title: Control of Peripheral Tolerance by Regulatory T Cell-Intrinsic Notch Signaling

status: Public on Jul 25 2015

city: Boston

first: Talal

last: Chatila

address: 1 Blackfan Circle Karp Family Building, RB10-214

department: Division of Immunology

institute: Harvard Medical School Division of Immunology The Boston Children's Hospital

summary: Notch receptors direct the differentiation of T helper (Th) cell subsets, but their influence on regulatory T (TR) cell responses is obscure. Interruption of Notch signaling in TR cells resulted in a super-regulatory phenotype, with suppression of TR cell Th1 programming and apoptosis as well as Th1 cell responses in systemic inflammation. In contrast, gain of function Notch1 signaling in TR cells resulted in lymphoproliferation, dysregulated Th1 responses and autoimmunity. To determine mechanisms by which Notch signaling may alter TR cell function, we compared the transcriptional profiles of splenic TR cells of Foxp3EGFPCre mice with those of Foxp3EGFPCreR26N1c/N1c (gain of function Notch signaling), Foxp3EGFPCreRBPJ∆/∆ (loss of function canonical Notch signaling), and Foxp3EGFPCreR26N1c/N1cRBPJ∆/∆ mice (gain of function/canonical loss of function Notch signaling).

overall_design: Regulatory T cells are isolated from the spleen of 6 weeks old males, based on the expression of CD3, TCRbeta, CD4 and GFP (Foxp3), after Red blood cell lysis by ACK and gate on lineage negative (CD8, B220, CD11b, CD11c, Gr1) cells. To reduce variability and increase cell number, cells from multiple mice were pooled for sorting and at least three replicates were generated for all groups. RNA from 4.0-5.0x104 cells was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays

first: Louis-Marie

last: Charbonnier


title: The Senescent Methylome and its relationship with cancer, ageing, and germline genetic variation in humans (methylation experiment 2)

status: Public on Jul 26 2015

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

type: Methylation profiling by genome tiling array

summary: Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. However, till now, biological markers that define senescence on a genome-wide scale have been limited. Here, we report a DNA methylomic analysis of actively dividing and deeply senescent normal human epithelial cells, identifying 3,852 senescence-associated differentially methylated positions (senDMPs). We find that this human senDMP signature is positively and significantly correlated with both cancer and ageing-associated methylomic dynamics. We also identify germline genetic variants, including those associated with the p16INK4A locus, that are associated with the presence of in vivo senDMP signatures. Importantly, we also demonstrate that the senDMP signature can be effectively reversed in a newly-developed protocol of transient cellular rejuvenation. The senDMP signature has significant potential for understanding some of the key (epi)genetic etiological factors that lead to cancer and age-related diseases in humans.

overall_design: Bisulphite converted DNA from the HMECs at early passage (EP), deep senescence (DS), deep senescence + p16 siRNA (DS+p16siRNA) at two different time points and FACS for cell cycle at EP were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: DNA methylation data from normal and chronic periodontitis patients from site OCI and USC

status: Public on Jul 29 2015

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

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

overall_design: Refer to individual Series


title: The Senescent Methylome and its relationship with cancer, ageing, and germline genetic variation in humans

status: Public on Jul 24 2015


title: p21 Regulates LC Radiation Resistance

city: New York

first: Jeremy

last: Price

state: NY

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

type:
Expression profiling by array
Third-party reanalysis

summary:
Treatment with ionizing irradiation (IR) may lead to accumulation of tumor-infiltrating T regulatory (Treg) cells and subsequent tumor resistance to radiotherapy. Here we focused on the contribution of Langerhans cells (LCs) to this phenomenon because of their unique ability to resist depletion by high-dose IR. We found that LCs resisted apoptosis and rapidly repaired DNA damage post-IR. Particularly, we found that p21 was overexpressed in LCs, and that p21-deficient LCs underwent apoptosis and accumulated DNA damage following IR treatment. Wild-type, but not p21-deficient, LCs upregulated major histocompatibility complex class II molecules, migrated to the draining lymph nodes and increased Treg cell numbers upon exposure to IR. These findings suggest a means for manipulating LC IR-resistance to increase cutaneous tumor response to radiotherapy.
See above

overall_design: Cells were purified by flow cytometry and pooled until >10,000 cells/sample. At least 2 replicates of each sample were submitted.

middle: G

first: Juliana

last: Idoyaga


title: Gene expression data from HCC4006 and HCC4006ER cells

status: Public on Jul 31 2015

city: Tampa

first: Takeshi

last: Yoshida

state: FL

address: 12902 Magnolia Dr

department: Experimental Therapeutics

institute: H.Lee Moffitt Cancer Center

summary:
We generated erlotinib-resistant HCC4006 cells (HCC4006ER) by chronic exposure of EGFR-mutant HCC4006 cells to increasing concentrations of erlotinib. HCC4006ER cells acquired an EMT phenotype and activation of the TGF-β/SMAD pathway, while lacking both T790M secondary EGFR mutation and MET gene amplification.
We employed gene expression microarrays in HCC4006 and HCC4006ER cells to better understand the mechanism of acquired EGFR-TKI resistance with EMT. At the mRNA level, ZEB1 (TCF8), a known regulator of EMT, was >20-fold higher in HCC4006ER cells than in HCC4006 cells. Furthermore, numerous ZEB1 responsive genes, such as CDH1 (E-cadherin), ST14, and vimentin, were coordinately regulated along with increased ZEB1 in HCC4006ER cells.

overall_design: For each cell line, total RNA from triplicate samples was prepared and mixed equally. RNA samples (10 μg for each cell line; 500 ng/µL) were analyzed by Affymetrix Gene Profiling Array chip HG-U133 (Affymetrix, Santa Clara, CA) in the Moffitt Microarray Core. Data were normalized using MAS5, and differences in fold-change were calculated between HCC4006ER and HCC4006 cells (HCC4006ER/HCC4006).  A positive fold-change indicated a higher ratio in HCC4006ER cells, whereas a negative fold-change indicated higher expression in HCC4006 cells. Changes in gene expression ±1.5-fold were considered significant. Gene sets were analyzed by MetaCore (http://portal.genego.com; MetaCore, CA). Network data were integrated and visualized by Cytoscape (http://cytoscape.org/).

first: Lanxi

last: Song

first: Eric

last: Haura


title: Defective NK cells in AML patients at diagnosis are associated with blast transcriptional signatures of immune evasion

city: Paris

first: Nicolas

last: Dulphy

address: 1, avenue Claude Vellefaux

department: Institut de Recherche Saint-Louis

country: France

institute: UNIV PARIS

summary: Acute myeloid leukemia (AML) is a heterogeneous group of malignancies which may be sensitive to the natural killer (NK) cell anti-tumor response. However, NK cells are frequently defective in AML. Here, we found in an exploratory cohort (n = 46) that NK-cell status at diagnosis of AML separated patients in two groups with a different clinical outcome. Patients with a deficient NK-cell profile, including reduced expression of some activating NK receptors (e.g. DNAM-1, NKp46 and NKG2D) and decreased IFN-g production, had a significantly higher risk of relapse (P = 0.03) independently of cytogenetic classification in multivariate analysis. Patients with defective NK cells showed a profound gene expression decrease in AML blasts for cytokine and chemokine signaling (e.g. IL15, IFNGR1, IFNGR2, CXCR4), antigen processing (e.g. HLA-DRA, HLA-DRB1, CD74) and adhesion molecule pathways (e.g. PVR, ICAM1). A set of 388 leukemic classifier genes defined in the exploratory cohort was independently validated in a multicentric cohort of 194 AML patients. In total, these data evidenced the interplay between NK-cells and AML blasts at diagnosis allowing an immune-based stratification of AML patients independently of clinical classifications.

overall_design: 5 normal AML cells were compared with 8 NK deficient AML cells.

first: Meyling

last: Cheok


title: Expression data from coronary heart disease in Chinese Han people

status: Public on Jul 23 2015

city: Changchun

first: Bo

middle: Fan

last: Meng

address: Xiantai Street 126 of Changchun of Jilin Province

country: China

institute: the Department of Cardiology, China–Japan Union Hospital, Jilin University,

summary:
The genetics, social, cultural and environmental factors pose a great challenge for the diagnosis and treatment of coronary heart disease among different racial groups. We aimed to identify the differentially expressed genes involved in coronary heart disease in Chinese Han people as an aid for screening and diagnosing coronary heart disease.
We used microarrays to detail the global programme of gene expression to identify the differentially gene between the patients with coronary heart disease and healthy people in Chinese Han people

overall_design: Three patients with coronary heart disease and three healthy people in Chinese Han people were recruited,total RNA of each samples were extracted from peripheral blood to hybridize with Affymetrix microarrays.

first: Fanbo

first: Lin

last: Fan


title: Affymetrix GeneChip Mouse Gene 1.0 arrays of RNA extracted from gastrocnemius muscle of 4 global Ppp3cb KO mice and 4 corresponding WT littermates, and  4 skeletal muscle-specific Ppp3r1Mlc1fCre KO and 4 corresponding WT littermates.

status: Public on Jul 22 2015

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Global deficiency of catalytic subunit Ppp3cb, and tissue-specific ablation of regulatory subunit Ppp3r1 from skeletal muscle but not adipose tissue or liver led to protection from high-fat diet induced obesity and comorbid sequelæ.
Ser637 hyperphosphorylation of dynamin-related protein 1 (Drp1) in skeletal muscle of calcineurin-deficient mice was associated with mitochondrial elongation into power-cable shaped filaments, increased mitochondrial respiration, but attenuated exercise performance.

overall_design: Mice used for microarray analyses were all male, and chronically exposed to HFD for at least 8 weeks.

first: Matthias

middle: H

last: Tschöp

first: Paul

middle: T

last: Pfluger


title: Effect of TET1 overexpression on DNA methylation levels of HEK293 cells

status: Public on Jul 16 2015

city: Essen

first: Bernhard

last: Horsthemke

address: Hufelandstrasse 55

department: Universitaetsklinikum Essen

country: Germany

institute: Institut fuer Humangenetik

summary: We compared TET1 overexpressing cells to uninduced cells with endogenous TET1 transcript levels to determine DNA methylation changes.

overall_design: TET1 overexpression

first: C

last: Grosser

first: B


title: DNA methylation data from 12 normal and 10 chronic periodontitis patients from site OCI

first: Daniel

summary: Microarray methylation (Infinium¨HumanMethylation 450 BeadChip from Illumina) was performed on 12 normal and 10 chronic periodontitis (CP) patients

overall_design: Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Aline

last: Planello

first: Rajat

last: Singhania


title: Evaluation of the whole genome amplification of bisulfite modified DNA

city: Wako-shi

first: Junko

last: Ueda

state: Saitama-ken

address: Hirosawa 2-1

department: BSI

country: Japan

institute: RIKEN

summary: We compared genom-wide DNA methylation profiles between whole genome amplified bisufite-modified DNA and non-amplified DNA.

overall_design: 3 samples were bisulfite-converted, non-amplified DNA (technical triplicate). 6 samples were amplified with EpiTect® Whole Bisulfitome from 10ng or 50ng of bisulfite-converted DNA. All samples were hybridized to the Illumina Infinium HumanMethylation450.

first: Miki

last: Bundo

first: Fumiko

last: Sunaga

first: Tadafumi

last: Kato

first: Kiyoto

last: Kasai

first: Kazuya

last: Iwamoto


title: Expression data from germ-free and conventional mice fed lard or fish oil for 11 weeks

status: Public on Jul 14 2015

city: Gothenbrug

first: Robert

last: Caesar

address: Gothenburg University

department: Wallenberg Laboratory

country: Sweden

institute: Gothenburg University

summary: Dietary lipids and gut microbiota may both influence adipose tissue physiology. By feeding conventional and germ-free mice high fat diets with different lipid compositon we aimed to investigate how dietary lipids and the gut microbiota interact to influence inflammation and metabolism in epididymal adipiose tissue (EWAT)

overall_design: Wild-type C57Bl/6 male mice 11 weeks of age were fed isocaloric diets (45% kcal fat) with either menhaden fish oil (Research Diets, D05122102) or lard (Research Diets, D10011202) for 11 weeks. Epididymal WAT samples were harvested at the end of the experiment and analyzed by microarray.

first: Fredrik

last: Bäckhed


title: Effect of TET1 and TET3 overexpression on the transcriptome of HEK293 cells

summary: We compared TET1 and TET3 overexpressing cells to uninduced cells with endogenous levels of the respective transcript to determine global gene expression changes.

overall_design: TET1 overexpression, TET3 overexpression

first: L

last: Klein-Hitpass


title: Effect of the simultaneous knockdown of TET1, TET2 and TET3 on the transcriptome of HEK293 cells

summary: We compared TET triple knockdown cells to control cells treated with non-targeting siRNAs to determine global gene expression changes.

overall_design: TET triple knockdown


title: Expression data from XP-A and XP-V cells after UVC exposure

city: Kobe

first: Seiji

last: Takeuchi

address: Kusunoki-cho 7-5-1, Chuou-ku

institute: Kobe University

summary:
XPA is required for Nucleotide Excision Repair system, which could function to repair DNA damage induced by the UV. UV damage on the genomic DNA cannot be removed, thus persistence of damage could affect the transcriptional machinary.
We used the microarray to investigate the global expression profiles in the XP-A and XP-V cells in the low dose of UVC comparing with fibroblast from healthy person.

overall_design: Human primary fibroblasts were developed from the skin of healthy person and two XP patients (XP-A and XP-V). We evaluated global expression profiles comparing the UVC-exposed (0.5J/m2, 5J/m2) with non-exposed sample.

first: Toshiro

last: Matsuda

first: Ryusuke

last: Ono

first: Chikako

last: Nishigori


title: Effect of the simultaneous knockdown of TET1, TET2 and TET3 on DNA methylation levels of HEK293 cells

first: Bernhard

last: Horsthemke

summary: We compared TET triple knockdown cells to control cells treated with non-targeting siRNAs to determine DNA methylation changes.

first: C

first: B


title: Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

status: Public on Jul 15 2015

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute


title: Analysis of differentially expressed genes in A549 after treatment with Sulforaphene

city: Beijing

first: Zhou

last: Mo

address: North Third Ring Road No. 15

institute: Beijing University of Chemical Technology

summary: This study aimed to identify differential expressed genes before and after treatment with Sulforaphene, using the A549 lung cancer cell line as a model.

overall_design: There were a total of 4 samples examined. Two replicates have been included (2 control samples and 2 test samples).

first: Ming

last: Yang

first: Qipeng

last: Yuan

first: Mo

last: Zhou


title: Gene expression profiling on isogenic lines expressing wild-type and mutant forms of SMARCA2 and SMARCA4

status: Public on Jul 21 2015

city: Houston

first: Parantu

last: Shah

state: TX

address: 1515 Holcombe Blvd

institute: The UT MD Anderson Cancer Center

summary:
SMARCA2 and SMARCA4 are two mutually exclusive ATPase subunits of SWI/SNF complex. SMARCA4 deficient lung cancer population selectively depend on SMARCA2 for cancer growth phenotype. Rescue experiments with ectopic expression of wild-type, bromodomain mutant and ATPase dead SMARCA2 and SMARCA4 highlight that ATPase domain is the drug target.
In this study, we performed genome-wide microarray and differential gene expression profiling on isogenic lung cancer lines expressing cDNA rescue constructs for wild-type, bromodomain mutant and ATPase dead SMARCA2 and SMARCA4

overall_design: RNA was extracted from A549 and H1299 cells expressing wild-type, bromodomain mutant or ATPase dead SMARCA2 and SMARCA4 cDNA

middle: K

first: Bhavatarini

last: Vangamudi

first: Jannik

middle: N

last: Andersen


title: Expression data from mouse CD4+ T cells

city: Los Angeles

first: Ruili

state: CA

address: 2250 Alcazar St HSC CSA103

institute: University of Southern California

summary:
Hydrogen sulfide (H2S) is an endogenous gasotransmitter and is capable of regulating various endogenous signaling pathways, inculding inflamation and immune response. In mammals, H2S is mainly generated by two pyridoxal-5'-phosphate-dependent enzymes, termed cystathionine β-synthase (CBS) and cystathionine γ-lyase (CSE). CBS-deficient mice showed autoimmune disorders. H2S play important roles in T cell development and differentiation, especially Treg cells development and differentiation.
We used microarrays to detail the global gene expression of WT and CBS-deficient CD4+ T cells.

overall_design: CD4+ T cells from WT and CBS-deficient mice were isolated for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the homogeneous populations of mice at 6 weeks in order to increase the temporal resolution of expression profiles.

first: Songtao

last: Shi


title: Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells

type: Methylation profiling by high throughput sequencing

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


title: Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network [RIP-chip]

summary: In embryonic stem cell (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors that regulate the ESC state are not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 Ubiquitin Ligase Protein Makorin-1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems-level analyses we compiled a MKRN1-centered interactome in undifferentiated ESCs at the proteomic and ribonomic level. Proteomic analyses revealed that MKRN1 is a novel RNA-binding protein that exists within messenger ribonucleoprotein (mRNP) complexes in undifferentiated ESC populations. In accordance with its presence in mRNPs, MKRN1 is mobilized to stress granules (SG) upon arsenite-induced stress, yet MKRN1 is not required for SG formation. RIP-chip analysis revealed that MKRN1 associates with mRNAs encoding functionally related regulatory proteins involved in diverse processes such as cell differentiation, apoptosis, or secreted proteins. Thus, our unbiased systems level analyses supports a role for MKRN1 as a novel RNA-binding protein and a potential gene regulatory protein within the ESC GRN.

overall_design: Five samples are included from this single ribonucleoprotein immunoprecipitation (RIP) experiment. Total (Input) or Immunoprecipitated (RIP) RNA was derived from mouse R1 embryonic stem cell (ESC) clones constitutively expressing either the pCAGGS::FLAG:MKRN1 fusion protein (FLAG:MKRN1) or the pCAGGS::FLAG:Ctrl construct (FLAG:Ctrl); the latter was used as a control lysate to identify background from anti-FLAG immunoprecipitation. Total (Input) RNA was harvested from an aliquot of FLAG:MKRN1 and FLAG:Ctrl ESC lysates taken prior to initiating the immunoprecipitation step. RIP RNA was obtained from FLAG:MKRN1 and FLAG:Ctrl ESC lysates following immunoprecipitation with anti-FLAG or anti-IgG antibodies. Sample 1: Input FLAG Control - total RNA obtained from bulk FLAG:Ctrl ESC lysates prior to RNA immunoprecipitation.  Sample 2: Input FLAG MKRN1 - total RNA obrtained from bulk FLAG:MKRN1 ESC lysates prior to RIP. Sample 3: anti-FLAG RIP FLAG Control - Immunoprecipitated RNA resulting from FLAG immunoprecipitation from bulk FLAG:Ctrl ESC lysates. This control sample indicates background RNA that is immunoprecipitated with FLAG antibodies from ESC lysates that do not express the FLAG:MKRN1 fusion protein. Sample 4: anti-FLAG RIP FLAG MKRN1 - immunoprecipitated RNA resulting from FLAG immunoprecipitation of FLAG:MKRN1 fusing protein from FLAG:MKRN1 ESC lysates. This sample represents the treatment group. Sample 5: anti-IgG RIP FLAG MKRN1 - Immunoprecipitated RNA resulting from immunoprecipitation with IgG control antibodies from FLAG:MKRN1 ESC lysates. This control sample indicates background RNA that is immunoprecipitated with IgG and beads from the FLAG:MKRN1 ESC lysate.

middle: L

first: Paul

middle: A

last: Cassar

first: Richard

last: Carpenedo


title: Microarray and Pathway Analysis Reveal Distinct Mechanisms Underlying Cannabinoid-Mediated Modulation of LPS-Induced Activation of BV-2 Microglial Cells

status: Public on Jul 09 2015

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Cannabinoids are known to exert immunosuppressive activities. However, the mechanisms which contribute to these effects are unknown. Using lipopolysaccharide (LPS) to activate BV-2 microglial cells, we examined how Δ9-tetrahydrocannabinol (THC), the major psychoactive component of marijuana, and cannabidiol (CBD) the non-psychoactive component, modulate the inflammatory response.

overall_design: Microarray analysis of genome-wide mRNA levels was performed using Illumina platform and the resulting expression patterns analyzed using the Ingenuity Pathway Analysis to identify functional subsets of genes, and the Ingenuity System Database to denote the gene networks regulated by CBD and THC.

first: Ana

last: Juknat

first: Maciej

last: Pietr

first: Ewa

last: Kozela

first: Neta

last: Rimmerman

first: Rivka

last: Levy

first: Fuying

last: Gao

first: Daniel

last: Geschwind

first: Zvi

last: Vogel


title: A DNA Hypomethylation Signature Predicts Novel Anti-Tumor Activity of LSD1 Inhibitors in SCLC (BeadChip)

city: Collegeville

first: David

last: Soong

state: PA

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline

summary: Epigenetic dysregulation has emerged as an important mechanism in cancer.  Alterations in epigenetic machinery have become a major focus for new targeted therapies.  The current report describes the discovery and biological activity of a cyclopropylamine containing inhibitor of Lysine Demethylase 1 (LSD1), GSK2879552.  This small molecule is a potent, selective, orally bioavailable, mechanism-based irreversible inhibitor of LSD1.  A proliferation screen of cell lines representing a number of tumor types indicated that small cell lung carcinoma (SCLC) is sensitive to LSD1 inhibition.  The subset of SCLC lines and primary samples that undergo growth inhibition in response to GSK2879552 exhibit DNA hypomethylation of a signature set of probes suggesting this may be used as a predictive biomarker of activity.  The targeted mechanism coupled with a novel predictive biomarker make LSD1 inhibition an exciting potential therapy for SCLC, a highly prevalent, rarely cured, tumor type representing approximately 15% of all lung cancers.

overall_design: DNA methylation profiling was performed using Infinium 450K methylation arrays on SCLC cell lines, patient derived xenografts, and patient samples. Data was processed and normalized using GenomeStudio V2011.1

first: Helai

middle: P

last: Mohammad

first: Kimberly

last: Smitheman

first: Chandrashekhar

middle: D

last: Kamat

first: Kelly

last: Federowicz

first: Glenn

last: Van Aller

first: Jess

last: Schneck

first: Jeff

last: Carson

first: Yan

last: Liu

first: Michael

last: Butticello

first: William

last: Bonnette

first: Shelby

last: Gorman

last: Degenhardt

first: Yuchen

last: Bai

last: McCabe

first: Melissa

last: Pappalardi

first: Jiri

last: Kasparec

first: Xinrong

last: Tian

first: Ken

last: McNulty

first: Megan

last: Rouse

first: Patrick

last: McDevitt

first: Thau

last: Ho

first: Michelle

last: Crouthamel

first: Nestor

last: Concha

first: Charles

last: McHugh

last: Miller

first: Dashyant

last: Dhanak

first: Peter

last: Tummino

first: Christopher

last: Carpenter

first: Neil

last: Johnson

first: Christine

last: Hann

first: Ryan

last: Kruger


title: PAK1 is a Therapeutic Target in Acute Myeloid Leukemia and Myelodysplastic Syndrome

status: Public on Jul 11 2015

city: Bronx

first: Ashley

middle: M

last: Pandolfi

address: 1300 Morris Park Chanin 606

department: Cell Biology

institute: Albert Einstein College of Medicine

summary:
Poor clinical outcome of Acute Myeloid Leukemia (AML) and Myelodysplastic Syndrome (MDS) has been attributed to failure of current chemotherapeutic regimens to target leukemic stem cells. We recently identified p21-activated kinase (PAK1) as a downstream effector molecule of H2.0-like homeobox (HLX), a gene functionally relevant for AML pathogenesis. In this study, we find that inhibition of PAK1 activity by small molecule inhibitors or by RNA interference leads to profound leukemia-inhibitory effects both in vitro and in vivo. Inhibition of PAK1 induces differentiation and apoptosis of AML cells through downregulation of MYC oncogene and a core network of MYC target genes. Moreover, we find that PAK1 up-regulation occurs during disease progression and is relevant for patient survival in MDS. Importantly, we find that inhibition of PAK1 inhibits primary human leukemic cells including immature leukemic stem cell-enriched populations. Our studies highlight PAK1 as a novel target in AML and MDS, and support the use of PAK1 inhibitors as a therapeutic strategy in these diseases.
To obtain insight into the molecular mechanism for the induction of apoptosis and differentiation resulting from PAK1 inhibition in AML, we performed gene expression microarrays following treatment with either IPA-3 or FRAX-597.

overall_design: RNA was isolated from THP-1 cells after 5 hours of treatment with IPA-3 (6 ug/mL), FRAX-597 (2 ug/mL) or an equal volume of DMSO using Trizol Reagent (Invitrogen).

first: A

first: R

last: Stanley

first: U

last: Steidl


title: Defective NK cells in AML patients at diagnosis are associated with blast transcriptional signatures of immune evasion

first: Nicolas

last: Dulphy

summary: Acute myeloid leukemia (AML) is a heterogeneous group of malignancies which may be sensitive to the natural killer (NK) cell anti-tumor response. However, NK cells are frequently defective in AML. Here, we found in an exploratory cohort (n = 46) that NK-cell status at diagnosis of AML separated patients in two groups with a different clinical outcome. Patients with a deficient NK-cell profile, including reduced expression of some activating NK receptors (e.g. DNAM-1, NKp46 and NKG2D) and decreased IFN-g production, had a significantly higher risk of relapse (P = 0.03) independently of cytogenetic classification in multivariate analysis. Patients with defective NK cells showed a profound gene expression decrease in AML blasts for cytokine and chemokine signaling (e.g. IL15, IFNGR1, IFNGR2, CXCR4), antigen processing (e.g. HLA-DRA, HLA-DRB1, CD74) and adhesion molecule pathways (e.g. PVR, ICAM1). A set of 388 leukemic classifier genes defined in the exploratory cohort was independently validated in a multicentric cohort of 194 AML patients. In total, these data evidenced the interplay between NK-cells and AML blasts at diagnosis allowing an immune-based stratification of AML patients independently of clinical classifications.

overall_design: Gene expression analysis were performed on CD56bright and CD56dim NK cells sorted from patients with impaired or normal CD56bright NK cells (n=2 for each patients? group) and from 3 HC

first: Zena

last: KHAZNADAR

last: DULPHY

first: Antoine

last: TOUBERT

last: NAZARET

first: Severine

last: CROZE

first: Joel

last: LACHUER


title: An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

city: Moscow

first: Maria

last: Shutova

state: Russia

address: Gubkina 3

department: Epigenetics

country: Russia

institute: Vavilov Institute of General Genetics, Russian Academy of Sciences

summary: The pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the three germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the “gold standard” of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, three types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and three pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that five iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of “the best iPSC line” selection and confirmed it on an independent dataset.

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. For each line there are a biological (different passages) or technical (same passage) replicate.

middle: V

first: Anastasia

last: Surdina

first: Dmitry

middle: S

last: Ischenko

first: Vladimir

last: Naumov

first: Aleksandra

last: Bogomazova

first: Ekaterina

last: Vassina

last: Alekseev

last: Lagarkova

first: Sergey

last: Kiselev


title: Engagement of the Aryl Hydrocarbon Receptor in Mycobacterium tuberculosis–Infected Macrophages Has Pleiotropic Effects on Innate Immune Signaling

city: Montreal

first: John

last: White

state: Quebec

address: Room 1109, McIntyre Medical Buiding, 3655 Prom Sir William Osler

department: Physiology

institute: McGill University

summary: Understanding the mechanisms of host macrophage responses to Mycobacterium tuberculosis (M.tb.) is essential for uncovering potential avenues of intervention to boost host resistance to infection. Macrophage transcriptome profiling revealed M.tb. infection strongly induced expression of several enzymes controlling tryptophan (Trp) catabolism. This included indole 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2), which catalyze the rate-limiting step in the kynurenine pathway, producing ligands for the aryl hydrocarbon receptor (AHR). The AHR and heterodimeric partners AHR nuclear translocator (ARNT) and RELB are robustly expressed, and AHR and RELB levels further increased during infection. Infection enhanced AHR/ARNT and AHR/RELB DNA binding, and stimulated expression of AHR target genes, including that encoding the inflammatory cytokine IL1beta. AHR target gene expression was further enhanced by exogenous kynurenine, and exogenous Trp, kynurenine or synthetic agonist indirubin reduced mycobacterial viability. Comparative expression profiling revealed that AHR ablation diminished expression of numerous genes implicated in innate immune responses, including several cytokines. Notably, AHR depletion reduced expression of IL23A and IL12B transcripts, which encode subunits of interleukin 23 (IL23), a macrophage cytokine that stimulates production of IL22 by innate lymphoid cells. The AHR directly induced IL23A transcription in human and mouse macrophages through near-upstream enhancer regions. Taken together, these findings show that AHR signaling is strongly engaged in Mtb-infected macrophages, and has widespread effects on innate immune responses. Moreover, they reveal a cascade of AHR-driven innate immune signaling, as IL1B (IL-1β) and IL23 stimulate T cell subsets producing IL22, another direct target of AHR transactivation.

overall_design: Gene expression profiling of Mycobacterium tuberculosis Infected THP-1 monocytic cells following siRNA-mediated Aryl hydrocarbon receptor (AHR) knockdown.

first: Babak

last: Memari

first: Manuella

last: Bouttier

first: Vassil

last: Dimitrov

first: Marc

last: Ouellette

first: Marcel

last: Behr

first: Jorg

last: Fritz


title: Symmetrical dose-dependent DNA methylation profiles in children with deletion or duplication of chromosome 7q11.23

city: Toronto

first: Lucy

last: Osborne

address: 7360 Medical Sciences Building, 1 Kings College Circle

department: Medicine

institute: University of Toronto

summary: Genome wide DNA methylation in blood derived DNA from individuals with deletion or duplication of 7q11.23

overall_design: Bisulfite converted DNA was hybridized onto the Illumina Infinium HumanMethylation450 BeadChip array

first: Emma

last: Strong


last: Shutova

summary:
The pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the three germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the “gold standard” of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, three types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and three pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that five iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of “the best iPSC line” selection and confirmed it on an independent dataset.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network [expression]

first: William

last: Stanford

overall_design: Expression profiling by microarray of mESC populations 6 days post transient transfection with pLKO.1 shGFP or pLKO.1 shMKRN1 plasmids.  Transfected mESC populations were subjected to four days of puromycin selection to remove non-transfected cells prior to lysing the resultant puromycin-resistant populaton for RNA extraction.  Differential gene expression in shMKRN1-transfected ESC populations was compared to shGFP-transfected control ESC populations.

first: Paul

last: Cassar

first: Richard

last: Carpenedo


title: Expression data from C4-2 cells

status: Public on Jul 13 2015

city: Philadelphia

first: Karen

last: Knudsen

state: Pennsylvania

institute: Thomas Jefferson University - Kimmel Cancer Center

summary:
Evaluation of the genome wide impact on gene expression of DNA-PK knockdown or enzymatic inhibition.
DNA-PK expression is elevated in multiple tumor types.  DNA-PK has recently been implicated in transcriptional regulation, so understanding genes modulated by DNA-PK may provide insight into disease progression

overall_design: 6 samples were analyzed. A genome-wide expression array was performed on a GeneChip Human Gene 2.0ST Array (Affymetrix, 902112) with C4-2 cells depleted of DNA-PK or treated with DNA-PK inhibitor for 24 hours

middle: E

first: Jonathan

middle: F

last: Goodwin


title: Expression data for triple-negative breast cancer (TNBC) cells following chemotherapy

status: Public on Jul 10 2015

first: Xinyu

last: Deng

address: 650 Charles E Young Dr.

department: Surgery

institute: University of California Los Angeles

summary:
The mechanisms behind drug resistance and sensitivity in breast cancers relies on complex signalling pathways that involve the up or downregulation of certain genes. Many of these genes are involved in adhesion, growth, epithelial/mesenchymal transitions, and apoptosis.
We used microarrays to assess differences in gene expression in triple-negative breast cancer cells in response  to treatment.

overall_design: We examined the triple-negative human cell line HCC1806 treated with docetaxel or control DMSO. The purpose is to find out the early drug induced changes in this cell line.

first: Helena

last: Chang


title: EAG2 potassium channel with evolutionarily conserved function as a brain tumor target

status: Public on Jul 08 2015

city: Boston

first: Adrian

last: Dubuc

state: Massachussetts

address: 75 Francis St, 5-5066 Shapiro Building

institute: Brigham and Women's Hospital

summary:
Characterizing the impact of pharmacological and shRNA-mediated silencing of EAG2 in medulloblastoma.
Medulloblastoma (MB) is the most common pediatric CNS malignancy. Previously, we demonstrated that overexpression of the ion channel EAG2, identified in a subset of histological and molecular subtypes of this disease, functionally contributes to tumor progression (PMID: 22855790). Here, we demonstrate the evolutionarily conserved function of EAG2 potassium channel in promoting brain tumor growth and metastasis, delineate downstream pathways and uncover a co-option mechanism for different potassium channels to regulate mitotic cell volume and tumor progression. We show that EAG2 potassium channel is enriched at the trailing edge of migrating MB cells to regulate local cell volume dynamics, thereby facilitating cell motility. We identify the FDA- approved antipsychotic drug thioridazine as an EAG2 channel blocker that reduces xenografted MB growth and metastasis, and present a case report of repurposing thioridazine for treating a human patient. Our findings thus illustrate the potential of targeting ion channels in cancer treatment.

overall_design: The goal of this analysis was to determine the transcriptional consequences of  pharmacological (i.e. astemizole) or shRNA-mediated inhibition/suppression of EAG2 in low passage medulloblastoma cell lines. This analysis was performed in an effort to characterize evolutionarily conserved role of EAG2 in mediating tumor growth and metastasis. Pathway analysis was subsequently performed and compared to results obtained in a Drosophila model.

first: Xi

last: Huang


title: A DNA Hypomethylation Signature Predicts Novel Anti-Tumor Activity of LSD1 Inhibitors in SCLC (microarray)

first: David

last: Soong

overall_design: To gain insight into the mechanism of LSD1 inhibition in inhibiting growth in SCLC cell lines, the effect of GSK2879552 on gene expression was evaluated in 6 SCLC lines, three sensitive to the growth inhibitory effects of GSK2879552 and three resistant. Expression was measured on Affy HG-U133_PLUS_2 microarrays at three time points (2, 4, and 7 days) with replicates.

first: Helai

last: Mohammad

first: Kimberly

last: Smitheman

first: Chandrashekhar

last: Kamat

first: Kelly

last: Federowicz

first: Glenn

last: Van Aller

first: Jess

last: Schneck

first: Jeff

last: Carson

first: Yan

last: Liu

first: Michael

last: Butticello

last: Bonnette

first: Shelby

last: Gorman

last: Degenhardt

first: Yuchen

last: Bai

last: McCabe

first: Melissa

last: Pappalardi

first: Jiri

last: Kasparec

first: Xinrong

last: Tian

first: Ken

last: McNulty

first: Megan

last: Rouse

first: Patrick

last: McDevitt

first: Thau

last: Ho

first: Michelle

last: Crouthamel

first: Nestor

last: Concha

first: Charles

last: McHugh

last: Miller

first: Dashyant

last: Dhanak

first: Peter

last: Tummino

first: Christopher

last: Carpenter

first: Neil

last: Johnson

first: Christine

last: Hann

first: Ryan

last: Kruger


title: Gene expression annalysis of peripheral blood cells in patients with chronic kidney disease

status: Public on Jul 07 2015

city: Kanazawa

first: Shinji

last: Kitajima

address: 13-1 Takara-machi

institute: Kanazawa University hospital

summary: Genes related to sleep and wakefulness were evaluated by RNA microarray in patients, including CKD,HD patients and control subjects.

overall_design: RNA microarray analysis was performed in 19 patients without diabetes. The patients were divided into three groups: HT group (8 hypertension patients with eGFR of >60 mL/min/1.73 m2), CKD group (7 patients not on dialysis with eGFR of <60 mL/min/1.73 m2) and HD group (4 HD patients).

first: Yasunori

last: Iwata

first: Kengo

last: Furuichi

first: Akihiro

last: Sagara

first: Yasuyuki

last: Shinozaki

first: Tadashi

last: Toyama

first: Norihiko

last: Sakai

first: Miho

last: Shimizu

first: Takeshi

last: Sakurai

first: Shuichi

last: Kaneko

first: Takashi

last: Wada


title: Expression profiles in 3 different B-cell lymphoma cell lines treated by 92 FDA approved compounds

city: New York

first: Andrea

last: Califano

address: 1130 St. Nicholas Avenue, Rm. 906

institute: Columbia University

summary:
Identifying the Mechanism of Action (MoA) of drugs is critical for the development of new drugs, understanding their side effects, and drug repositioning. However, identifying drug MoA has been challenging and has been traditionally attempted only though large experimental setups with little success. While advances in computational power offers the opportunity to achieve this in-silico, methods to exploit existing computational resources are still in their infancy. To overcome this, we developed a novel method to identify Drug Mechanism of Action using Network Dysregulation (DeMAND).
The method is based on the realization that drugs affect the protein activity of their targets, but not necessarily their mRNA expression levels. In contrast, the change in protein activity directly affects the mRNA expression levels of downstream genes. Based on this hypothesis, DeMAND identifies drug MoA by comparing gene expression profiles following drug perturbation with control samples, and computing the change in the individual interactions within a pre-determined integrated transcriptional and post-translational regulatory model (interactome).

overall_design: This dataset includes GEPs in 3 different B-cell lymphoma cell lines (OCI-LY3, OCI-LY7 and U2932) at 6, 12, and 24hrs. 92 FDA approved compounds were used at a concentration of IC20 at 24h. DMSO was used as control at each time-point. A total of 828 samples and 29 control samples were available for analysis. Total RNA was isolated with the RNAqueous-96 Automated Kit (Ambion) on the Janus automated liquid handling system (Perkin Elmer Inc.), quantified by NanoDrop 6000 spectrophotometer and quality checked by Agilent Bioanalyzer. 300ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol and hybridized on the Human Genome U219 96-Array Plate (Affymetrix). Hybridization, washing, staining and scanning of the array plates were performed on the GeneTitan Instrument (Affymetrix) according to manufacturer’s protocols.

first: Jung

last: Woo

first: Yishai

last: Shimoni

first: Mukesh

last: Bansal

first: MicHeLa

last: Mattioli

first: Charles

last: Karan


title: Transcribed ultraconserved region 339 promotes carcinogenesis by sequestering tumor suppressor microRNAs

first: Muller

last: Fabbri

address: 4650 Sunset Blvd

institute: University of South California - Children's hospital Los Angeles

summary: The transcribed ultraconserved regions (T-UCRs) are a family of long non-coding RNAs implicated in human carcinogenesis. The mechanism of action of T-UCRs and the factors regulating their expression in human cancers are poorly understood. In this study we show that high expression of uc.339 correlates with lower survival in 204 non-small cell lung cancer (NSCLC) patients. We also show that uc.339 found up-regulated in archival NSCLC samples, functions as a decoy for miR-339-3p, -663-3p and -95-5p. As a result, Cyclin E2, a direct target of these microRNAs is up-regulated, promoting cancer growth and migration. We provide evidence from cell lines and primary samples suggesting that TP53 directly regulates uc.339. Our results support a key role for uc.339 in lung cancer.

overall_design: 4 experimental groups in triplicate (total: 12 samples). A339= A549 infected with a lentivirus over-expressing uc.339; AE= A549 infected with an empty lentivirus (control of A339); L339= LoVo infected with a lentivirus over-expressing uc.330; LE= LoVo infected with an empty lentivirus (control of L339). 1-2-3 refer to each experiment.

first: Ivan

last: Vannini

first: Kishore

middle: B

last: Challagundla

first: Meropi

last: Plousiou

first: Erika

last: Bandini

first: Francesca

last: Fanini

first: Giorgia

last: Paliaga

first: Melissa

last: Crawford

first: Manuela

last: Ferracin

first: Ramana

last: Davuluri

first: Zhihi

last: Guo

first: Maria

last: Cortez

first: Cristina

last: Ivan

first: Xinna

last: Zhang

first: Cecilia

last: Fernandez-Cymering

first: Leng

last: Han

first: Petra

last: Wise

first: Silvia

last: Carloni

first: Hui

last: Ling

first: Mariam

last: Murtadha

first: Barbara

last: Gitlitz

first: Ite

last: Laird-Offringa

first: Patrick

last: Nana-Sinkam

first: Massimo

last: Negrini

first: Han

last: Liang

first: Dino

last: Amadori

first: Amelia

last: Cimmino

first: George

last: Calin


title: Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [Methylation]

status: Public on Jul 03 2015

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: We performed genome-wide DNaseI hypersensitive site in FLT3-ITD and WT patient samples. We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. We examined association patterns of FLT3 ITD and WT AMLs and found that FLT3-ITD signaling is associated with common gene expression and chromatin signature.

overall_design: Examination of DNA methylation patterns in  FLT3 ITD and WT AML via microarray study.

first: Sally

last: James

first: Anetta

last: Ptasinska

first: Joaquin

last: Zacarias-Cabeza

first: Maria

middle: R

last: Imperato

first: Salam

last: Assi

first: Jason

last: Piper

first: Sascha

last: Ott

first: Constanze

last: Bonifer

first: Peter

last: Cockerill


title: Gene expression profiling from TS1 and TS2 cells in biological duplicates (A and B)

status: Public on Jul 01 2015

city: Brussels

first: Lorraine

last: Springuel

address: 74, Avenue Hippocrate

department: Brussels Branch

country: Belgium

institute: Ludwig Institute for Cancer Research

summary: TS1 and TS2 are T-lymphocyte derived cell lines that striclty depend on the presence of interleukin-9 for growth and survival. The goal of the study was to compare gene expression profiles between those 2 cell lines.

overall_design: TS1 and TS2 cell lines were maintained in vitro under the same conditions. RNA was extracted from biological duplicates ( 2 X 2 samples = 4 samples).

first: Jean-Christophe

last: Renauld

first: Laurent

last: Knoops


title: mRNA Expression data from human osteosarcoma (OS)

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

institute: Oita University

summary:
To explore possible oncogenic factors in OS, we used a microarray-based approach to profile changes in the expression of mRNAs in five OS cell lines and human mesenchymal stem cells (hMSCs).
We used a microarray-based approach to profile the mRNA expression of OS

overall_design: Human OS cell lines were analyzed with genome-wide expression arrays.

first: Kazuhiro

last: Tanaka


title: DNA methylation data from 11 periodontitis cases and 12 age-matched healthy individuals

first: Daniel

last: De Carvalho

address: 101 College Street, room 9-302

institute: Ontario Cancer Institute

summary: Microarray methylation (Infinium® HumanMethylation450 BeadChip from Illumina) was performed on gingival tissue samples from 11 periodontitis cases and 12 age-matched healthy individuals.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: D

first: A

last: Souza


title: MET after transient Twist activation results in de novo gain of malignant traits

status: Public on Jul 02 2015

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
During Epithelial-Mesenchymal Transition (EMT), apical-basal polarized epithelial cells are converted to front-to-back polarized mesenchymal cells that only form loose cell-cell adhesions. These phenotypic changes are accompanied by acquisition of increased motility and invasiveness. EMT programs are orchestrated by pleiotropic transcription factors (TFs), such as Twist1 and Snail1 and effect morphogenetic steps during embryogenesis, including mesoderm formation and neural crest migration. EMTs have also been implicated in the acquisition of aggressive traits by carcinoma cells, including the ability to complete several steps of the metastatic cascade as well as propagation of the tumor by single cells (clonogenicity), a defining trait of tumor-initiating or cancer stem cells. However, the molecular links between the expression of EMT-TFs, the process of EMT and acquisition of clonogenicity remain obscure.
Using inducible Twist1 or Snail1 expressed in CD24-positive mammary epithelial cells, we show that clonal growth in anchorage independence and EMT are induced sequentially and independently: clonogenic potential is induced prior to EMT and requires transient TF-activity. By contrast, EMT depends on continuous TF-activation over a longer period. In 3D-collagen assays, continuous Twist1 activity suppresses colony formation, whereas transient activation induces highly invasive growth independently of EMT. In conclusion, our results demonstrate that transient Twist1 activation suffices to drive tumor progression of CD24-positive breast epithelial cells, assessed by invasive as well as anchorage-independent clonal growth, whereas chronic Twist1 exposure can suppress these traits of aggressive tumor cells.

overall_design: We performed gene expression microarray analysis on CD24high and CD24negative populations derived from HMLE-Twist1-ER or HMLE-Snail1-ER cell lines upon various culture conditions

first: Johanna

last: Schmidt

first: Elena

last: Panzilius

first: Martin

last: Irmler

first: Christina

last: Scheel


title: Comparison of the gene expression profiles of carfilzomib-resistant derivatives versus parental human myeloma cell lines

city: Washington

first: Robert

last: Hawley

state: DC

address: 2300 I Street NW, Suite 431

department: Anatomy and Regenerative Biology

institute: George Washington University

summary: KMS-11 and KMS-34 cells were exposed to stepwise increasing concentrations of carfilzomib over a period of 18 weeks: cells adapted to growth in 4 nM carfilzomib by 4 weeks, in 6 nM in another 6 weeks and in 12 nM after a further 8 weeks. The resulting cell cultures, denoted KMS-11/Cfz and KMS-34/Cfz, respectively, retained resistance to carfilzomib even when tested after removal of selective pressure for approximately 8 weeks.

overall_design: KMS-11/Cfz and KMS-34/Cfz cells were profiled for gene expression after 1 week of growth in the absence of carfilzomib together with parental KMS-11 and KMS-34 cells which had not been selected in the drug (triplicate samples).

first: Irene

last: Riz

first: Teresa

middle: G


title: Gene expression data from HEK-293T cells transfected with miR-194 mimics

city: Shanghai

first: Chunyang

last: Bao

state: Shanghai

address: Shanghai Medical College, Fudan University 1207 Rm., 2# Bldg., 270 Dong An Rd.

department: Fudan University Shanghai Cancer Center

institute: Fudan University

summary: Nuclear factor κB (NF-κB) pathway plays an important role in hepatocellular carcinoma (HCC) progression. miR-194 was previously shown to reduce the induction of NF-κB activity upon addition of tumor necrosis factor α (TNFα). To clarify the molecular mechanism responsible for the effect of miR-194 on NF-κB pathway, mRNA microarray assays were performed to identify the genes that were suppressed by miR-194.

overall_design: HEK-293T cells transfected with miR-194 mimics were cultured for RNA extraction and hybridization on Affymetrix mRNA microarrays. These were compared against the control, which were HEK-293T cells transfected with negative control mimics.

first: Yan

last: Li

first: Shenglin

last: Huang

first: Xianghuo

last: He


title: DNA methylation of estrogen regulated enhancers defines endocrine sensitivity in breast cancer

city: Darlinghurst

last: Zotenko

state: NSW

address: 384 Victoria St.

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: Expression of estrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy as part of their adjuvant care, but does not guarantee patient response. However, the molecular factors that define endocrine response in ESR1-positive breast cancer patients remain poorly understood. Here, we characterize the DNA methylome of endocrine sensitivity and demonstrate the potential impact of differential DNA methylation on endocrine response in breast cancer.  We show that DNA hypermethylation occurs predominantly at estrogen-responsive enhancers and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1-activity; thus providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers. Conversely, we delineate that ESR1-responsive enhancer hypomethylation is critical in transition from normal mammary epithelial cells to endocrine responsive ESR1-positive cancer.  Cumulatively these novel insights highlight the potential of ESR1-responsive enhancer methylation to both predict ESR1-positive disease and stratify ESR1-positive breast cancer patients as responders to endocrine therapy.

overall_design: Methylation profiling with Illumina's HumanMethylation450K array was performed on ESR1-positive hormone sensitive MCF7 cells, and three different well characterised endocrine resistant MCF7-derived cell lines; tamoxifen-resistant (TAMR), fulvestrant-resistant (FASR) and estrogen deprivation resistant (MCF7X) cells.  For each cell line two biological replicates were profiled bringing the number of samples to eight.


title: Transcriptomic Changes in TGF-β1 Differentiated and PGE2 Dedifferentiated Myofibroblasts

status: Public on Jun 30 2015

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary:
These data show that the genes that distinguish myofibroblasts from fibroblasts are myriad, and that some genes not traditionally associated with myofibroblast differentiation may serve as novel therapeutic targets for fibrosing disorders.
Gene expression levels were assessed from total RNA on the Affymetrix U219 microarray.

overall_design: Here, we use transforming growth factor-β1 (TGF-β1) and prostaglandin E2 (PGE2), which has recently been shown to reverse myofibroblast differentiation, to investigate the transcriptomic changes that occur during TGF-β1-induced differentiation and PGE2-induced de-differentiation of myofibroblasts.

first: Steven


title: Infection exposure promotes ETV6-RUNX1 precursor B cell leukemia revealing secondary genomic alterations in histone modification genes

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: We used microarrays to investigate gene expression changes in ETV6/RUNX1 proB and preB cells

overall_design: Bone marrow proB and preB cells of four ETV6/RUNX1 mice compared with bone marrow proB and preB cells of three WT mice and three Pax5+/- mice.

first: Guillermo

last: Rodríguez-Hernández

first: Julia

last: Hauer

first: Alberto

last: Martín-Lorenzo

first: Daniel

last: Schaefer

first: Christoph

last: Bartenhagen

first: Idoia

last: García-Ramírez

first: Franziska

last: Auer

first: Inés

last: González-Herrero

first: Lucia

last: Ruiz-Roca

first: Vera

last: Okpanyi

first: Ute

last: Fischer

last: Dugas

first: Sanil

last: Bhatia

first: Marta

last: Suquia

first: María

last: Trincado

first: Angel

last: Sanchez

first: Oscar

last: Blanco

first: Maria

last: García-Cenador

first: Francisco

middle: J

last: García-Criado

first: César

last: Cobaleda

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Carolina

last: Vicente-Dueñas

last: Sánchez-García

first: Arndt

last: Borkhardt


title: Redefining the role of eIF4E dose in development, cancer, and protein synthesis

city: San Francisco

first: Davide

last: Ruggero

address: 1450 3rd St. Room HD-319

department: Helen Diller Cancer Center

institute: UCSF

summary: eIF4E, the major cap-binding protein, has long been considered limiting for translating the mammalian genome. However, the requirement for eIF4E dose at an organismal level remains unexplored. By generating an Eif4e haploinsufficient mouse, we surprisingly found that 50% reduction in eIF4E, while compatible with normal development and global protein synthesis, significantly impeded cellular transformation and tumorigenesis. Genome-wide translational profiling uncovered a translational program induced by oncogenic transformation and revealed a critical role for eIF4E dose specifically in translating a network of mRNAs enriched for a unique 5’UTR signature. In particular, we demonstrate that eIF4E dose is essential for translating mRNAs regulating reactive oxygen species (ROS) that fuel transformation and cancer cell survival in vivo. Therefore, mammalian cells have evolved surplus eIF4E levels that cancer cells hijack to drive a translational program supporting tumorigenesis

overall_design: Total cellular RNA and high MW polysome associated RNA were isolated from matched untransformed and tranformed WT and Eif4e+/- MEFs for analysis on Affymetrix Mouse Gene 1.0 ST arrays. The difference in log2 RMA intensity between matched polysomal RNA and total RNA was taken to quantify translational efficiency (TE).

first: Morgan

last: Truitt

first: Taku

last: Tokuyasu


title: Gene expression profiling of BDC2.5 CD4T cells isolated from NOD mice after in vivo antigen stimulation with either DEC205+ or DCIR2+ DCs.

city: Bethesda

first: Kristin

middle: V.

last: Tarbell

state: MD

address: Bldg.10, CRC, 5W-5940, 10 Center Drive

department: Diabetes, Endocrinology, and Obesity Branch

institute: National Institute of Diabetes and Digestive and Kidney Diseases

summary:
We identified DCIR2+DCs but not DEC205+DCs as able to induce peripheral T cell tolerance in pre-diabetic autoimmune NOD mice. To determine what distinct genetic programs are elicited in the auto-reactive CD4 T cells early after stimulation by these two DC subsets, we utilized adoptive transfer of BDC2.5 CD4 T cells into NOD mice, which were then given chimeric antibody to deliver the beta-cell specific antigen to either DCIR2+DCs or DEC205+DCs, leading to BDC2.5 CD4 T cell specific stimulation in vivo. The analysis shows that the negative transcriptional factor Zbtb32 (ROG) is up-regulated more in BDC2.5 CD4 T cells after stimulated with a antigen via DCIR2+DCs presentation, compared with DEC205+DCs, suggesting the involvement of Zbtb32 in DCIR2+DCs-mediated auto-reactive T cell tolerance in disease ongoing NOD mice.
The BDC2.5 CD4 T cells after 14 hour of injection with a 100 ng of anti-DCIR2-BDC, anti-DEC205-BDC antibody, or PBS as a control to NOD mice, were sorted by BD FACSAria and their expression profile was analyzed using Affymetrix chips.

overall_design:
NOD mice with transferred BDC2.5 T cell were injected with 100 ng of anti-DCIR2-BDC (NOD_DCIR2-BDC), anti-DEC205-BDC antibody (NOD_DEC-BDC), or PBS (NOD_PBS) as a control. After 14 hours, BDC2.5 CD4 T cells were sorted by BD FACSAria and their expression profile was analyzed using Affymetrix microarray chips. Each sample has a biological duplicate.
Raw data were preprocessed with the RMA algorithm in Partek, and averaged expression values were used for analysis.

first: Jeffrey

last: Price

first: Chie

last: Hotta-Iwamura

first: Yongge

last: Zhao

first: Nicole

last: Beauchamp


title: whole-genome SNP-CN and DNA methylation data from cell lines originating from patients with multiple myeloma

city: Atlanta

first: Jeanne

last: Kowalski

address: 1365-B Clifton Rd. NE.

department: Winship Cancer Institute

institute: Emory University

type: Genome binding/occupancy profiling by SNP array

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

overall_design: Refer to individual Series


title: Disturbance of gene expression in primary human hepatocytes by hepatotoxic pyrrolizidine alkaloids: a whole genome transcriptome analysis

city: Berlin

first: Stefanie

last: Hessel

address: Max-Dohrn-Straße 8-10

institute: Federal Institute for Risk Assessment

summary: 1,2-unsaturated pyrrolizidine alkaloids (PA) are plant metabolites predominantly occurring in the plant families Asteraceae and Boraginaceae. Acute and chronic PA poisoning causes severe hepatotoxicity. So far, the molecular mechanisms of PA toxicity are not well understood. To analyze its mode of action, primary human hepatocytes were exposed to a non-cytotoxic dose of 100 µM of four structurally different PA: echimidine, heliotrine, senecionine, senkirkine. Changes in mRNA expression were analyzed by a whole genome microarray. Employing cut-off values with a |fold change| of 2 and a q-value of 0.01, data analysis revealed numerous changes in gene expression. In total, 4556, 1806, 3406 and 8623 genes were regulated by echimidine, heliotrine, senecione and senkirkine, respectively. 1304 genes were identified as commonly regulated. PA affected pathways related to cell cycle regulation, cell death and cancer development. The transcription factors TP53, MYC, NFκB and NUPR1 were predicted to be activated upon PA treatment. Furthermore, gene expression data showed a considerable interference with lipid metabolism and bile acid flow. The associated transcription factors FXR, LXR, SREBF1/2, and PPARα/γ/δ were predicted to be inhibited.   In conclusion, though structurally different, all four PA significantly regulated a great number of genes in common. This proposes similar molecular mechanisms, although the extent seems to differ between the analyzed PA as reflected by the potential hepatotoxicity and individual PA structure.

overall_design: Primary human hepatocytes (Clonetics® Normal Human Hepatocytes from Lonza, Walkersville, USA) were treated for 24 h with 100 µM echimidine, heliotrine, senecionine, senkirkine or solvent control (1 % acetonitrile) in triplicate. Prior to RNA isolation, cells were washed three times with pre-warmed PBS. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. For genome-wide microarray analysis quality and concentration of RNA was determined using Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA, USA). Affymetrix GeneChip hybridization (HG-U133 Plus 2.0) was conducted with 250 ng RNA according to the manufacturer’s instructions.

first: Claudia

last: Luckert

first: Dido

last: Lenze

first: Alfonso

last: Lampen


title: mRNA and miRNA expression data from human osteosarcoma (OS)

first: Masanori

last: Kawano

type: Expression profiling by high throughput sequencing

platform_organism:
Homo sapiens
synthetic construct


title: Omic Personality: Implications of Stable Transcript and Methylation Profiles for Personalized Medicine [DNA Methylation]

first: Greg

last: Gibson

state: Georgia

address: North Ave NW

department: School of Biology

institute: Georgia Institute of Technology

summary:
Background:   Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic response.  We report a pilot study quantifying gene expression and methylation profile consistency over time, addressing the reasons for individual uniqueness, and its relation to N=1 phenotypes.
Methods:  Whole blood samples from 4 African American women, 4 Caucasian women, and 4 Caucasian men drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNASeq, miRNASeq, and Illumina Methyl-450 arrays.  Standard regression approaches were used to evaluate the proportion of variance for each type of omic measure that is among individuals, and to quantify correlations among measures and with clinical attributes related to wellness.
Results:  Longitudinal omic profiles are in general highly consistent over time, with an average of 67% of the variance in transcript abundance, 42% of CpG methylation level (but 88% for the most differentiated CpG per gene), and 50% of miRNA abundance among individuals, which are all comparable to 74% of the variance among individuals for 74 clinical traits.  One third of the variance can be attributed to differential blood cell type abundance, which is also fairly stable over time, and a lesser amount to eQTL effects, whereas seven conserved axes of covariance that capture diverse aspects of immune function explain over half of the variance.  These axes also explain a considerable proportion of individually extreme transcript abundance, namely approximately 100 genes that are significantly up- or down-regulated in each person and are in some cases enriched for relevant gene activities that plausibly associate with clinical attributes.  A similar fraction of genes have individually divergent methylation levels, but these do not overlap with the transcripts, and fewer than 20% of genes have significantly correlated methylation and gene expression.
Conclusions:  People express an “omic personality” consisting of peripheral blood transcriptional and epigenetic profiles that are constant over the course of a year and reflect various types of immune activity.  Baseline genomic profiles can provide a window into the molecular basis of traits that might be useful for explaining medical conditions or guiding personalized health decisions.

overall_design: Whole blood samples from 12 subjects drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNASeq, miRNASeq, and Illumina Methyl-450 arrays.

first: Rubina

last: Tabassum

first: Ambily

last: Sivadas

first: Vartika

last: Agrawal

first: Haozheng

last: Tian

first: Dalia

last: Arafat


title: Quantification of regenerative potential in primary human mammary epithelial cells

first: Johannes

last: Beckers

summary:
We present an organoid regeneration assay in which freshly dissociated human mammary epithelial cells from healthy donors are grown in adherent/rigid or floating/compliant collagen I gels. In both conditions, luminal progenitors (CD49f+EpCAM+) form spheres, whereas basal cells (CD49fhiEpCAM-) generate branched ductal structures. However, in compliant but not rigid collagen gels, branching ducts form alveoli at their tips, express basal and luminal markers at correct positions and display contractility, which is required for alveologenesis. Thereby, branched structures generated in compliant collagen gels resemble terminal ductal-lobular units (TDLUs), the functional units of the mammary gland.
Moreover, the membrane metallo-endopeptidase CD10 as an additional surface marker enriches for TDLU-formation and reveals the presence of stromal cells within the CD49fhiEpCAM- population. In summary, we describe a defined in vitro assay system to quantify cells with regenerative potential and systematically investigate their interaction with the physical environment at distinct steps of morphogenesis.

overall_design: Comparison of three cell populations derived from FACS-sorted primary human mammary epithelial cells: luminal progenitors, CD10+ basal cells and CD10- basal cells.

first: Jelena

last: Linnemann

first: Haruko

last: Miura

first: Lisa

middle: K

last: Meixner

first: Martin

last: Irmler

first: Uwe

last: Kloos

first: Benjamin

last: Hirschi

first: Harald

last: Bartsch

first: Steffen

last: Sass

first: Fabian

last: Theis

first: Christian

last: Gabka

first: Karl

last: Sotlar

first: Christina

middle: H

last: Scheel


title: Ten day time course of the effect of influenza A infection on spleen gene expression in mice

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: These data were generated as part of a study to model gene regulatory networks influenced by influenza infection. Other tissue compartments included in the study were blood, lung, and lymph node.

overall_design: RNA was extracted from spleens of female mice that did not have any experimental treatment (n = 3, labeled as T-9) or that received intranasal administration of influenza A virus either immediately before (n = 3, T0) or 1 to 10 days before being euthanized for tissue collection (T1 through T10, n =3-4 per day). Gene expression profiles were determined with comprehensive microarrays (Affymetrix Mouse Gene ST 1.0).

last: Zand


title: Slit2/Robo axis is mandatory for neural remodeling  in pancreatic cancer.

city: Quebec

first: Ezequiel

middle: L

last: Calvo

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: Pancreatic Ductal Adenocarcinoma (PDA) is a critical health issue in cancer field with little new therapeutic options. Several evidences support an implication of intra-tumoral microenvironment (stroma) on PDA progression. However, its contribution to the role of neuroplastic changes within pathophysiology and clinical course of PDA, mainly through tumor recurrence and neuropathic pain, remains unknown neglecting a putative therapeutic window. Here, we report that intra-tumoral microenvironment is a mediator of PDA Associated Neural Remodeling (PANR). With laser capture microdissection of stromal/tumoral compartment from human PDA followed by cDNA based microarray analyses we highlighted numerous factors expressed by stromal compartment that could impact on neuroplastic changes; among them, the Slit2/Robo axon guidance pathway. Using co-culture in vitro, we showed that stromal secreted Slit2 increases DRG neurite outgrowth and Schwann cells migration/proliferation by modulating N-Cadherin/β-Catenin signaling. Importantly, Slit2/Robo signaling inhibition disrupts this stromal/neural connection. Finally, we revealed in vivo that Slit2 expression is correlated with neural remodeling within Human and mouse PDA. These results demonstrate the implication of microenvironment, through secretion of axon guidance molecule, in PANR. Furthermore, it provides rationale to investigate the disruption of stromal/neural compartment dialogue by using Slit2/Robo pathway inhibitors for treatment of pancreatic cancer recurrence and associated pain.

overall_design: Freshly frozen tissue samples of PDACs were obtained from patients who underwent surgery. Patients underwent hemipancreaticoduodenectomy or distal pancreatectomy. No distant metastases were revealed at initial diagnosis. Histological examination confirmed diagnosis of PDAC in all cases. Prior to surgery all patients had signed an informed consent form that had been approved by the local ethics committee. Frozen sections were obtained from tissue samples of three tumors. After a brief staining sections were dehydrated and epithelial and stromal compartment has been microdissected using the PALM system. The microdissected material was immediately dissolute in a buffer containing β-mercaptoethanol and RNA carrier, and frozen before RNA extraction. Fifteen ug of total RNA was converted to biotinylated cRNA and hybridised to a human oligonucleotide array U133 Plus 2.0 (Genechip, Affymetrix, Santa Clara, CA).

first: Veronique

last: Secq

first: Julie

last: Leca

first: Fabienne

last: Guillaumond

first: Paulina

last: Skrobuk

first: Jeremy

last: Nigri

first: Sophie

last: Lac

first: Marie-Noëlle

last: lavault

first: Thi-thien

last: Bui

first: Atul

last: Thakur

first: Noëlle

last: Callizot

first: Rémy

last: Steinschneider

first: Patrice

last: Berthezene

first: Nelson

last: Dusetti

first: Corinne

last: Bousquet

first: Stéphane

last: Garcia

last: Vasseur

first: Juan

last: Iovanna

first: Richard

last: Tomasini


title: Expression data from prostate cancer and benign prostate glands

city: Aarhus N

first: Martin

middle: Mørck

last: Mortensen

address: Brendstrupgaardsvej 100

department: Dept. of Urology

country: Denmark

institute: Aarhus University Hospital

summary: Prostate cancer is a leading cause of cancer death amongst males. The main clinical dilemma in treating prostate cancer is the high number of indolent cases that confer a significant risk of over diagnosis and over treatment. In this study we have performed a genome expression profiling of tumor tissue specimens from 36 patients with prostate cancer to identify transcripts that delineate aggressive and indolent cancer. We included normal prostate biopsies from 14 patients in our analysis. Unsupervised hierarchical cluster analysis separated the cancer samples into two groups with a significant overrepresentation of tumors from patients with biochemical recurrence in one of the groups (Chi2, p=0.02). The samples were separated by basically three clusters of genes that showed differential expression between the two sample clusters - totaling 371 transcripts. Ingenuity Pathway Analysis revealed that one cluster contained genes associated with invasive properties of the tumor, another genes associated with the cell cycle, and the last cluster genes involved in several biological functions. We successfully validated the transcripts association with recurrence using two publicly available patient datasets totaling 669 patients. Twelve genes were found to be independent predictors of recurrence in multivariate logistical regression analysis.

first: Mørck

first: Lars

last: Dyrskjøt


title: DNA methylation data from cell lines originating from patients with multiple myeloma

first: Jeanne

last: Kowalski

summary: We performed genome-wide DNA methylation profiling of KMS11, MM.1S, and RPMI8226 multiple myeloma cell lines to identify methylation changes distinct to each cell line

overall_design: Three multiple myeloma cell lines (KMS11, MM.1S, and RPMI8226) with two replicates each

first: Lawrence

last: Boise

first: Sagar

last: Lonial

first: Michael

last: Rossi


title: Novel culture conditions facilitating the induction of naïve pluripotency in human embryonic stem cells

status: Public on Jun 29 2015

city: Leiden

first: Nannan

last: He

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

summary: We report a novel culture condition inducing naive pluripotency in hESCs in a rapid, robust and reproducible way. These naive hESCs were similar to mESCs exhibiting domed colony morphology, increased single survival, reduced doubling time, upregulation of naive pluripotency-specific genes, unbiased lineage-specific differentiation, hypomethylation, separate clustering profile from parental primed hESCs and were dependent on signalling pathways similar to naive mESCs.

overall_design: Global DNA methylation analysis of naive hESCs and their parental primed hESC counterparts.

first: Galbha

last: Duggal

first: Sabitri

last: Ghimire

first: Dorien

last: Brokaert

first: Tom

last: Deroo

first: Margot

last: Van der Jeught

first: Sharat

last: Warrier

first: Sylvie

last: Lierman

first: Luc

last: Peelman

first: Ann

last: Van Soom

first: Bjorn

last: Menten

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele

first: Matthias

last: Roost

first: Roderick

last: Slieker

first: Bastiaan

middle: T

last: Heijmans

first: Dieter

last: Deforce

first: Petra

last: De Sutter

first: Susana

last: Chuva De Sousa Lopes

last: Heindryckx


title: The Chromatin Remodeller CHD7 Lies Upstream of Semaphorin, Slit/Robo and Calcium Handling Pathways during Cardiovascular Development

city: London

first: Matt

last: Burney

address: 30 Guilford Street

department: Developmental Biology of Birth Defects

institute: University College London Institute of Child Health

summary: Chromatin remodelling provides a key mechanism for the regulation of gene expression through dynamic alterations in nucleosome occupancy at promoters and enhancers. Haploinsufficiency for the ATP-dependent chromatin remodeller chromodomain-helicase-DNA-binding protein 7 (CHD7) causes human CHARGE syndrome. CHARGE is characterised by a distinct pattern of congenital anomalies, including cardiovascular malformations, and has traditionally been considered a neurocristopathy. We present a new perspective, by showing severe structural cardiovascular defects following ablation of Chd7 in the anterior mesoderm and other cardiac-related lineages. We identify multiple downstream pathways affected by the loss of Chd7 and disruption of excitation-contraction coupling in cardiomyocytes. Furthermore, we demonstrate CHD7 binding at the Sema3C promoter and alterations to the local chromatin structure in vivo, indicating direct transcriptional regulation. This work therefore provides novel insights into the etiology of heart defects arising in CHARGE syndrome and reveals a requirement for CHD7 activity in mesodermal cardiac progenitors.

overall_design: We performed microarrays on whole hearts dissected from E11.5 and E13.5 embryos, resulting from crossing Chd7fl/+;Mesp1-Cre mice with Chd7fl/fl mice. This ablates Chd7 expression specifically in the mesoderm, from which the heart derives.

first: Sophie

last: Payne

first: Matthew

first: Karen

last: McCue

first: Nelo

last: Popal

first: Sean

last: Davidson

first: Robert

last: Anderson

first: Peter

last: Scambler


title: Ten day time course of the effect of influenza A infection on mediastinal lymph node gene expression in mice

first: Stephen

last: Welle

summary: These data were generated as part of a study to model gene regulatory networks influenced by influenza infection. Other tissue compartments included in the study were blood, lung, and spleen.

overall_design: RNA was extracted from mediatinal lymph nodes of female mice that did not have any experimental treatment (n = 3, labeled as T-9) or that received intranasal administration of influenza A virus either immediately before (n = 3, T0) or 1 to 10 days before being euthanized for tissue collection (T1 through T10, n =3 per day). Gene expression profiles were determined with comprehensive microarrays (Affymetrix Mouse Gene ST 1.0).

first: Martin

last: Zand


title: Effect of knock down of LASP-1 on human breast cancer cells

status: Public on Jun 26 2015

city: Nashville

first: Dayanidhi

last: Raman

state: TN

address: PRB436, 23rd Ave S @ Pierce

department: Cancer Biology

institute: Vanderbilt Universirty


title: Ten day time course of effects of influenza A infection in mice on gene expression in blood, spleen, lymph node, and lung


title: Effect of knock down of LASP-1 on basal-like breast cancer cells (MDA-MB-231)

summary:
Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MDA-MB-231S (sorted for high surface expression of  CXCR4) and MDA-Bone-Un (Mouse bone metastasized MDA-MB-231 cells) human basal-like breast cancer cells cultured in 3D-Matrigel was performed.
Changes in transcript levels of key microRNAs 29B1 and 29B2, miRLet7F1, miR519A1, MMP9, MMP1, FAM75D4, Interferons a7 and a17, Glycine receptor a3, CADM2 and claudin12

overall_design: Non-silencing (control) and LASP-1 knock down MDA-MB-231-S and MDA-Bone-Un cells were cultured on 3D-Matrigel, total RNA was extracted and analyzed - 1 biological replicate each

first: Nichole

last: Duvall-Noelle


title: Gene expression data of C57BL/6, Il1a-knockout and Il1b-knockout mice at 24 hours after spinal cord injury

status: Public on Jun 27 2015

city: Québec

first: Steve

last: Lacroix

state: Québec

address: 2705, boul. Laurier

department: Médecine moléculaire

institute: Centre de recherche du Centre hospitalier universitaire (CHU) de Québec - CHUL

summary: We have previously shown that Il1a-knockout (KO) mice exhibit rapid (at day 1) and persistent improvements in locomotion associated with reduced lesion volume compared with Il1b-KO mice and C57BL/6 controls after traumatic spinal cord injury (SCI). To investigate the mechanism by which Il1a mediates its detrimental effect, we analyzed the transcriptome of the injured spinal cord of Il1a-KO, Il1b-KO and C57BL/6 mice at 24 hours after SCI using GeneChip microarrays.

overall_design: Il1a-KO, Il1b-KO and C57BL/6 mice were subjected to a 50-kdyn SCI and a 6-mm spinal cord segment centered over the site of contusion extracted for RNA isolation and microarray analysis.


title: The effect of Nebulin-Deficiency on Skeletal Muscle

status: Public on Jun 25 2015

city: Tucson

first: Henk

last: Granzier

state: AZ

address: 1656 E Mabel St.

institute: University of Arizona

summary: Nebulin is a giant filamentous protein that is coextensive with the actin filaments of the skeletal muscle sarcomere.  Nebulin mutations are the main cause of nemaline myopathy (NEM), with typical NEM adult patients having low expression of nebulin, yet the roles of nebulin in adult muscle remain poorly understood.   To establish nebulin’s functional roles in adult muscle we performed studies on a novel conditional nebulin KO (Neb cKO) mouse model in which nebulin deletion was driven by the muscle creatine kinase (MCK) promotor.  Neb cKO mice are born with high nebulin levels in their skeletal muscle but within weeks after birth nebulin expression rapidly falls to barely detectable levels  Surprisingly, a large fraction of the mice survives to adulthood with low nebulin levels (<5% of control), contain nemaline rods, and undergo fiber-type switching towards oxidative types.  These microarrays investigate the changes in gene expression when nebulin is deficient.

overall_design: Two skeletal muscle groups were studied: Quadriceps (which is markedly smaller in the Neb cKO mice relative to control) and Soleus (which is not significantly smaller in the Neb cKO relative to control).  Six biological replicates for each muscle group were selected; all are age-matched males.

first: John

last: Smith

first: Justin

last: Kolb

first: Frank

last: Li

first: Danielle

last: Buck


title: Expression profile of primary and wound metastatic lesions of melanoma

city: Shinanomachi Shinjuku-ku

first: Keitaro

last: Fukuda

state: Tokyo

department: Dermatology

institute: Keio University School of Medicine

summary:
The phenomenon that metastatic lesion developed on injured sites has long been recognized in a number of cancers, such as melanoma. The factors associated with wound healing that attract circulating tumor cells have remained unknown, however.
A patient with acral lentiginous melanoma presented with a metastatic lesion that appeared 1 month after trauma. To explore the molecular mechanism underlying the promotion of wound metastasis in melanoma, we performed microarray analysis of the metastatic lesions (n = 2) and the primary lesions (n = 3) of the patient.

overall_design: Using Human Genome U133 Plus 2.0 array, we compared global gene expression profiles of tissues derived from the patient’s primary (n = 3) and wound metastatic (n = 2) lesions to search for particular biological functions in genes of which expression intensities were increased in the wound metastasic lesions of melanoma.


title: Ten day time course of the effect of influenza A infection on lung gene expression in mice

summary: These data were generated as part of a study to model gene regulatory networks influenced by influenza infection. Other tissue compartments included in the study were blood, lymph node, and spleen.

overall_design: RNA was extracted from lungs of female mice that did not have any experimental treatment (n = 3, labeled as T-9) or that received intranasal administration of influenza A virus either immediately before (n = 1, T0) or 1 to 10 days before being euthanized for tissue collection (T1 through T10, n =1-3 per day). Gene expression profiles were determined with comprehensive microarrays (Affymetrix Mouse Gene ST 1.0).


title: Ten day time course of the effect of influenza A infection on peripheral blood monocyte gene expression in mice

summary: These data were generated as part of a study to model gene regulatory networks influenced by influenza infection. Other tissue compartments included in the study were lung, lymph node, and spleen.

overall_design: RNA was extracted from peripheral blood monocytes of female mice that did not have any experimental treatment (n = 3, labeled as T-9) or that received intranasal administration of influenza A virus either immediately before (n = 3, T0) or 1 to 10 days before being euthanized for tissue collection (T1 through T10, n =3 per day). Gene expression profiles were determined with comprehensive microarrays (Affymetrix Mouse Gene ST 1.0).


title: TCF12 Expression Profiles in HNSCC

status: Public on Jun 24 2015

city: Taipei

first: Yi-Fen

last: Chen

address: No. 155, Li-Nong St., Section 2,

department: Institute of Oral Biology

country: Taiwan

institute: National Yang-Ming University

summary: To investigate the regulation of TCF12 on downstream genes in OSCC, we performed GeneChip analysis using OECM1 expression cell subclones and HSC3 knockdown cell subclones.

overall_design: 4 samples

first: Yi Fen

first: Cheng Chieh

last: Yang

first: Shou Yen

middle: Y

last: Kao

first: Chung Ji

last: Liu

first: Shu Chun*

last: Lin

first: Kuo Wei*

middle: W

last: Chang


title: caArray_harri-00137: Predictors of Resistance to Preoperative Trastuzumab and Vinorelbine for HER2-Positive Early Breast Cancer

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: To assess pathologic complete response (pCR), clinical response, feasibility, safety, and potential predictors of response to preoperative trastuzumab plus vinorelbine in patients with operable, human epidermal growth factor receptor 2 (HER2)-positive breast cancer. EXPERIMENTAL DESIGN: 48 patients received preoperative trastuzumab and vinorelbine weekly for 12 weeks. Single and multigene biomarker studies were done in an attempt to identify predictors of response. RESULTS: 8 of 40 (20%) patients achieved pCR (95% confidence interval, 9-36%). Of 9 additional patients recruited for protocol-defined toxicity analysis, 8 were evaluable; 42 of 48 (88%) patients had clinical response (16 patients, clinical complete response; 26 patients, clinical partial response). T(1) tumors more frequently exhibited clinical complete response (P = 0.05) and showed a trend to exhibit pCR (P = 0.07). 5 (13%) patients experienced grade 1 cardiac dysfunction during preoperative treatment. Neither HER2 nor estrogen receptor status changed significantly after exposure to trastuzumab and vinorelbine. RNA profiling identified three top-level clusters by unsupervised analysis. Tumors with extremes of response [pCR (n = 3) versus nonresponse (n = 3)] fell into separate groups by hierarchical clustering. No predictive genes were identified in pCR tumors. Nonresponding tumors were more likely to be T(4) stage (P = 0.02) and express basal markers (P < 0.00001), growth factors, and growth factor receptors. Insulin-like growth factor-I receptor membrane expression was associated with a lower response rate (50% vs 97%; P = 0.001). CONCLUSIONS: Preoperative trastuzumab plus vinorelbine is active and well tolerated in patients with HER2-positive, operable, stage II/III breast cancer. HER2-overexpressing tumors with a basal-like phenotype, or with expression of insulin-like growth factor-I receptor and other proteins involved in growth factor pathways, are more likely to be resistant to this regimen.

overall_design:
harri-00137
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133_Plus_2
Organism: Homo sapiens (ncbitax)


title: Association of DNA Methylation with Acute Mania and Inflammatory Markers

status: Public on Jun 22 2015

city: Baltimore

first: Sarven

last: Sabunciyan

address: 600 N. Wolfe Street, Blalock 1146

department: Pediatrics

institute: Johns Hopkins University

summary: Genome wide DNA methylation profiling of serum samples from 20 individuals hospitalized with acute mania and 20 unaffected controls using the Illumina 450K methylation arrays.

overall_design: Bisulphite converted DNA from the 40 samples were hybridised to the Illumina HumanMethylation450 BeadChip arrays

first: Robert

last: Yolken

first: Faith

last: Dickerson


title: Expression data of squamous cervical carcinoma after chemotherapy

status: Public on Jun 23 2015

city: Kyoto

first: Naoki

last: Horikawa

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University

summary: The patients with locally advanced squamous cervical cancer (SCC) were examined in this study.  All patients received neoadjuvant chemotherapy followed by radical hysterectomy. Tumor response against NAC was determined based on RECIST criterior. Gene-expression profiles of SCC were determined using Human Genome GeneChip arrays U133.

overall_design: SCC patients who had undergone radical hysterectomy after NAC were studied. To identify molecular signatures to predict response to NAC using Irinotecan/Nedaplatin, gene expression profiles were compared between NAC Reponder and Non-responder.

first: N

first: T

last: Baba


title: The RALA pathway can maintain the proliferation of KRAS- and BRAF-mutated cancer cells

status: Public on Jun 20 2015

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

summary: By silencing of RALA, a downstream member of the RAS signal transduction pathway, we aimed to determine whether genes downstream of a mutated KRAS (codon 12 or 13) or a mutated BRAF can have significant functions in colorectal cancer carcinogenesis.

overall_design:
RALA was silenced in three colorectal cancer cell lines (SW480, HCT116 and HT29). Effects were normalized to mock-transfected cells and the effects of scramble siRNA were excluded.
SW480, HCT116 and HT29 cell lines were treated with the PI3K inhibitor LY294002 or DMSO.

last: Gyorffy

first: Iwona

last: Stelniec-Klotz

first: Reinhold

last: Schäfer


title: Identifying pH independent hypoxia induced genes in human squamous cell carcinomas in vitro

city: Århus C

first: Brita

middle: Singers

last: Sørensen

address: Nørrebrogade 44

department: Dep Experimental Clinical Oncology

institute: Aarhus Univesity Hospital

summary: Background: Genes upregulated by low oxygen have been suggested as endogenous markers for tumor hypoxia. Yet, most of the genes investigated have shown inconsistent results, which have led to concerns about their ability to be true hypoxia markers. Previous studies have demonstrated that expression of hypoxia induced genes can be affected by extracellular pH (pH e ). Methods: Five different human cell lines (SiHa, FaDu DD, UTSCC5, UTSCC14 and UTSCC15) were exposed to different oxygen concentrations and pH (7.5 or 6.3), and gene expression analyzed with microarray (Affymetrix - Human Genome U133 Plus 2.0 Array). Results: An analysis of two of the cell lines using SAM identified 461 probesets that were able to separate the four groups “ Normal oxygen, normal pH ” , “ Low oxygen, normal pH ” , “ Normal oxygen, low pH ” and “ Low oxygen, low pH ” . From here it was possible to identify a fraction of probesets induced at low oxygen independent of pH in these two cell lines, this fraction included HIG2, NDRG1, PAI1 and RORA. Further verifi cation by qPCR highlighted the necessity of using more cell lines to obtain a robust gene expression profi les. To specifi cally select pH independent hypoxia regulated genes across more cell lines, data for FaDu DD, UTSCC5, UTSCC14 and UTSCC15 were analyzed to identify genes that were induced by hypoxia in each cell line, where the induction was not affected by low pH, and where the gene was not signifi cantly induced by low pH alone. Each cell line had 65 – 122 probesets meeting these criteria. For genes to be considered as target genes (hypoxia inducible pH independent), genes had to be present in three of four cell lines. Conclusion: The result is a robust hypoxia profile unaffected by pH across cell lines consisting of 27 genes. This study demonstrates a way to identify hypoxia markers by microarray, where other factors in the tumor microenvironment are taken into account.

overall_design: Five cell lines, four HNSCC (FaDuDD, UTSCC5, UTSCC14 and UTSCC15) and one cervical (SiHa). Hypoxia was achieved by continually gassing the cells in an airtight chamber for 24 hours with either atmo- spheric air, 5%, 1%, 0.1%, 0.01% or 0% oxygen, sup-  plemented with 5% CO 2 and nitrogen, at 37ºC. To simulate acidosis, pH of the medium (without sodium bicarbonate) was buffered with 20 mM tris (Hydroxym- ethyl) aminomethane (TRIS) base (Sigma), 20 mM 2-(N-Morpholino)ethanesulfonic acid (MES) (Sigma)  and 0.52 g/l NaHCO 3 (Sigma) and titrated to 6.3 or 7.4. The pH adjusted media was applied immediately before the induction of hypoxia. No replicates.

middle: S

first: Jens

last: Overgaard

first: Jan

last: Alsner


title: Expression data from IL-1β-stimulated immature human enterocytes treated with probiotic-conditioned media

city: Charlestown

first: Kriston

last: Ganguli

state: MA

address: 114 16th street

institute: Mass General Hospital for Children

summary:
The conditioned media from Bifidobacterium infantis (BCM) and Lactobacillus acidophilus (LCM) were reported to promote maturation of innate immune response gene expression, which explained the protective effects of probiotics in clinical necrotizing enterocolitis. We used microarray analysis to investigate the expression of genes involved in regulation of BCM and LCM in IL-1β stimulated immature human enterocytes.
The H4 cells (a human nontransformed primary intestinal epithelial cell line) were pretreated with BCM or LCM (15%) for 30 minutes, and then stimulated with or without IL-1β (10 ng/mL) for 4 h. Cell media and IL-1β stimulation were negative and positive control, respectively. RNA was extracted for mcroarray analysis.

overall_design: A total of six treatments (triplicates for each) were included in this study. As one RNA sample in IL-1β-stimulated cells treated with BCM was dropped due to bad quality, seventeen samples were analyzed.  Various treatments were compared to the nagative control (cell media alone). Genes with  a fold-change ≥2 and a p value ≤ 0.05 were selected.

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