title: Platelet-derived growth factor receptor signaling is required for postnatal tendon growth

status: Public on Mar 08 2017

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

summary: Platelet-derived growth factor receptor (PDGFR) signaling plays an important role in the embryonic formation of many different tissues. There is a family of PDGF isoforms which signal through the PDGF receptors α (PDGFRα) and β (PDGFRβ). PDGF regulates many key cellular processes of mesenchymal cell function including proliferation, differentiation, migration and extracellular matrix (ECM) synthesis. While PDGF has been used to enhance flexor tendon healing in vivo, its role in postnatal tendon growth has remained largely unexplored. To determine the importance of PDGFR signaling in postnatal tendon growth, we performed pharmacological blockade of PDGFRα and PDGFRβ, and then induced tendon growth via mechanical overload using the hindlimb synergist ablation model. Our hypothesis was that inhibition of PDGFR signaling will restrict normal growth of tendon tissue in response to mechanical loading.

overall_design: 10 pooled samples total. Equal amounts of RNA isolated from four individual tendons were pooled into a single sample for microarray analysis, and two pooled samples from each group were analyzed. RNA was pooled because gene expression from a pooled sample is similar to the average of the individual samples composing the pooled sample.

first: Kristoffer

middle: B

last: Sugg

first: James

last: Markworth

first: Nathaniel

middle: P

last: Disser

first: Andrew

middle: M

last: Rizzi

first: Jeffrey

middle: R

last: Talarek

first: Dylan

last: Sarver


title: Suppression of epithelial mesenchymal transition by a novel Traf2- and Nck-interacting kinase inhibitory compound

city: Tokyo

first: Teppei

last: Sugano

address: Sendagi, Bunkyo-ku

country: Japan

institute: Graduate School of Medicine,

summary:
Recently, we found that a novel Traf2- and Nck-interacting kinase (TNIK) inhibitor, named NCB-0846, was capable of attenuating tumor-initiating cells among human colorectal cancer. The cross link between EMT and cancer stemness has been revealed in several studies and other group showed another TNIK inhibitor named KY-05009 had inhibited the TGF-β-induced EMT. Therefore we evaluated whether this small-molecule compound could have efficacy to inhibit TGF-β-induced EMT.
NCB-0846 reduced the expression of mesenchymal markers (Vimentin and N-cadherin) and upregulated the expression of epithelial marker E-cadherin in A549 and H2228 non-small cell lung cancer cells. NCB-0846 suppressed the phosphorylation and nuclear translocation of Smad proteins and also inhibited migration, invasion, and metastasis. NCB-0846 inhibited TGF-β1-induced EMT through the down-regulation of TGF-β receptor-1 (TβRI) in mRNA levels. MiR-186-5p and miR-320 family were identified as candidate miRNAs that could target TβRI and we found that miR-186-5p and miR-320s inhibited TβRI expression.  NCB-0846 might be a novel therapeutics drugs that targets the invasion and metastasis through inhibiting TGF-β-induced EMT in lung cancer.

overall_design: EMT related markers and ability of migration, invasion, and metastasis  were examined  after exposure to TGF-B1 only or co-treated with TGF-B1 and NCB-0846 or NCB-970.

last: sugano

first: Mari

last: Masuda

first: Yuko

last: Uno

first: Hideki

last: Moriyama

first: Naoko

last: Goto

first: Masahiro

last: Seike

first: Masaaki

last: Sawa

first: Akihiko

last: Gemma

first: Tesshi

last: Yamada


title: HCoV-229E infection of the human HuH7 cell line [Experiment B]

status: Public on Mar 15 2017

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: The aim of the experiment is to identify changes in host gene expression upon infection of Huh7 hepatoma carcinoma cells  with human coronavirus HCoV-229E as compared to uninfected cells and in comparison to cells stimulated by IL-1alpha (10ng/ml) for 1h. All experiments have been performed at 33°C which is required for sufficient viral entry/replication. Also included are two samples which have been treated with a heat inactivated coronavirus (56°C for 5min).

overall_design: Single-color hybridization of RNA from HuH7 cells. Duplicates.

first: Michael

last: Kracht

last: Poppe


title: Effects of anti-complement component 5 antibody targeting MG4 domain on the normal retina

status: Public on Mar 07 2017

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: This study aims to investigate the effects of anti-complement component 5 antibody targeting MG4 domain on normal retina.

overall_design: Mice were treated with intravitreal injection of anti-C5 antibody (1 or 10 μg/1 μL PBS). At 7 days after the injection, retinas were prepared from the enucleated eyes. Four retinas from 4 mice were put into a microcentrifuge tube for further analyses. 'Control', 'Therapeutic' and 'Toxic' groups mean that the mice received intravitreal PBS, 1 μg of anti-C5 antibody and 10 μg of anti-C5 antibody. Three biological replicates were included for each group.

first: Dong

last: Jo

first: Jin

first: Wonjun

last: Yang

first: Hyori

first: Shinjae

last: Jang

first: Dongjo

first: Minseok

last: Chang

first: Kihwang

last: Lee

first: Junho

last: Chung

first: Jeong


title: Expression data of differentially regualted genes in TH-MYCN mouse tumors after immunotherapy

city: Stockholm

first: Per

last: Kogner

address: Karolinska University Hospital

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

country: Sweden

institute: Karolinska Institutet

summary: In order to understand differentially regulated gene expression after the different treatments, 4 size matched tumors of each group were analyzed by microarrays.

overall_design:
TH-MYCN mice were treaded for 10 days with BLZ945 (CSF-1R inhibitor, Novartis), anti-PD-1/L1 antibodies, are the combination of both. Control mice remained untreated.
Heterozyous TH-MYCN mice were treated for 10 days as soon as they had a palpable tumor in their abdomen. At day 10, mice were sacrificed, tumors were weighed and snap frozen. Tumors were kept at -80degree until further analysis.

first: Nina

last: Eissler


title: Immunostimulatory endogenous nucleic acids drive the lesional inflammation in cutaneous lupus erythematosus

status: Public on Mar 01 2017

city: Bonn

first: Joerg

last: Wenzel

address: Sigmund Freud Str 25

department: Dermatology

institute: University of Bonn

summary:
Cutaneous lupus erythematosus (CLE) is a photosensitive autoimmune disease characterized by a strong type-I-interferon (IFN) associated inflammation. Keratinocytes are known to determine the interface-dermatitis-pattern in CLE by production of proinflammatory cytokines in the lower epidermis. These cytokines drive a cytotoxic anti-epithelial immune response resulting in keratinocytic cell death and release of endogenous nucleic acids (eNA). We hypothesized that these eNA (RNA- and DNA-motifs) have the capacity to activate innate immune pathways in keratinocytes via pathogen-recognition-receptors (PRR).
Gene expression analyses revealed an excessive activation of innate immune response pathways with strong expression of IFN-regulated cytokines in CLE skin lesions. Cultured keratinocytes produce large amounts of these cytokines in response to stimulation of PRR with eNA. UV-stimulation enhances the immunogenicity of eNA and induces CLE-like skin lesions in knockout mice lacking the cytosolic DNase TREX1.
Our results provide evidence for a pathogenetic role of endogenous nucleic acids in CLE. They are released within the cytotoxic inflammation along the dermo-epidermal junction and have the capacity to drive the LE-typical inflammation. UV-irradiation supports this inflammation by generation of highly immunostimulatory DNA motifs (8-OHG).
These findings explain the photosensitivity of lupus patients and identify pathways of the innate immune system as targets for future therapies.

overall_design: Lesional skin biopsies were taken from patients with active, untreated lupus skin disease (Chronic discoid lupus erythematosus = CDLE, n=6; subacute cutaneous lupus erythematosus =  SCLE, n=5). Healthy control (HC) specimens were obtained from healthy skin of 5 patients undergoing plastic surgery. In every case, two 4mm punch biopsies were taken. One was flash-frozen in liquid nitrogen and afterwards processed for mRNA isolation and gene expression analyses. The second biopsy was fixed in 5% formalin solution overnight, and was proceeded for histological investigation.

first: Benedikt

last: Scholitissek


title: Synergistic effects of space radiation and microgravity (miRNA WT and dys-mutant)

city: Dalian

first: Ying

last: Gao

state: Liaoning

address: Linghai Road 1

country: China

institute: Dalian Maritime university

summary:
Space radiations and microgravity both could cause DNA damage in cells, but the eﬀects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceﬂight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed.
The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.

overall_design: In our study, wild type and dys-1 mutant strains of C.elegans endured four conditions during shenzhou-8 spaceflight mission, including spaceflight static condition(ss), spaceflight 1-g centrifugal condition(sc), ground control condition(gc) and no-transport control. Limited to the quantity of worm samples, we performed technical-repeat test but not sample-repeat test. Accordingly, eight miRNA microarrays were performed.

first: Yeqing

last: Sun


title: lncRNA expression of CRC liver metastasis

status: Public on Feb 28 2017

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

institute: Sun Yat-sen University Cancer Center

summary: The purpose of this study is to identify lncRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 439 miRNAs were identified to be differentially expressed between 7 primary CRC tissues with liver metastases and 8 CRC tissues without liver metastases from 15 patients by Arraystar lncRNA microarrays

overall_design: 7 CRC with liver metastasis and 8 CRC without liver metastasis were subjected to microarray to select differentially expressed lncRNAs

first: D

middle: L

first: R

middle: H

last: Xu


title: Synergistic effects of space radiation and microgravity (miRNA WT and ced-1 mutant)

summary:
Space radiations and microgravity both could cause DNA damage in cells, but the eﬀects of microgravity on DNA  damage response to space radiations are still controversial.A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceﬂight environment and space radiations environment during 16.5-day Shenzhou-8 space mission was performed.
The analyzation this study are further described in Gao, Y., Xu, D., Zhao, L., Zhang, M. and Sun, Y. (2015) Effects of microgravity on DNA damage response in Caenorhabditis elegans during Shenzhou-8 spaceflight. International journal of radiation biology, 91, 531-539.

overall_design: In our study, wild type and ced-1 mutant strains of C.elegans endured three conditions during shenzhou-8 spaceflight mission, including spaceflight static condition(ss), spaceflight 1-g centrifugal condition(sc) and ground control condition(gc).  Limited to the quantity of worm samples, we performed technical-repeat test but not sample-repeat test.Accordingly，six miRNA microarrays were performed.


title: Development of gene expression signatures of GPCR family.

city: Nanchang

first: Jian-feng

last: Zheng

state: Jiangxi

address: No.1 Min De Road

institute: Nanchang University

summary: In human HCC tumors, matching paracancerous specimens, and normal liver specimens, a targeted gene expression microanalysis was used to screen alterations in GPCR family gene expression.

overall_design: A targeted gene expression microanalysis was used to screen alterations in GPCR family in 3 human HCC tumors, matching paracancerous specimens, and 3 normal liver specimens.

first: Qiong

last: Wu

first: Jin-xian

first: Yu

first: Li-li

last: Cai

first: Xiao-zhong

last: Wang

first: Wu-hua

last: Guo


title: Synergistic effects of space radiation and microgravity

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

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

overall_design: Refer to individual Series


title: TSA induced gene expression variation on breast cancer cell SKBR3

city: Xi'an

first: Ting

address: Changlexilu Road

department: Biochemistry and Molecular Biology

institute: the Fourth Military Medical University

summary: To explore TSA influence on human breast cancer cells, we attempt to analyze genes differentially expressed between TSA treated and untreated SKBR3 cells, which will hopefully provide clues for TSA target genes.

overall_design: Gene expression in human breast cancer cell SKBR3 was measured at 24 hours after treated with 330nM TSA. Three independent experiments were performed at each time using different donors for each experiment.

first: Lintao

last: Jia

first: Lei

first: Guoyin

last: Li


title: Integrin-regulated gene expression in immortalized keratinocytes

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

country: USA

institute: SUNY-University at Albany

summary:
Gene-level analysis of gene expression in immortalized mouse keratinocyte lines that express integrins alpha3beta1 and alpha9beta1 in different combinations.
The integrins alpha3beta1 and alpha9beta1 are expressed highly in the epidermis, but their roles in regulating gene expression programs that promote normal or pathological wound healing have not been explored previously.  In order to identify genes that are regulated by these integrins in keratinocytes, we used microarray approaches to identify integrin-dependent genes in mouse keratinocytes that were immortalized with SV40 large T antigen (i.e., MK cells).

overall_design: We used the Affymetrix Mouse Exon 1.0 ST platform to analyze biological replicates of MK cell lines that were derived from alpha3-null mice (MK546), as well as variants of this line in which human integrin subunits alpha3 and/or alpha9 were expressed in different combinations.  Array data was processed by Affymetrix Exon Array Computational Tool.

first: C

last: DiPersio

first: Livingston

last: Van deWater

first: Whitney

last: Longmate


title: mRNA Expression Data from Murine Hearts of Pcyt2+/- Male and Female Mice at 8 Months of Age

status: Public on Feb 17 2017

city: Guelph

first: Marica

last: Bakovic

state: Ontario

address: 50 Stone Rd E

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

summary:
Hearts were collected from Pcyt2+/- male and female mice at 8 months of age
The microarray approach allows the investigation of gene expression changes of all genes in Pcyt2+/- male and female hearts.

overall_design: There are a total of 8 samples, 4 from Pcyt2+/- males 8 months old and 4 from  Pcyt2+/- females 8 months old.


title: Long non-coding RNAs and mRNAs in nasopharyngeal carcinoma metastasis

status: Public on Feb 22 2017

first: Jun

last: Ma

address: 651 Dongfeng Road East

summary: Increasing evidence has demonstrated a significant role for long non-coding RNAs (lncRNAs) in tumorigenesis. However, their functions in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, a model compared high and low metastatic NPC cell lines (5-8F vs. 6-10B and S18 vs. S26)was constructed to determine the expression profile of lncRNAs using the microarray analysis, and we found 167 lncRNAs and 209 mRNAs were differentially expressed. Validationof 26 significantly dysregulated lncRNAs by qRT-PCR showed the expression patterns of 22 lncRNAs were in accordance with the microarray data. Furthermore, the expression level of ENST00000470135, which was the most upregulated lncRNA in high metastatic cell lines, was significantly higher in NPC cell lines and tissues with lymph node metastasis（LNM）and knocking down ENST00000470135 suppressed the migration, invasion and proliferation of NPC cells in vitro. In conclusion, our study revealed expression patterns of lncRNAs in NPC metastasis. The dysregulated lncRNAs may act as novel biomarkers and therapeutic targets for NPC.

overall_design: Total RNA recovered from two sets of cell lines (5-8F vs. 6-10B and S18 vs. S26) were used to acquire different expression profiles of mRNAs and lncRNAs in high metastatic potential and low metastatic potential nasopharyngeal carcinoma cell lines.

first: Xin

last: Wen

last: Liu


title: FUS/TLS acts as an aggregation-dependent modifier of polyglutamine disease model mice

status: Public on Feb 12 2017

first: Yoshihiro

last: Kino

address: 2-522-1 Noshio, Kiyose

institute: Meiji Pharmaceutical University


title: Identification of LncRNA Expression Signatures for breast cancer brain metastasis (BCBM)

city: Houston

first: chunru

last: lin

state: TX

address: 1515 Holcombe Blvd

department: Molecular & Cellular Oncology

institute: MD Anderson Cancer Center

summary: To identify BCBM-relevant lncRNAs, we assessed the expression profiles of lncRNAs in parental MDA-MB-231 (231-PAR) cells and isogenic brain metastatic cells (231-BRN), which were isolated from brain-seeking 231-PAR cells

overall_design: LncRNA Expression profiling analysis of the 231-PAR and 231-BRN by Arraystar Human LncRNA Array v3.0.

first: Shouyu

first: Liuqing

last: Yang

first: Chunru

last: Lin


title: FUS/TLS acts as an aggregation-dependent modifier of polyglutamine disease model mice (II)

summary:
FUS/TLS is an RNA/DNA-binding protein associated with neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Previously, we found that a prion-like domain in the N-terminus of FUS/TLS mediates co-aggregation between FUS/TLS and mutant huntingtin, the gene product of Huntington's disease (HD). Here, we show that heterozygous knockout of FUS/TLS worsened the phenotypes of model mice of Huntington's disease (HD) but not spinal and bulbar muscular atrophy (SBMA). This difference was correlated with the degree of pathological association between disease proteins and FUS/TLS. Co-aggregation between FUS/TLS and mutant huntingtin resulted in the depletion of free FUS/TLS protein in HD mice that was detected as a monomer in SDS-PAGE analysis. Recently, we found that FUS/TLS paralogs, TAF15 and EWS, were up-regulated in homozygous FUS/TLS knockout mice. These two proteins were up-regulated in both HD and FUS/TLS heterozygote mice, and were further elevated in HD-TLS+/- double mutant mice, consistent with the functional impairment of FUS/TLS. These results suggest that FUS/TLS sequestration by co-aggregation is a rate-limiting factor of disease phenotypes of HD and that inclusions may have an adverse aspect, rather than being simply benign or protective. In addition, our results highlight inclusions as repositories of potential modifiers of neurodegeneration.
Gene expression profiles were analyzed to examine the effects of FUS/TLS heterozygosity in mouse with or without the transgene of mutant androgen receptor.

overall_design: To examine the effect of FUS/TLS heterozygosity on the transcriptome of spinal and bulbar muscular atrophy (SBMA) model mice, we crossed FUS/TLS heterozygous knockout mice with SBMA model mice. We extracted total RNA from the spinal cord of these mice at 8 weeks and used for a microarray analysis. The samples are SBMA transgenic mice with FUS/TLS heterozygosity (SBMA_TLS+/-), SBMA mice with normal FUS/TLS (SBMA_TLS+/+), non-SBMA-transgenic mice with FUS/TLS heterozygosity (NT_TLS+/-), and non-SBMA-transgenic mice with normal FUS/TLS (NT_TLS+/+).

first: Nobuyuki

last: Nukina


title: Dysregulated gene expression pathways in mice models of HR-MDS and AML post MDS mimic human disease

status: Public on Feb 11 2017

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: In spite of the recent discovery of genetic mutations in most MDS, pathophysiology of those disorders remain poorly known, and few animal are available. We performed global exome specific gene expression profiling and functional pathway analysis in purified Sca1+ spleen cells of two MDS transgenic mouse models developed by our group. Those models mimic high-risk MDS (HR MDS) and AML post MDS, depending on the transgene promoters used (MRP8NRASD12/tethBCL-2 and MRP8NRASD12/MRP8hBCL-2 respectively). We found common deregulated pathways in both models showing disease continuum. The most significantly deregulated pathways identified have previously been reported in MDS patients such as cell cycle, DNA replication/damage/repair, apoptosis, immune responses and canonical Wnt pathways. Interestingly, this analysis highlights other deregulated pathways such as non-canonical Wnt pathways including Rho signaling and circadian rhythm that may be critical in a human MDS setting.

overall_design: MRP8NRASD12/tethBCL-2 and MRP8[NRASD12/hBCL-2] double transgenic mice were analyzed by enriching for primitive Sca1+ cells from splenocytes. RNA was extracted analyzed for gene expression profiles using exon specific arrays.

first: Patricia

last: Krief

first: Laura

last: Guerenne

first: Stephanie

last: Beurlet

first: Rose-Ann

last: Padua


status: Public on Feb 09 2017

city: chuo-ku

first: Yu

last: Fujita

state: Tokyo

address: 5-1-1 Tsukiji

department: Research of Molecular Functions and Targets

institute: National Cancer Center Research Institute

summary: In general, microRNAs (miRNAs) regulate gene expression by repressing translation or promoting the degradation of their target genes. To strategically identify direct microR-197 (miR-197) target genes, we first performed mRNA microarray analyses of A549, PC14, and PC14CDDP cells that were transiently transfected with either pre-miR-197 or LNA-miR-197 and their controls. We observed that 1037 predicted target genes exhibited expression alterations consistently across the three different lung cancer cell lines.

overall_design: To detect the mRNAs in cells, 100 ng of total RNA was labelled and hybridised using a SurePrint G3 Human GE v2 8x60K Microarray (Agilent Technologies) according to the manufacturer’s protocol. Hybridisation signals were detected using a DNA microarray scanner (Agilent Technologies).

first: Takahiro

last: Ochiya


title: miR-135b expression effect on myxoid liposarcoma cell line

first: Yutaka

last: Nezu

address: Tsukiji 5-1-1, Chuo-ku

department: Molecular and Cellular Medicine

institute: National Cancer Center, Research Institute

summary: miR-135b expression is higher in myxoid liposarcoma cell lines than in adipose-derived mesenchymal cell line, as well as in myxoid liposarcoma tumors than in adjacent normal prostate tissues.To further investigate the molecular mechanisms regulated by miR-135b, we performed mRNA microarray analysis of cell cultures from myxoid liposarcoma cell line after transfections with miR-135b mimic or negative control.

overall_design: mRNA expression of cell cultures from myxoid liposarcoma cell line 2645-94 after transient transfection with miR-135b mimic or negative control were measured.


title: The CD4+ CD52 low T Cells Contributes to the Development of Systemic Lupus Erythematosus through the CCR8/TARC Pathways

status: Public on Feb 14 2017

city: Nagasaki

first: Masataka

last: Umeda

state: Nagasaki

department: Unit of Advanced Preventive Medical Sciences

institute: Nagasaki University Graduate School of Biomedical Sciences

summary: Objective: CD52 is a cell-surface glycoprotein that is widely expressed in lymphocytes. CD4+CD52high T cells inhibit the activation of CD4+CD52low T cells through the release of cell-surface CD52. The role of the immune regulation of these cells in systemic lupus erythematosus (SLE) is unknown. Methods: Blood samples obtained from SLE patients, rheumatoid arthritis (RA) patients and 33 healthy controls (HC). The expressions of CD4+CD52high T cells and CD4+CD52low T cells were analyzed by flow cytometry. To determine the genetic characteristics of these cells from SLE, we performed cDNA microarrays and examined the function of the genes in in-vitro. Results: The expression of CD4+CD52low T cells in the SLE was significantly higher than HC and non-SLE and its expression were positively correlated with SLEDAI, anti-ds-DNA antibodies and IgG. The population of circulating follicular helper like T cells (Tfh like cells) were increased in SLE and its expression was positively correlated with CD4+CD52low T cells. The microarray analysis revealed that the expression of chemokine receptor 8 (CCR8) is increased in CD4+CD52low T cells. In addition, in vitro experiments using CD4 T cells from patients with SLE showed that thymus and activation-regulated chemokine (TARC), known as a ligand of CCR8, induced the conversion of CD4+CD52high T cells into CD4+CD52low T cells. Conclusion: Our data suggest that increased CD4+CD52low T cells along with increased Tfh like cells are involved in the pathogenic autoantibodies production and that TRAC may contributes to the development of SLE via an aberrant induction of CD4+CD52low T cells.

overall_design: CD4+ CD52low T cells and CD4+ CD52high T cells from five SLE patients were sorted by sorting flow cytometry. The expression of messenger RNA from each populations was analyzed by microarray analysis.

first: Kunihiro

last: Ichinose

first: Atsushi

last: Kawakami


title: Reseveratrol and Rosiglitazone regulation of liver gene expression in ZDF rats

status: Public on Feb 07 2017

first: David

last: Mutch

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

summary: The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.

overall_design: A total of 5 microarrays were run for each group, for a total of n=20 samples. For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Rat Gene 2.1 ST array strips, according to the manufacturer’s instructions (Affymetrix Inc., Fremont, CA, USA).

first: Monica

last: Wong


title: Reseveratrol and Rosiglitazone regulation of blood gene expression in ZDF rats

summary: The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and whole blood.


title: FUS/TLS acts as an aggregation-dependent modifier of polyglutamine disease model mice (I)

first: Yoshihiro

last: Kino

summary:
FUS/TLS is an RNA/DNA-binding protein associated with neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Previously, we found that a prion-like domain in the N-terminus of FUS/TLS mediates co-aggregation between FUS/TLS and mutant huntingtin, the gene product of Huntington's disease (HD). Here, we show that heterozygous knockout of FUS/TLS worsened the phenotypes of model mice of Huntington's disease (HD) but not spinal and bulbar muscular atrophy (SBMA). This difference was correlated with the degree of pathological association between disease proteins and FUS/TLS. Co-aggregation between FUS/TLS and mutant huntingtin resulted in the depletion of free FUS/TLS protein in HD mice that was detected as a monomer in SDS-PAGE analysis. Recently, we found that FUS/TLS paralogs, TAF15 and EWS, were up-regulated in homozygous FUS/TLS knockout mice. These two proteins were up-regulated in both HD and FUS/TLS heterozygote mice, and were further elevated in HD-TLS+/- double mutant mice, consistent with the functional impairment of FUS/TLS. These results suggest that FUS/TLS sequestration by co-aggregation is a rate-limiting factor of disease phenotypes of HD and that inclusions may have an adverse aspect, rather than being simply benign or protective. In addition, our results highlight inclusions as repositories of potential modifiers of neurodegeneration.
Gene expression profiles were analyzed to examine the effects of FUS/TLS heterozygosity in mouse with or without the transgene of mutant huntingtin exon 1.

overall_design: To examine the effect of FUS/TLS heterozygosity on the transcriptome of Huntington's disease model mice, we crossed FUS/TLS heterozygous knockout mice with HD model mice. We extracted total RNA from the striatum of these mice at 8 weeks and used for a microaaray analysis. The samples are HD transgenic mice with FUS/TLS heterozygosity (HD_TLS+/-), HD mice with normal FUS/TLS (HD_TLS+/+), non-HD-transgenic mice with FUS/TLS heterozygosity (NT_TLS+/-), and non-HD-transgenic mice with normal FUS/TLS (NT_TLS+/+).


title: Reseveratrol and Rosiglitazone regulation of red tibialis anterior (red TA) gene expression in ZDF rats


title: Acute dietary fat intake initiates alterations in energy metabolism and insulin resistance

status: Public on Feb 02 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
BACKGROUND. Dietary intake of saturated fat is a likely contributor to nonalcoholic fatty liver disease (NAFLD) and insulin resistance, but the mechanisms that initiate these abnormalities in humans remain unclear. We examined the effects of a single oral saturated fat load on insulin sensitivity, hepatic glucose metabolism, and lipid metabolism in humans. Similarly, initiating mechanisms were examined after an equivalent challenge in mice.
METHODS. Fourteen lean, healthy individuals randomly received either palm oil (PO) or vehicle (VCL). Hepatic metabolism was analyzed using in vivo 13C/31P/1H and ex vivo 2H magnetic resonance spectroscopy before and during hyperinsulinemic-euglycemic clamps with isotope dilution. Mice underwent identical clamp procedures and hepatic transcriptome analyses.
RESULTS. PO administration decreased whole-body, hepatic, and adipose tissue insulin sensitivity by 25%, 15%, and 34%, respectively. Hepatic triglyceride and ATP content rose by 35% and 16%, respectively. Hepatic gluconeogenesis increased by 70%, and net glycogenolysis declined by 20%. Mouse transcriptomics revealed that PO differentially regulates predicted upstream regulators and pathways, including LPS, members of the TLR and PPAR families, NF-κB, and TNF-related weak inducer of apoptosis (TWEAK).
CONCLUSION. Saturated fat ingestion rapidly increases hepatic lipid storage, energy metabolism, and insulin resistance. This is accompanied by regulation of hepatic gene expression and signaling that may contribute to development of NAFLD.

overall_design: We performed gene expression microarray analysis of liver derived from mice treated with palm oil under euglycemic hyperinsulinemic clamps and control animals.

first: Elisa

last: Álvarez Hernández

first: Sabine

last: Kahl

first: Anett

last: Seelig

first: Paul

last: Begovatz

first: Martin

last: Irmler

first: Yuliya

last: Kupriyanova

first: Bettina

last: Nowotny

first: Peter

first: Christian

last: Herder

first: Cristina

last: Barosa

first: Filipa

last: Carvalho

first: Jan

last: Rozman

first: Susanne

last: Neschen

first: John

middle: G

last: Jones

last: Hrabe de Angelis

first: Michael

last: Roden


title: Transcriptional Profiling of Dysregulated lncRNAs in B cells Response to Active Tuberculosis

status: Public on Jan 30 2017

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

institute: weifang medical universtiy

summary: Role of lncRNAs in human adaptive immune response to active tuberculosis (TB) infection is largely unexplored. The objective of this study was to characterize lncRNA expression profile in primary human B cell response to active TB infection using mcroarray assay.

overall_design: Patients with active pulmonary TB (male/female=13:18) with a mean age of 42.1±15.5 yr (ATB group) were recruited from Weifang No. 2 People’s Hospital of Shandong Province, China. Diagnosis of active pulmonary TB was based on both sputum smear and culture positive or at least one sputum culture positive, as well as typical pulmonary TB clinical symptoms. Healthy subjects (male/female=15:20) with a mean age of 40.3±13.9 yr (control group) were enrolled from the staff of Weifang Medical University, were free of clinical symptoms of any infectious disease, and had no close contact of a TB patient. All involved subjects had no history of TB, diabetes, tumor or other infectious disease. Three samples randomly selected from each group (male/female=1:2,BT1,BT2 and BT3 for ATB group, CB1,CB2 and CB3 for controls) were used in the microarray assay and all of the samples were used for further RT-qPCR confirmation.

first: Yurong

last: Fu

first: Zhengjun

last: Yi

first: Xianqin

last: Xu

first: Junfang

last: Xue

first: Wenping

last: Duan


title: lncRNA expression in leukemia

status: Public on Jan 13 2017

city: stanford

first: chunjiang

last: he

address: 265 campus drive

institute: stanford university

summary: Global analysis of differentially expressed lncRNAs between AML and control samples

overall_design: Total RNA from bone marrow mononuclear cells were extracted using TRIzol reagent following the manufacturer's instructions. ArrayStar lncRNA array V3 was performed to detect the differentially expressed lncRNAs and mRNAs.

first: Chunjiang

last: He

first: Lijun

last: Lei

first: Siyu

last: Xia


title: Hyperglycemic Memory – New insights into a thought to be known topic

status: Public on Feb 01 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Hyperglycemic memory is part of the pathogenesis of diabetic retinopathy. We established a novel mouse model of intermediate-term hyperglycemic memory and demonstrated that changes in gene expression and microvascular damage in the neurovascular unit of the diabetic retina persist after euglycemic reentry, indicating memory.
Using microarrays and functional annotation clustering of full genome expression data, genes meeting the criteria for hyperglycemic memory were attributed to the cytoskeletal and nuclear compartments of cells of the neurovascular unit.

overall_design: 12-weeks-old STZ-diabetic animals (DC12W), 6-weeks-old STZ-diabetic animals receiving isogenic pancreatic islet transplantation for further 6 weeks (DC+Tx@12W) and age-matched controls (NC) were analyzed after 6 (@6W) and 12 weeks (@12W).

first: Patrick

last: Friedrichs

first: Hans-Peter

last: Hammes


title: Deficiency of myeloid-related proteins 8 and 14 (Mrp8/Mrp14) does not block inflammaging but prevents steatosis

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

summary: The Mrp8 and Mrp14 proteins (calprotectin) accumulate within tissues during aging and may contribute to chronic inflammation. To address this possibility, we evaluated calprotectin-deficient Mrp14-KO and wild-type (WT) mice at 5 and 24 months of age. However, there was no evidence that age-related inflammation is blunted in KO mice. Inflammation makers were in fact elevated in livers from old KO mice, and microarray analysis revealed more consistent elevation of genes specifically expressed by B-cells and T-cells. Adipose-specific genes, however, were less consistently elevated in aged KO mice, suggesting an anti-steatosis effect of Mrp8/14 deficiency. Consistent with this, genes decreased by the anti-steatosis agent SRT1720 were decreased in old KO compared to old WT mice. Expression of lipid metabolism genes was altered in KO mice at 5 months of age, along with genes associated with development, biosynthesis and immunity. These early-age effects of Mrp8/14 deficiency, in the absence of any external stressor, were unexpected. Taken together, our findings demonstrate a pro-steatosis rather than pro-inflammatory role of calprotectin within the aging liver. This appears to reflect a developmental-metabolic phenotype of Mrp14-KO mice that is manifest at a young age in the absence of pro-inflammatory stimuli.

overall_design: Gene expression was compared between Mrp14-KO and wild-type (WT) mice at young and old ages (5 and 24 months, respectively). Expression was profiled in 5-8 mice per group (young-WT: n = 5; young-KO: n = 5; old-WT: n = 6; old-KO: n = 8)

first: Nicole

last: Ward

first: Johann

middle: E

last: Gudjonsson


title: Colon tumor samples from mice with Braf V600E, Cdx2-/-, or both, as well as control colon, and tumors from Apc-/- mice.

status: Public on Jan 10 2017

first: Rork

last: Kuick

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

summary: We tamoxifen treated 8-12 week old mice that had floxed alleles of the following: 1) both Apc alleles (giving rise to Apc truncation/inactivation); 2) both Cdx2 alleles (giving rise to Cdx2 inactivation; 3) one Braf allele, that upon Cre-mediated recombination gives a Braf V600E mutant allele (details below), and 4) the combination of both the Cdx2 alleles and the BrafV600E allele. All four of those groups also had a CDX2P-CreERT2 transgene that expresses Cre recombinase fused to a tamoxifen-regulated fragment of the estrogen receptor ligand binding domain. CreERT2 expression occurs only in tissues where the Cdx2 gene is expressed, which is almost exclusively in adult mouse cecum and colon epithelium. A fifth group of mice had the floxed Cdx2 alleles, but no CDX2P-CreERT2 gene.  Treating the mice having CDX2P-CreERT2 with tamoxifen permits the Cre recombinase to enter the cell nucleus and recombine the Apc, Braf, and/or Cdx2 alleles containing loxP sequence elements. Mice were treated with intraperitoneal injection of tamoxifen dissolved in corn oil. Three mice per group were used.   The control mice did not develop tumors or any morphological or histological changes in their epithelium, but their colons were used to create the 3 control samples. To obtain the BrafV600E allele we used a genetically engineered mouse line previously described by Dankort et al. (Genes Dev 2007, 21:379-84) that can express the BrafV600E mutant protein following Cre-mediated recombination. The  Braf(CA) (Braf-Cre-activated) allele mice carry a gene-targeted allele of Braf, where Braf sequences from exons 15-18 are present in the normal mouse Braf intron 14, followed by a mutated exon 15 (carrying the V600E mutation). The exon 15-18 sequence element is flanked by loxP sites. In the absence of Cre-mediated recombination, the Braf(CA) allele expresses a wild type Braf protein. Following Cre-mediated recombination,  the Braf exon 15-18 element is removed, and the Braf(CA) allele then encodes the Braf V600E protein (from the introduced mutated exon 15).  RNA was purified from tumor or normal tissue, and targets for Affymetrix arrays were synthesized from the mRNAs.  We used Affymetrix Mouse Gene 2.1 ST arrays, which hold 41345 probe-sets, but we largely analyzed just those 25216 probe-sets that were mapped to Entrez gene IDs.  Raw data was processed with the Robust Multi-array Average algorithm (RMA).  Data is log2-transformed transcript abundance estimates. We fit a one-way ANOVA model to the five groups of samples.  We supply a supplementary excel workbook that holds the same data as the data matrix file, but also holds the probe-set annotation at the time we analyzed the data, and some simple statistical calculations, which selects subsets of the probe-sets as differentially expressed between pairs of groups, as well as significant Cdx2-/- by Braf V600E interactions. It also gives the homologous human gene IDs we used for enrichment testing, which were 1-to-1 best homologs according to build 68 of NCBI's Homologene. A second supplementary sheet shows the data we enrichment tested after collapsing to distinct human homologs, joins of the results of tests with GSE4045 data and of tests with TCGA data to the mouse genes, and the intersections of selected genes in those data set with our gene selections in mouse.  Consumers should consider obtaining more up-to-date probe-set annotation for the array platform.

overall_design: Three colon tumor samples from 3 mice with conditional knockout of Apc, 3 colon tumors samples from 3 mice with conditional knockout of Cdx2, 3 colon tumor samples from 3 mice with conditional rearrangement of Braf to yield Braf V600E mutations, 3 colon tumor samples from 3 mice with both the Cdx2 knockout and the Braf V600E mutation, and 3 samples from the colons of 3 control mice (who had floxed Cdx2 alleles but no Cre recombinase transgene).

first: Naoya

last: Sakamoto

first: Ying

last: Feng

first: Carmine

last: Stolfi

first: Yuki

last: Kurosu

first: Maranne

last: Green

first: Kazuhiro

last: Sentani

first: Wataru

last: Yasui

first: Martin

last: McMahon

first: Karin

last: Hardiman

first: Jason

last: Spence

first: Joel

middle: K

last: Greenson

first: Kathleen

last: Cho

first: Eric

last: Fearon


title: Th22 cells form a distinct T helper lineage from Th17 cells in vitro with unique transcriptional properties and Tbet-dependent Th1 plasticity

status: Public on Jan 16 2017

city: New Lambton Heights

first: Maximilian

last: Plank

state: Australia

address: Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

summary: To determine the transcriptional profile of Th22 cells and allow comparative analysis with Th17 cells

overall_design: A total of 6 samples was arrayed. 2 samples for each Naïve, Th17 and Th22 cells.

middle: W

first: Gerard

last: Kaiko

first: Steven

last: Maltby

first: Jessica

last: Weaver

first: Hock

last: Tay

first: Scott

last: Durum

first: Paul

middle: S

last: Foster


title: Microarray analysis on fat bodies of fruit fly (Drosophila melanogaster) larvae fed with either a semi-purified diet only or a semi-purified diet supplemented with palm fruit juice (PFJ)

status: Public on Jan 06 2017

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary: PFJ (4 ml for a final concentration of 19,000 mg gallic acid equivalent (GAE) per kg diet or 0.86 mg GAE per kcal diet) was supplemented to larvae of fruit flies (Drosophila melanogaster) given a semi-purified diet to observe for possible effects on energy metabolism and lifespan. Fat bodies extracted from these larvae were used five days since the egg stage for gene expression studies. Results from the microarray data analysis carried out show that fruit fly larva fat bodies given PFJ had up-regulated heat shock protein genes, while cell cycle and growth genes were down-regulated.

overall_design: Total RNA obtained from fat bodies of fruit fly (Drosophila melanogaster) larvae given PFJ in a semi-purified diet (five days since the egg stage) were compared to controls (two replicates in the treatment group versus two replicates in the control group, with each replicate containing total RNA from ten larva fat bodies).

first: Soon

first: K

middle: C

last: Hayes

first: Ravigadevi

last: Sambanthamurthi


title: Microarray analysis on fruit fly (Drosophila melanogaster) larvae and fat bodies of fruit fly larvae fed with either a semi-purified diet only or a semi-purified diet supplemented with palm fruit juice (PFJ)

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

overall_design: Refer to individual Series


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency

status: Public on Apr 07 2017

city: New York

first: Frederique

last: Ruf-Zamojski

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center


title: A novel LSD1 inhibitor T-3775440 induces transdifferentiation in AML cell lines

status: Public on Jan 01 2017

city: Fujisawa

first: Yoshinori

last: Ishikawa

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

institute: Takeda Pharmaceutical Company Ltd.

summary: We describe the anti-leukemic activity and mechanism of action of T-3775440, a novel irreversible LSD1 inhibitor. Cell growth analysis of leukemia cell lines revealed that acute erythroleukemia (AEL) and acute megakaryoblastic leukemia cells (AMKL) are highly sensitive to this compound. T-3775440 treatment enforced transdifferentiation-like phenotypic change from erythroid/megakaryocytic lineages into granulomonocytic lineage. Our findings provide the rationale for testing LSD1 inhibitors as potential treatments with a novel mechanism of action for AML, particularly AEL and AMKL.

overall_design: Total RNA obtained from cells treated with or without 100 nM of T-3775440 for 24 hours in vitro. Effects of T-3775440 on AML cells lines were compared that of DMSO-treated control.

first: Koji

last: Yamamoto


title: Gene expression analysis of RNAs isolated from WT and ZIP7-depleted human mesenchymal stem cells

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to identify the roles of ZIP7 in hMSCs , we performed a gene expression microarray analysis for the RNAs isolated from WT and ZIP7-depleted hMSCs

overall_design: Duplicate experiments were performed for WT and ZIP7 knock-down human mesenchymal stem cells. Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturer's protocols.

first: Bum-Ho

last: Bin

first: Jinhyuk

last: Bhin


title: Microarray analysis on fruit fly (Drosophila melanogaster) larvae fed with either a semi-purified diet only or a semi-purified diet supplemented with palm fruit juice (PFJ)

summary: PFJ (4 ml for a final concentration of 19,000 mg gallic acid equivalent (GAE) per kg diet or 0.86 mg GAE per kcal diet) was supplemented to larvae of fruit flies (Drosophila melanogaster) given a semi-purified diet to observe for possible effects on energy metabolism and lifespan. Larvae were used five days since the egg stage for gene expression studies. Results from the microarray data analysis carried out show that fruit fly larvae given PFJ had up-regulated transport and metabolic processes, while development and morphogenesis processes were down-regulated.

overall_design: Total RNA obtained from larvae of fruit flies (Drosophila melanogaster) given PFJ in a semi-purified diet (five days since the egg stage) were compared to controls (three replicates in the treatment group versus three replicates in the control group, with each replicate containing total RNA from three to four larvae).

first: S


title: Development of gene expression signatures for the HDF and MDA-MB-231 cells that received TP4 (a cationic antimicrobial peptide) treatment

status: Public on Dec 31 2016

city: Yilan

first: Chen-Hung

last: Ting

state: Taiwan

address: 23-10 Dawen Rd., Jiaoxi

department: Marine research station, Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Triple-negative breast cancer (TNBC) lacks therapeutic target and is difficult to treat. We report a cationic antimicrobial peptide (CAP), tilapia piscidin 4 (TP4), derived from Nile tilapia (Oreochromis niloticus), selectively toxic to TNBC. Here we aim to identify potential target in TNBC cell response to TP4 treatment by microarray study and to further address the role of TP4-resposive genes involved in TNBC cell death.

overall_design: TNBC (MDA-MB-231) cells and control (HDF) cells were treated with TP4 at 14 ug/mL for 6hr. Duplicated total RNA samples (i.e. two mock treated and two TP4 treated groups in each cell-line) were collected for further microarray study.

first: Yi-Chun

last: Chen

first: Jyh-Yih


title: Gene expression profiles from human splenic macrophages, sinusoid lining cells and HUVECs

city: Barcelone

first: Carolina

middle: Mercedes

last: Barra

address: Aiguader 88

country: Spain

institute: IMIM

summary: Compared to typical endothelial cells (HUVEC) and splenic macrophages (CD14+CD45+), SLCs have phenotype closer to splenic macrophages.

overall_design: Unstimulated splenic macrophages and SLCs were FACSorted from the collagenase digested spleen of 4 adult healthy subjects, and 4 HUVEC samples were collected and digested for RNA isolation and Agilent analysis.

first: Irene

last: Puga

first: Andrea

last: Cerutti


title: Astrocyte-specific transcriptional response to glucocorticoid receptor activation in the central nervous system

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary:
Many studies indicated in an indirect way that astrocytes are a major target for transcriptional responses induced by glucocorticoids in the CNS, implying that glial cells an important consituent of stress responses.   To address this issue directly we have generated astrocyte-specific conditional GR knockout mice (Cx30GRko) using Cre/loxP system utilizing connexin 30 promoter driving expression of CreERT2 recombinase.
Genome wide analysis of molecular effects of astrocytic GR knockout would allow for dissecting the glial cell-type specific components of stress response mediated by glucocorticoids

overall_design: We have analyzed 4 groups (5 mice/group): control animals injected with saline, Cx30GRko animals injected with saline, control animals injected with GR agonist dexamethasone (Dex, 4 mg/kg, i.p.) and Cx30GRko animals injected with Dex (4 mg/kg, i.p.). Spinal cord (tissue characterized by the highest efficiency of Cre-mediated recombination) samples were collected 4h after injections.

first: M

last: Slezak

last: Tertil

last: Korostynski

first: R

last: Przewlocki


title: Gene expression profiles of naïve PC-9 cells and PC-9GR cells that are resistant to gefitinib.

city: Kodaira

first: Hirohiko

last: Hohjoh

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

summary: We investigated gene expression profiles of gefitinib-resistant PC-9 (PC-9GR) cells as well as naïve PC-9 cells. The data exhibited marked differences in the expression profiles between them.

overall_design: Total RNAs were extracted from naïve PC-9 cells and PC-9GR cells that were resistant to gefitinib, and examined by Agilent-028004 SurePrint G3 Human GE 8x60K Microarrays.

first: Masaki

last: Takahashi


title: TWS119 treatment of human memory T cells

status: Public on Dec 15 2016

city: Baltimore

first: Yen-Ling

last: Chiu

state: MD

address: 733 N. Broadway, BRB 615

institute: Johns Hopkins University

summary:
We want to identify gene expression pattern in memory cells in response to Wnt pathway activation
human memory T cells from peripheral blood from three healthy individuals were stimulated with anti-CD3/CD28 in the presence and absence of TWS119, a Wnt pathway activator. DMSO was added as control vehicle.

overall_design: 3 samples in each group

first: Jonathan

last: Schneck


title: Muscle Developmental Defects in Heterogeneous Nuclear Ribonucleoprotein A1 Knockout Mice

status: Public on Dec 05 2016

city: Kaohsiung

first: Ting-Yuan

last: Liu

address: 100 Shih-Chuan 1st Road

department: Graduate Institute of Medicine, College of Medicine

institute: Kaohsiung Medical University

summary:
Transcriptome analysis of total RNA samples from heart tissue of knockout mice
Alternative splicing is the main mechanism to increase protein diversity from an mRNA. Heterogeneous ribonucleoprotein (hnRNP) family members are vital regulators of alternative splicing. The hnRNP A1 is the most well-known protein in this family, but its role in embryonic development is not well understood. We generated hnRNP A1 knockout mice to study the function of hnRNP A1 in vivo. The hnRNP A1-depleted mice showed embryonic lethality because of muscle developmental defects. In a previous study, cellular hnRNP A2/B1 was reported to be capable of compensating for the expression of hnRNP A1. However, this phenomenon did not occur in the hnRNP A1 heterozygous mice in vivo. We demonstrated that hnRNP A1 regulated muscle-related genes expression and alternative splicing.  In summary, our data demonstrated that hnRNP A1 plays a critical role in embryonic muscle development. Understanding the effects of hnRNP A1 in vivo may help to define the function of hnRNP A1 in alternative splicing.

overall_design: We analyzed total RNA from heart of knockout mice (3 males) using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Yu-Chia

first: Yuh-Jyh

last: Jong

first: Chien-Chin

last: Lee

first: Jan-Gowth

last: Chang

first: Yung-Fu


title: Rational selection of syngeneic preclinical tumor models for immunotherapeutic drug discovery

status: Public on Dec 07 2016

city: Cambridge

first: John

last: Prime

address: Aaron Klug Building

department: Oncology Research

country: United Kingdom

institute: Medimmune

type: Genome variation profiling by genome tiling array


title: To determine transcriptome of gnotobiotic mice fed fiber-rich and fiber-free diets

status: Public on Nov 21 2016

first: Eric

middle: Charles

last: Martens

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

summary:
Despite accepted health benefits of dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic model, in which mice were colonized with a synthetic human gut microbiota, we elucidated the functional interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defence against pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation promoted greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium, but only in the presence of a fiber-deprived microbiota that is pushed to degrade the mucus layer. Our work reveals intricate pathways linking diet, gut microbiome and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.
Germ-free mice (Swiss Webster) were colonized with synthetic human gut microbiota comprising of 14 species belonging to five different phyla (names of bacterial species: Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides caccae, Bacteroides uniformis, Barnesiella intestinihominis, Eubacterium rectale, Marvinbryantia formatexigens, Collinsella aerofaciens, Escherichia coli HS, Clostridium symbiosum, Desulfovibrio piger, Akkermansia muciniphila, Faecalibacterium prausnitzii and Roseburia intestinalis). These mice were fed either a fiber-rich diet or a fiber-free diet for about 6 weeks. The mice were then sacrificed and their cecal tissues were immediately flash frozen for RNA extraction. The extracted RNA was subjected to microarray analysis based on Mouse Gene ST 2.1 strips using the Affy Plus kit. Expression values for each gene were calculated using robust multi-array average (RMA) method.

overall_design: Fiber-rich diet group contained 4 replicate mice (2 independent experiments) and Fiber-free diet group contained 3 replicate mice (2 independent experiments)

first: Mahesh

last: Desai


title: Rational selection of syngeneic preclinical tumor models for immunotherapeutic drug discovery [exon array]

summary: Murine syngeneic tumor models are the cornerstone of novel immuno-oncology (IO)-based therapy development but the molecular and immunological features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Within a panel of commonly-used murine syngeneic tumor models, we showed variable responsiveness to IO-therapies. We employed aCGH, whole-exome sequencing, exon microarray analysis and flow cytometry to extensively characterise these models and revealed striking differences that may underlie these contrasting response profiles. We identified strong differential gene expression in immune-related pathways and changes in immune cell-specific genes that suggested differences in tumor immune infiltrates between models. We further investigated this using flow cytometry, which showed differences in both the composition and magnitude of the tumor immune infiltrates, identifying models that harbor ‘inflamed’ and ‘non-inflamed’ tumor immune infiltrate phenotypes. Moreover, we found that immunosuppressive cell types predominated in syngeneic mouse tumor models that did not respond to immune-checkpoint blockade, whereas cytotoxic effector immune cells were enriched in responsive models. A cytotoxic cell-rich tumor immune infiltrate has been correlated with increased efficacy of IO-therapy in the clinic and these differences could underlie the varying response profiles to IO-therapy between the syngeneic models. This characterisation highlighted the importance of extensive profiling and will enable investigators to select appropriate models to interrogate the activity of IO-therapies as well as combinations with targeted therapies in vivo.

overall_design: Mouse syngeneic tumour cell lines were grown in vitro n=1 and in vivo n ≈5 subcutaneously on the backs of mice from their parental strain or orthotopically (see sample records for specific details for each mouse model). Mice were sacrificed when tumours reached an average of 200 mm3.  In vitro samples underwent aCGH analysis and transcriptomics analysis while in vivo tumor samples along with a draining lymph node and spleen sample were taken from the same mouse and underwent transcriptomics analysis. Whole exome sequencing and immunophenotyping were also performed on these syngeneic models to in all give a multiomic characterisation of these models.

first: Suzanne

middle: I

last: Mosely

first: Richard

last: Sainson

first: Jens-Oliver

last: Koopmann

first: Dennis

middle: Y

last: Wang

first: Danielle

last: Greenawalt

first: Miika

middle: J

last: Ahdesmaki

first: Rebecca

last: Leyland

first: Stefanie

last: Mullins

first: Luciano

last: Pacelli

last: Marcus

first: Judith

last: Anderton

first: Amanda

last: Watkins

first: Jane

last: Coates Ulrichsen

first: Philip

last: Brohawn

first: Brandon

last: Higgs

first: Matthew

last: McCourt

first: Hazel

last: Jones

first: James

middle: A

last: Harper

first: Michelle

last: Morrow

first: Viia

last: Valge-Archer

first: Ross

last: Stewart

first: Simon

last: Dovedi

first: Robert

last: Wilkinson


title: A long noncoding RNA signature in Ulcerative Colitis

status: Public on Nov 08 2016

city: Los Angeles

first: David

middle: Miguel

last: Padua

state: CA

department: Medicine-Division of Digestive Diseases

institute: UCLA

summary:
Background & Aims: Inflammatory bowel diseases (IBD) are clinically manifested as ulcerative colitis (UC) and Crohn’s Disease (CD). Novel high throughput technologies revealed new categories of genes, including the long non-coding RNAs (lncRNAs), which have been involved in the pathogenesis of different human diseases; however the role and function of lncRNAs in the UC pathogenesis has not been evaluated.
Methods: The gene expression patterns for both non-coding (lncRNAs) and coding (mRNA) transcripts were profiled in UC (n=8) and control (n=7) patients by ArrayStar assays.  The differentially expressed genes were used to develop lncRNA signatures in UC samples. Ingenuity Software Analysis (IPA) program was used to identify the up-stream regulators of IFNG-AS1. Jurkat T cells were activated by PMA/ionomycin and IFNG and TNF protein levels were assessed by ELISA assay. Two anti-sense molecules were designed and used to block IFNG-AS1 expression levels. Colonic tissues from TNBS-treated and IL10-/- mice were used to extract RNA and examine INFG-AS1 expression by real-time PCR.
Results: A unique set of lncRNAs was found to be differentially expressed between UC (n=15) and control samples (n=16). Of these, IFNG-AS1 was among the highest statistically significant lncRNAs (fold change: 5.27, p-value: 7.07E-06).  Bioinformatic analyses showed that IFNG-AS1 was associated with the IBD susceptibility loci SNP rs7134599 and its genomic location is adjacent to the inflammatory cytokine, interferon-gamma (IFNG). Using the TNBS and IL10-/- mouse models of colitis, we found increased colonic expression of this lncRNA during active colitis.  Utilizing the Jurkat T cell model system, we explored the mechanisms of action and found that IFNG-AS1 can positively regulate IFNG expression.
Conclusions:   Novel lncRNA signatures were identified to differentiate UC patients with active disease, in remission and control subjects. A subset of these lncRNAs was found to be associated with the clinically validated IBD susceptibility loci.  IFNG-AS1 was one of these differentially expressed lncRNAs in UC patients and was found to regulate the key inflammatory cytokine, IFNG, in CD4 T cells.  Taken together, our study revealed novel lncRNA signatures deregulated in ulcerative colitis and identified IFNG-AS1 as a novel regulator of IFNG inflammatory responses, suggesting the potential importance of non-coding RNA mechanisms on regulation of IBD-related inflammatory responses.

overall_design: 19 overall samples were analyzed.  Colonic resection samples from 8 Active Ulcerative colitis, 4 Inactive Ulcerative colitis, 7 control samples

middle: M

first: Dimitrios

last: Iliopoulos


title: Muscle Biopsy: oxygen vs air treatment

status: Public on Nov 23 2016

city: Birmingham

first: Stanley

middle: Ikenna

last: Ejiofor

state: West Midlands

address: Mendelsohn Way

department: Clinical and Experimental Medicine

institute: University of Birmingham

summary:
Transcriptional profiling comparing muscle biopsies from vastus lateralis in patients with COPD
Patients randomised in cross over study to 3months of air and 3months oxygen therapy with muscle biopies taken at baseline and following each intervention.

overall_design: Matched pair design

first: Chirag

last: Dave

first: Stuart

last: Egginton

first: Alice

last: Turner


title: Gene Expression data from LPS (2 hour) - treated PPP2CA alpha conditional knockout Bone Marrow Derived Macrophages (PP2ACαfl/fl;lyM-Cre, cre-loxp mediated exon1 deletion in myeloid cells)

status: Public on Nov 04 2016

city: Ann arbor

first: Lei

last: Sun

address: 109 Zina Pitcher Place, BSRB 4478

department: Pediatrics

summary:
PP2A regulates inflammatory cytokine/chemokine gene expression by dephosphorylating protein kinases at multiple signaling pathways from stimulated cells. In this dataset, Affymetrix mouse Gene ST 2.1 Array was used to assay total RNA extracted from LPS-treated PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre) and the control BMDM (PP2ACαfl/fl)
In this dataset, we include the expression data obtained from LPS-stimulated PP2ACα conditional knockout BMDM (PP2ACαfl/fl;lyM-Cre) and control BMDM (PP2ACαfl/fl). The data are used to obtain 1080 genes that are differentially expressed in response to LPS stimulation

overall_design: Four total samples (2 control samples and 2 experimental samples) were analyzed. Gene expression data was first calculated with a robust multi-array average of background-adjusted, normalized, and log-transformed intensity values applying the Robust Multi-Array Average algorithm (RMA).  The mean optical background level for each array was subtracted from the signal intensity for each probe. The normalized data were then transformed to the log2 scale. A signal log2 ratio of 1.0 corresponds to an increase of the transcript level by two-fold change (2 FC) and -1.0 indicates a decrease by two-fold change (-2 FC). A 1.5-fold or greater was used as the cutoff value by which a final gene list of 1,080 genes were selected as differentially expressed genes between LPS-stimulated BMDM derived from the myeloid-specific PP2ACα knockout mice (PP2ACαfl/fl;lyM-Cre) versus BMDM from the PP2ACαfl/fl mice

first: Thomas

middle: P

last: Shanley


title: Expression profiling in LIN28A, SET7/9, and TUT4 depleted H9 cells, or in the silent mutations (siR) of  LIN28A and LIN28A-K135R overexpressed H9 cells

city: Daejeon

first: Seung-Kyoon

last: Kim

address: 99 Daehak-ro, Yuseong-gu,

department: Convergent Bioscience and Informatics

institute: Chungnam National University

summary: A developmentally regulated RNA binding protein, LIN28A and its homolog LIN28B may share a similar mechanism to regulate the processing of let-7 microRNAs (miRNAs) in embryonic stem cells (ESCs) or certain cancer cells, although their predominant localization is different in cells. However, little is known about the regulatory mechanism of LIN28A for miRNA processing in the nucleus. Here, we show that SET7/9, a known histone methyltransferase, associates with LIN28A in vivo and in vitro. SET7/9-mediated methylation significantly leads to the nuclear retention and protein stability of LIN28A, and remarkably regulated RNA binding ability of LIN28A to pri-let-7. Using RNAi knockdown approach, we find that the methylated nuclear form of LIN28A may function in the nucleoli by sequestering the primary let-7 miRNA to block their processing through a Tut4 (Zcchc11)-independent mechanism to regulate human ESC pluripotency. We propose a new insight toward the understanding of the molecular mechanism for post-translational methylation of nuclear LIN28A along modulating pluripotency by regulating pri-let-7 miRNAs in human ESCs.

overall_design: Expression expression changes upon depletion of LIN28A, SET7/9, or TUT4 in H9 human embryonic stem cells, or in the silent mutations of LIN28A and LIN28A-K135R overexpressed H9 human embryonic stem cells. H9 was tracked by microarray profiling. Agilent one-color experiment, Organism: Human, Agilent SurePrint G3 Human Gene Expression, 8x60K, Labeling kit: Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology; G4140-90040)

first: Sang

first: Jung

last: Choi

first: Yong-Mahn

last: Han

first: Daeyoup

last: Lee


title: Targeting metastasis stem cells through the fatty acid receptor CD36 (I)

status: Public on Dec 16 2016

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Metastasis is the leading cause of cancer-related deaths. For most human cancers, the identity of the cells that initiate and promote metastasis is still unknown, hampering our ability to develop therapies to prevent or inhibit the spread of tumour cells to distant sites. Using an orthotopic model of human oral squamous cell carcinoma (OSCC), we have now identified a subpopulation of CD44bright cells within the primary lesion with the highest potential to develop lymph node and lung metastasis. This population is slow-cycling, expresses high levels of the receptor CD36 at the cell membrane and relies on fatty acid metabolism to thrive in lymph nodes and bronchoalveolar environments. Importantly, inhibition of CD36 by either shRNA or neutralizing monoclonal antibodies severely impairs metastatic spread of primary OSCC patient samples and established cell lines. Further underscoring its importance, CD36 overexpression in poorly disseminating tumours confers an aggressive metastatic behavior. Analyses of public gene expression data indicate that the presence of the signature-defining CD36+ cells also strongly correlates with a poor prognosis in patients with lung SCC, ovarian cancer, bladder cancer, or luminal breast cancer. By identifying metastasis-promoting cells and then targeting them with CD36 inhibition, novel anti-metastatic therapies could be developed for patients with these types of tumours.

overall_design: 4 biological replicates from SCC-25 cell line were included (set 8A, set 8B, set 9B and set 10A). From each biological replicate, 3 independent cell populations were sorted DID+,DID- and CD44. From set 8B, an additional technical replicate was done.

first: Salvador

last: Aznar-Benitah

first: Stefania

last: Mejetta

first: Camille

last: Stephan-Otto Attolini


title: NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors.

city: Bethesda

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Gene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. Given that the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone-like) mouse photoreceptors. We identified a large-scale, sharp transition in the transcriptome landscape between postnatal days 6 and 10 concordant with rod morphogenesis. Rod-specific temporal DNA methylation corroborated gene expression patterns. De novo assembly and alternative splicing analyses revealed previously unannotated rod-enriched transcripts and the role of NRL in transcript maturation. Furthermore, we defined the relationship of NRL with other transcriptional regulators and downstream cognate effectors. Our studies provide the framework for comprehensive system-level analysis of the GRN underlying the development of a single sensory neuron, the rod photoreceptor.

overall_design: GFP positive cells from Nrlp-GFP mouse retinas at post-natal ages P2, P4, P6, P10, P12, P21, and P28 were isolated by flow sorting by FACSAria II (Becton Dickinson) into RNAlater (Invitrogen). Total RNA was extracted by RNeasy Mini Kit (Qiagen) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). Five nanograms of high quality of total RNA (RIN: >7.0) was used as input for exon array target preparation. Affymetrix Mouse Exon 1.0 ST arrays were performed using targets prepared from WT-Ovation RNA-Amplification System (NuGEN). Gene-level core RMA intensity values for each GeneChip® Mouse Exon 1.0 ST array were collected using Affymetrix Expression Console Software (Affymetrix) with MoEx-1_0-st-v1.r2.dt1.mm8.core.mps.

first: Jung-Woong

first: Hyun-Jin

last: Yang

first: Lina

last: Zelinger

first: Gökhan

last: Karakülah

first: Norimoto

last: Gotoh

first: Alexis

last: Boleda

first: Linn

last: Gieser

first: Felipe

last: Giuste

first: Thad

last: Whitaker

first: Ashley

last: Walton

first: Raphael

last: Vilasmil

first: Koray

middle: D

last: Kaya

first: Jennifer

last: Barb

first: Peter

last: Munson

first: Vijender

last: Chaitankar

first: Tiziana

last: Cogliati

first: Anand

last: Swaroop


title: Examine the expression profiles of lncRNAs in early stage lung squamous cell carcinoma

status: Public on Oct 19 2016

city: Shanghai

first: cheng

last: zule

address: NO.865 Changning Street

institute: Shanghai Institute of Microsystem And Information Technology,Chinese Academy of Sciences

summary: To further understand the expression pattern of long non-coding RNAs in early stage lung squamous cell carcinoma (SCC), we have employed the Arraystar Human LncRNA Microarray V3.0 profiling as a discovery platform to identify lncRNAs which are differentially expressed in early stage lung SCC. Three pairs of tumor tissues and adjacent normal tissues of early stage lung SCC patients are used for microarray analysis.

first: Zule

last: Cheng

first: Hongju

last: Mao


title: arrayCGH from human mesenchymal stem cells (hMSC) and hMSC after adipogenic and osteogenic differentiation

status: Public on Oct 20 2016

city: Saarbruecken

first: Valentina

last: Galata

state: Saarland

address: Campus, E2.1

department: Chair for Clinical Bioinformatics

institute: Saarland University

summary: hMSCs (Lonza) were differentiated towards adipocytes with three cycles of adipocyte differentiation induction and maintenance. hMSCs were differentiated towards osteocytes with osteogenic differentiation medium for 3 days and for 7 days. ArrayCGH experiments were performed before differentiation induction, after 2 and 3 cycles of adipogenic differentiation induction and after 3 days and 7 days of osteogenic differentiation induction.

overall_design: Genomic DNA was isolated form hMSCs before differentiation induction, after 2 and 3 cycles adipogenic differentiation induced cells and from 3-day and 7-day osteogenic differentiation induced cells.

first: Ulrike

last: Fischer


title: Microarray on osteoblasts made from bone marrow stromal cells from Bmp2 flox/flox and Bmp2; Prx1-Cre mice

city: Boston

first: Valerie

last: Salazar

state: MA

address: 188 Longwood Avenue REB 513

department: Developmental Biology

institute: Harvard School of Dental Medicine

summary: Enhanced BMP or canonical Wnt (cWnt) signaling are therapeutic strategies employed to enhance bone formation and fracture repair, but the mechanisms each pathway utilizes to specify cell fate of bone-forming osteoblasts remain poorly understood. Among all BMPs expressed in bone, we find that singular deficiency of Bmp2 blocks the ability of cWnt signaling to specify osteoblasts from limb bud or bone marrow progenitors. When exposed to cWnts, Bmp2-deficient cells fail to progress through the Runx2/Osx1 checkpoint and thus do not upregulate multiple genes controlling mineral metabolism in osteoblasts. Cells lacking Bmp2 after induction of Osx1 differentiate normally in response to cWnts, supporting pre-Osx1+ osteoprogenitors as a critical source and target of BMP2. Our analysis furthermore reveals Grainyhead-like 3 (Grhl3) is to date an unidentified transcription factor in the osteoblast gene regulatory network that is induced during bone development and bone repair, and acts upstream of Osx in a BMP2-dependent manner. The Runx2/Osx1 transition therefore receives critical regulatory inputs from BMP2 that are not compensated for by cWnt signaling, and this is mediated at least in part by induction and activation of Grhl3.

overall_design: Gene level differential expression analysis was performed with Affymetrix Mouse ST 2.1 microarrays on bone marrow stromal cells from Bmp2F/F or Bmp2Prx1Δ/Δ mice that were differentiated for 7 days in osteogenic medium alone, plus BMP2 (100 ng/ml), plus Wnt3a (40 ng/ml), or BMP2 plus Wnt3a.  Cultures were performed in biological triplicates using pooled cells from n≥3 mice/genotype. Traditional cDNA, generated from 1 ug total RNA using EcoDry Premix (Clonetech), was used for pre-microarray and post-microarray validation by QPCR.  Eight cDNA libraries were made from 100 ng total RNA using WT Expression Kit (Ambion): 1 pooled sample from 3 independent cultures of Bmp2F/F cells grown in osteogenic medium (33.33 ng each for a total of 100 ng); 1 pooled sample from 3 independent cultures of Bmp2Prx1Δ/Δ cells + BMP2 + Wnt3a (33.33 ng each for a total of 100 ng); 3 samples from 3 independent cultures of Bmp2F/F cells + Wnt3a (100 ng each); and 3 samples from 3 independent cultures of Bmp2Prx1Δ/Δ cells + Wnt3a (100 ng each).  Data was analyzed with Expression Console and Transcriptome Analysis Console v3.0 (free from Affymetrix). Gene expression was reported as linear fold change relative to Bmp2Prx1Δ/Δ cells + Wnt3a, and p-value was calculated by one-way between-subject ANOVA for unpaired samples.

first: Vicki

last: Rosen


title: lncRNA in chronic lymphocytic leukemia cells and normal B cells with and without stimulation

status: Public on Oct 04 2016

city: Columbus

first: Kevin

middle: R

last: Coombes

state: Ohio

address: 340E Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University Wexner Medical Center

summary: Analysis of lncRNA expression in negatively selected pooled peripheral blood CLL samples compared to pooled peripheral blood normal B-cells with or without stimulation with CD40 ligand.

overall_design: Primary B-cells were isolated and treated in vitro with CD40L. RNAwas iolated from cells for gene expression analysis. Two pools of RNA from CLL patient samples (P1 and P2, n=5 per pool) with mixed clinical and molecular histories, unstimulated or stimulated with CD40 ligand (PeproTech), were compared to a pool of healthy donor B cells (NB, n=6) unstimulated or stimulated with CD40 ligand.

first: Cecelia

last: Miller

first: Erin

last: Hertlein


title: mRNA expression profiles in decidualized and non-decidualized endometriotic cyst stromal cells (ECSCs).

status: Public on Oct 12 2016

city: yufu city

first: yoko

last: aoyagi

address: 1-1 Idaigaoka hamasamachi

institute: oita university

summary: To identify the mRNAs which regulate the decidualization of ECSCs, we explored differentially expressed mRNAs between untreated ECSCs (n=4) and decidualized ECSCs (n=4) using gene expression microarray.   The mRNA expression profiles in untreated ECSCs and decidualized ECSCs were obtained, then the mRNAs were filtered by signal intensity (50.0<, at least one out of 8 samples have values within range) and flags (at least 58% of cases have good flags).  We established the criteria for regulated genes: Z-score ≥2.0 and ratio ≥2.0-fold for up-regulated genes, and Z-score ≤–2.0 and ratio ≤0.5 for down-regulated genes.

overall_design: The primary culture of untreated ECSCs and decidualized ECSCs were utilized. Decidualization of cultured ECSCs was induced by 12 days-culture with a combination of 0.5 mM of dibutyryl-cAMP and 100 nM of dienogest in the presence of 10% charcoal-stripped heat-inactivated FBS. Total RNA was extracted from these samples, and gene expression microarray analysis was performed. The mRNAs differentially expressed between untreated ECSCs and decidualized ECSCs were identified, and aberrantly expressed mRNA in ECSCs were defined as the decidualization related mRNA.

first: Yoko

last: Aoyagi

first: Kaei

last: Nasu


title: miRNA expression profiles in decidualized and non-decidualized endometriotic cyst stromal cells (ECSCs).

summary: To identify the miRNAs which regulate the decidualization of ECSCs, we explored differentially expressed miRNAs between untreated ECSCs (n=4) and decidualized ECSCs (n=4) using miRNA microarray.   The miRNA expression profiles in untreated ECSCs and decidualized ECSCs were obtained, then the miRNAs were filtered by signal intensity (50.0<, at least one out of 8 samples have values within range) and flags (at least 17% of cases have good flags).  We established the criteria for regulated genes: ratio ≥2.0-fold for up-regulated genes and ratio ≤0.5 for down-regulated genes.

overall_design: The primary culture of untreated ECSCs and decidualized ECSCs were utilized. Decidualization of cultured ECSCs was induced by 12 days-culture with a combination of 0.5 mM of dibutyryl-cAMP and 100 nM of dienogest in the presence of 10% charcoal-stripped heat-inactivated FBS. Total RNA was extracted from these samples, and miRNA microarray analysis was performed. The miRNAs differentially expressed between untreated ECSCs and decidualized ECSCs were identified, and aberrantly expressed miRNA in ECSCs were defined as the decidualization related miRNA.


title: miRNA expression profiles in decidualized and non-decidualized normal endometrial stromal cells (NESCs).

summary: To identify the miRNAs which regulate endometrial decidualization, we explored differentially expressed miRNAs between untreated NESCs (n=4) and decidualized NESCs (n=4) using miRNA microarray.   The miRNA expression profiles of untreated NESCs and decidualized NESCs were obtained, then the miRNAs were filtered by signal intensity (50.0<, at least one out of 8 samples have values within range) and flags (at least 13% of cases have good flags).  We established the criteria for regulated genes: ratio ≥2.0-fold for up-regulated genes and ratio ≤0.5 for down-regulated genes.

overall_design: The primary culture of untreated NESCs and decidualized NESCs were utilized. Decidualization of cultured NESCs was induced by 12 days-culture with a combination of 0.5 mM of dibutyryl-cAMP and 100 nM of dienogest in the presence of 10% charcoal-stripped heat-inactivated FBS. Total RNA was extracted from these samples, and miRNA microarray analysis was performed. The miRNAs differentially expressed between untreated NESCs and decidualized NESCs were identified, and aberrantly expressed miRNA in NESCs were defined as the decidualization related miRNA.


title: mRNA expression profiles in decidualized and non-decidualized normal endometrial stromal cells (NESCs).

summary: To identify the mRNAs which regulate endomrtial decidualization, we explored differentially expressed mRNAs between untreated NESCs (n=4) and decidualized NESCs (n=4) using gene expression microarray.   The mRNA expression profiles of untreated in NESCs and decidualized NESCs were obtained, then the mRNAs were filtered by signal intensity (50.0<, at least one out of 8 samples have values within range) and flags (at least 43% of cases have good flags).  We established the criteria for regulated genes: Z-score ≥2.0 and ratio ≥2.0-fold for up-regulated genes, and Z-score ≤–2.0 and ratio ≤0.5 for down-regulated genes.

overall_design: The primary culture of untreated NESCs and decidualized NESCs were utilized. Decidualization of cultured NESCs was induced by 12 days-culture with a combination of 0.5 mM of dibutyryl-cAMP and 100 nM of dienogest in the presence of 10% charcoal-stripped heat-inactivated FBS. Total RNA was extracted from these samples, and gene expression microarray analysis was performed. The mRNAs differentially expressed between untreated NESCs and decidualized NESCs were identified, and aberrantly expressed mRNA in NESCs were defined as the decidualization related mRNA.


title: HeLa cells: Control vs. GPRC5A depletion at different stages of adhesion to Matrigel

city: Helsinki

first: Daria

last: Bulanova

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

summary: Transcriptional profiling of HeLa cervical carcinoma cells comparing cells with siRNA- or shRNA-mediated depletion of GPRC5A vs. cells carrying non-targeting siRNA or shRNA after 45 min and 6 h of adhesion to 10% Matrigel matrix. The goal was to determine the effect of GPRC5A depeltion on the global gene expression following the adhesion process.

overall_design: Four-condition experiment, GPRC5A depletion vs. control cells, two time points (45 min and 6 h of adhesion to Matrigel). Biological replicates: 2 replicates per silencing construct, 2 silencing RNAi constructs for GPRC5A vs. two non-targeting RNAi constructs

first: Teemu

last: Laajala


title: A transcriptomic analysis of the bioactive properties of a polypropylene surgical mesh modified with silver-containing microparticles.

status: Public on Oct 03 2016

city: Barcelona

first: Maria

middle: Teresa

last: Quiles

address: Pg Vall Hebron 119-129

department: General Surgery Research Group

institute: Vall Hebron Research Institute - Vall Hebron University Hospital

summary: Permanent synthetic meshes are a prized option to promote soft-tissue support and repair in several surgical procedures. Contrariwise, the risk to develop biomaterial-associated infection (BAI) has not been solved. Intrinsically antibacterial materials, such as those that include metals with antimicrobial activity as part of their composition, are an advanced approach to be further explored for BAI prevention. In this study, a panel of in vitro, ex vivo and in vivo assays was used to compare a novel polypropylene-based surgical mesh modified with silver-containing microparticles with a commercially available similar device normally used for hernia repair. To comprehensively identify specific mechanisms of how the new silver-containing meshes influence the full host-tissue response in the presence and absence of infection, prostheses were screened for cytotoxicity, biological integration and transcriptomic responses, and additional antibiofilm production behaviour.  Silver-modified polypropylene meshes exhibited good properties in terms of mechanical and cytotoxic values, as well as a modest prevention of biofilm formation. Moreover, they promoted connective tissue deposition and angiogenesis and, outstandingly, induced “immunomodulating” effects that may be potentially useful in the clinical context. Overall, the results substantiate the potential use of polypropylene surgical meshes modified with silver-containing microparticles as a means to prevent  BAI in soft tissue repair.

overall_design: New silver-containing permanent polypropylene meshes were compared with a conventional lightweight polypropylene mesh commonly used in abdominal wall reconstructive surgery). Meshes (3 sq cm each) were placed onto the pre-fascia avascular plane and fixed in 7-wk-old male Sprague-Dawley Hairless rats (n=8 per mesh). Half of the implanted meshes (n=4) were directly inoculated with a suspension of Staphylococcus aureus-Xen 29 strain obtained from the exponential phase of growth (107 CFU). After 10 days, rats were euthanized and the engrafted prostheses together with the surrounding tissues were explanted by cutting around the area. Half of each implant was frozen for total RNA extraction. Once isolated, biological pools each containing 3 individual replicates of an equal quantity of RNA from each animal were constructed. Gene expression was analyzed in 3 different pools per condition using the Affymetrix Rat Gene 2.1 ST 16-Array Plate.

middle: T

first: Christine

last: Weis

first: Pau

last: Turon

last: Arbos


title: Expression profiles in decidualized and non-decidualized endometriotic cyst stromal cells (ECSCs) and normal endometrial stromal cells (NESCs)

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

overall_design: Refer to individual Series


title: Gene expression analysis of imatinib-resistant GIST

status: Public on Dec 27 2016

city: Tsukiji, Chuuoo-ku

first: Momoko

last: NAGAI

department: Department of Bioinformatics

institute: National Cancer Center Research Institute

summary: To reveal mechanisms for acquired imatinib resistance in gastrointestinal stromal tumor (GIST), we have analyzed several cell lines with resistance to imatinib.

overall_design: The parental cell line, T1, was cultured exposed to imatinib, doses of which were increased in a stepwise manner where we selected survived cells until normal cell growth resumed. Thus, we independently established imatinib-resistant GIST cell lines, which exhibited more than 500 times IC50 values (over 10 μM) for imatinib compared to the parental line. R2, RA2, R8, and R9 are fully resistant cell lines. T117 was exposed only for 7 weeks.

first: Tsuyoshi

last: Takahashi

first: Mamoru

last: Kato


title: DNA methylation alternations in the offspring adipose from chromium restriction diet dams

status: Public on Sep 08 2016

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

type: Methylation profiling by genome tiling array

summary: Maternal chromium restriction may disturb susceptibility in offspring. Adipose from maternal chromium diet has 1214 CpG  sites that exhibit differential DNA methylationregulated compared to control.

overall_design: We performed DNA methylation array analyses of offspring adipose from chromium restriction dams and control diet dams at 32 week (n=3 per group).

first: Xiaofang

last: Sun

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: Expression profiles of lncRNAs in bladder cancer

status: Public on Oct 21 2016

city: Chongqing

first: Zhenyu

last: Zhong

address: No. 1 Yixueyuan Road

institute: Chongqing Medical University

summary: To explore non-coding and coding expression profiling and their biological functions in bladder cancer, we surveyed the lncRNA and mRNA expression signature of bladder cancer and para-cancer tissues using microarray for four patients. Thousands of significantly changed lncRNAs and mRNAs were identified. Our findings provide a novel perspective on transcriptional group and lay the foundation for future research of potential roles of lncRNAs in bladder carcinoma.

overall_design: Total RNA from four pairs of human bladder carcinomas and matched para-carcinomas were used for microarray analysis.

first: Jun-Xia

last: Chen


title: Genes expression after ZNF717 knockdown in liver cancer

status: Public on Sep 14 2016

first: Chong

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Using the highly sensitive lncRNA array (Arraystar human lncRNA microarray V3), we screened the lncRNAs and mRNA abundant in shZNF717-HepG2 and shCtrl-HepG2 cell lines, and the functions of ZNF717 in liver cancer were analyzed along the following research.

overall_design: Liver cancer cell lines HepG2 with shZNF717 or without shZNF717 treatment were individually profiled the lncRNA and mRNA expression


title: Changes of lncRNA expression in primary human skin fibroblasts after irradiation with UVA or UVB

city: Yokohama

first: Kazuyuki

last: Yo

address: 560 Kashio-cho, Totsuka-ku

department: Skin Research Department

institute: POLA Chemical Industries, Inc.

summary: In response to ultraviolet radiation (UVR), cells alter gene expression, switching on a variety of damage response pathways. Long non-coding RNA (lncRNA) is thought to play critical roles in regulating expression of protein-coding genes. We hypothesized that lncRNAs also regulate gene expression following UV exposure and screened for changes in lncRNA expression in human primary fibroblasts after irradiation with longwave UV (UVA) or shortwave UV (UVB).

overall_design: Gene expression profiles in primary human skin fibroblasts were determined 6 and 24 hours after single exposures to 200 kJ/m2 UVA or 500 J/m2 UVB. In addition, gene expression profiles were also determined 24 hours after three daily exposure to 100 kJ/m2 UVA or 200 J/m2 UVB. Triplicate samples of sham-irradiated cells and duplicate samples of irradiated cells were examined. Labeled cRNA were hybridized onto the Human LncRNA Array v3.0 (Arraystar). This array has been designed specifically for the detection of lncRNAs. It contains 30,586 probes for lncRNAs and 26,109 probes for mRNAs.

first: K

first: T

last: Rünger


title: Expression data from muscle samples following synergist ablation

status: Public on Sep 30 2016

city: Ann Arbor

first: Jonathan

middle: Paul

last: Gumucio

address: 109 Zina Pitcher Pl

department: Orthopaedic Surgery

institute: University of Michigan

summary: We used microarrays to detail the program of gene expression underlying the growth of the plantaris muscle following synergist ablation-induced supraphysiological overload

overall_design: Rats were subjected to bilateral Achilles tenectomy surgeries, where the Achilles tendon is removed to ablate the gastrocnemius and soleus muscles, which places a robust stimulus for growth in the synergist plantaris muscle. We measured the expression of transcripts at time 0, 3, 7 and 28 days post surgery on Affymetrix Rat Gene 2.1 ST arrays.

first: Schwartz

last: Andrew

first: Gumucio

last: Jonathan

first: Mendias

last: Christopher


title: Spinal motor neuron-enriched secreted protein R-spondin 2 induces Wnt-mediated neuromuscular junction formation

status: Public on Sep 11 2016

city: Nagoya

first: Kinji

last: Ohno

address: 65 Tsurumai, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

summary: Identification of genes that are specifically expressed at the spinal motor neurons

overall_design: Spinal motor neurons and posterior column of adult C57Bl/6 mice are lasercapture-microdissected and analyzed by Affymetrix Mouse Exon Array in triplicate.

first: Hiroaki

last: Nakashima

first: Bisei

last: Ohkawara


title: Expression data from GSS/101LL brain regions

status: Public on Oct 28 2016

city: Easter Bush

first: Jean

last: Manson

state: Midlothian

address: The Roslin Institute Building

department: The Neurobiology Division

institute: The Roslin Institute, The University of Edinburgh

summary:
Gerstmann Strausller Scheinker (GSS) human prion disease homogenate is i.c. inoculated into mice exhibiting a proline to leucine alteration at codon 101 of the murine prion protein gene (101LL). This results in a disease with an incubation period of approximately 291 days. Normal brain homogenate i.c. inoculated into 101LL mice which are aged matched are used as controls.
We used microarrays to detail the gene expression changes occurring in individual GSS/101LL brain regions compared to NBH/101LL, but also the differences in gene expression between different GSS/101LL brain regions.

overall_design: In this study we set out to decipher differences in gene expression between different GSS/101LL brain regions. To achieve this, we compared four different brain regions (brain stem, cerebellum, thalamus and cerebral cortex). Each file represents individual samples, but three replicates are used for each brain region of each exposure type (i.e. NBH or GSS), with the exception of GSS Cortex pool (ii) which failed quality control analysis.

first: Tom

last: Freeman

first: V

middle: H

last: Perry

first: James

last: Alibhai


title: HIPSTR lncRNA knockdown in HEK293 cells

city: São Paulo

first: Sergio

last: Verjovski-Almeida

state: São Paulo

address: Av. Vital Brasil 1500

country: Brazil

institute: Instituto Butantan

summary: HIPSTR is a conserved lncRNA that is transcribed antisense to TFAP2A gene. Unlike previously reported antisense lncRNAs, HIPSTR expression does not correlate with the expression of its antisense counterpart. HIPSTR depletion in HEK293 and H1BP cells predominantly affects genes involved in early organismal development and cell differentiation.

overall_design: HEK293 cells were transfected with antisense oligonucleotides (ASOs) targeting HIPSTR (ASO #1 or ASO #2) or control scrambled ASO (ASO CTL); transfection with each ASO was done in triplicate.

first: Dinar

last: Yunusov

first: Leticia

last: Anderson


title: SOX7 and ETS factors regulate an endothelial transcriptional program during vascular development

status: Public on Oct 29 2016

city: Manchester

first: Andrew

middle: Joshua

last: Lilly

address: Wilmslow Road

department: Stem Cell Haematopoiesis

institute: CRUK Manchester Institute

summary: Vascular development involves complex changes in gene expression necessary to dictate the behaviour of differentiating endothelial cells within the emerging vascular network.  However, the transcriptional programs regulating vascular development are poorly understood.  Here we use a microarray approach to profile the genes regulated in response to SOX7 overexpression.

overall_design: CD41 hematopoietic precursors (HPCs) were treated with and without dox for 12 and 24 hours in duplicate

first: Valerie

last: Kouskoff


title: Expression data on 3T3-L1 adipocytes treated with leukemia cell-conditioned media

status: Public on Oct 22 2016

city: Los Angeles

first: Steve

last: Mittelman

address: 4546 W Sunset Blvd

department: Endocrinology

institute: Children's Hospital Los Angeles

summary: We used Affymetrix microarray to survey the global gene expression changes in adipocytes that have been treated with acute lymphoblastic leukemia cell conditioned media.

overall_design: 3T3-L1 adipocytes were treated with 8093 murine ph+ acute lymphoblastic leukemia cell conditioned media for 24 hours. Then cells were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Steven


title: Adipose tissue stromal cells from lean, obese, and formerly obese mice

status: Public on Sep 01 2016

first: Carey

middle: N

last: Lumeng

address: 109 Zina Pitcher Place

summary:
Adipose tissue stromal cells contribute to the regulation of adipose tissue in lean and obese states.  Myeloid cells such as adipose tissue macrophages (ATMs) and dendritic cells (ATDCs) undergo both quantitative and qualitative changes with obesity.  Due to similarity in markers the identify of adipose tissue dendritic cells and macrophages has been elusive. We have refined prior protocols to unambiguously discern ATM and ATDC in mice. We used microarrays to compare the profiles of ATMs and ATDC from gonadal adipose tissue from lean, obese, and formerly obese mice. We also isolated preadipocytes (PA) from lean and obese mice for comparison.
Male C57Bl/6 mice were fed normal diet (ND) or high fat diet (HFD) for 16 weeks.  Weight loss (WL) mice were switched from the HFD to ND for 8 weeks. RNA was purified from FACS sorted cell populations (live cells only) obtained from gonadal/epididymal adipose tissue depots.  ATMs were defined as CD11c+ (CD45+CD64+ CD11c+) or CD11c- (CD45+CD64+ CD11c-) ATMs.  ATDC were defined as CD64- CD11c+.  PA were defined as CD31- CD45- Sca1+ PDGFRA+.

overall_design: For ATM and ATDC analysis, 2 pools of cells from 4 ND mice were analyzed and 3 pools of 3-4 HFD mice were analyzed.  For PA, 3 pools of 3-4 ND and HFD mice were analyzed.  Due to the paucity of cells, CD11c+ ATM in ND mice were not purified.