand how ESCs maintain its identity. We reported a gene named PHB is essential for hESC self- renewal.
We used microarrays to find out the potential mechanisms regulated by PHB in maintaining hESC identity.

overall_design: hESCs were reverse transfected with NT and PHB siRNA respectively. Four days after transfection, cells were collected for TRIzol extraction and hybridization on Affymetrix microarrays.

first: Yanwu

last: Zeng

first: Chunliang

last: Li

first: Junjie

last: Gu

first: Laixiang

last: Ge

first: Fan

last: Tang

first: Ying

last: Jin


title: Aberrant connective tissue differentiation towards cartilage and bone underlies human keloids in African Americans

status: Public on Dec 20 2016

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

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

institute: Mount SinaiSchool of Medicine

summary: Pilot study: Observational clinical study

overall_design: To characterize keloids in African Americans, we performed transcriptional profiling of biopsies from large chronic keloids, adjacent nonlesional (NL) skin (n=3) and a newly formed keloid lesion using Affymetrix HGU133 2.0 plus arrays. Quantitative RT-PCR (qRT-PCR) and immunohistochemistry staining were done to confirm increased expression of relevant genes

first: Judilyn

last: Fuentes-Duculan

last: Suárez-Fariñas

first: Sandra

last: Garcet

first: Michael

last: Tirgan

first: James

middle: G

last: Krueger


title: Changes of myocardial gene expression and protein composition in patients with dilated cardiomyopathy after immunoadsorption with subsequent immunoglobulin substitution

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

summary:
Immunoadsorption with subsequent immunoglobulin substitution (IA/IgG) represents a therapeutic approach for patients with dilated cardiomyopathy (DCM). Here, we studied which molecular cardiac alterations are initiated after this treatment.
Transcription profiling of endomyocardial biopsies with Affymetrix whole genome arrays was performed on 33 paired samples of DCM patients collected before and six months after IA/IgG. Therapy-related effects on myocardial protein levels were analysed by label free proteome profiling for a subset of 23 DCM patients. Data were analysed regarding therapy-associated differences in gene expression and protein levels by comparing responders (defined by improvement of left ventricular ejection fraction ≥ 20% relative and ≥5% absolute) and non-responders.
Responders to IA/IgG showed a decrease in serum N-terminal proBNP levels in comparison to baseline which was accompanied by a decreased expression of heart failure markers such as angiotensin converting enzyme 2 or periostin. However, despite clinical improvement even in responders IA/IgG did not trigger general inversion of DCM associated molecular alterations in myocardial tissue. Transcriptome profiling revealed reduced gene expression for connective tissue growth factor, fibronectin, and collagen type I in responders. In contrast, in non-responders after IA/IgG, for fibrosis associated genes and proteins showed elevated levels whereas values were reduced or maintained in responders.
Thus, improvement of LV function after IA/IgG seems to be related to a reduced gene expression of heart failure markers and pro-fibrotic molecules as well as reduced fibrosis progression.

overall_design: gene expression and protein profiling of DCM patients before and after IA/IgG therapy

first: Gourav

last: Bhardwaj

first: Elke

last: Hammer

first: Daniel

last: Beug

first: Leif

last: Steil

first: Yvonne

last: Reinke

first: Kerstin

last: Weitmann

first: Markus

last: Grube

first: Christiane

last: Trimpert

first: Karin

last: Klingel

first: Reinhard

last: Kandolf

first: Wolfgang

last: Hoffmann

first: Matthias

last: Nauck

first: Marcus

last: Dörr

first: Klaus

last: Empen

first: Stephan

middle: B

last: Felix

first: Uwe

last: Völker


title: Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis

city: Palo Alto

first: Thomas

middle: A

last: Rando

state: CA

address: 3801 Miranda Ave

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

summary:
The platelet-derived growth factor receptor alpha (PDGFRα) exhibits divergent effects in skeletal muscle. At physiological levels, signaling through this receptor promotes muscle development in growing embryos and proper angiogenesis in regenerating adult muscle. However, either increased PDGF ligands or enhanced PDGFRα pathway activity causes pathological fibrosis. This excessive collagen deposition, which is seen in aged and diseased muscle, interferes with proper muscle function and limits the effectiveness of gene- and cell-based therapies for muscle disorders. Although compelling evidence exists for the role of PDGFRα in fibrosis, little is known about the cells through which this pathway acts. Here we show that PDGFRα signaling regulates a population of muscle-resident fibro/adipogenic progenitors (FAPs) that play a supportive role in muscle regeneration but may also cause fibrosis when aberrantly regulated. We found that FAPs produce multiple transcriptional variants of PDGFRα with different polyadenylation sites, including an intronic variant that codes for a protein isoform containing a truncated kinase domain. This variant, upregulated during regeneration, acts as a decoy to inhibit PDGF signaling and to prevent FAP over-activation. Moreover, increasing expression of this isoform limits fibrosis in vivo, suggesting both biological relevance and therapeutic potential of modulating polyadenylation patterns in stem cell populations.
We used microarrays to explore the biological effects of altering intronic polyadenylation of PDGFRα in FAPs.

overall_design: FAPs were isolated from the uninjured hindlimbs of C57Bl/6 mice. Cells were plated at 1 x 10^6 cells per well in 12-well plates. Cells were grown for 2.5 days in DMEM supplemented with 10% FBS. The media was switched to Ham’s F10 supplemented with 10% horse serum and transfected with 10 µM control or experimental AMO as indicated for 48 hours. The media was then replaced with Opti-Mem and cells re-transfected with 10 µM AMO with 50uM PDGF-AA or control. After 48 hours, the cells were lysed and RNA prepared with the RNeasy Mini Kit as per the manufacturer’s instructions (Qiagen). The microarray data was obtained using Affymetrix Mouse 1.0 ST. Each biological replicate represents cells pooled from 2 mice.

first: Alisa

last: Mueller


title: BRAF V600E mutant colorectal cancer subtypes based on gene expression

status: Public on Nov 28 2016

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Insitute of Medical Reseach

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

overall_design: Refer to individual Series


title: Expression data from Tp80-Treated HCV replicon cell, Huh7/RepFeo.

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary:
Tp80 is a novel antiviral compound. Antiviral mechanism of Tp80 is the inhibition of the viral genome replication through the recoverly of GPx2 expression downregulated by HCV infection.
We used microarrays to evaluated the effect of Tp80 on the transcriptome of HCV replicon cells, compared with Non-infected host cells or non-treated HCV replicon cells.

overall_design: Huh7/RepFeo cells were incubated withTp80 or DMSO at the concentration of 10µM for 48 hours, and cellular RNAs were collected and subjected to microarray analysis. DMSO treated Huh7 cells were used as the noninfected control.

first: Bao

last: Nguyen

first: Yukiko

last: Okuno

first: Masahiko

last: Ajiro

last: Iida

first: Masatsugu

last: Denawa

first: Makoto

last: Yamamoto

first: Naoya

last: Sakamoto

first: Hiroyuki

last: Kagechika

first: Masatoshi

last: Hagiwara


title: Mesenchymal stromal cell transcriptome study

status: Public on Nov 23 2016

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary:
Transcriptomes of mesenchymal stromal cells from bone marrow (bmMSC) were compared to MSC from term placenta (pMSC).
Cells were expanded under GMP-compliant conditions. The transcriptome was explored to compare the regenerative potential of bmMSCs and pMSCs in a pre-clinical and eventually in a clinical context

overall_design: 25 samples, 11 bone marrow (no replicates) from male and female donors, 14 healthy human term placentas from planned cesareans. The study was approved by the Ethics Committee

first: W

last: Aicher

first: K


title: Expression data from meduallar thymic epithelial cells and thymic or splenic B cells

status: Public on Dec 12 2016

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

country: Israel

institute: Weizmann Institute

summary:
Aire is a transcriptional regulator that induces promiscuous expression of thousands of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive.
We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells.

overall_design: Mature EpCAM+MHC-II high mTECs, Immature EpCAM+MHC-II low mTECs, and EpCAM+Ly51+ cTECs were flow-sorted from thymi isolated from thymi of C57BL/6 6weeks old mice. CD19+Aire.GFP+ thymic B cells and CD19+ Splenic B cells were flow sorted from thyme or spleen, respectively, of C57BL/6 Adig 6weeks old mice. Typically, 3 mice were pooled to obtain 30-60 thousand sorted TECs or thymic B cells, which were then analyzed by gene expression profiling. Specifically, total RNA was extracted from ~30,000 pooled sorted cells using Trizol. Purified total RNA was then amplified using the MessageAmp RNA kit (Ambion). Biotinylated cRNA was then hybridized to Affymetrix Mouse Gene 1-ST arrays by the genomics core at the Weizmann Institute.

first: J


title: Radiogenomics of glioblastoma: Machine-learning based classification of molecular characteristics using multiparametric and multiregional MRI features

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary:
Background:To evaluate the association of multiparametric and multiregional MRI-features with key molecular characteristics in patients with newly-diagnosed glioblastoma.
Methods:Retrospective data evaluation was approved by the local ethics committee of the University of Heidelberg (ethics approval number: S-320/2012) and informed consent was waived. Preoperative MRI-features were correlated with key molecular characteristics within a single-institutional cohort of 152 patients with newly-diagnosed glioblastoma. Preoperative MRI-features (n=31) included multiparametric (anatomical, diffusion-, perfusion-, and susceptibility-weighted images) and multiregional (contrast enhancing and non-enhancing FLAIR-hyperintense) information with (histogram) quantification of tumor volumes, volume ratios, apparent diffusion coefficients, cerebral blood flow / volume (CBF / CBV) and intratumoral susceptibility signals. Molecular characteristics determined with the Illumina Infinium HumanMethylation450 array included global DNA-methylation subgroups (e.g. mesenchymal (MES), RTK I “PGFRA”, RTK II “classic”), MGMT-promoter methylation status and hallmark copy-number-variations (EGFR-, PDGFRA-, MDM4- and CDK4-amplification; PTEN-, CDKN2A-, NF1- and RB1-loss). Univariate analyses (voxel-lesion-symptom-mapping for tumor location, Wilcoxon-test for all other MRI-features) as well as machine-learning models were applied to study the strength of association and discriminative value of MRI-features for predicting underlying molecular characteristics.
Results: There was no tumor location predilection for any of the assessed molecular parameters (permutation-adjusted p>0.05 each). Univariate imaging parameter associations were noted for EGFR amplification and CDKN2A loss, both demonstrating increased nrCBV and nrCBF values (performance of these parameters, as assessed by the area under the ROC curve ranged from 63 to 69%, FDR-adjusted p<0.05, respectively). Subjecting all MRI-features to machine-learning-based classification allowed to predict EGFR amplification status and the RTK II “classic” GB subgroup with a moderate, yet significantly greater accuracy (63% for EGFR [p<0.01] and 61% for RTK II [p=0.01]) than the prediction by chance, whereas prediction accuracy for all other molecular parameters was non-significant (p>0.05, all models).
Conclusions: In summary, we found univariate associations between established MRI-features and molecular characteristics, however not of sufficient strength to allow the generation of machine-learning classification models for reliable and clinically meaningful prediction of the assessed molecular characteristics in patients with newly-diagnosed glioblastoma.

overall_design: The Illumina Infinium HumanMethylation450 array (Illumina, San Diego, USA) data from n=152 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Sturm et al. Cancer Cell. 2012 Oct 16;22(4):425-37)

first: Philipp

last: Kickingereder

first: David

last: Bonekamp

first: Annekathrin

last: Kratz

first: Martha

last: Nowosielski

first: Sina

last: Burth

first: Antje

last: Wick

last: Eidel

first: Heinz-Peter

last: Schlemmer

first: Alexander

last: Radbruch

first: Jürgen

last: Debus

first: Christel

last: Herold-Mende

first: Andreas

last: Unterberg

last: Jones

first: Stefan

last: Pfister

first: Woflgang

last: von Deimling

last: Bendszus

last: Capper


title: Inhibition of Akt Signaling in PIK3R2 Overexpressing Colon Cancer Stem Cells Reduces Tumor Growth due Apoptosis and Decreased Mucin Production

status: Public on Dec 06 2016

city: Gainesville

first: M Cecilia

last: Lopez

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

overall_design: Affymetrix microarray analysis was used to assess gene expression differences between ALDH+ and ALDH- cells enriched from primary human tumor xenografts

first: Sugong

last: Chen

first: Robert

middle: C

last: Fisher

first: Steven

last: Signsb

first: L

last: Molina

first: Anitha

middle: K

last: Shenoy

first: Maria-Cecilia

first: Henry

middle: V

last: Baker

first: John

last: Koomen

first: Y

first: Haley

last: Gittlemane

first: Jill

last: Barnholtz-Sloane

first: Samaneh

last: Kamalib

first: Annamarie

last: Berg

middle: D

last: Appelman

first: Lyle

last: Moldawer

first: Emina

last: Huang


title: The GEP of Treg subpopulations A and B and matchd T conventional

status: Public on Nov 22 2016

city: London

first: Shahram

last: Kordasti

state: London

address: Rayne Institute, 123 Coldharbour Lane

country: United Kingdom

institute: King's College London

summary: Transcriptom analysis of Treg subpopulations based on CD4,CD25,CD127,CCR4,CD45RO and CD95 expression

overall_design: We have analysed sorted Treg subpopulations based on CD4,CD25,CD127,CCR4,CD45RO and CD95 expression

first: Benedetta

last: Costantini

first: Thomas

last: Seidl

first: Giovanni

last: Povoleri

first: Ghulam

last: Mufti


title: Expression data from GFP control and GFP-PRDM1 transduced H9 hESCS

status: Public on Dec 11 2016

city: Taipei

first: I-Ying

last: Lin

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: The mechanisms of transcriptional regulation underlying human primordial germ cell differentiation are largely unknown. Transcriptional repressor Prdm1/Blimp1 is known to play a critical role in controlling germ cell specification in mice. We show that ectopic expression of PRDM1 in hESCs promotes the generation of cells exhibiting transcriptomic features of early primordial germ cells.

overall_design: To consolidate if hESCs expressing ectopic GFP-PRDM1 displayed gene expression signature similar to that in germline lineage, we compared the transcription profiles of H9 hESCs transduced with GFP-PRDM1 and GFP control vectors on days 7 and 17.

first: Ching-Yu

last: Chuang

first: Nardnisa

last: Sintupisut

first: Chen-Hsiang

last: Yeang

first: Hung-Chih

last: Kuo

first: Kuo-I


title: Epigenome analysis of intracranial aneurysm and superficial temporal artery samples

city: Beijing

first: Jia

last: Wang

address: Tian Tan Xili 6#

department: Neurosurgery

institute: Beijing Tian Tan Hospital, Capital Medical University

summary: Genomic DNA of intracranial aneurysm and matched superficial temporal artery from same patient (n=9) was extracted  with QIAamp DNA Mini Kit (Qiagen, Valencia, CA). A total of 500 of genomic DNA was bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA) and then analyzed on an Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA) following the manufacturer’s instructions.

overall_design: Genomic DNA of intracranial aneurysm and matched superficial temporal artery from the 9 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Lanbing

last: Yu

first: Jizong

last: Zhao


title: Control of secreted protein gene expression and the mammalian secretome by the metabolic regulator PGC-1a

first: Neri

last: Minsky

address: 1230 York Avenue

institute: Rockefeller University

summary: Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes and signal molecules.  In this study  we demonstrate, unexpectedly, that PGC-1α, a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate expression of diverse genes encoding secreted molecules and extracellular matrix (ECM) components to modulate the secretome.  We show that both endogenous and exogenous PGC-1α down-regulate expression of numerous genes encoding secreted molecules. Mechanistically, results obtained using mRNA stability measurements as well as intronic RNA expression analysis are consistent with a transcriptional effect of PGC-1α on expression of genes encoding secreted proteins. Interestingly, PGC-1α requires the central heat shock response regulator HSF1 to affect some of its targets, and both factors co-reside on several target genes encoding secreted molecules in cells.  Finally, using a mass spectrometric analysis of secreted proteins, we demonstrate that PGC-1α modulates the secretome of mouse embryonic fibroblasts (MEFs).

overall_design:
Cells were grown in 12-well plates and control adenoviruses (Ad-control) or PGC-1alpha (Ad-PGC-1α) encoding adenoviruses were directly added to the culture medium where indicated.
PGC-1α KO and PGC-1α WT differentiated brown adipocytes were examined.

first: Rober

last: Roeder


title: Expression data from Alzheimer's disease (AD) model mouse and AD model mouse overexpressing human mitochondrial transcriptional factor A (hTFAM)

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To delineate the mechanism underlying the amelioration of AD pathophysiology by hTFAM, we performed gene expression profiling using hippocampal RNAs from the AD model mouse and AD model mouse overexpressing human TFAM.
One-way ANOVA of microarray data from hippocampus revealed that the gene expression profile is most significantly altered in the hippocampi of ADh/hTFAMh mice. Comparative analyses of the brains of ADh/WT and ADh/hTFAMh mice showed that the expression of genes involved in cancer, endocrine system disorders, and organismal injury and abnormalities were significantly altered. Among the genes whose expression was significantly altered by hTFAM expression, transthyretin, encoded by the Ttr gene, binds Aβ and inhibits its aggregation.

overall_design: Hemizygous 3xTg-AD mice harboring hemizygous APPSwe and tauP301L transgenes with a hemizygous Psen1M146V mutation (ADh/WT), and hemizygous 3xTg-AD mice with the hemizygous hTFAM transgene (ADh/hTFAMh) were used in this study, (male, n=3 for each group). RNA samples prepared from hippocampi were subjected to microarray analysis using the Affymetrix Mouse Gene 1.0 ST platform (GPL6246).

first: Sugako

last: Oka


title: Confirmation dataset of Transcriptome Sequencing (RNAseq) data utilizing Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development

status: Public on Nov 21 2016

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

type: Expression profiling by high throughput sequencing

summary: This dataset complements GSE76207. Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies (Eikrem et al., PLoS One. 2016 Feb 22;11(2):e0149743. doi: 10.1371/journal.pone.0149743. eCollection 2016. PMID: 26901863) with FFPE confirmation dataset from clear cell renal cell carcinoma (ccRCC) patients. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol. The goal of the study is to compare the discovery and the confirmation data and to assess the utilization of the data for ccRCC biomarker development.

overall_design:
RNA from paired ccRCC and normal human renal biopsies were sequenced using the Illumina HiSeq 2500; platform GPL16791.

In accordance with local ethics committee, raw sequence data cannot be provided.  Please contact the submitter for the sequence data.

first: Oystein

last: Eikrem

first: Christian

last: Beisland

first: Karin

last: Hjelle

first: Arnar

last: Flatberg

first: Andreas

last: Scherer

first: Lea

last: Landolt

first: Trude

last: Skogstrand

first: Sabina

last: Leh

first: Vidar

last: Beisvag

first: Hans-Peter

last: Marti


title: Expression data of Intracranial aneurysm

first: Jia

last: Wang

summary:
Intracranial aneurysm is a cerebrovascular disorder in which degeneration of intima and internal elastic lamina of a cerebral artery or vein causes a localized dilation or ballooning of the blood vessel. Different molecular mechanisms are involved in sIA formation in patients.
We used microarrays to detail the gene expression of intracranial aneurysm.

overall_design: Intracranial aneurysm and matched superficial temporal artery were selected for RNA extraction and hybridization on Affymetrix microarrays. We compared intracranial aneurysm (IA) wall tissues with control superficial temporal artery walls

first: Lanbing

last: Yu


title: Intronic polyadenylation of PDGFRα in stromal stem cells attenuates muscle fibrosis

first: Thomas

last: Rando

summary:
The platelet-derived growth factor receptor alpha (PDGFRα) exhibits divergent effects in skeletal muscle. At physiological levels, signaling through this receptor promotes muscle development in growing embryos and proper angiogenesis in regenerating adult muscle. However, either increased PDGF ligands or enhanced PDGFRα pathway activity causes pathological fibrosis. This excessive collagen deposition, which is seen in aged and diseased muscle, interferes with proper muscle function and limits the effectiveness of gene- and cell-based therapies for muscle disorders. Although compelling evidence exists for the role of PDGFRα in fibrosis, little is known about the cells through which this pathway acts. Here we show that PDGFRα signaling regulates a population of muscle-resident fibro/adipogenic progenitors (FAPs) that play a supportive role in muscle regeneration but may also cause fibrosis when aberrantly regulated. We found that FAPs produce multiple transcriptional variants of PDGFRα with different polyadenylation sites, including an intronic variant that codes for a protein isoform containing a truncated kinase domain. This variant, upregulated during regeneration, acts as a decoy to inhibit PDGF signaling and to prevent FAP over-activation. Moreover, increasing expression of this isoform limits fibrosis in vivo, suggesting both biological relevance and therapeutic potential of modulating polyadenylation patterns in stem cell populations.
We used microarrays to explore the biological effects of altering intronic polyadenylation of PDGFRα in FAPs in vivo.

overall_design: Tibialis anterior muscles from C57Bl/6 mice were each injured with 30 µL of 50% v/v glycerol and injected with the indicated vivo morpholino (VMO) after 3 days. FAPs were then isolated from the muscles 2 days post-VMO injection. Cells were lysed and the RNA was prepared with the RNeasy Mini Kit as per the manufacturer’s instructions (Qiagen). The microarray data were obtained using Affymetrix Mouse 1.0 ST. Each biological replicate represents cells pooled from 4 mice.

first: Alisa

last: Mueller


title: Expression data for 59 primary tumors from patients with colorectal cancer

city: Parkville

first: Oliver

last: Sieber

summary: mRNA from 59 primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. Mutation status for several genes were determined using Sanger sequencing.

overall_design: 59 colorectal cancers samples were analyzed for both microarray expression (Plus2.0 platform) and mutation status of several genes.


title: Comparison of R1, R2 and R3

status: Public on Nov 24 2016

first: Pierre

last: Guermonprez

address: 1st floor NHH, Guy's Campus,

department: CIBCI

summary:
3 samples of R1, R2 and R3 bone marrow monocytes were compared from 3 biological replicates in 3 separate experiments.
R1, R2 and R3 were sorted from triplicate experiments from pools of mice

overall_design: Ly6Chi CD115+ cells from murine bone marrow was sorted into the Flt3-CD11c- (R1), Flt3+CD11c- (R2), Flt3+CD11c+ (R3) cells for analysis of their transcriptional profiles

first: Shinelle

last: Menezes


title: DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with Caveolin-1

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Epigenetic modifications have been shown to be important in developmental tumors as Ewing sarcoma. We profiled the DNA methylation status of 15 primary tumors and 7 cell lines using the Infinium Human Methylation 450k. Differential methylation analysis between Ewing sarcoma and reference samples revealed 1,166 hypermethylated and 864 hypomethylated CpG sites (Bonferroni p<0.05, δ-β-value with absolute difference of >0.20) corresponding to 392 and 470 genes respectively. Gene Ontology analysis of genes differentially methylated in Ewing sarcoma samples showed a significant enrichment of developmental genes. Membrane and cell signal genes were also enriched, among those, 11 were related to caveola formation. We identified differential hypermethylation of CpGs located in the body and S-Shore of the PTRF gene in Ewing sarcoma that correlated with its repressed transcriptional state. Reintroduction of PTRF/Cavin-1 in Ewing sarcoma cells revealed a role of this protein as a tumor suppressor. Restoration of caveolae in the membrane of Ewing sarcoma cells, by exogenously reintroducing PTRF, disrupts the MDM2/p53 complex, which consequently results in the activation of p53 and the induction of apoptosis.

overall_design: 15 primary tumors (Ewing Sarcoma) and 7 Ewing's sarcoma cell lines were interrogated for methylation levels using the Infinium HumanMethylation450k microarray.

first: Oscar

last: Tirado

first: Juan

last: Huertas-Martinez


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends on Lhx2 [123cre:double knockout]

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

summary:
Conditional deletion of Lhx2, and to a lesser extent, Emx2 in olfactory neurons alters odorant receptor expression frequency.
GeneChip microarrays were used to measure odorant receptor mRNAs and test whether their abundance was affected in knockout mice

overall_design: Cre recombinase expression specific to immature and mature neurons was used to conditionally delete floxed Lhx2 and Emx2 genes.


title: Comparative gene expression profiling analysis of primary urothelial cells at early passage 2 and late passage 8

first: Clara Ibel

last: Chamorro Jimenez

address: Center for Molecular Medicine (CMM) Karolinska University Hospital L8:02 Sweden

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

summary:
In vitro propagated urothelial cell could be ideal material in regenerative medicine.  The fine characterization of the laboratory produced cells before transplantation is important. Here we aimed to characterize changes in gene expression and cell proliferation in urothelial cells expanded in vitro.
Gene expression profiling was performed using Affymetrix HG-U133 Plus 2 microarrays. We identified distinct classes of down- and up-regulated genes during this process.

overall_design: Human primary urothelial cells were isolated from bladder washes,  and propadated in vitro for several passages. RNA was collected from cells at early passage 2 and late passage 8.  In total samples from 3 different donors were analyzed using the Afimetrix, human Genome U133 set (HG-U133) plus 2.

first: Clara

last: Chamorro

first: Said

last: Zeiai

first: Gisela

last: Reinfeldt Engberg

first: David

last: Brodin

first: Agneta

last: Nordenskjöld

first: Magdalena

last: Fossum


title: Pancreatic adenocarcinoma associated fibroblast cells

city: Hangzhou

first: Donger

last: Zhou

address: Jiefang Road 88#

institute: Zhejiang University

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

overall_design: Refer to individual Series


title: Gene expression profiles in CDX2P-G19Cre;Apcflox/flox;Tgfbr2flox/flox and CDX2P-G19Cre;Apcflox/flox mouse tumors

city: Hiroshima City

first: MASASHI

last: MIGUCHI

state: Please Select

address: 3-2-1 Kasumi Minami-Ku

institute: Hiroshima University

summary: Mutations in TGFBR2, a component of the transforming growth factor (TGF)-β signaling pathway, occur in high-frequency microsatellite instability (MSI-H) colorectal cancer (CRC). In mouse models, Tgfbr2 inactivation in the intestinal epithelium accelerates the development of malignant intestinal tumors in combination with disruption of the Wnt-β-catenin pathway. However, no studies have further identified the genes influenced by TGFBR2 inactivation following disruption of the Wnt-β-catenin pathway. We previously described CDX2P-G19Cre;Apcflox/flox mice, which is stochastically null for Apc in the colon epithelium. In this study, we generated CDX2P-G19Cre;Apcflox/flox;Tgfbr2flox/flox mice, with simultaneous loss of Apc and Tgfbr2. These mice developed tumors, including adenocarcinoma in the proximal colon. We compared gene expression profiles between tumors of the two types of mice using microarray analysis.

overall_design: Tumors in two genetically engineered mice at 3 weeks of age.  CDX2P-G19Cre;Apcflox/flox;Tgfbr2flox/flox mice’ and CDX2P-G19Cre;Apcflox/flox mice’ were selected by LMD6500 laser capture microdissection device for RNA extraction and hybridization on Affymetrix microarrays.

first: Masashi

last: Miguchi

first: Takao

last: Hinoi


title: Epigenome analysis of pancreatic adenocarcinoma associated fibroblast cells.

summary: Genome wide DNA methylation profiling of cancer associated fibroblasts. The hypothesis tested in the present study was that tumor induced DNA methylation in cancer associated fibroblasts. Results showed DNA methlation status in cancer associated fibroblasts changed  after coculture with pancreatic cancer cells.

overall_design: Mesenchymal stem cells and 09.05CAFs which was primary cultured fibroblasts either cultured alone or co-cultured with pancreatic tumor cells then purified by anti-FAP antibody coupled Dynabeads. DNA were abtained and DNA methylation were compared between cultured alone and cocultured.

first: Lei

last: Zheng


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends on Lhx2 [OmpCre:Lhx2]

summary:
Conditional deletion of Lhx2, and to a lesser extent, Emx2 in olfactory neurons alters odorant receptor expression frequency. This series describes 1 of the 5 array experiments.
GeneChip microarrays were used to measure odorant receptor mRNAs and test whether their abundance was affected in conditional knockout mice

overall_design: Cre recombinase expression specific to immature and mature neurons was used to conditionally delete floxed Lhx2 gene.


title: Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice

city: Urbana

first: William

last: Helferich

state: Illinois

address: 905 S Goodwin Avenue

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Champaign

summary:
Scope: Soy flour diet (MS) prevented isoflavones from stimulating MCF-7 tumor growth in athymic nude mice, indicating that other bioactive compounds in soy can negate the estrogenic properties of isoflavones. The underlying signal transduction pathways to explain the protective effects of soy flour consumption were studied here.
Methods and results: Ovariectomized athymic nude mice inoculated with MCF-7 human breast cancer cells were fed either MS or purified isoflavone mix (MI), both with equivalent amounts of genistein. Positive controls received estradiol pellets and negative controls received sham pellets. GeneChip-Human-Genome-U133 Plus-2.0 Array platform was used to evaluate gene expressions, and results were analyzed using bioinformatics approaches. Tumors in MS-fed mice exhibited higher expression of tumor-growth-suppressing genes ATP2A3 and BLNK, and lower expression of oncogene MYC. Tumors in MI-fed mice expressed higher level of oncogene MYB and lower level of MHC-I and MHC-II, allowing tumor cells to escape immunosurveillance. MS-induced gene expression alterations were predictive of prolonged survival among estrogen-receptor-positive breast cancer patients, whilst MI-induced gene changes were predictive of shortened survival.
Conclusion: Our findings suggest dietary soy flour affects gene expression differently than purified isoflavones, which may explain why soy foods prevent isoflavones-induced stimulation of MCF-7 tumor growth in athymic nude mice.

overall_design: Ovarectomized athymic nude mice at 28 days of age were randomly assigned to four groups: soy flour (MS), purified isoflavone mix (MI), negative control (NC) and positive control (PC). MS and MI groups contained equivalent amounts of genistein, and both PC and NC groups received no genistein. All mice were fed AIN93G diet, with corn oil substituted with soy oil. Mice in the PC group received 2 milligram estradiol (E2) pellets and mice in the NC group received sham pellets. AIN93G based MI and MS diets contained 750 ppm genistein aglycone and were individually formulated and balanced to contain equal amounts of protein, carbohydrate and fat. All mice were euthanized 12 weeks after inoculation of MCF-7 tumor cells and tumors were immediately frozen by submersion into liquid nitrogen. All of the experimental procedures were approved by the Illinois Institutional Animal Care and Use Committee (Protocol ID 13315) and were conducted in accordance with the regulations described in the Committee’s Manual.

first: Yunxian

last: Liu


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends Lhx2 [OmpCre:Emx2]


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends on Lhx2 [123Cre:Emx2]


title: Pan-Raf co-operates with PI3K-dependent signaling and critically contributes to myeloma cell survival independently of mutated RAS

city: Würzburg

first: Claus

last: Scholz

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

summary:
The most common oncogenic mutations in multiple myeloma (MM) affect N- and K-RAS leading to constitutive activation of RAS-dependent signaling. Signal transduction via RAS, Raf and MAPK has been well described as a canonical pathway. In accordance with this assumption, we showed that the activity of the MEK/ERK module is strictly dependent on pan-Raf activity. However, inhibition of MEK/ERK has no or only minor effects on MM cell survival, whereas oncogenic Ras and pan-Raf critically contribute to survival of multiple myeloma cells. Therefore, we aimed to learn more about Raf-dependent but MEK-independent signaling effectors.
We analyzed gene expression profiles in INA-6 cells after either pan-Raf inhibition with SB-590885 or MEK inhibition with PD-325901.

overall_design: Four biological replicates from each experimental group were analyzed with Affymetrix HGU133 Plus 2.0 microarrays.

first: Elisabeth

last: Müller

first: Manik

last: Chatterjee


title: The lncRNA HOTAIR Modulates DNA-Methylation in Mesenchymal Stem Cells via Triple Helix Formation (methylation)

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Long non coding RNAs are implemented in epigenetic changes and regulation of gene expression. HOTAIR is a promising lncRNA concerning epigenetic regulation. We performed HOTAIR overexpression and knockdown experiments in mesenchymal stromal cells derived from bone marrow. After two weeks cells were harvested and RNA and DNA were isolated. Analysis of gene expression was performed with Human Gene 2.0 ST Array (Affymetrix, Santa Clara, USA). Analysis of DNA methylation was performed with Infinium HumanMethylation450 BeadChips (Illumina, San Diego, USA)

overall_design: DNA methylation profiles of BM-MSC upon HOTAIR retroviral Overexpression and siRNA mediated Knockdown.

first: Marie

last: Kalwa

first: Sonja

last: Hänzelmann

first: Chao-Chung

last: Kuo

first: Sylvia

last: Joussen

first: Eduardo

last: Fernandez-Rebollo

first: Björn

last: Rath

first: Carmen

last: Koch

first: Andrea

last: Hofmann

first: Shih-Han

last: Lee

first: Andrew

middle: E

last: Teschendorff

first: Bernd

last: Denecke

first: Qiong

last: Lin

first: Martin

last: Widschwendter

first: Ivan

last: Costa


title: The lncRNA HOTAIR Modulates DNA-Methylation in Mesenchymal Stem Cells via Triple Helix Formation


title: The lncRNA HOTAIR Modulates DNA-Methylation in Mesenchymal Stem Cells via Triple Helix Formation (expression)

overall_design: Gene expression profiles of BM-MSC upon HOTAIR retroviral Overexpression and siRNA mediated Knockdown.


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends on Lhx2

first: Tim

last: McClintock


title: BW25113 Rif pre-treated persister cells vs. stationary phase BW25113 wild-type

status: Public on Nov 20 2016

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: E. coli K-12 BW25113 persister cells generated via rifampicin pre-treatment  relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

overall_design:
BW25113 wild-type, pre-treated with refampicin 30 min, ampicillin 3 h; BW25113 wild-type OD at 600 nm of 3.0, ampicillin 30 mins.
Medium: LB
ampicillin 20 ug/mL used to generate persisters; ampicillin 5 ug/mL added to stationary phase BW25113 wild-type

first: Hazel

middle: F

last: O'Connor

first: Michael

last: Benedik


title: Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons Depends on Lhx2 [123Cre:Lhx2]


title: RNA profiling of mouse mammary tumor cell redirection in vitro model.

status: Public on Nov 18 2016

city: Clemson

first: Alex

last: Feltus

address: 302C Biosytstems Research Complex

department: Genetics & Biochemistry

institute: Clemson University

summary: We have developed an in vitro system of cancer cell redirection that employs the 1:50 ratio of cancer cells to normal cells.  Using our in vitro system of cancer cell redirection we investigated the genetic profiles of erbB2-overexpressing mammary tumor-derived cells as they undergo the redirection phenomenon.

overall_design: 6 cell groups with measured in triplicate

first: Brian

middle: W

last: Booth

first: Frank


title: Dynamic response of EGF stimulation in lung cancer cells [EGF]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for the detection of significant expression dynamics often fail when the expression dynamics show a large heterogeneity, and often cannot cope with irregular and sparse measurements.

overall_design: H1975 NSCLC cells were seeded in 6-well-plates with 1,33x10(-5) cells per well. After incubation for 3 days, cells were washed 3 times and supplemented with medium without FCS for overnight starvation. The following day, cells were stimulated with 50 ng/ml of EGF diluted in starvation medium. Samples were harvested after 0, 0.5, 1, 2, 4, 6, 8, 12, 24 and 48 hours. Total cellular RNA was isolated with the NucleoSpin RNA II kit according to the manufacturers' instructions. After amplification, labeling with biotin and fragmentation of the RNA, hybridization with GeneChip Human Gene 2.0 ST Array was performed for 16 h at 45°C. Subsequently, washing and staining was performed using an Affymetrix Fluidics Station 450 and the microarray was scanned using an Affymetrix GeneArray Scanner 3000.

first: Kai

last: Breuhahn

first: Benedikt

last: Müller


title: Change in Expression in U937 under MIXL1 enforced overexpression

city: Houston

first: Lalitha

last: Nagarajan

state: TX

address: 6767 Bertner

department: Genetics

institute: Unviersity of Texas MD Anderson Cancer Center

summary:
While the role of the paired-type homeobox transcription factor MIXL1 in early embryonic development has been previously established, very little is known about the role of MIXL1 in adult hematopoiesis.
To determine what role MIXL1 plays in adult hematopoietic cells, we established an enforced expression model for MIXL1 in the cell line U937, then analyzed the changes of gene expression caused by increased expression of MIXL1 by microarray analysis.

overall_design: In attempt to identify the downstream role of MIXL1 in adult hematopoietic cells, we used previously established MIXL1 overexpression line (HL004-MIXL) and empty vector control (HL003-Vec) clones of the AML cell line U937.  Both cell lines were grown for 24 hours at a starting concentration of 5x10^4/ml in 90% RMPI/10% FBS before being harvested for RNA.  The RNA was then compared by microarray analysis, with the empty vector control sample (HL003-Vec) used as a control sample for the purposes of analysis.

first: Raymond

last: Aaron

first: Nagarajan

last: Lalitha


title: Dynamic response of EGF stimulation in lung cancer cells [controls]

overall_design: H1975 NSCLC cells were seeded in 6-well-plates with 1,33x10(-5) cells per well. After incubation for 3 days, cells were washed 3 times and supplemented with medium without FCS for overnight starvation. The following day, cells were stimulated in starvation medium. Samples were harvested after 0, 0.5, 1, 2, 4, 6, 8, 12, 24 and 48 hours. Total cellular RNA was isolated with the NucleoSpin RNA II kit according to the manufacturers' instructions. After amplification, labeling with biotin and fragmentation of the RNA, hybridization with GeneChip Human Gene 2.0 ST Array was performed for 16 h at 45°C. Subsequently, washing and staining was performed using an Affymetrix Fluidics Station 450 and the microarray was scanned using an Affymetrix GeneArray Scanner 3000.


title: Dynamic response of EGF stimulation in lung cancer cells


title: Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_05_Methylation]

status: Public on Nov 15 2016

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

summary: Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. Our results indicate that DNA demethylation and histone acetylation are coordinated to generate the transcriptional program associated with memory cells. Conversely, EM and TEMRA cells share a very similar epigenetic landscape. Nonetheless, the TEMRA transcriptional program predicts an innate immunity phenotype associated with genes never reported in these cells, including several mediators of NK cell activation (VAV3 and LYN) and a large array of NK receptors (KIR2DL3, KIR2DL4, KIR2DL1, KIR3DL1, KIR2DS5, etc.). In addition, we identified up to 161 genes that encode transcriptional regulators, some of unknown function in CD8+ T cells, that were differentially expressed in the course of differentiation. Overall, these results provide new insights into the regulatory networks involved in memory CD8+ T cell maintenance and T cell terminal differentiation.

overall_design: Genome-wide changes in DNA methylation in human CD8+ T cell subsets isolated from peripheral blood were generated by HumanMethylation450 (HM450) BeadChips (Illumina Inc.)

first: Ramón

last: Rodriguez

first: Carlos

last: Lopez Larrea

first: José

last: Luis Lavín


title: Gene expression comparison between histone H2A.Z WT and K102Q in MCF7 breast cancer cell line

status: Public on Nov 17 2016

city: Taipei

first: Shu-Chun

last: Teng

address: No.1 Jen Ai Road Section 1

department: Department of Microbiology

institute: National Taiwan University

summary: The study aims to elucidate the effect of histone H2A.ZK102me2 on gene expression in MCF-7 breast cancer cell line.  Results provide insight into the role of H2A.ZK102me2 in breast cancer cell.

overall_design: The H2A.ZWT and H2A.ZK102Q protein were stably overexpressed while endogenous H2A.Z was knocked down in MCF-7 cells. Their total RNA was isolated for genomic expression profiling with Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Cheng-Hui

last: Tsai

first: Yun-Ju

last: Chen

first: Chia-Jung

last: Yu

first: Wen-Hong

last: Kuo

first: Ming-Chieh

last: Lin

first: Nei-Li

last: Chan

first: Kou-Juey

last: Wu


title: Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

institute: University of Stirling

type:
Expression profiling by array
Third-party reanalysis


title: Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice [HDAC9 transgenic]

summary: Histone deacetylase 9 (HDAC9) is expressed in B cells, and its overexpression has been observed in B-lymphoproliferative disorders, including B-cell non-Hodgkin lymphoma (B-NHL). We examined HDAC9 protein expression and copy number alterations in primary B-NHL samples, identifying high HDAC9 expression among various lymphoma entities and HDAC9 copy number gains in 50% of diffuse large B-cell lymphoma (DLBCL). To study the role of HDAC9 in lymphomagenesis, we generated a genetically engineered mouse (GEM) model that constitutively expressed an HDAC9 transgene throughout B-cell development under the control of the immunoglobulin heavy chain (IgH) enhancer (Eμ). Here, we report that the Eμ-HDAC9 GEM model develops splenic marginal zone lymphoma and lymphoproliferative disease (LPD) with progression towards aggressive DLBCL, with gene expression profiling supporting a germinal center cell origin, as is also seen in human B-NHL tumors. Analysis of Eμ-HDAC9 tumors suggested that HDAC9 might contribute to lymphomagenesis by altering pathways involved in growth and survival, as well as modulating BCL6 activity and p53 tumor suppressor function. Epigenetic modifications play an important role in the germinal center response, and deregulation of the B-cell epigenome as a consequence of mutations and other genomic aberrations are being increasingly recognized as important steps in the pathogenesis of a variety of B-cell lymphomas. A thorough mechanistic understanding of these alterations will inform the use of targeted therapies for these malignancies. These findings strongly suggest a role for HDAC9 in B-NHL and establish a novel GEM model for the study of lymphomagenesis and, potentially, preclinical testing of therapeutic approaches based on histone deacetylase inhibitors.

overall_design: FLAG-epitope-tagged full-length human HDAC9 cDNA was cloned into the pEμSR vector, placing the HDAC9-sequence-containing oligonucleotide cassette downstream of the immunoglobulin heavy chain (IgH) enhancer (Eμ) and the SRα potent promoter (Bodrug et al., 1994). The Eμ-HDAC9 transgenic fragment was isolated from the vector by enzymatic digestion using the NotI restriction sites and injected into B6CBAF1 pronuclei. Mice were backcrossed and maintained in a C57BL/6 background to generate three transgenic lines: 1468, 1469 and 1839. PCR genotyping was performed using SV40 primers: F: 5′-GGAACTGATGAATGGGAGCA-3′ and R: 5′-GCAGTGCAGCTTTTTCCTTT-3′. Mice were housed and maintained in accordance with UK Home Office regulations. Animals were monitored and analyzed from birth to 23 months of age and sacrificed if showing signs of illness. Statistical analysis was performed using Prism (GraphPad Software). Kaplan–Meier cumulative survival and the log-rank (Mantel–Cox) test were used to determine tumor-free survival and the χ2 test was used to compare B-NHL incidence in HDAC9 mice versus wild-type controls. P<0.05 was considered statistically significant. All experimental protocols were monitored and approved by The Institute of Cancer Research Animal Welfare and Ethical Review Body, in compliance with guidelines specified by the UK Home Office Animals (Scientific Procedures) Act 1986 and the United Kingdom National Cancer Research Institute guidelines for the welfare of animals in cancer research (Workman et al., 2010). ARRIVE guidelines were applied when reporting in vivo experiments (Kilkenny et al., 2010).


title: Expression data for analysis of genes regulated by EWS/FLI1 protein levels in Ewing sarcoma cell line A673

status: Public on Nov 16 2016

city: Zurich

first: Maria

middle: Elka

last: Gierisch

address: Steinwiesstrasse 32

department: Department of Oncology

country: Switzerland

institute: University Children's Hospital Zurich

summary:
Comparison of gene expression profile of Ewing sarcoma cells which have an exchange of the endogenous EWS/FLI1 to either wild-type or a turnover-deficient mutant EWS/FLI1. Most target genes are saturated as only a few target genes are soly driven by increasing protein amount.
The effect of a stable EWS/FLI1 mutant on global gene expression was evaluated in A673 Ewing sarcoma cells.

overall_design: A doxycycline-inducible shRNA construct directed against the 5'UTR of  endogenous EWS/FLI1 was stably transduced into A673 cells and used for silencing.  Further, a doxycycline-inducible overexpression construct was used to simultaneously express either a flag-tag, 3xflag-EWS/FLI1 or 3xflag-EWS/FLI1 K380R. RNA used for expression profiling was isolated from these A673 cells after 24h and 48h doxycycline-induction. Controls cells were uninduced samples from each cell line construct.

first: Beat

last: Schäfer

first: Marco

last: Wachtel


title: Incoming human papillomavirus 16 genome is lost in PML protein-deficient HACAT keratinocytes.

city: Shreveport

first: Martin

last: Sapp

state: LA

address: 1501 Kings Hwy

department: Microbiology and Immunology

institute: LSU Health

summary:
Human papillomaviruses (HPVs) target PML nuclear bodies during infectious entry and PML protein is important for efficient transcription of incoming viral genome.We used shRNA to knockdown PML protein in HaCaT keratinocytes to further investigate the role of PML protein in HPV entry.
We used microarrays to compare the transcriptome of PML protein-deficient with vector control-transduced HaCaT cells.

overall_design: HaCaT cells were transduced with lentiviruses expresing shRNA directed against PML or scrambled control. Stable cell lines were then selected with puromycin. A PML-deficient single-cell clone and vector control cells were used to isolate total RNA.

first: Malgorzata

last: Bienkowska-Haba

first: Wioleta

last: Luszczek

first: Timothy

middle: R

last: Keiffer

first: Lucile

last: Guion

first: Stephen

last: DiGiuseppe

first: Rona

last: Scott


title: Gene expression induced by DOT1L and Menin inhibition in cell line models of leukemia

status: Public on Nov 14 2016

city: Basel

first: Swann

last: Gaulis

address: Postfach

department: Oncology Research

institute: Novartis Institutes for Biomedical Research

summary:
Gene expression upon DOT1L inhibition, or Menin inhibition, or a combination of DOT1L and Menin inhibiting agents, was assessed in several MLL-rearranged human cell lines and a mouse model of MLL-AF9 leukemia.
The goal of the study was to explore the mechanisms by which the EPZ0004777 and MI-2-2 chemicals collaborate to induce differentiation and cell death in MLL-AF4 and MLL-AF9 leukemias.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2 compounds and combinaison thereof, 1 concentration & 1 timepoint per treatment, DMSO control, 3 biological replicates

first: Vanessa

middle: J

last: Craig

first: Ralph

last: Tiedt


title: Loss of the Inhibitory Immune Checkpoint CD85j/LILRB1 on Malignant Plasma Cells Contributes to Immune Escape in Multiple Myeloma

city: Barcelona

first: Ester

last: Lozano

address: Rosselló, 153

department: Hemato-Oncology

institute: IDIBAPS

summary:
Mechanisms of immune regulation may control proliferation of aberrant plasma cells (PCs) in patients with the asymptomatic monoclonal gammopathy of undetermined significance (MGUS) preventing progression to active multiple myeloma (MM). We investigated the role of CD85j (LILRB1), an inhibitory immune checkpoint for B cell function, in MM pathogenesis.
We used microarrays to gain insight into the molecular mechanisms underlying CD85j functions in myeloma cells.

overall_design: MM cell lines (U266, RPMI-8226, ARP-1) were lentivirally transduced to express CD85j-GFP or GFP-control in the presence of 8 µg/mL polybrene. Lentiviral particles were generated using HEK293T cells and the Lenti-vpak packaging kit (packaging plasmids and MegaTran1.0 transfection reagent)  with Lenti ORF clone of human LILRB1, transcript variant 1, pLenti-C-mGFP vector purchased from OriGene Technologies, Inc. (Rockville, MD, USA). After 3 days, cells were FACS-sorted and total RNA was isolated using Trizol® reagent according to the manufacturer's guidelines. RNA samples had a RNA integrity number (RIN) above 8 determined using a Bioanalyzer 2100 instrument (Agilent Technologies).

first: Carlos

last: Fernandez de Larrea


title: NPM-ALK expression levels identify two distinct signatures in Anaplastic Large Cell Lymphoma of Childhood

status: Public on Nov 04 2016

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary: Anaplastic large-cell lymphoma (ALCL) makes up approximately 15% of paediatric non-Hodgkin's lymphomas of childhood. The vast majority of them is associated with the t(2;5)(p23;q35) translocation that results in the expression of a hybrid oncogenic tyrosine kinase, NPM-ALK. In order to investigate ALCL  biological characteristics we used  transcriptional profiling approach. Genome-wide gene expression profiling, performed on 23 paediatric ALCL and  12 reactive lymph nodes specimens, showed two novel ALCL subgroups based on their NPM-ALK expression levels (named  (ALK low and ALK high). Gene set enrichment analysis revealed, in ALK low samples, a positive enrichment of genes involved in the Interleukin signaling pathway, whereas we found  increased expression of genes related to cell cycle progression and division in  ALK high tumour samples, such as Aurora Kinase A (AURKA)  and B (AURKB). Growth inhibition was observed upon administration of AURKA and AURKB inhibitors Alisertib and Barasertib and it was associated with perturbation of the cell cycle and induction of apoptosis. In conclusion we identified two novel ALCL subgroups, which display unique biological characteristics suggesting sensitivity to distinct targeted therapies.

overall_design: Gene expression was measured on Affymetrix in 23 Anaplastic Large Cell Lymphoma patients and 12 reactive lymph nodes.

first: Silvia

last: Bresolin

first: Lara

last: Mussolin


title: Prolonged activation of innate antiviral gene signature after childbirth is determined by IFNL3 genotype

status: Public on Nov 08 2016

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Maternal innate and adaptive immune responses are modulated during pregnancy to concurrently defend against infection and tolerate the semi-allogeneic fetus. The restoration of these systems after childbirth is poorly understood. We reasoned that enhanced innate immune activation may extend beyond gestation while adaptive immunity recovers.  To test this hypothesis, the transcriptional profiles of total PBMCs following delivery in healthy women were compared to those of non-pregnant control subjects. Interestingly, interferon stimulated genes (ISGs) encoding proteins such as IFIT1, IFIT2, and IFIT3, as well as signaling proteins such as STAT1, STAT2, and MAVS, were enriched postpartum. Antiviral genes were primarily expressed in CD14+ cells and could be stratified according to genetic variation at the interferon-λ3 gene (IFNL3, also named IL28B) single nucleotide polymorphism (SNP) rs12979860. Antiviral gene expression was sustained beyond six months following delivery in mothers with a CT or TT genotype but resembled baseline non-pregnant control levels following delivery in mothers with a CC genotype. CT and TT IFNL3 genotypes have been associated with persistent elevated ISG expression in individuals chronically infected with hepatitis C virus. Together these data suggest that postpartum, the normalization of the physiological rheostat controlling interferon signaling is dependent on IFNL3 genotype.

overall_design: Two different analyses were performed:  1) Set1- Two non-pregnant controls (NPC 354 and 357) were compared against two patients post-partum  (ID7 and ID8); 2) Set 2- Two non-pregnant controls (NPC 354 and 357) were compared against two patients post-partum (ID10 and ID12)

first: Aryn

last: Price

first: Dana

last: Tedesco

first: Mona

last: Prasad

first: Kimberly

last: Workowski

first: Christopher

middle: M

last: Walker

first: Mehul

middle: S

last: Suthar

first: Jonathan

last: Honegger

first: Arash

last: Grakoui

first: Steve

last: Bosinger


title: Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation

status: Public on Nov 12 2016

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

summary:
Study question:  Do short-term and long-term exposures to low dose folic acid supplementation alter DNA methylation in sperm?
Summary answer:  No alterations in sperm DNA methylation patterns were found following the administration of low dose folic acid supplements of 400 μg/day for 90 days (short-term exposure) or when pre-fortification of food with folic acid and post-fortification sperm samples (long-term exposure) were compared.
What is known already:  Excess dietary folate may be detrimental to health and DNA methylation profiles due to folate’s role in one carbon metabolism and the formation of S-adenosyl methionine, the universal methyl donor.  DNA methylation patterns are established in developing male germ cells and have been suggested to be affected by high dose (5 mg/day) folic acid supplementation.
Participants/materials, setting, methods:  Blood and seminal plasma folate levels were measured in participants before and following the 90-day treatment with placebo or supplement.  Sperm DNA methylation was assessed using the whole genome and genome-wide techniques, MassArray epityper, restriction landmark genomic scanning, methyl-CpG immunoprecipitation and Illumina HumanMethylation450 Bead Array.
Main results and the role of chance:  Following treatment, supplemented individuals had significantly higher levels of blood and seminal plasma folates compared to placebo. Initial first generation genome-wide analyses of sperm DNA methylation showed little evidence of changes when comparing pre- and post-treatment samples.  With Illumina HumanMethylation450 BeadChip arrays, no significant changes were observed in individual probes following low-level supplementation; when compared with those of the post-fortification cohort, there were also few differences in methylation despite exposure to years of fortified foods.
Limitations, reasons for caution:  This study was limited to the number of participants available in each cohort, in particular those who were not exposed to early (pre-1998) fortification of food with folic acid.  While genome-wide DNA methylation was assessed with several techniques that targeted genic and CpG rich regions, intergenic regions were less well interrogated.
Wider implications of the findings:  Overall, our findings provide evidence that short term exposure to low dose folic acid supplements of 400 μg/day, over a period of 3 months, a duration of time that might occur during infertility treatments, has no major impact on the sperm DNA methylome.

overall_design: Study design, size, duration:  This is a control versus treatment study where genome-wide sperm DNA methylation patterns were examined prior to fortification of food (1996-1997) in men with no history of infertility at baseline and following 90-day exposure to placebo (n=9) or supplement containing 400 μg folic acid/day (n=10).  Additionally, pre-fortification sperm DNA methylation profiles (n=19) were compared with those of a group of post-fortification (post-2004) men (n=8) who had been exposed for several years to dietary folic acid fortification.

first: Donovan

last: Chan

first: Serge

last: McGraw

first: Kathleen

last: Klein

first: Lynn

last: Wallock

first: Carolin

last: Konermann

first: Christoph

last: Plass

first: Peter

first: Bernard

last: Robaire

first: Robert

last: Jacob

first: Celia

last: Greenwood


title: Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions (cerebellum DBCBB).

status: Public on Nov 10 2016

city: Exeter

last: Mill

address: RD&E NHS Foundation, Trust Campus, Barrack Rd

department: Medical School, RILD Building

institute: University of Exeter

summary: Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular etiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, many residing in the vicinity of genes previously implicated in schizophrenia including NCAM1, SYNPO, GBP4, PRDM9, GADD45B and DISC1. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with etiological variation in complex disease.

overall_design: 33 post-mortem brain (cerebellum) samples were obtained from the Douglas Bell-Canada Brain Bank (DBCBB; 16 schizophrenia and 17 controls), Montreal, Canada. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.

first: J

last: Viana

first: E

last: Hannon

last: Dempster

first: R

last: Pidsley

last: Macdonald

first: O

last: Knox

first: H

last: Spiers

first: C

last: Troakes

first: S

last: Al-Saraj

first: G

last: Turecki

first: L

last: Schalkwyk


title: Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions (hippocampus LNDBB).

first: Jonathan

overall_design: 27 post-mortem brain (hippocampus) samples were obtained from the  London Brain Bank for Neurodegenerative Disorders (LBBND; 14 schizophrenia and 13 controls), London, UK. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.


title: Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions (striatum DBCBB).

overall_design: 33 post-mortem brain (striatum, putamen) samples were obtained from the Douglas Bell-Canada Brain Bank (DBCBB; 16 schizophrenia and 17 controls), Montreal, Canada. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.


title: Differential gene expression in neuroblastoma cells after transfection with control siRNA, MYCN siRNA or TFAP4 siRNA.

status: Public on Nov 02 2016

city: Randwick

first: Chengyuan

last: Xue

state: NSW

address: PO Box 81

department: Molecular Diagnostics

institute: Children's Cancer Institute

summary: We analyed the gene expression profiles after knocking down MYCN or TFAP4. Results showed that transcription factor MYCN and TFAP4 commonly regulats a subset of genes that may contribute to neuroblastoma cells proliferation and migration.

overall_design: Neuroblastoma BE(2)-C cells were transfected with control siRNA, MYCN siRNA1, MYCN siRNA2, TFAP4 siRNA1 and TFAP4 siRNA2, respectively. Total RNA was extracted from cells 30 hours after each transfection and subjected to gene expression study by Affymetrix microarray.

first: Tao

last: Liu


title: Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions (striatum LNDBB).

overall_design: 49 post-mortem brain (striatum, putamen) samples were obtained from the  London Brain Bank for Neurodegenerative Disorders (LBBND; 21 schizophrenia and 28 controls), London, UK. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.


title: Determination of mRNA expression profile for Flp-In T-REx 293 cells inducibly expressing ΔE302/3 Torsin1a for 72 hours

city: Durham

first: Nicole

last: Calakos

state: NC

address: 311 Research Dr

department: Neurology

institute: Duke University

summary: Dystonia is a centrally driven movement disorder characterized by often painful twisting motions and postures. The majority of dystonia cases are idiopathic and sporadic, although a significant number of rare inherited forms have defined genetic causes. However, regardless of etiology, the biological mechanisms for nearly all forms of dystonia are still largely unknown and there are currently no disease-modifying treatments.  Here we show a common role for impaired functioning of the eIF2α stress-response pathway in rare inherited and common sporadic forms of dystonia.  We first identified a potential role for the eIF2α pathway in dystonia through a genome-wide RNAi screen aimed at correcting a DYT1 dystonia-related cellular phenotype. Mechanistically, we find that the corrective effect is mediated by activating the eIF2α pathway through an eIF2α-phosphorylation and ATF4 transcription factor-dependent mechanism. We further find evidence that this pathway is impaired in DYT1 patient-derived cell lines, suggesting a role in pathogenesis. Notably, pathogenicity of reduced eIF2α pathway signaling is supported by another known cause of dystonia, DYT16, which is due to loss-of-function mutations in the PRKRA gene that encodes an eIF2α kinase activator. Here, we demonstrate that sporadic cervical dystonia patients share a rare, conserved, loss-of-function ATF4 mutation. Finally, we show that pharmacologically enhancing eIF2α signaling improves DYT1-related phenotypes in both a cultured cell system and a mouse model.  Our results identify eIF2α signaling as a novel pathway in the pathogenesis of multiple forms of dystonia.  Our work also shows that the eIF2α pathway constitutes an attractive biological target for the development of dystonia therapeutics.

overall_design: 3 independent biological samples were plated and induced with tetracyline (5µg/mL) for 72hr prior to cell harvest and total RNA extraction.

first: Zachary

last: Caffall


title: Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions

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

overall_design: Refer to individual Series


title: Expression data from human osteosarcoma cells after transfected miR-199a-3p

status: Public on Nov 01 2016

city: Boston

first: Zhenfeng

last: Duan

state: Massachusetts

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

summary: The U-2OS and KHOS osteosarcoma cell lines were seeded into the 100mm cell culture plate, then transfected miRSelect pEP-miR-199a-3p or miRSelect pEP-miR-Null into the two cell lines with Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours. After that, total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Gene Chip U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 is first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 25-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-199a-3p treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 foldchange or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

overall_design: Evaluate the effect of miR-199a-3p regulated gene expression in osteosarcoma cells

first: Chao

last: Han


title: Investigating the influence of the homoebox transcription factor IRX1 on gene expression

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: We used microarrays to investigate differential gene expression in HEK293T cells after transfection of the transgene of  Iroquois 1 (IRX1). Microarray analysis revealed differential gene expression patterns of HEK293T cells after transient expression of IRX1. In total 8400 genes were deregulated by IRX1.

overall_design: IRX1 transfection

last: Marschalek

first: A

last: Kühn


title: Zeb2 regulates commitment to plasmacytoid dendritic cell and monocyte fate

city: St. Louis

first: Xiaodi

last: Wu

state: Missouri

address: 4940 Parkview Pl

institute: Washington University/HHMI


title: Major depression MDD suicide brain study

first: Therese

last: Murphy

address: RILD building

department: University of Exeter Medical School

summary:
Background: Major Depressive Disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for MDD suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesized that regulatory genomic processes are involved in the pathology of both MDD and suicidality.
Methods: Genome-wide patterns of DNA methylation were assessed in depressed MDD suicide completers (n=20) and compared to non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25)). Analyses focussed on identifying differentially methylated regions (DMRs) associated with suicidal depression, and epigenetic variation was explored in the context of polygenic risk scores for major depression and MDD suicide. Weighted gene co-methylation network analysis was used to identify modules of co-methylated loci associated with depressed MDD suicide completers and polygenic burden for MDD and MDD suicide attempt.
Results: We identified a DMR upstream of the PSORS1C3 gene, subsequently validated using bisulfite-pyrosequencing and replicated in a second set of MDD suicide samples, which is characterized by significant hypomethylation in both cortical brain regions in MDD MDD suicide cases. We also identified discrete modules of co-methylated loci associated with polygenic risk burden for MDD suicide attempt, but not major depression. MDD suicide-associated co-methylation modules were enriched among gene networks implicating biological processes relevant to depression and suicidality, including nervous system development and mitochondria function.
Conclusions: Our data suggest there are coordinated changes in DNA methylation associated with MDD suicide that may offer novel insights into the molecular pathology associated with depressed MDD suicide completers.

overall_design: Tissue (n=75) from two regions of the cortex (Brodmann area 11 (BA11, n=40) and Brodmann area 25 (BA25, n=35)) from 20 MDD MDD suicide cases and 20 non-psychiatric sudden death controls

first: Bethany

last: Crawford

first: Emma

middle: L

last: Dempster

first: Eilis

last: Hannon

first: Joe

last: Burrage

first: Gustavo

last: Kaminsky

last: Mill


title: Epigenomic deconvolution of breast tumors reveals metabolic coupling between constituent cell types

city: Houston

first: Ronak

middle: Y

last: Patel

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary:
Cancer progression is dependent on both cell-intrinsic processes and interactions between different cell types that constitute tumor tissue. To access this information, we develop Epigenomic Deconvolution (EDec), an in silico method that provides estimates of cell type composition of complex tissues, such as solid tumors, as well as CpG methylation and gene transcription within constituent cell types. By applying EDec to breast tumors from TCGA we detect changes in immune cell infiltration, and a striking change in stromal fibroblast to adipocyte ratio across breast cancer subtypes. We further show that a decrease in stromal adipocyte content and increase in fibroblast content is associated with a reduction of mitochondrial activity in stromal cells and a concomitant increase in oxidative metabolism in cancerous epithelial cells. These findings highlight the role of stromal cell type composition in the establishment of patterns of metabolic coupling such as the previously proposed reverse Warburg effect.
Raw data files were not provided for this Series. Submitters did not have permission to share the raw data.

overall_design: Epigenomic Deconvolution was applied to the set of 39 primary breast tumor methylation profiles to infer average methylation profiles of constituent cell types and proportions of constituent cell types in each sample. Estimated methylation profiles of constituent cell types were compared (Pearson correlation) against methylation profiles of 6 breast cancer cell lines, CD8+ T-cell, HMEC cell line, and cancer associated fibroblast cell line. Comparison results indicate that, starting from breast tumor methylation profiles, the deconvolution technique was able to infer methylation profiles of constituent cell types that resembled those of cell types expected to be the major constituents of breast tumor tissue samples.

first: Vitor

last: Onuchic

first: Ryan

last: Hartmaier

first: David

middle: N

last: Boone

first: Michael

last: Samuels

first: Wendy

last: White

first: Vesna

last: Garovic

first: Steffi

last: Oesterreich

first: Matt

last: Roth

first: Adrian

last: Lee

first: Aleksandar

last: Milosavljevic


title: Zeb2 regulates commitment to plasmacytoid dendritic cell and monocyte fate (part 2)

first: Xiaodi

last: Wu

summary: Recent studies have identified Zeb2 as a transcription factor important for the final maturation of natural killer cells and effector CD8+ T cells. We show that Zeb2 is required for the development of two myeloid cell types, the monocyte and the plasmacytoid dendritic cell, and clarify that this factor is not required for the development of classical dendritic cells.

overall_design: Ly-6C(hi) monocytes and neutrophils were isolated by FACS from the bone marrow (BM) of untreated or poly(I:C)–treated Zeb2-sufficient mice and from the BM of poly(I:C)–treated Mx1-Cre-driven Zeb2-deficient mice.

first: Kenneth

last: Murphy


title: Zeb2 regulates commitment to plasmacytoid dendritic cell and monocyte fate (part 1)

overall_design: CD24+ classical dendritic cells (cDCs) were isolated by FACS from the spleen of Zeb2-sufficient mice, and CD172a+ cDCs were isolated by FACS from the spleen of Zeb2-sufficient and CD11c-Cre-driven Zeb2-deficient mice.


title: DNA methylation data from brain samples of human subjects with Huntington's disease

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
Human DNA methylation Beadchip v1.2 was used to profile n=475 samples from various brain regions of subjects with Huntington's disease and control samples.
The main goal of the study was to relate Huntington's disease status to measures of epigenetic age acceleration based on DNA methylation data. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.

overall_design: We analyzed n=475 samples (215 Huntington's disease, 125 Alzheimer's disease, and 135 control samples). The samples represent various brain regions (frontal lobe, parietal lobe, occipital lobe, caudate nucleus, cingulate gyrus, cerebellum, hippocampus, etc) from 65 human subjects.


title: Beta-catenin hyperactivation in embryonic pancreas

city: Seville

last: Cano

state: Seville

address: Manuel siurot s/n

institute: Institute of Biomedicine of Sevilla

summary: We used microarrays to detail the global programme of gene expression underlying beta catenin activation in embryonic pancreas.

overall_design: Pancreas were obtained at E13.5 developmental stage from control and Pdx-Cre beta catenin-exon3 floxed (active) embryos

middle: A

first: Ana

middle: I

last: Rojas


title: Gene expression profiling of lung cancer cells following treatment with dasatinib

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
Mechanisms of resistance and sensitivity to the multi-targeted kinase inhibitor dasatinib are unknown. We previously found that lung cancer cells with kinase-inactivating BRAF mutations are sensitive to dasatinib and undergo senescence whereas cells with wild type BRAF are resistant.
To better understand mechanisms underlaying the differential sensitivity of lung cancer cells to dasatinib, we performed gene expression profiling of lung cancer cells with (sensitive) and without (resistant) kinase-inactivating BRAF mutations

overall_design: A549 and H661 dasatinib-resistant lung cancer cells and H1666 and Cal12 dasatinib-sensitive cells were treated with vehicle (control) or 150 nM dasatinib for 72 h (8 samples). Total RNA was isolated and whole transcriptomes were profiled using the Human Gene U133A plus 2.0 platform from Affymetrix.

first: Shaohua

last: Peng

first: Banibrata

last: Sen

first: Faye

last: Johnson


title: Analysis of gene expression in HIV transgenic mice (TG26) with lymphoma in comparison to asymptomatic TG26 mice, and background control (FVBN).Tg26 carries a pNL4-3 HIV-1 provirus lacking part of the gag-pol region, rendering the virus non-infectious.

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: About 15% of the TG26 mice develop lymphoma. HIV protein expression is observed, particularly the protein p17/Matrix. Total cellular RNA from spleen and lymph nodes from 3 groups of animals: FVB/N controls (n=3), Tg26 asymptomatic (n=6), and Tg26 with lymphoma (n=6). Results provide insights into the gene expression program in animals with lymphoma.

overall_design: Gene expression analysis was performed using Affymetrix GeneChip Mouse Gene 1.0 ST to identify genes and pathways associated wirh B Cell Lymphoma in HIV-1 Transgenic Mice. Raw data pre-processing was monitored using standard diagnostic plots (i.e., 2-D image plots, RNA degradation plots, MA-plots, and box plots). Affymetrix microarray data were normalized at probe-level by using the Frozen Robust Multiarray Analysis (fRMA) method. A generalized linear model approach, coupled with empirical Bayes standard errors shrinkage, and including coefficients for data heterogeneity as derived from surrogate variable analysis (SVA), was used for identifying differentially expressed genes between animal groups. Correction for multiple testing was performed using the Benjamini–Hochberg method.

first: Virginia

last: Carroll

first: Alfredo

last: Garzino-Demo

first: Robert

middle: C

last: Gallo

first: Joseph

last: Bryanta

first: Mark

middle: K

last: Lafferty