title: Exploring chronic drug effects on microengineered human liver cultures using global gene expression profiling

city: Chicago

first: Brenton

middle: Robert

last: Ware

state: IL

address: 851 S Morgan St

department: Biomedical Engineering

institute: University of Illinois at Chicago

summary: Global gene expression profiling is useful for elucidating a drug?s mechanism of action (MOA) on the liver; however, such profiling in rats is not very sensitive for predicting human druginduced liver injury, while de-differentiated monolayers of primary human hepatocytes (PHHs) do not permit chronic drug treatment. In contrast, micropatterned co-cultures (MPCCs) containing PHH colonies and 3T3-J2 fibroblasts maintain a stable liver phenotype for 4-6 weeks. Here, we used MPCCs to test the hypothesis that global gene expression patterns in stable PHHs can be used to distinguish clinical hepatotoxic drugs from their non-liver-toxic analogs and understand the MOA prior to the onset of overt hepatotoxicity. We found that MPCCs treated with the clinical hepatotoxic/non-liver-toxic pair, troglitazone/rosiglitazone, at each drug?s reported and non-toxic Cmax (maximum concentration in human plasma) level for 1, 7, and 14 days displayed a total of 12, 269, and 628 differentially expressed genes, respectively, relative to the vehicle-treated control. Troglitazone modulated >75% of transcripts across pathways such as fatty acid and drug metabolism, oxidative stress, inflammatory response, and complement/coagulation cascades. Escalating rosiglitazone?s dose to that of troglitazone?s Cmax increased modulated transcripts relative to the lower dose; however, over half the identified transcripts were still exclusively modulated by troglitazone. Lastly, other hepatotoxins (nefazodone, ibufenac, and tolcapone) also induced a greater number of differentially expressed genes in MPCCs than their non-liver-toxic analogs (buspirone, ibuprofen, and entacapone) following 7 days of treatment. In conclusion, MPCCs allow evaluation of time- and dose-dependent gene expression patterns in PHHs treated chronically with analog drugs.

overall_design:
[a] We used Affymetrix microarrays to profile the global gene expression of MPCCs treated with either rosiglitazone or troglitazone relative to DMSO-only controls for 24 hours, 7 days, or 14 days. Global gene expression changes were evaluated as drug-treated conditions against DMSO-only controls.
[b] We used Affymetrix microarrays to profile the global gene expression of MPCCs treated with a known hepatotoxin or its non-toxic structural analog relative to a DMSO-only control for 7 days.

middle: R

first: Michael

last: McVay

first: Wendy

middle: Y

last: Sunada

first: Salman

last: Khetani


title: Analysis of DNA methylation and gene expression in TET1 depleted colorectal cancer cells

status: Public on Jan 01 2017

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data comparing BEL7402 HCC cells grown in the presence or absence of 10ng/ml hepatocyte growth factor (HGF)

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

country: China

institute: The University of Hong Kong

summary:
To identify genes regulated by HGF
Affymetrix Human Genome 2.0 ST GeneChip microarray

first: Terence

middle: K


title: Expression profiles of human NK cell subsets

city: Frankfurt

first: Evelyn

last: Ullrich

address: Theodor-Stern-Kai 7

department: Childrens Hospital

country: Germany

institute: Goethe University

summary: It is known that natural killer (NK) cells are a heterogeneous population of functionally distinct NK cell subsets. Here we report on different genomic, phenotypic and functional properties of human NK cell subsets derived from peripheral blood, thymus and bone marrow. NK cell subpopulations were defined via expression of CD56 and CD16.

overall_design: Gene expression was measured in NK cell subsets freshly sorted from human tissues. Three different batches were analysed.


title: An epithelial paracrine pathway that induces an asthmatic phenotype through a neuropeptide-Y induced mechanism

status: Public on Jan 02 2017

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Asthma is one of the most common chronic diseases in the world and its incidence is rising. While most treatments for asthma involve reducing symptoms including blunting of the reactive inflammatory response, little is understood about the role of the airway epithelium in this disease.

overall_design: To explore the role of the airway epithelium in asthma, we performed lung resistance and airway compliance testing after exposure to methacholine (Mch) on adult control (Scgb1a1-Cre) and Scgb1a1-Cre:Foxp1flox/flox:Foxp4flox/flox (Foxp1/4DKO) mutants,  and did  larger proximal airway microarray analysis, respectively.

first: Shanru

last: Li

middle: P

first: Edward

middle: E

last: Morrisey


title: Drug Discovery For Diamond Blackfan Anemia Using Reprogrammed Hematopoietic Progenitors

city: Boston

first: Melissa

last: Kinney

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Diamond-Blackfan anemia (DBA) is a congenital disorder characterized by the failure of erythroid progenitor differentiation, severely curtailing red blood cell production. Because many DBA patients fail to respond to corticosteroid therapy, there is considerable need for therapeutics for this disorder. Identifying therapeutics for DBA requires circumventing the paucity of primary patient blood stem and progenitor cells. To this end, we adopted a reprogramming strategy to generate expandable hematopoietic progenitor cells from induced pluripotent stem cells (iPSCs) from DBA patients. Reprogrammed DBA progenitors recapitulate defects in erythroid differentiation which were rescued by gene complementation. Unbiased chemical screens identified SMER28, a small molecule inducer of autophagy, which enhanced erythropoiesis in a range of in vitro and in vivo models of DBA. SMER28 acted through autophagy factor ATG5 to stimulate erythropoiesis and upregulate expression of globin genes. These findings present an unbiased drug screen for hematological disease using iPSCs and identify autophagy as a therapeutic pathway in DBA.

overall_design: CB CD34+ progenitors were transduced with shLUC or shRPS19 were treated with DMSO or SMER28. CD34-5F cells transduced with shLUC or shATG5 and were treated with DMSO or SMER28.

first: Sergei

last: Doulatov

first: Linda

middle: T

last: Vo

first: Elizabeth

last: Macari

first: Lara

last: Wahlster

middle: A

first: Alison

middle: M

last: Taylor

first: Jessica

last: Barragan

first: Manav

last: Gupta

first: Katherine

last: McGrath

first: Hsiang-Ying

last: Humphries

first: Alex

last: DeVine

first: Anupama

last: Narla

first: Blanche

last: Alter

first: Alan

middle: H

last: Beggs

first: Suneet

last: Agarwal

first: Benjamin

middle: L

last: Ebert

first: Hanna

last: Gazda

first: Harvey

middle: F

last: Lodish

first: Colin

last: Sieff

first: Thorsten

last: Schlaeger

first: Leonard

middle: I

last: Zon

first: George

middle: Q

last: Daley


title: DNA methylome analysis of skin samples from punch tissue biopsy of 322 healthy female individuals and total body naevus count

status: Public on Jan 04 2017

city: London

first: Tim

last: Spector

address: Westminster Bridge road

department: Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

summary:
Genome wide genomic DNA profiling with the HumanMethylation450 BeadChip (450k) of skin samples. The skin tissue DNA was derived from a peri-umbilical punch biopsy (adipose tissue was removed from the biopsy before freezing) from 322 healthy female twins of the TwinsUK cohort.
Family structure is present in this data. If the samples are related they will share a similar Relatedness identification ID either monozygotic_twinpair_* or dizygotic_twinpair_*

overall_design: Bisulphite converted DNA from the 322 samples were hybridised to the Illumina HumanMethylation450 BeadChip

first: Leonie

last: Roos

first: Jordana

last: Bell


title: Clonal isolates of PC3 cells overexpressing RWDD4

city: Bethesda

first: Jean

last: Winter

state: MD

address: 50 South Driver

department: NHGRI

institute: NIH

summary:
We identified RWDD4 as prostate cancer metastases genes by analyzing QTL, transcript profiles and SNP associations with aggressive disease phenotypic traits in transgenic mice and human cohorts
RWDD4 was futher validated as a metastases gene in vitro and in vivo utilizing prostate cancer cell lines overexpressing the gene, and we used microarray to analyze the changes in transcripts

overall_design: Human prostate cancer cell line PC-3 was cloned with etither a control (empty) p-Lenti vector, or a p-Lenti vector containing the RWDD4 gene. Cells were selected using blastocydin followed by propagation of 4 clonal isolates for RNA extraction and hybridization onto Affymetrix array

first: Nigel

last: Crawford


title: Mitochondrial deficiency impairs hypoxic induction of HIF-1 transcriptional activity and retards tumor growth

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

institute: Institute of Medical Science, The University of Tokyo

summary: Mitochondria can be involved in regulating cellular stress response to hypoxia and tumor growth, but little is known about that mechanistic relationship. Here, we show that mitochondrial deficiency severely retards tumor xenograft growth with impairing hypoxic induction of HIF-1 transcriptional activity. Using mtDNA-deficient rho0 cells, we found that HIF-1 pathway activation was comparable in slow-growing rho0 xenografts and rapid-growing parental xenografts. Interestingly, we found that ex vivo rho0 cells derived from rho0 xenografts exhibited slightly increased HIF-1alpha expression and modest HIF-1 pathway activation regardless of oxygen concentration. Surprisingly, rho0 cells, as well as parental cells treated with oxidative phosphorylation inhibitors, were unable to boost HIF-1 transcriptional activity during hypoxia, although HIF-1alpha protein levels were ordinarily increased in these cells under hypoxic conditions. These findings indicate that mitochondrial deficiency causes loss of hypoxia-induced HIF-1 transcriptional activity and thereby might lead to a constitutive HIF-1 pathway activation as a cellular adaptation mechanism in tumor microenvironment.

overall_design:
Human colon cancer HT-29 cells and mtDNA-deficient HT-29 rho0 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We examined the gene expression change in xenografts in nude mice, cells under hypoxia, and cells treated with bortezomib (BZM).
HT29_rho0n cells: mtDNA-deficient HT-29 cells (normal HT-29 rho0 cells).
HT29_rho0x cells: Isolated from xenografts of HT29 rho0 cells in mice, and cultured in dishes (i.e., HT29_rho0x cells were established from HT29_rho0n cells).

first: Naomi

last: Haga

first: Aki

last: Furuno

first: Satomi

last: Tsukahara

first: Junko

last: Sakurai

first: Shigeo

last: Sato

first: Yuri

last: Tani

first: Akihiro

last: Tomida


title: MicroRNA-196b-5p is a prognostic factor in colorectal cancer patients and influences cancer cell migration and metastases formation through regulation of HOXB7 and GalNT5

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary:
Background: MicroRNA-196b-5p (miR-196b-5p) has been previously involved in carcinogenesis, though its role in colorectal cancer (CRC) patients and biology remains controversially. In our current study, we systematically explored the clinical significance and biological relevance of miR-196b-5p, as well as the underlying molecular mechanisms regulated by miR-196b-5p in colorectal cancer.
Methods: In this study, we measured miR-196b-5p expression by quantitative RT-PCR and explored its prognostic value in two independent patient cohorts of 292 CRC patients. In a panel of CRC cell lines, using transient and stable gain and loss of function experiments, we evaluated the impact on in vitro proliferation, chemo-sensitivity and migration/invasion as well as in vivo metastases-formation. The molecular mode of action was characterized by mRNA transcriptome profiling, target prediction tools, luciferase-interaction assays, and pheno-copy gene knock-down experiments for potential target genes.
Results: Our clinical data indicate that low levels of miR-196b-5p in CRC are significantly associated with metastatic disease and poor patient outcome in both independent cohorts (p<0.05). A loss of function of miR-196b-5p led to increased cancer cell migration/invasion and metastases formation, which can be partly explained by direct interaction with HOXB7 and GalNT5 mRNA, which both of them influence CRC cell migration.
Conclusion: In conclusion, our data suggest that low levels of miR-196b-5p are associated with poor prognosis in CRC. MiR-196b-5p has an effect on CRC progression through genes important for cancer cell migration and metastases.

overall_design: three biological replaicates of stably transduced HCT116 miR-196b overexpressing cells or empty vector transtuced cells as control cells

first: Verena

last: Stiegelbauer

first: Daniela

last: Schwarzenbacher

first: Martin

last: Pichler


title: Identification Of Neuroblastoma Metastasis Associated Genes

city: Toronto

first: David

last: Kaplan

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

summary: Metastatic relapse is the major cause of death in neuroblastoma (NB), yet there are no therapies to specifically target metastases. To understand the molecular mechanisms mediating NB metastasis, we developed a mouse model using intracardiac injection and in vivo selection to isolate metastatic subpopulations that exhibited a higher propensity for bone and central nervous system metastases. Gene expression profiling revealed two distinct subtypes, primary and metastatic, with differential regulation of 412 genes and multiple pathways including CADM1, SPHK1, and YAP/TAZ whose expression independently predicted survival. Loss- and gain-of-function experiments with these genes demonstrated a rescue of metastatic phenotypes in multiple NB cell lines in vitro or in vivo. Treatment with the compounds SKI II and Verteporfin that target SPHK1 and YAP/TAZ, respectively, inhibited NB metastasis in vivo. In addition, using gene expression profiling from the metastatic subpopulations, a gene signature (MET-75) was identified that predicts NB survival of patients with metastatic disease. This model therefore identifies genes regulating metastasis and candidate therapeutics for metastatic NB

overall_design: We analysed 16 samples, 4 representing primary NB models and 12 representing metastatic NB models.


title: Integrative computational biology and molecular determinants of rectal cancer resistance to chemoradiotherapies

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

summary:
Gene expression analysis identified a CRC related signature of differentially expressed genes discriminating patients Responder and Non Responder to radiochemotherapy
Gene expression signatures of CRC samples Responder and Non Responder to radiochemotherapy were analyzed using supervised analyses

overall_design: Patients with CRC have been studied using class comparison and class prediction analyses to identify markers characterizing Responders and Non Responders to radiochemotherapy

first: Marco

last: Agostini


title: Prospective identification of resistance mechanisms to HSP90 inhibition in KRAS mutant cancer cells [HG-U133_Plus_2]

status: Public on Dec 31 2016

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Inhibition of the HSP90 chaperone results in depletion of many signaling proteins that drive tumorigenesis, such as downstream effectors of KRAS, the most commonly mutated human oncogene. As a consequence, several small-molecule HSP90 inhibitors are being evaluated in clinical trials as anticancer agents. To prospectively identify mechanisms through which HSP90-dependent cancer cells evade pharmacologic HSP90 blockade, we generated multiple mutant KRAS-driven cancer cell lines with acquired resistance to the purine-scaffold HSP90 inhibitor PU-H71. All cell lines retained dependence on HSP90 function, as evidenced by sensitivity to short hairpin RNA-mediated suppression of HSP90AA1 or HSP90AB1 (also called HSP90α and HSP90β, respectively), and exhibited two types of genomic alterations that interfere with the effects of PU-H71 on cell viability and proliferation: (i) a Y142N missense mutation in the ATP-binding domain of HSP90α that co-occurred with amplification of the HSP90AA1 locus, (ii) genomic amplification and overexpression of the ABCB1 gene encoding the MDR1 drug efflux pump. In support of a functional role for these alterations, exogenous expression of HSP90α Y142N conferred PU-H71 resistance to HSP90-dependent cells, and pharmacologic MDR1 inhibition with tariquidar or lowering ABCB1 expression restored sensitivity to PU-H71 in ABCB1-amplified cells. Finally, comparison with structurally distinct HSP90 inhibitors currently in clinical development revealed that PU-H71 resistance could be overcome, in part, by ganetespib (also known as STA9090) but not tanespimycin (also known as 17-AAG). Together, these data identify potential mechanisms of acquired resistance to small molecules targeting HSP90 that may warrant proactive screening for additional HSP90 inhibitors or rational combination therapies.

overall_design: Gene expression was profiled in PU-H71-sensitive and resistant A549 und SW480 cell lines  [n=2 sensitive A549 clones, n=2 resistant A549 clones, n=2 sensitive SW480 clones, n=2 resistant SW480 clones].

first: Arefeh

last: Rouhi

first: Stefan

last: Fröhling

first: Claudia

last: Scholl


title: The role of Foxp1/2/4 in lung endoderm identity

first: Michael

last: Morley

summary: Our previous work has demonstrated an important role for the Foxp1/2/4 subfamily of transcriptional repressors in promoting lung epithelial differentiation. However, the overall role of this transcription factor subfamily in early lung endoderm identity is unknown.

overall_design: To explore the overall role of Foxp1/2/4r subfamily in early lung endoderm identity , we performed microarray analysis of Shh-Cre control and Foxp1/2/4Shh-CreDKO mutant lungs at E14.5, 3 embryos, respectively.

first: Shanru

last: Li

first: Edward

last: Morrisey


title: Prospective identification of resistance mechanisms to HSP90 inhibition in KRAS mutant cancer cells

type:
Expression profiling by array
SNP genotyping by SNP array


title: Genome wide methylation analysis of breast cancer epithelia, adjacent normal epithelia, breast cancer cell lines, and blood DNA from healthy individuals

city: Kyoto

first: Natsue

last: Uehiro

address: 54 Kawaharacho, Shogoin, Sakyo-ku

department: Department of Breast Surgery

institute: Kyoto University

summary: To define methylation markers of breast cancer for circulating tumor DNA, we compare the methylation characteristics of breast cancer and blood DNA of healthy individuals.

overall_design: Bisulphite converted DNA from the 119 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

first: Fumiaki

last: Sato

first: Masakazu

last: Toi


title: Specific myelomonocytic cells heavily infiltrate orthotopic lung tumors and display a hypoxia-driven micro-RNA expression signature that directs tumor-supporting functions and negatively impacts on clinical outcome

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: Targeting immunomodulatory pathways has ushered a new era in lung cancer therapy. Further progress requires deeper insights into the nature and dynamics of immune cells in the lung cancer micro-environment.  Dendritic cells (DCs) represent a heterogenous and highly plastic immune cell system with a central role in controlling immune responses. The intratumoral infiltration and activation status of DCs emerge as clinically relevant parameters in lung cancer.  In this study we used an orthotopic preclinical model of lung cancer to interrogate the transcriptome of lung tumor-infiltrating DCs and extract novel biologically and clinically relevant information.  Lung tumor-infiltrating leukocytes expressing generic DC markers were found to predominantly consist of CD11b+ cells which, compared to peritumoral lung DC counterparts, strongly over-express the T cell inhibitory molecule PD-L1 and acquire classic markers of tumor-supporting macrophages (TAM) on their surface. Transcriptome analysis of these CD11b+ tumor-infiltrating DCs (TIDCs) indicates impaired anti-tumoral immunogenicity, confirms the skewing towards TAM-related features, and indicates exposure to a hypoxic environment. In paralled, TIDCs display a specific micro-RNA signature dominated by the prototypical lung cancer oncomir miR-31. Hypoxia was found to drive intrinsic miR-31 expression in CD11b+DCs. Conditioned medium of mir-31-overexpressing CD11b+DCs induces pro-invasive lung cancer cell shape changes and is enriched with the pro-metastatic factors S100A8 and S100A9. Finally, analysis of TCGA datasets reveals that the TIDC-associated miRNA signature has a negative prognostic impact in non-small cell lung cancer.  Together, these data suggest a novel mechanism through which lung cancer co-opts the plasticity of the DC system to support tumoral progression.  Targeting immunomodulatory pathways has ushered a new era in lung cancer therapy. Further progress requires deeper insights into the nature and dynamics of immune cells in the lung cancer micro-environment.  Dendritic cells (DCs) represent a heterogenous and highly plastic immune cell system with a central role in controlling immune responses. The intratumoral infiltration and activation status of DCs emerge as clinically relevant parameters in lung cancer.  In this study we used an orthotopic preclinical model of lung cancer to interrogate the transcriptome of lung tumor-infiltrating DCs and extract novel biologically and clinically relevant information.  Lung tumor-infiltrating leukocytes expressing generic DC markers were found to predominantly consist of CD11b+ cells which, compared to peritumoral lung DC counterparts, strongly over-express the T cell inhibitory molecule PD-L1 and acquire classic markers of tumor-supporting macrophages (TAM) on their surface. Transcriptome analysis of these CD11b+ tumor-infiltrating DCs (TIDCs) indicates impaired anti-tumoral immunogenicity, confirms the skewing towards TAM-related features, and indicates exposure to a hypoxic environment. In paralled, TIDCs display a specific micro-RNA signature dominated by the prototypical lung cancer oncomir miR-31. Hypoxia was found to drive intrinsic miR-31 expression in CD11b+DCs. Conditioned medium of mir-31-overexpressing CD11b+DCs induces pro-invasive lung cancer cell shape changes and is enriched with the pro-metastatic factors S100A8 and S100A9. Finally, analysis of TCGA datasets reveals that the TIDC-associated miRNA signature has a negative prognostic impact in non-small cell lung cancer.  Together, these data suggest a novel mechanism through which lung cancer co-opts the plasticity of the DC system to support tumoral progression.

overall_design: Orthotopic model of lung cancer by inoculating Lewis lung carcinoma (LLC) cells into the airways of immunocompetent syngeneic C57BL/6 hosts were used to study the transcriptomic differences between tumoral and peritumoral tissue.

first: Karim

last: Vermaelen

first: Lotte

last: Pyfferoen


title: Analysis of DNA methylation in TET1 depleted colorectal cancer Colo320DM cells

first: Hiromu

last: Suzuki

summary: We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established three stable TET1 knockdown clones and negative control clones of Colo320DM cells, and carried out DNA methylation analysis with HumanMethylation450 BeadChip.

overall_design:
RNAi-induced TET1 knockdown was accomplished using a BLOCK-iT Pol II miR RNAi Expression Vector kit (Thermo Fisher Scientific). Two sets of oligonucleotides targeting TET1 were purchased from Invitrogen and ligated into a pcDNA6.2-GW/EmGFP-miR vector (Thermo Fisher Scientific). Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 1.0 mg/ml G418. GFP-positive colonies were isolated, and knockdown efficiencies were analyzed using RT-qPCR.
Please note that the idat files linked as Series supplementary file contains raw data for multiple samples, as indicated in the corresponding sample description field.


title: 1,25-dihydroxyvitamin D3 triggers an anti-inflammatory response in brain pericyte

city: La tronche

first: didier

last: wion

address: fortuné ferrini

country: France

institute: INSERM

summary: Background: Epidemiology and experimental studies suggest 1,25-dihydroxyvitamin D3 plays a neuroprotective role in neurodegenerative diseases including Alzheimer's disease. Most of the experimental data on the genes regulated by this hormone in brain cells have been obtained with neuron and glial cells. Emerging evidence demonstrates pericyte plays a critical role in brain function that encompasses its classical function in the control and maintenance of the blood brain barrier. However, the gene response of brain pericyte to 1,25D remains to be investigated. Methods: The transcriptomic response of human brain pericytes to 1,25-dihydroxyvitamin D3 was analyzed.  Results were confirmed by RT-qPCR for the genes of interest. Results: We demonstrate that human brain pericyte in culture responds to 1,25-dihydroxyvitamin D3 by regulating genes involved in the control of neuro-inflammation. We also showed that pericytes respond to the pro-inflammatory cytokines TNF-alpha and Interferon gamma by inducing the expression of the gene involved in the synthesis of 1,25-dihydroxyvitamin D3 named CYP27B1. Conclusion: Taken together these results suggest that neuro-inflammation could trigger the synthesis of 1,25-dihydroxyvitamin D3 by brain pericytes, which will in turn respond to the hormone by a global anti-inflammatory response.

overall_design: Four samples were analysed, two replicates for control samples and two replicates treated with 1,25D3.

first: Marie-France

last: Nissou

first: Audrey

last: Guttin

first: Cyril

last: Zenga

first: Francois

last: Berger

first: Jean-Paul

last: Issartel

first: Didier

last: Wion


title: Analysis of DNA methylation in TET1 depleted colorectal cancer HCT116 cells

summary: We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established two stable TET1 knockdown clones and negative control clones of HCT116 cells, and carried out DNA methylation analysis with HumanMethylation450 BeadChip.

overall_design: RNAi-induced TET1 knockdown was accomplished using a BLOCK-iT Pol II miR RNAi Expression Vector kit (Thermo Fisher Scientific). Two sets of oligonucleotides targeting TET1 were purchased from Invitrogen and ligated into a pcDNA6.2-GW/EmGFP-miR vector (Thermo Fisher Scientific). Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 0.6 mg/ml G418. GFP-positive colonies were isolated, and knockdown efficiencies were analyzed using RT-qPCR.


title: Insulin and glucose alter death-associated protein kinase 3 (DAPK3) DNA methylation in human skeletal muscle

city: Stockholm

first: Juleen

last: Zierath

address: Von Eulersväg 4a

department: Molecular medicine and surgery

country: Sweden

institute: Karolinsk Institutet

summary: DNA methylation marks are altered by environmental factors. We tested the hypothesis that DNA methylation is altered in skeletal muscle in response to either insulin or glucose exposure. We performed a genome-wide DNA methylation analysis in skeletal muscle from healthy men before and after insulin exposure. DNA methylation of selected genes was determined in skeletal muscle from healthy and type 2 diabetic men before and after a glucose tolerance test. Insulin reduced DNA methylation in the calcium pump ATP2A3 gene. Insulin increased DNA methylation in the gene body of death-associated protein kinase 3 (DAPK3), a gene involved in cell proliferation, apoptosis and autophagy. DAPK3 methylation was reduced in type 2 diabetic patients. Carbohydrate ingestion reduced DAPK3 DNA methylation in healthy and type 2 diabetic men, suggesting glucose may play a role. In support of this, DAPK3 DNA methylation was inversely correlated with the glucose concentration 2 hours after an oral glucose test. Insulin and glucose exposure acutely alter the DNA methylation profile of skeletal muscle, supporting recent evidence that DNA methylation constitutes a rapidly and adaptive epigenetic mark. Furthermore, insulin and glucose modulate skeletal muscle DAPK3 DNA methylation in a reciprocal manner suggesting a feedback control on the epigenome.

overall_design: Skeletal muscle biopsies from 3 different healthy volunteers incubated in either control buffer (biopsy 1) or buffer+120nM insulin (biopsy 2) for one hour.

first: Jonathan

last: Mudry


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [shTET2 - H2O2 - methylation]

city: Baltimore

first: Stephen

middle: B

last: Baylin

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University SOM

summary: Genome wide DNA methylation profilings (Bisulfite (BS), or oxidative bisulfite (oxBS)) were done for A2780 cells 1) infected with control virus, no H2O2 (Scr_mock) treatment, 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2), and 3) infected with shTET2 virus, with H2O2 treatment  (30 min plus 2.5 h resting) (shTET2_H2O2). Each genomic DNA was splitted equally to two aliquots. One aliquote was subjected to oxidation (oxBS) and one to mock oxidation (BS) prior to bisulfite treatment (CEGX protocol). The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs. 5hmC levels were calculated by subtracting oxBS values from BS values.

first: Yang

last: Zhang

first: Zhihong

last: Wang

first: Wenbing

last: Xie

first: Yi

last: Cai

first: Limin

last: Xia

first: Hariharan

last: Easwaran

first: Ray-Whay

last: Chiu


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [A2780 damage time points - methylation]

summary: Genome wide DNA methylation profiling of A2780 cells untreated (mock), treated with H2O2 for 30 min (H2O2 30 min), or treated with H2O2 for 30 min with additional 2.5 hour resting ( H2O2 3h) . The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs.

overall_design: A2780 cells were either untreated (mock), treated with H2O2 for 30 min and harvested immediately (H2O2 30 min), or treated with H2O2 for 30 min, replace with fresh medium and rested fro an additional 2.5 hour ( H2O2 3h). Mock cells were harvested at 30 min time point.


title: Restoring miR-150-5p to an estrogen receptor positive breast cancer cell line [ZR-75-1]

city: Aurora

first: Jennifer

last: Richer

state: CO

address: Mail Stop 8104, RC1N 5th Floor P18-5127, 12800 E. 19th Ave.

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary:
The objective of these experiments is to identify novel direct and indirect targets of miR-150-5p in breast cancer cell lines. The goal is that these will give direction as to what targets or pathways may be contributing to the reduced growth observed in these cell lines upon restoration of miR-150-5p. A therapy directed towards one or more critical subtype-specific targets could be developed as a therapeutic for breast cancer patients.
Using has-miR-150-5p mirVana miRNA mimic (Ambion, 4464066), miR-150-5p was restored to an estrogen receptor positive breast cancer cell line, ZR-75-1.

overall_design: Cells were transfected in triplicate for 48 hours with either mock, negative control, or mimic, and RNA isolated from each sample was hybridized onto Affymetrix GeneChip® Human Gene Array 2.0 ST ( probesets).

first: R

last: Heinz

first: N

middle: S

last: Spoelstra

first: H

last: Gu

first: J


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress

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

overall_design: Refer to individual Series


title: Expression data from 0Month (New Born) Slovak Children with high PCBs exposure

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

summary:
Exposure to Polychlorinated Biphenyls (PCBs) is known to cause serious health effects in human both in pre- and post-natal period. The knowledge of gene expression will help us to develop early disease or disorder biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of high PCB exposure from the cord blood of the PCB-exposed newborn in Slovakia to understand the molecular mechanism of PCB related toxic effect and its functional implications during fetal development.

overall_design:
High PCB Exposed 0 month Slovak Children
Extraction of total RNA was performed by using Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

first: Somiranjan

last: Ghosh

first: Partha

last: Mitra

first: Tomas

last: Trnovec

first: Lubica

last: Pulkovicova

first: Sovcikova

last: Eva


title: Impaired calcineurin signaling in dendritic cells and macrophages increases susceptibility to aspergillosis through pentraxin-3 downregulation

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Treatment of post-transplant patients with immunosuppressive drugs targeting the calcineurin-NFAT pathway, such as Cyclosporine A or Tacrolimus, are commonly associated with a higher incidence of opportunistic infections, such as Aspergillus fumigatus, which can lead to severe life-threating conditions. A component of the A. fumigatus cell wall, β-glucan, is recognized by dendritic cells via the Dectin-1 receptor, triggering downstream signaling that leads to calcineurin-NFAT binding, NFAT translocation, and transcription of NFAT-regulated genes. Here, we address the question of whether calcineurin signaling in CD11c-expressing cells, such as DCs, has a specific role in the innate control of A. fumigatus. Impairment of calcineurin in CD11c-expressing cells (CD11ccrecnb1loxP) significantly increased susceptibility to systemic A. fumigatus infection and to intranasal infection in irradiated mice undergoing bone marrow transplant. Global expression profiling of bone marrow-derived DCs identified calcineurin-regulated processes in the immune response to infection, including expression of pentraxin-3, an important anti-fungal defense protein. These results suggest that calcineurin inhibition directly impairs important immunoprotective functions of myeloid cells, as shown by the higher susceptibility of CD11ccrecnbloxP mice in models of systemic and invasive pulmonary aspergillosis, including after allogeneic bone marrow transplantation. These findings are relevant to the clinical management of transplant patients with severe Aspergillus infections.

overall_design: Conditional calcineurin knock-out bone marrow-derived dendritic cells and their littermates controls were stimulated with Aspergillus fumigatus morphotypes in order to identify genes regulated through calcineurin signaling.

first: Jan

last: Fric

first: Teresa

last: Zelante

first: Alicia

last: Wong

first: Andrea

last: Mencarelli

first: Geraldine

last: Koh

first: Francesca

last: Zolezzi

first: Michael

last: Poidinger

first: Paola

last: Ricciardi-Castagnoli


title: Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver [array]

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary:
In mammals, the circadian clock controls behavioral, physiological and cellular rhythms. Part of this daily variation is controlled by transcription-translation feedback loops in sync with the light-dark phase. On the other hand, daily rhythms in expression of a multitude of genes are related to nutrient-response cycles. Time-resolved mapping of DNase I hypersensitive sites (DHS) throughout the day can identify details of the regulatory interplay between metabolism and the internal clock at a molecular level.
Here, we report a genome-wide analysis of mammalian DHS using high‐throughput sequencing of DNase tags from mouse liver with a resolution of 4 h (12 h light/12 h dark). Among the 65’000 DHS sites identified, a significant proportion of distal DHS showed a diurnal cycle, suggesting a fine regulation of oscillating genes by enhancers, which we seek to understand better.
Using PolII and H3K27ac ChIP-seq, we characterize the DHS and study the dynamics of each mark in wild-type and Bmal1-KO mice. We use the sequence motif content of each DHS and a linear regression model to explain DHS temporal behaviour in terms of phase and amplitude. We monitor the temporal expression of target genes in order to understand the phase-specific regulation in the circadian context.
Interestingly, DHS associated with circadian genes tend to be time-correlated with expression, Pol II and H3K27ac marks. The Bmal1-KO phenotype in light-dark conditions show a proportion of DHS with circadian rhythms associated with transcription factors related to metabolism, due to food entrainment and systemic cues.

overall_design:
We examined 7 samples, each consisting of a pool of RNAs extracted from the whole liver of 5 mice in BMAL1-KO phenotype. Samples were collected at times ZT2, ZT6, ZT10, ZT14, ZT18, ZT22, and ZT26 (ZT0/24 and ZT12 are the times when the lights are switched on and off, respectively).

Contributor: CycliX Consortium

first: Irina

last: Krier

first: Teem

last: Andersin

first: Sunil

last: Raghav

first: Donatella

last: Canella

first: Federica

last: Gilardi

first: Alexandra

last: Kalantzi

first: Matteo

last: Dal Peraro

first: Nouria

last: Hernandez

first: Ueli

last: Schibler

first: Bart

last: Deplancke

first: Felix

last: Naef


title: IL-10 Receptor Signaling is essental for Tr1 cell function in vivo

status: Public on Dec 30 2016

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Interleukin-10 (IL-10) is essential to maintain intestinal homeostasis. CD4+ T regulatory type 1 (TR1) cells produce large amounts of this cytokine and being therefore currently examined in clinical trials as T-cell therapy in patients with inflammatory bowel disease (IBD). However, factors and molecular signals sustaining TR1 cell regulatory activity still need to be identified in order to optimize the efficiency and to ensure the safety of these trials. We investigated the role of IL-10 signaling in mature TR1 cells in vivo.   Double IL-10eGFP Foxp3mRFP reporter mice and transgenic mice with impairment in IL-10 receptor signaling were used to test the activity of TR1 cells in a murine IBD model, a model that resembles the trials performed in humans. The molecular signaling was elucidated in vitro. Finally, we used human TR1 cells, currently employed for cell therapy, to confirm our results.   We found that murine TR1 cells expressed functional IL-10 receptor α. TR1 cells with impaired IL-10 receptor signaling lost their regulatory activity in vivo. TR1 cells required IL-10 receptor signaling in order to activate p38 MAP kinase, thereby sustaining IL-10 production, which ultimately mediated their suppressive activity. Finally, we confirmed these data using human TR1 cells.  In conclusion TR1 cell regulatory activity is dependent on IL-10 receptor signaling. These data suggest that in order to optimize TR1 cell-based therapy, IL-10 receptor expression has to be taken into consideration.

overall_design: Expression analysis of IL10RA-WT TR1 and IL-10RA-Impaired TR1 cells isolated from small intestine of anti-CD3 treated mice.

first: Leonie

last: Brockmann

first: Nicola

last: Gagliani

first: Anastasios

middle: D

last: Giannou

first: Jan

last: Kempski

first: Penelope

last: Pelczar

first: Maria

last: Geffken

first: Bechara

last: Mfarrej

first: Francis

middle: J

last: Huber

first: Johannes

last: Herkel

first: Yisong

middle: Y

last: Wan

first: Enric

last: Esplugues

first: Manuela

last: Battaglia

first: Christian

last: Krebs

first: Richard

last: Flavell

first: Samuel


title: A Molecular Profile of Colorectal Cancer to Guide Therapy

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

institute: Duke University


title: Allergen-specific oral immunotherapy combined with kakkonto enhances the efficacy of the oral immunotherapy in a murine food allergy model

status: Public on Dec 29 2016

city: Toyama

first: Takeshi

last: Yamamoto

address: 2630 Sugitani

institute: University of Toyama

summary: Oral immunotherapy (OIT) has been considered a promising approach for food allergies (FAs). However, the current OIT strategy is limited in terms of the long-term efficacy and safety. We have previously demonstrated that kakkonto, a traditional Japanese herbal medicine, suppresses the occurrence of allergic symptoms in a murine model of ovalbumin (OVA)-induced FA, which is attributed to the induction of the Foxp3+ CD4+ regulatory T cells. In this study, we established an OIT model using the FA mice with already established allergic symptoms and determined whether kakkonto could improve the efficacy of OIT. The OIT method consisted of initially administrating a very small amount of OVA and slowly increasing the amount. Allergic symptoms decreased in the OIT-treated FA mice. OIT significantly downregulated Th2 immune response-related gene expression in the FA mouse colon, and decreased a level of mouse mast cell protease-1, a marker of mast cell degranulation in the FA mouse plasma. Furthermore, the concomitant use of kakkonto significantly enhanced the effectiveness of OIT on the allergic symptoms, the Th2 immune responses and the mast cell degranulation in the OIT-treated FA mice. In addition, OIT significantly increased the population of Foxp3+ CD4+ regulatory T cells in the FA mouse colon, and this population was further increased by OIT in combination with kakkonto. Furthermore, the combined therapy with kakkonto reduced the expression of RA-degrading enzyme CYP26B1 mRNA in the FA mouse colon. These findings indicated that the combination of OIT with kakkonto represents a promising approach for FA treatment.

overall_design: To elucidate the mechanism underlying therapeutic effects of oral immunotherapy (OIT) and combined therapy of OIT and kakkonto, we established an OIT model using the food allergy mice with already established allergic symptoms. Kakkonto was administrated 1 h before each oral heated OVA challenge for a combination therapy. Total RNA was extracted from the proximal colon.

first: Yuka

last: Nagata

first: Michie

last: Hayashi

first: Shusaku

first: Makoto

last: Kadowaki


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [A2780 TET2 KO - methylation]

first: Stephen

last: Baylin

summary: Genome wide DNA methylation profiling of A2780 control cells (Scr_1 and Scr_2), and A2780 TET2 KO clones (KO1.1, KO1.36, and KO2.32). The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs.

overall_design: A2780 cells were infected with either Control or LentiCRISPR virus against TET2 gene for 2 days, followed by puromycin selection. Single clones were selected and validated after ~8 weeks selection in puromycin. Genome wide DNA methylation of control and KO clones were profiled.

first: Yang

last: Zhang

first: Zhihong

last: Wang

first: Wenbing

last: Xie

first: Yi

last: Cai

first: Limin

last: Xia

first: Hariharan

last: Easwaran

first: Ray-Whay

last: Chiu


title: Persistent organic pollutants alter DNA methylation during human adipocyte differentiation

status: Public on Dec 27 2016

city: Wageningen

first: Myrthe

last: van den Dungen

address: Tuinlaan 5

country: Netherlands

institute: Wageningen University

summary: Genome-wide DNA methylation profiling was performed in human mesenchymal stem cells (hMSCs) differentiated into adipocytes (day 10) while being continuously exposed to either one of three different persistent organic pollutants (POPs), namely TCDD, PFOS, and TBT. The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to measure DNA methylation of unexposed differentiated adipocytes and compared to POP-exposed differentiated adipocytes. Our aims were to 1) measure genome-wide DNA methylation changes upon POP exposure during adipocyte differentiation in primary hMSCs and 2) investigate the relationship between DNA methylation and gene expression regulation after POP-exposure in a panel of 84 adipocyte-related genes.

overall_design: Bisulphite converted DNA from four independent experiments was hybridised to the Illumina Infinium 450K Human Methylation Beadchip. The comparison was made between unexposed adipocytes and POP-exposed adipocytes.

middle: W

last: Van den Dungen

first: Albertinka

last: Murk

first: Wilma

last: Steegenga

first: Dieuwertje

last: Kok


title: Acetylation enhances TET2 function in protecting against abnormal DNA methylation during oxidative stress [A2780 TET2KD damage 3h - methylation]

summary: Genome wide DNA methylation profiling of A2780 cells 1) infected with control virus, no H2O2 (Scr_mock), 2) infected with control virus with H2O2 treatment (30 min plus 2.5 h resting) (Scr_H2O2), 3) infected with shTET2 virus, no H2O2 (shTET2_mock), and 4) infected with shTET2 virus, with H2O2 treatment  (30 min plus 2.5 h resting) (shTET2_H2O2, two biological replicates). The Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) was used to obtain DNA methylation profiles across approximately 450,000 CpGs.


title: Gene expression analysis of DAC treated AML: high impact or tumor suppressor gene expression changes

city: Ulm

first: Stephan

middle: Rainer

last: Bohl

address: Alber Einstein Allee 23

department: Internal Medicine III

institute: University Hospital of Ulm

summary: DAC represents a therapeutic option for elderly AML patients. However, there is still a lack of data for valid biomarkers in respect to response. We executed a gene expression analysis prior to treatment to evaluate gene expression patterns associated with response that might be used to predict DAC therapy outcome. In our cohort an objective ORR of 27% was seen. In a class comparison analysis 333 genes were identified that correlated significantly with response. In this gene signature genes that were prior associated with adverse outcome to regular chemotherapy were enriched in the response group. Interistingly for the non response cohort TSG showed an increased expression, suggesting that epigenetic silencing due to promoter hypermethylation might play a lesser role in theses leukemia pathogenesis.

overall_design: Gene expression was profiled in 45 AML samples in DAC treated patients prior to therapy. Response n=20, non response n=18, unknown n=7)

middle: R

first: Lars

last: Bullinger


title: lung adenocarcinoma DNA methylation

city: Tokushima city

first: Koichiro

last: Kajiura

department: Department of Thoraci,Endocrine Surgery and Oncology

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

summary: The aim of this study is to identify the gene affected carcinogenesis by DNA methylation in early lung adenocarcinoma

overall_design: 24 samples were all exracted fresh frozen sample from early adenocarcinoma. Smokers(B.I.>800) group was 6 cases with paired tumor and non-tumor tissue. Non-smoker group was 6 cases as well.

first: Kiyoshi

last: Masuda


title: Expression data from undifferentiated and differentiated human ES cells

status: Public on Dec 23 2016

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
GCNF controls the level of Oct4 expression during ES cell differentiation and early mouse embryonic development. GCNF was overexpressed in H9 human ES cells using Tet-On Inducible system.
mRNA microarray analysis demonstrated that overexpression of GCNF globally regulates gene expression in undifferentiated and differentiated hES cells.  Within altered genes, GCNF down-regulated 36% of the genes, and up-regulated 64% of the genes in undifferentiated hES cells. In addition, GCNF also showed a regulatory gene pattern that is different from RA treatment during hES cell differentiation.

overall_design: Undifferentiation (d0) hES cells were treated with 1 ug/ml Doxycycline (Dox) or without Dox; Differentiation (d6) hES cells were treated with 1 uM RA or 1 ug/ml Dox for six days. We wanted to investigate GCNF regulation of gene expression both in undifferentiation ES cells (d0 vs do+dox) and differentiation ES cells (d6+RA vs d6+Dox).

first: Hongran

first: Austin

last: Cooney


title: Somatic Loss of Wild-Type Kras Enhances Cancer Fitness and Promotes MEK Dependence

status: Public on Dec 22 2016

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

summary: Investigating therapeutic “outliers” that show exceptional responses to anti-cancer treatment can reveal unexpected synthetic lethal interactions and uncover biomarkers of drug sensitivity. Preclinical trials investigating primary murine acute myeloid leukemias (AMLs) generated by retroviral insertional mutagenesis in KrasG12D “knock-in” mice showed that the MEK inhibitor PD0325901 (PD901) extended survival while the pan-phosphoinositide 3-kinase (PI3K) inhibitor GDC-0941 was ineffective. One outlier PD901-treated AML had a four-fold improvement in survival, and exhibited intrinsic drug resistance at relapse. This resistant leukemia arose from an evolutionary precursor of the dominant drug-sensitive AML, and KrasG12D was duplicated in both AML clones. Loss of wild-type (WT) Kras both enhanced the competitive fitness of the dominant clone and rendered it more sensitive to MEK inhibition. Similarly, colorectal cancer cell lines with loss of WT KRAS are more sensitive to MEK inhibitors, and CRISPR-Cas9-mediated replacement of WT KRAS with a mutant allele sensitized a heterozygous mutant HCT116 cells to drug treatment. In a large prospectively characterized cohort of tumors from patients with advanced and metastatic cancers, 642 of 1168 (55%) with KRAS mutations exhibited allelic imbalance. Together, these studies demonstrate that serial genetic changes at the Kras/KRAS locus are frequent in cancer, and can modulate competitive fitness and MEK dependency.

overall_design: Total bone marrow was harvested from secondary transplant recipient mice, subjected to red blood cell lysis, and total RNA was harvested using the RNeasy mini kit (Qiagen) and hybridized to a Gene 1.0 ST array (Affymetrix) according to the manufacturer's instructions. Sensitive and resistant specimens were run in triplicate. Raw data were processed with aroma.affymetrix (Bengtsson et al., 2008) and background corrected with RMA followed by quantile normalization and summarization using the RMA probe-level model (PLM) to obtain gene-level summaries. Statistically significant differential expression between sensitive and resistant cells was determined with a moderated empirical Bayes approach (Smyth, 2004) and multiple hypothesis correction was performed. Significant genes were those with a False Discovery Rate (FDR) of <1%.

first: Michael

last: Burgess

first: Eugene

last: Hwang

first: Rana

last: Mroue

first: Craig

middle: M

last: Bielski

first: Anica

last: Wandler

first: Ari

last: Firestone

first: Amy

last: Young

first: Jennifer

last: LaCap

first: Lisa

last: Crocker

first: Saurabh

last: Asthana

first: Elizabeth

last: Davis

first: Jin

last: Xu

first: Keiko

last: Akagi

first: Michelle

last: Le Beau

first: Qing

last: Li

first: David

last: Stokoe

first: Deepak

last: Sampath

first: Barry

last: Taylor

first: Marie

last: Evangelista

first: Kevin

last: Shannon


title: Expression data from orthotopic tumors and the MCF7 and HCC1937 breast cancer cell lines

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL


title: Expression data from a triple-negative BRCA1-mutated ortho-xenograft treated with sirolimus

summary: Inhibitors of the mechanistic target of rapamycin (mTOR) are currently used to treat advanced metastatic breast cancer. However, whether an aggressive phenotype is sustained through adaptation or resistance to mTOR inhibition remains unknown. Here, complementary studies in human tumors, cancer models and cell lines reveal transcriptional reprogramming that supports metastasis in response to mTOR inhibition. This cancer feature is driven by EVI1 and SOX9. EVI1 functionally cooperates with and positively regulates SOX9, and promotes the transcriptional upregulation of key mTOR pathway components (REHB and RAPTOR) and of lung metastasis mediators (FSCN1 and SPARC). The expression of EVI1 and SOX9 is associated with stem cell-like and metastasis signatures, and their depletion impairs the metastatic potential of breast cancer cells. These results establish the mechanistic link between resistance to mTOR inhibition and cancer metastatic potential, thus enhancing our understanding of mTOR targeting failure.

overall_design: A metastatic triple-negative BRCA1-mutated (germline) breast tumor orthotopically engrafted in nude mice was treated with sirolimus (5 mg/kg) or DMSO (control) for approximately 60 days. Subsequently, RNA was extracted, processed, and hybridized on Affymetrix microarrays.

first: Helena

last: Aguilar

first: Francesca

last: Mateo

first: Alberto

last: Villanueva

first: Miguel

middle: A


title: Genome-wide DNA methylation study in Chinese Systemic Lupus Erythematosus

status: Public on Dec 21 2016

city: Hong Kong

first: Brian

last: Chung

state: Hong Kong

address: 102 Pokfulam Road

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Epigenetic alternations in addition to genetic factors are important contributors to the pathogenesis of Systemic Lupus Erythematosus (SLE). Recent studies revealed that aberrant changes in DNA methylation occur in SLE patients, and potentially contributes to the pathogenesis. Using genome-wide DNA methylation microarray, the Illumina Infinium HumanMethylation450 BeadChip, we compared the DNA methylation level of white blood cells between Chinese female SLE patients with that of healthy controls.  There was no difference in global levels of DNA methylation between SLE patients and controls. However, we identified 36 CpG sites with differential loss of DNA methylation and 8 CpG sites with differential gain of DNA methylation, representing 26 genes and 7 genes respectively. Surprisingly, nearly half of the hypomethylated CpG sites were located in the CpG shores, which implicated the functional importance of loss of DNA methylation in the CpG shores in SLE.

overall_design: The DNA methylation data of 12 SLE was compared with 10 sex- and ethnic-matched healthy controls. All the patients are self-reported to be Chinese and all met the criteria of the American College of Rheumatology for SLE diagnosis. Genomic DNA was bisulfite converted and DNA methylation was measured by HumanMethylation450 BeadChip.

middle: H

first: Kit

last: Yeung

first: Sanaa

last: Choufani

first: Mo

last: Mok

first: Wai

middle: L

last: Wong

first: Christopher

middle: C

last: Mak

first: Wanling

last: Yang

first: Pamela

middle: P

last: Lee

first: Wilfred

first: Yi-an

last: Chen

first: Daria

last: Grafodatskaya

first: Raymond

first: Chak

last: Lau

first: Tak

last: Chan

first: Rosanna

last: Weksberg

first: Yu-Lung


title: DNA methylation analysis in multi-locus imprinting disturbances

first: Julia

last: Kolarova

address: Albert-Einstein-Allee 11

department: Institute of Human Genetics

institute: University Hospital Ulm

summary: The aim of our study was to characterize the genotypic and phenotypic extent of multi-locus imprinting disturbances. Therefore, we analyzed the DNA methylation pattern of 37 individuals with different DNA methylation disturbances. Of these 37 individuals 17 were previously diagnosed with a multi-locus methylation disturbance (MLID) and the remaing 20 were diagnosed with a typical single locus imprinting disorder (SLID). We compared the DNA methylation of these 37 individuals to the DNA methylation of 38 evaluable individuals born small for gestational age. Our analysis revealed  21/37 individuals with a multi-locus methylation disturbances, characterzied by an aberrant DNA methylation in more than one imprintend gene region. Validation analyses were performed by bisulfite-pyrosequencing in the two imprinted gene regions ZDBF2 and FAM50B. Our analyses revealed each one patient previously diagnosed with Temple- and Angelman syndrome to have MLID.  Furthermore, we showed that many of the aberrantly methylated imprinted gene regions in patients with MLID are not associated with the so far known typical imprinting disorders.

overall_design: Bisulfite converted DNA of peripheral blood from 37 individuals with DNA methylation disturbances and 39 individuals born small for gestationale age, serving as controls, were hybridized to the Illumina Infinium HumanMethylation450k Bead Chip array.

first: Susanne

last: Bens

first: Jasmin

last: Beygo

first: Karin

last: Buiting

first: Almuth

last: Caliebe

first: Thomas

last: Eggermann

first: Gabriele

last: Gillessen-Kaesbach

first: Dirk

last: Prawitt

last: Thiele-Schmitz

first: Matthias

last: Begemann

first: Thorsten

last: Enklaar

first: Jana

last: Gutwein

first: Andrea

last: Haake

first: Ulrike

last: Paul

last: Richter

first: Lukas

last: Soellner

first: Inga

last: Vater

first: David

last: Monk

first: Bernhard

last: Horsthemke

first: Ole

last: Ammerpohl

first: Reiner

last: Siebert


title: Expression data in JDCaP prostate cancer xenograft model before and after expression of AR splice variants

status: Public on Dec 25 2016

city: Fujisawa

first: Daisuke

last: Nakata

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

institute: Takeda Pharmaceutical Company

summary: Our previous study using nude rats revealed that the parental JDCaP xenografts predominantly expressed full-length androgen receptor (AR) whereas the relapsed JDCaP xenografts after castration acquired AR splice variants including AR-V7 and ARv567es. To understand molecular mechanisms underlying the acquisition of AR splice variants in the JDCaP model, we performed microarray analysis using RNA samples of the xenografts without castration (Parent), the relapsed xenografts overexpressing full-length AR and AR-V7 (ARhiV7hi), and the relapsed xenografts expressing ARv567es (ARv567es).

overall_design: The JDCaP xenografts without castration (Parent), the relapsed JDCaP xenografts after castration which overexpressed full-length AR and AR-V7 (ARhiV7hi), and which expressed ARv567es (ARv567es), were harvested for RNA extraction and hybridization on Affymetrix microarrays (n = 3 each). The Parent samples were used as a control.

first: Yusuke

last: Nakayama


title: Gene expression comparison between Ebf2 -/- and WT P2 Sciatic nerves

city: Genova

first: Anna

middle: Margherita

last: Corradi

address: Viale Benedetto XV 3

department: Dimes

institute: University of Genova

summary:
Ebf genes regulate differentiation of several cell type. Ebf2 is expressed in Schwann cells and Ebf2-/- mice show among other phenotypical abnormalities a delay in the onset of myelination associated to a decreased expression of genes regulating myelination. In addition at one month of age Ebf2-/- mice show decreased motor conduction velocity and morphological alteration in sciatic nerves. Ebf2 target genes are unknown. To identify Ebf2 target genes with a role in myelination, we compared the expression profiles of sciatic nerves isolated from P2 Wt and Ebf2-/- mice by microarray analysis.
We used microarray to find Ebf2 candidate target genes by comparing gene expression of Ebf2-/- sciatic nerve and wt nerves 2 days postnatally (P2) a time point in which Ebf2-/- pups present a delay in the onset of myelination.

overall_design: We set up several Ebf2+/- X Ebf2+/- breeding couples and monitored births every day. The day after birth (P1) we genotype the pups. At P2 we isolated and cut sciatic nerves and we pooled nerves according to genotype. The single pool include 12 nerves and we  constituted 3 pools of wt nerves and 2 pools of Ebf2-/- nerves.

first: Diego

last: Moruzzo

first: Ignazio

last: Piras

first: Fabrizio

last: Serra

first: Alessandro

last: Bulfone


title: Phenotypic spectrum and extent of DNA methylation defects associated with multi-locus imprinting disturbances

first: Julia

last: Kolarova

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

overall_design: Refer to individual Series


title: Gene profiling of HER2 breast cancer patients treated with adjuvant trastuzumab

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

institute: Institut Jules Bordet

summary: The human epidermal growth factor receptor 2 (HER2) gene encodes a tyrosine kinase receptor that controls important signal transduction pathways in breast cancer.  Amplification and overexpression of the HER2 gene occurs in approximately 20% of breast cancers and is associated with an aggressive clinical phenotype. Trastuzumab, a humanized monoclonal antibody that targets HER2 showed exceptional efficacy in the treatment of breast cancer. In the adjuvant treatment of breast cancer patients, five randomized trials showed significant benefit of trastuzumab, with a reduction in the rate of recurrence of approximately 50% and improvement in the rate of survival of approximately 30%. In the current study, positive early stage breast cancer samples treated with adjuvant trastuzumab provided by institute Jules Bordet (IJB) and KUL. Gene expression and clinical outcome data were available. to better understand the genetic regulations and effects of the trastuzumab, we profile the the genes expression of positive early stage breast cancer samples treated with adjuvant trastuzumab.

overall_design: The dataset (as part of the FP7 EU consortium) is composed of 94 HER2 positive early stage breast cancer samples treated with adjuvant trastuzumab provided by the Jules Bordet Institute (IJB) and the Katholieke Universiteit Leuven (KULeuven) for patients followed between 2002 and 2011. The average age of these patients is 52.9 and their median follow-up time is 4.96 years. After hybridization on the chips, the quality controls were performed following the recommandation posted on http://www.arrayanalysis.org/.

first: Debora

last: Fumagalli

first: Sherene

last: Loi

first: Samira

last: Majjaj

first: Patrick

last: Neven

first: Sibylle

last: Loibl

first: Carsten

last: Denkert

first: Christos

last: Sotiriou


title: Lung inflammatory milieu in mice with chronic CD4+ T cell mediated auto-immune inflammation of the lung

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

summary: Noncommunicable chronic respiratory diseases (CRDs) such as chronic obstructive pulmonary disease (COPD) and asthma affect hundreds of millions of people and are associated with increasing morbidity and mortality. CRDs are multifactorial disorders and despite different etiologies they commonly manifest in pulmonary structural (airway remodeling, emphysema) and/or functional changes. In this study we used mice intrinsically developing autoimmune-mediated lung inflammation associated with lung pathology and immune imprinting partly comparable to hallmarks of CRD. The so called SPC-HAxTCR-HA transgenic mice (BALB/c genetic background), express a neo-self antigen (influenza A virus hemagglutinin, HA) on lung alveolar epithelial type II cells in the presence of HA-specific CD4+ T cells leading to the establishment of chronic lung inflammation. In order to characterize the inflammatory lung milieu of SPC-HAxTCR-HA mice in comparison to SPC-HA control mice (lacking HA-specific CD4+ T cells), we performed whole lung tissue transcriptional analyses (n = 3 / group). 378 transcripts were found to be differentially expressed in SPC-HAxTCR-HA lungs. 326 of those were up-regulated and 52 were down-regulated compared to SPC-HA control mice.

overall_design: In total six microarrays were performed. Per mouse group (SPC-HAxTCR-HA, SPC-HA) three individual replicates were analyzed.

last: Boehme

first: Sabine

last: Stegemann-Koniszewski

first: Nicole

last: Peters

first: Andrea

last: Autengruber

first: Joseph

last: Wissing

first: Lothar

last: Jänsch

first: Dunja

last: Bruder


title: Insights into carcinogenic mechanisms of colorectal carcinoma lacking β-catenin/TCF regulated transcription.

city: Helsinki

first: Johanna

last: Lotsari-Salomaa

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

summary:
We sought to identify the carcinogenic mechanisms involved in RKO cell line with no evidence of activated β-catenin/TCF regulated transcription, by comparison its gene expression profile to that of group of colorectal cancer cell lines selected to be mismatch repair
deficient similar to RKO and having activate Wnt signaling.

overall_design: Comparison of expression profiles of cancer cell lines with respect to Wnt signaling status.

first: Wael

last: Abdel-Rahman

middle: E

first: Sippy

last: Kaur


title: Gene expression profiles of human immature dendritic cells  and macrophages after 6h of co-cultivation with Aspergillus fumigatus and platelet rich plasma

status: Public on Dec 20 2016

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

institute: University Hospital of Würzburg

summary: In a whole-transcriptome study, cellular responses of DCs and macrophages confronted with the fungi A. fumigatus, platelet rich plasma (PRP) or the combination of A.fumigatus and PRP were investigated. Therefore DCs and macrophages of three independent donors were harvested after 6 hours co-culture with A. fumigatus, platelet rich plasma (PRP) or the  combination of A.fumigatus and PRP and analyzed with Affymetrix whole genome expression arrays. In general, transcriptomic analysis revealed a cell type dependent clustering. Only little effects were obeserved by addition of PRP. Furthermore a clustering of A.fumigatus stimulated cells whether PRP was present or not, was observed. However, significant differences in the immune response of A.fumigauts stimuled DC and macrophages were determined.

overall_design: Human DCs and macrophages were generated from 3 independent, healthy blood donors. DCs/macrophages were either left untreated or co-cultivated  with Aspergillus fumigatus 46645 germ tubes (MOI 1), PRP (1:30) or the combination of  Aspergillus fumigatus 46645 germ tubes (MOI 1) + PRP (1:30) for 6h.

first: Marcus

last: Dittrich


title: Epigenetic Activation of WNT5A Drives Glioblastoma Stem Cell Differentiation and Invasive Growth [ChIP-Seq]

status: Public on Dec 17 2016

city: Pittsburgh

first: Baoli

last: Hu

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Chromatin landscape comparisons of matched NSCs and derivative GSCs reveal activation of WNT5A and an EC signature

Raw data are not available for these records.

overall_design: Examination of 4 different histone modifications in matched NSCs and derivative GSCs

first: Qianghu

last: Wang

first: Y

first: Sujun

last: Hua

first: Charles-Etienne

last: Sauvé

first: Derrick

last: Ong

first: Zheng

last: Lan

first: Qing

last: Chang

first: Yan

last: Ho

first: Marta

last: Monasterio

first: Xin

last: Lu

first: Yi

last: Zhong

first: Jianhua

last: Zhang

first: Pingna

last: Deng

first: Zhi

last: Tan

first: Guocan

first: Wen-ting

last: Liao

first: Lynda

last: Corley

first: Haiyan

last: Yan

first: Junxia

first: Yongping

last: You

first: Ning

last: Liu

first: Linbo

last: Cai

first: Gaetano

last: Finocchiaro

first: Joanna

last: Phillips

first: Mitchel

middle: S

last: Berger

first: Denise

last: Spring

first: Jian

first: Erik

last: Sulman

first: Gregory

middle: N

last: Fuller

last: Chin

first: Roeland

middle: G

last: Verhaak

first: Ronald

last: DePinho


title: Transcriptional response of colon or small-intestinal tissues to bacterial colonization ex-vivo

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We analyzed the transcriptional profile of colon and small-intestinal (SI) tissues in response to ex-vivo colonization with members of the gut microbiota. Tissues were dissected from SPF or GF mice, and connected to the ex-vivo gut organ culture system. Then, microbial cultures or fecal samples were infused into the lumen, and tissues were processed in different time points, as indicated below.

overall_design: A small 3-5 mm segment of the proximal colon or SI terminal ileum of mice was placed directly into TRIzol.

first: Nissan

last: Yissachar

first: Yan

last: Zhou

first: Lloyd

last: Ung

first: Nicole

last: Lai

first: James

middle: F

last: Mohan

first: Allen

last: Ehrlicher

first: David

last: Weitz

first: Dennis

last: Kasper

first: Isaac

last: Chiu

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: CD133+CD24lo defines a 5-Fluorouracil-resistant colon cancer stem cell-like phenotype

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: Metastatic human colon carcinoma cell lines LS411N and SW620 were cultured in the presence of increased concentration of 5-FU. The selected stable cell lines (LS411N-5FU-R and SW620-5FU-R) are CD133+ that are resistant to 5-FU. However, FACS-sorted CD133+ cells from LS411N and SW620 are not resistant to 5-FU, suggesting that only a subset of CD133+ cells are 5-FU-resistant colon cancer stem cells. A global gene expression profiling was performed to identify differentiated expressed genes between LS411N-CD133+ cells and LS411N-5FU-R, and between SW620-CD133+ and SW620-5FU-R cells. These differentially expressed genes are potentially responsible for the colon cancer stem cell phenotypes and chemoresistance.

overall_design: gene expression comparisions between LS411N-CD133+ and LS411N-5FU-R cells, and between SW620-CD133+ and SW620-5FU-R cells.

first: Amy

middle: V

last: Paschall


title: Whole-genome profiling of the liver transcriptome in Trpm6 gene deficient mice and control littermates.

status: Public on Dec 14 2016

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

institute: Ludwig-Maximilians-Universität München

summary:
To attain deeper insight into metabolic alterations in Trpm6 gene deficient mice we used microarrays for profiling of hepatic transcripts of Trpm6 ko and control mice.
We identified a set of gene networks up- or down-regulated in the liver of Trpm6 gene deficient mice.

overall_design: Liver tissues were collected from 12-13 weeks old Trpm6 deficient (n=3) and control (n=4) male littermates.

first: Vindi

last: Jurinovic

first: Thomas

last: Gudermann


title: A Molecular Profile of Colorectal Cancer to Guide Therapy [PDCCEs]

city: Durham

last: Hsu

address: 905 S. LaSalle St. Rm 3008

institute: Duke University

summary:
The ability to dissect heterogeneity in colorectal cancer (CRC) is a critical step in developing predictive biomarkers. The goal of this study was to develop a gene expression based molecular subgrouping model, which predicts the likelihood that patients will respond to specific therapies.

Using microarray data compiled from 848 CRC patients, we developed a subgrouping model based on 23 activated oncogenic pathway expression signatures. Stability of the model was validated in two independent data sets.  To test the capacity of our model to predict patient response to specific targeted therapies and to determine the sensitivity of the subgroups to chemotherapy in vivo, we treated patient-derived colorectal cancer explants (PDCCEs) predicted to have high mTOR pathway activity with everolimus or oxaliplatin.
Results: A molecular profile of the discovery dataset revealed 8 molecular subgroups of colorectal cancer (MSCC).  Both validation sets also exhibited 8 MSCC and demonstrated significant similarities to the discovery dataset. MSCC predicted to have active mTOR pathway signaling were more sensitive to everolimus compared to MSCC predicted to have low mTOR pathway activity (p=0.016).  Furthermore, MSCCs displayed differential sensitivities to oxaliplatin (p<0.05).

 The ability to predict oncogenic signaling pathway activation is a powerful tool that may be used to sub-classify CRCs into clinically relevant MSCCs. Patterns of pathway activation may be used to target specific therapies in CRC patients and identification of sensitivities of MSCC to specific drugs can be a powerful approach to guide therapy for CRC patients.

overall_design: 133 (non-replicate) primary and metastatic colorectal cancer tissue samples were used in this analysis.

first: Joshua

last: Uronis

first: Jeffrey

middle: B

last: Van Deusen

first: Ellie

last: Proussaloglou

first: Michael

last: Gatza

last: Datto

first: Joseph

last: Lucas

first: William

middle: T

last: Barry

last: Morse

first: Christopher

last: Mantyh

first: H

middle: K

last: Lyerly

first: Bryan

last: Clary


title: The Role of a Non-Canonical Splice Variant of the Helios Gene in the Differentiation of Jurkat T Lymphoblasts

status: Public on Dec 15 2016

city: Tianjin

first: Feifei

last: Liu

address: 94 Weijin Road

department: School of Medicine

institute: Nankai University

summary:
In this study, the ectopic overexpressions of the wild-type Helios-1, non-canonical short isoforms Helios-Δ190-1186, Helios-Δ326-1431, and control in the Jurkat cells were utilized as the routine in vitro model of the T-cell acute lymphoblastic leukemia (T-ALL).
We compared the microarray data for transcriptional analysis of the Jurkat cells with stable overexpression of full-length Helios-1, non-canonical short isoforms Helios-Δ190-1186, Helios-Δ326-1431, and mock transfected control.

overall_design: Gene expression profiling was performed on Jurkat cells stably expressing Helios-1, as well as short variants Helios-Δ190-1186 and Helios-Δ326-1431.

first: Liu

last: Feifei

first: Li

last: Yinghui


title: Epigenetic Activation of WNT5A Drives Glioblastoma Stem Cell Differentiation and Invasive Growth

first: Baoli

last: Hu

summary:
Chromatin and transcriptome comparisons of matched NSCs and derivative GSCs reveal activation of WNT5A and an EC signature
WNT5A-mediated GdEC differentiation and EC recruitment support the invasive growth of glioma cells in the brain parenchyma.

overall_design: Identify the GSC lineage differentiation based on gene expression in oncogenic transformation of human neuronal progenitor cells.

first: Qianghu

last: Wang

first: Y

first: Sujun

last: Hua

first: Charles-Etienne

last: Sauvé

first: Derrick

last: Ong

first: Zheng

middle: D

last: Lan

first: Qing

last: Chang

first: Yan

middle: W

last: Ho

first: Marta

last: Monasterio

first: Xin

last: Lu

first: Yi

last: Zhong

first: Jianhua

last: Zhang

first: Pingna

last: Deng

first: Zhi

last: Tan

first: Guocan

first: Wen-ting

last: Liao

first: Lynda

middle: J

last: Corley

first: Haiyan

last: Yan

first: Junxia

first: Yongping

last: You

first: Ning

first: Linbo

last: Cai

first: Gaetano

last: Finocchiaro

first: Joanna

last: Phillips

first: Mitchel

last: Berger

first: Denise

last: Spring

first: Jian

first: Erik

last: Sulman

first: Gregory

last: Fuller

last: Chin

first: Roeland

last: Verhaak

first: Ronald

last: DePinho


title: Host cell gene expression profile in Human respiratory syncytial virus (HRSV) infected Hep2 cells at 4, 8, 12 and 15 hours post infection

city: Singapore

first: Richard

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

institute: Nanyang Technological University

summary: We used the microarray data to analyze host cells response on Hep2 cells infected with HRSV.

overall_design: The HRSV infected Hep2 cells were harvested at 4, 8, 12 and 15 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to HRSV infection.

last: Sutejo

first: Hui

last: Chen

first: Boon

middle: H


title: Integrated genomic analyses of de novo pathways underlying atypical meningiomas [methylation]

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

summary: Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells (hESCs), thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways. In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation. Importantly, these primary atypical meningiomas do not harbor activating TERT promoter mutations, which have been reported in atypical tumors that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas, differentiating their profile from benign and progressed tumors and establishing novel therapeutic targets.

overall_design: Analysis of meningioma methylation data for each mutation subtype. Includes methylation data from 57 unique meningiomas and 3 controls.

last: Harmanci

first: Mark

last: Youngblood

first: Murat

last: Gunel


title: Langerhans dendritic cell differentiation and TGFbeta

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary: To identify genes with a potential role in Langerhans dendritic cell differentiation, progenitor cells from human cord blood were analyzed by Affymetrix GeneChip U133Plus 2.0 microarray profiling

overall_design: Human CD34+CD45Rahi hematopoietic progenitor cells were cultured for 2 days in GM-CSF, FLT3L, SCF and TNFa before TGFbeta was added or not. RNA was analyzed at 0h, 6h and 24h relative to addition of TGFbeta. Total RNA from 6 independent donors was isolated and combined into two separate pools (A and B), each containing RNA from 3 different donors.

first: Jennifer

last: Jurkin

first: Herbert

last: Strobl


title: VLX600 characterization

status: Public on Dec 07 2016

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

institute: Uppsala university

summary: Microarray based mRNA profiling was used to identify the mechanism of action for the small molecule VLX600.

overall_design: MCF7 cells were treated with the drug candidate VLX600 for 6h prior to RNA isolation

first: Marten

last: Fryknas


title: SOX9 Drives WNT Pathway Activation in Prostate Cancer [gene expression]

status: Public on Dec 28 2016

first: Fen

last: Ma

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC

summary:
SOX9 is critical for prostate development and is implicated in prostate cancer, we used transcriptome profiling in combination with SOX9 ChIP-seq to identify genes and pathways it regulates in normal or neoplastic epithelium.
We used microarrays to detail the global programme of gene expression in TMPRSS2/ERG fusion positive prostate cancer cell line with high basal expression of SOX9 by comparing the expression changes between SOX9 knockdown versus control.

overall_design: TMPRSS2/ERG fusion positive VCaP cell line with high basal SOX9 expression were transiently transfected with either control or two independent SOX9 SiRNAs for 72 hours. RNA were then extracted and subsequently hybridized to Affymetrix GeneCHIP Human Genome U133 plus 2.0 Arrays. Transcriptome profiling were done in biological duplicates by comparing SOX9 knockdown against control and differential gene expression was assessed.

first: Xin

last: Yuan

first: Steven

last: Balk


title: Preserving biological heterogeneity with personalized genomics batch correction

status: Public on Dec 12 2016

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary:
Motivation: Sample source, procurement process, and other technical variations introduce batch effects into genomics data. Algorithms to remove these artifacts enhance differences between known biological covariates, but also carry potential concern of removing intra-group biological heterogeneity and thus any personalized genomic signatures. As a result, accurate identification of novel subtypes from batch corrected genomics data is challenging using standard algorithms designed to remove batch effects for class comparison analyses. Nor can batch effects be corrected reliably in future applications of genomics-based clinical tests, in which the biological groups are by definition unknown a priori.
Results: Therefore, we introduce new algorithm, personalized-SVA (pSVA), blind to biological covariates corrected technical artifacts while retaining biological heterogeneity in genomic data. This algorithm facilitated accurate subtype identification in head and neck cancer from gene expression data in both formalin fixed and frozen samples. When applied to predict HPV status, pSVA improved cross- study validation even if the sample batches were highly confounded with HPV status in the training set.
Availability: All analyses were performed using R version 2.15.0. The code and data used to generate the results of this manuscript is available from https://sourceforge.net/projects/psva.

overall_design: 44 Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors that were either flash frozen (29) or preserved with FFPE (15), with 4 from both. Gene expression data from 38 of these samples was also measured using different amplification kits, and are available in GSE3292 and GSE10300. Data is log2 expression, obtained from fRMA normalization.

first: Christine

last: Chung


title: Clonal variation in drug and radiation response among glioma-initiating cells is linked to  proneural-mesenchymal transition (Methylation BeadChip)

status: Public on Dec 13 2016

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

institute: Uppsala University

summary: Intra-tumor heterogeneity is a hallmark of glioblastoma multiforme, and thought to negatively affect treatment efficacy. Here we establish libraries of glioma-initiating cell (GIC) clones from patient samples and find extensive molecular and phenotypic variability between clones, including a wide range of responses to radiation and drugs. This widespread variability was observed as a continuum of multitherapy resistance phenotypes linked to a proneural-to-mesenchymal shift in the transcriptome.

overall_design: Affymetrix Illumina 450k array analyses were performed according to the manufacturer's directions on DNA extracted from 16 clonal malignant glioma cultures and 1 bulk cultures representing the parental material used to derive clones.

first: Bengt

last: Westermark


title: Clonal variation in drug and radiation response among glioma-initiating cells is linked to  proneural-mesenchymal transition

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Characterization of Arginase Expression in Glioma-Associated Microglia and Macrophages

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Microglia (MG) and macrophages (MPs) represent a significant component of the inflammatory response to gliomas. When activated, MG/MP release a variety of pro-inflammatory cytokines, however, they also secrete anti-inflammatory factors that limit their cytotoxic function. The balance between pro and anti-inflammatory functions dictates their antitumor activity. To evaluate potential variations in MG and MP function in gliomas, we isolated these cells (and other Gr1+ cells) from intracranial GL261 murine gliomas by FACS and evaluated their gene expression profiles by microarray analysis. As expected, arginase 1 (Arg1, M2 marker) was highly expressed by tumor-associated Gr1+, MG and MP.  However, in contrast to MP and Gr1+ cells that expressed Arg1 shortly after tumor trafficking, Arg1 expression in MG was delayed and occurred in larger tumors. Interestingly, depletion of MPs in tumors did not prevent MG polarization, suggesting direct influence of tumor-specific factors on MG Arg1 upregulation. Finally, Arg1 expression was confirmed in human GBM samples, but most Arg1+ cells were neutrophils and not MPs. These findings confirm variations in tumor MG and MP polarization states and its dependency on tumor microenvironmental factors.

overall_design: The Affymetrix GeneChip Mouse Gene 1.0-ST array (Affymetrix, Santa Clara, CA) was used to define gene expression profiles from the samples.  Synthesis and labelling of cDNA targets, hybridization and scanning of GeneChips were carried out by the Microarray Core Facility at the City of Hope.  Due to the limited starting material, we used a modified two-cycle amplification protocol. Briefly, cRNA was generated using 10ng total RNA according to the manufacturer's protocol by using Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay in the first cycle of amplification. The cRNA was subjected to RiboMinus kit (Invitrogen, Carlsbad, CA) to remove rRNA. The resulted cRNA was used as the template for another round of amplification using the sense target labeling assay kit. Hybridization cocktails containing 5.5 g of fragmented, end-labeled cDNA were prepared and applied to GeneChip Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script. Arrays were scanned at 5-m resolution using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

first: I

last: Zhang

first: D

last: Alizadeh

first: J

last: Liang

first: L

first: H

last: Gao

first: Y

last: Song

last: Ren

first: M

last: Ouyang

first: X

last: D’Apuzzo

first: B

last: Badie


title: Cellular reactions to long-term volatile organic compound (VOC) exposures.

status: Public on Dec 05 2016

city: Innsbruck

first: Johanna

middle: M

last: Gostner

address: Innrain 80

department: Medical University Innsbruck

institute: Medical Biochemistry

summary:
A549 cells were grown at air liquid interphase (ALI) and exposed to airborne formaldehyde for three days. An exposure platform was developed for this purpose, which provided the volatile analyte in a humidified atmosphere. The platform was composed of a reference and an exposure chamber.
Treatments/ Sample code: (A) 0 ppm  (not = no treatment) in the exposure chamber and control cells in the reference chamber (co); (B) 0.1 ppm (01 FA)  in the exposure chamber and control cells in the reference chamber (co); and (C) 0.5 ppm (05FA) in the exposure chamber and control cells in the reference chamber (co)

overall_design: Each experiment was performed for three times. Chronological order of experiments was randomized. Formaldehyde concentrations could be changed in the atmosphere of the exposure chamber, no formaldehyde was present in the reference chamber (=control).

last: Zeisler

last: Alam

first: P

last: Gruber

last: Fuchs

first: K

last: Becker

last: Neubert

last: Kleinhappl

first: S

last: Martini

first: F

last: Überall


title: Targeted DNA methylation analysis of the imprinted loci FAM50B and ZDBF2 in a cohort of small for gestational age born children

status: Public on Dec 31 2016

city: Ulm

first: Julia

last: Kolarova

address: Albert-Einstein-Allee 11

department: Institute of Human Genetics

institute: University Hospital Ulm

summary: In this cohort of 52 individuals born small for gestational age we analyzed the DNA methylation of the two imprinted genes ZDBF2 and FAM50B using CpGs from these loci represented on the Illumina Infinium HumanMethylation450k Bead Chip.This cohort partly overlaps with an already published cohort analyzed for the potential influence of growth hormone therapy on the DNA methylation (GSE57205). Our analysis revealed one individual with a hypermethylation in ZDBF2.

overall_design: Bisulfite converted DNA of peripheral blood from 52 individuals  born small for gestational age were hybridized to the Illumina Infinium HumanMethylation450k Bead Chip array.

first: Susanne

last: Bens


title: A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome

status: Public on Dec 03 2016

first: Kasper

middle: Daniel

last: Hansen

state: Maryland

address: 615 N Wolfe St. E3527

department: Biostatistics

institute: Johns Hopkins

summary:
Kabuki syndrome is a Mendelian intellectual disability syndrome caused by mutations in either of two genes (KMT2D and KDM6A) involved in chromatin accessibility. We previously showed that an agent that promotes chromatin opening, the histone deacetylase inhibitor (HDACi) AR-42, ameliorates the deficiency of adult neurogenesis in the granule cell layer of the dentate gyrus, and rescues hippocampal memory defects in a mouse model of Kabuki syndrome (Kmt2d+/βGeo). Unlike a drug, a dietary intervention could be quickly transitioned to the clinic. Therefore, we have explored whether treatment with a ketogenic diet could lead to a similar rescue through increased amounts of beta-hydroxybutyrate, an endogenous HDACi. Here, we report that a ketogenic diet in Kmt2d+/βGeo mice modulates H3ac and H3K4me3 in the granular cell layer, with concomitant rescue of both the neurogenesis defect and hippocampal memory abnormalities seen in Kmt2d+/βGeo mice; similar effects on neurogenesis were observed upon exogenous administration of beta-hydroxybutyrate. These data suggests that dietary modulation of epigenetic modifications through elevation of beta-hydroxybutyrate may provide a feasible strategy to treat the intellectual disability seen in Kabuki syndrome and related disorders.
We used microarrays to query global gene expression changes in the hippocampus of wild type and Kmt2d+/βGeo (Kabuki syndrome model) mice on a regular diet to identify specific gene expression abnormalities in the hippocampus of the Kabuki syndrome mouse model.

overall_design: Two different microarray experiments were run using cDNA synthesized using RNA extracted from whole mouse hippocampi. In both, hippocampi were dissected from 1-2 month old wild type and Kmt2d+/βGeo mice (mouse model of Kabuki syndrome) on a standard diet. In the first experiment 4 wild type and 3 Kmt2d+/βGeo were profiled, and in the second experiment 3 wild type and 3 Kmt2d+/βGeo were profiled.

first: Genay

middle: O

last: Pilarowski

first: Hans

last: Bjornsson


title: Chromosome loop control of oncogenic MYC produces a common vulnerability in diverse cancers [4C-seq]

status: Public on Dec 24 2016

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The majority of human cancers become highly dependent on a deregulated MYC oncogene, thus identifying a common mechanism underlying MYC regulation could provide valuable targets for therapy. We show here that diverse tumor-specific super-enhancers acquired throughout the 3Mb MYC insulated neighborhood functionally interact with a single conserved site occupied by CTCF protein in the MYC promoter. CRISPR-mediated deletion analysis shows that this common CTCF site is required for super-enhancer looping to the MYC promoter, high MYC expression and rapid cell proliferation in multiple cancers. Targeted methylation of the MYC enhancer anchor by a dCAS9-DNMT3A-3L fusion protein abrogates CTCF binding with consequent loss of MYC expression, suggesting a common vulnerability and a novel approach for therapeutic targeting of aggressive cancers.

overall_design: 4C-seq in K562 and HCT-116 cells with or without deleted CTCF site

first: Jurian

last: Schuijers


title: DNA methylation analysis of lung adenocarcinoma and adjacent non-tumor tissues

status: Public on Dec 01 2016

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

summary: Genome wide DNA methylation profiling of lung adenocarcinoma and non-tumor adjacent tissues. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles. Samples included eight lung cancer and adjacent non-tumor tissues excised from a cohort of 8 patients with lung adenocarcinoma.

overall_design: DNA was extracted from frozen tissue samples using the Qiagen® Genomic DNA Mini Kit, as described by the manufacturer. DNA quantification was performed using a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo). The bisulfite conversion of DNA was conducted using the Zymo bisulfite gold kit. The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol. Processed methylation chips were scanned using an iScan reader (Illumina). All samples were processed at the same time to avoid chip-to-chip variation. Infinium Methylation data were processed using the Methylation Module of the GenomeStudio software package (v. 2011.1).

first: Fei

last: He

first: Zheng

last: Guo


title: Effects of NOTCH3 signalling on gene expression in breast cancer cells

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: MBA-MB-468 cells were grown and treated with combinations of NOTCH3 inhibiting antibody, NOTCH3 activating antibody, pan-NOTCH pathway inhibitors or activators.

overall_design: Two sets of experiments were performed, in which breast cancer cells in culture were treated with agonists or antagonists of elements of the NOTCH signaling pathway. Changes in gene expression were assessed using microarrays.

first: Lisa

last: Choy

first: Christian

last: Siebel