title: Influenza virus facilitates its infectivity by activating p53 to inhibit the expression of interferon-induced transmembrane proteins (IFITMs)

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary:
Transcriptome analysis of mock or H1N1 IAV PR8 infected p53WT A549 and p53null A549-KO3 cells by Affymetrix GeneChip Human Transcriptome 2.0 Arrays to achieve a set of genes those are regulated by p53 and responsive to IAV infection.
Influenza A virus infection activates cellular p53, however it has not been clear whether this process has pro- or anti- viral effects. In this study, using human isogenic p53 wildtype A549 cells and p53null A549-KO3 cells generated from the CRISPR/Cas9 technology, we report that p53null cells exhibit significantly reduced viral propagation property when infected with influenza A virus (H1N1/A/Puerto Rico/8/34). Here, using genome-wide microarray analysis we revealed that p53 regulates the expression of a large set of interferon-inducible genes, some of which are directly associated with viral infectivity and later experimentally validated to be responsible for p53-regulated IAV infectivity.

overall_design: We analyzed the gene expression profiling of H1N1 infected p53WT A549 and p53null A549-KO3 cells generated by CRISPR/Cas9 technology using Affymetrix Human Transciptome 2.0 Array with three technical replicates in each condition.

first: Bei

last: Wang

first: Zhiyong

last: Ye

first: Tze-Hau

last: Lam

first: Jinmiao

last: Chen

first: Mun-Kuen

last: Soh

first: Ee-Chee

last: Ren


title: DDX1 regulates alternative splicing and insulin secretion in pancreatic β cells

status: Public on May 02 2018

city: Beijing

first: Wen

last: Zhong

address: Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1. These DDX1-targeted alternative splicing genes are mainly associated with calcium ion binding, high voltage-gated calcium channel, and transmembrane transporter. Functionally, silencing DDX1 impairs calcium influx and insulin secretion in the pancreatic β cells. These results reveal an important role for DDX1 in the regulation of gene alternative splicing and insulin secretion in pancreatic β cells.

overall_design: To generate the transcriptomic profile mediated by DDX1, we constructed a DDX1 knockdown INS1 cell line (shDDX1) by stably expression short hairpin RNA (shRNA) targeting DDX1. Three independent preparations of shDDX1 and scramble cells were then RNA-sequenced. High-throughput sequencing was performed on a HiSeq 2500 (Illumina) system with paired ends 125bp in length.

first: Zonghong

last: Li

first: Maoge

last: Zhou

first: You

first: Tao

last: Xu


title: Deep sequencing  of microRNAs in transplanted corneas

status: Public on Apr 28 2018

city: Guangzhou

first: li

middle: Xiao

last: Lu

address: Baiyun Road

department: Nanfang Hospital

institute: Southern Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: We compared the levels of miRNA specific for DEGs in isograft corneas with those in normal corneas, as well as the levels of miRNA specific for DEGs in allograft corneas with those in isograft corneas, to gain a better understanding of molecular variables that affect corneal graft rejection pathways.
Methods: Illumina Hiseq 2500 deep sequencing was used to screen for differentially expressed genes (DEGs) in matched pairs of isograft corneas and normal corneas, allograft corneas and isograft corneas. Potential target genes among the DEGs were predicted using target prediction software (TargetScan, Miranda, miRDB, and CLIP), and the overlay portion was analyzed using the Gene Ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG). An analysis of the interactions between DEG proteins (PPI analysis) and a MetaCore software analysis.
Results: Our results showed that 22 miRNAs were significantly upregulated and 4 were significantly downregulated in the isograft group when compared with the control group (P < 0.01), while 17 miRNAs were significantly upregulated and 3 were significantly downregulated in the allograft group when compared with the isograft group (P < 0.01). Among the miRNAs with altered expression levels, miR-155-5p, miR-142-3p, miR-142-5p, and miR-223-3p displayed simultaneous changes in the above two comparisons. Potential target genes among the DEGs were predicted using target prediction software, and the overlay portion was analyzed using the Gene Ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG). GO and KEGG analyses showed that the DEGs were mainly involved in metabolic pathways, cytokine secretion, and tumor immunity functions. An analysis of the interactions between DEG proteins (PPI analysis) and a MetaCore software analysis of 4 key DEGs revealed that the genes regulated by miR-155-5p played important roles in the miRNA-mRNA regulatory network. Furthermore, the MetaCore analysis identified C/EBP beta, p53, and sp1 as key transcription factors in that network.
Conclusions:  Our study identified transplanted corneas-specific miRNA in matched pairs of isograft corneas and normal corneas, allograft corneas and isograft corneas. Furthermore, bioinformatics analysis of the key miRNA regulatory network revealed the molecular mechanisms, which suggests miRNAs may as new molecular targets for treating corneal injuries and corneal transplant rejection

overall_design: NSG of 3 normal corneas, 3 isograft corneas and 3 allograft corneas

first: Li

middle: X

first: Jing

last: Wu


title: Myeloma cells via E-cadherin convert pDCs to become tumor-promoting cells

status: Public on Apr 26 2018

city: CLEVELAND

first: ENGUANG

last: BI

state: OH

address: 9500 EUCLID AVE

department: CANCER BIOLOGY

country: USA

institute: CLEVELAND CLINIC LERNER RESEARCH INSTITUTE

summary: Analysis of gene expression change induced by myeloma cells in pDCs. The hypothesis tested in the present study was that myeloma cells inhibit pDCs function by direct contact. Results provide important information of gene expression change in the cocultured of pDCs and myeloma, such as IFNs and IFN regulatory genes, TLR9 signaling pathways.

overall_design: PDCs were obtained from human blood cells and cultured alone or with myeloma cell line ARP1 with or without CpG for 12 hours. Due to the sensitivity of pDCs, RNAs were obtained directly from different cell cultures instead of to sort the pDCs from cocultured. Microarray data were analyzed by comparing with different control.

first: Enguang

last: Bi

first: Hanyan

first: Laura

middle: C

last: Bover


title: Transcriptional response of M. tuberculosis to AX-35 treatment

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary: We report here lead optimisation efforts for molecule GW861072X, one of 177 leads published in a GSK-led phenotypic screening campaign by Balell et al. (2013), generating the AX series. Along with the parent compound AX-35, four other derivatives with mild to no cytotoxicity showed potent in vitro and ex vivo activity in infected THP-1 macrophages against M. tuberculosis. Isolation of resistant mutants to AX compounds in M. tuberculosis revealed mutations in the QcrB of the cytochrome bc1 oxidase, one of two terminal oxidases of the mycobacterial electron transport chain. Cross-resistance studies, transcriptomic analyses and bioenergetics flux assays provide further evidence of QcrB as the target of the AX compounds, and that AX compounds likely interact differently with the quinol binding pocket compared to other QcrB inhibitors. The transcriptomic and bioenergetic profiles obtained when M. tuberculosis was treated with AX-35 are similar to transcriptomic and respiratory signatures of other cytochrome bc1 oxidase inhibitors, whereby the pronounced role of the alternate terminal oxidase cytochrome bd in the respiratory adaptation of M. tuberculosis could be observed. Genes involved in utilisation and synthesis of triacylglycerol (TAG) were also additionally observed to be up-regulated with AX treatment, indicating a switch induced towards lipid metabolism under this particular stress.

overall_design: To gain insight into the initial adaptive response of M. tuberculosis to AX-35 treatment, the transcriptomes of wild-type H37Rv exposed to AX-35 at 10x and 30x MIC for a duration of four hours were examined. Two biological replicates were used for each condition.

first: Caroline

middle: S

last: Foo

first: Stewart

middle: T

last: Cole


title: Coreceptor delivery of paracrine APRIL to Golgic BCMA lowers immunogenicity of B-cell lymphoma

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

summary: APRIL is involved in the development of B-cell lymphomas. However, in tumors the source of APRIL is paracrine while one signaling receptor, BCMA, is intracellular, raising the question on how APRIL may signal. In fact, tumor cells internalized APRIL via their surface HSPG. Then, APRIL trafficked into endosomes to finally interact with Golgic BCMA, whose sequence harbors strong identities with sorting nexins. Intracellular APRIL/BCMA interactions activated the canonical NF-kB pathway, and mediated from tumor cells an immunosuppressive response including IL-10 upregulation. Absence of APRIL/BCMA interactions impaired tumor growth in mice, and APRIL internalization by tumor cells correlated with a reduced survival for patients. Taken together, the present study elucidates a fully intracellular signaling pathway, key to B-cell lymphoma development.

overall_design: Gene epression profiling of HBL-1 and BJAB cell lines treated by APRIL or EDA

first: Benoît

last: Manfroi

first: Karina

last: Lindner

first: Thomas

last: Matthes

first: Jean

middle: P

last: Issartel

first: Audrey

last: Guttin


title: Gene expression analysis of RNAs isolated from C646-untreated and C646-treated human keratinocytes

status: Public on Apr 19 2018

city: Pohang

first: Bhin

last: Jin-hyuk

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

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

summary: In order to identify the zinc responsive genes, we performed a gene expression microarray analysis for the RNAs isolated from C646-untreated and C646-treated human keratinocytes

overall_design: Duplicate experiments were performed for C646-untreated and C646-treated human keratinocytes. Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

first: Jinhyuk

last: Bhin

first: Bum-Ho

last: Bin


title: Gene expression profile of MRC5-CAFs transfected with control siRNA (si-Ctrl) or Dicer1 specific siRNA (si-Dicer1) for 72 hr

status: Public on Apr 10 2018

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

summary:
Ovarian cancer (OC) remains the leading cause of death in patients with gynecological malignancy. An improved understanding of the genomics has led to the separation of OC into histologically and molecularly defined subgroups. Based on molecular profiling in OC patients, subtype with a reactivated tumor stroma presented the worst prognosis, emphasizing the importance of tumor microenvironment especially stromal fibroblasts in fueling OC progression. Dicer1 is well recognized as the microRNA (miR) synthesis machinery, playing a crucial role in cellular maturation and development, and was generally considered to be a tumor suppressor gene that inhibited tumor initiation and metastasis. Dicer1 expression pattern and exact biological function was seldom studied in the stromal compartment. There was a recent study demonstrating that Dicer1 was involved in mouse embryonic fibroblast (MEF) development and maturation. Therefore, we are inspired to explore the expression and function of Dicer1 in stromal fibroblasts of OC patients. In this study, mRNA and microRNA gene expression profiling were conducted for MRC5-CAFs after silencing of Dicer1. By comparing the expression data of MRC5-CAFs transfected with control siRNA (si-Ctrl) or with Dicer1 specific siRNA (si-Dicer1) for 72 hr, we identified a set of differential expressed mRNA and microRNA in MRC5-CAFs after Dicer1 knockdown. This study was the first to investigate Dicer1 influence of stromal fibroblast gene expression and the underlying regulation mechanism, which held great importance in complementing our understanding of Dicer1 in OC initiation and development, and raises potent therapeutical targets in controlling OC metastasis
We used microarrays to profile the mRNA expression of MRC5-CAFs before and after Dicer1 knockdown, in order to identify molecular alteration exerted by Dicer1 in the context of stromal fibroblasts.

overall_design: Transcriptome profiling analyses were performed on 6 samples of MRC5-CAFs, including 3 samples of CAFs transfected with control siRNA (si-Ctrl) and 3 samples of CAFs transfected with Dicer1 specific siRNA (si-Dicer1) for 72 hr

first: Qinglei

last: Gao


title: Altered adipose lipid mobilization predicts long-term weight gain and impaired glucose metabolism

status: Public on Apr 13 2018

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

summary:
Factors predicting body weight gain and associated disturbed glucose metabolism remain to be established. Here we assessed the role of subcutaneous adipocyte lipid mobilization (lipolysis) in spontaneous long-term (>10 years) body weight changes. In two independent clinical cohorts we found that low stimulated lipolysis at baseline correlated inversely with body mass index changes over time. Disturbed lipolysis gave odds ratios of ≥4.6 for weight gain and ≥3.2 for development of insulin resistance and impaired fasting glucose/type 2 diabetes.
Baseline adipose mRNA expression of a set of established lipolysis-regulating genes was lower in weight gainers.

overall_design: To obtain insights into the transcriptional fingerprint underlying the observed lipolysis differences, we performed gene microarray analyses of subcutaneous adipose tissue samples from 13 weight gaining and 25 weight stable women available at baseline


title: BRD4 profiling identifies critical Chronic Lymphocytic Leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor [expression profiling]

status: Public on Apr 17 2018

city: Columbus

first: Hatice Gulcin

last: Ozer

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

summary: Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is over-expressed in CLL and is enriched proximal to genes up-regulated or de novo expressed in CLL with known function in disease pathogenesis and progression. These genes, including key members of the BCR signaling pathway, provide rationale for this therapeutic approach to identify new targets in alternative types of cancer.  Additionally, we describe PLX51107, a structurally distinct BET inhibitor with novel in vitro and in vivo pharmacologic properties that emulates or exceeds the efficacy of BCR signaling agents in pre-clinical models of CLL.  Herein, the discovery of the involvement of BRD4 in the core CLL transcriptional program provides a compelling rationale for clinical investigation of PLX51107 as epigenetic therapy in CLL and application of BRD4 profiling in other cancers.

overall_design: Microarray analysis for primary patient's derived B-CLL cells purifed under basal, stimulated and tretated conditions. A, B and C are pools of 3 individual CLL primary samples each. Samples were treated inbdividually, RNA extracted and equal amount of DNA was pooled for microarray analysis.

first: Rosa

last: Lapalombella

first: John

last: Byrd

first: Hatice

middle: G


title: MeDIP-chip result of 10 lung cancer patients

status: Public on Apr 21 2018

city: Kunming

first: Juan

last: Wang

state: Yunnna

address: No. 295 Xichang Road, Kunming, Yunnan Province, China.

department: Department of Clinical Laboratory

institute: Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China

type: Methylation profiling by genome tiling array

summary:
Compared with non-cancerous lung tissues, lung cancer in Xuanwei tissues expressed a total of 6,899 differentially methylated regions, including 5,788 hypermethylated regions and 1,111 hypomethylated regions.
Many differentially methylated regions have been found in lung cancer in Xuanwei.

overall_design: Differentially methylated regions were detected on 10 paired lung cancer in Xuanwei tissues and non-cancerous lung tissues by methylated DNA immunoprecipitation combined with microarray. For genome-wide methylation detection, equal quantities of gDNA from lung cancer or non-cancerous specimens from 10 patients were pooled respectively.

first: Yanliang

last: Zhang


title: Overexpression of PIK3CA in head and neck squamous cell carcinoma is associated with poor outcome and activation of the YAP pathway

status: Public on Apr 02 2018

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary:
Objectives: Phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) is commonly altered in many human tumors, leading to the activation of p110α enzymatic activity that stimulates growth factor-independent cell growth. PIK3CA alterations such as mutation, gene amplification and overexpression are common in head and neck squamous cell carcinoma (HNSCC) and. We aim to explore how these alterations and clinical outcome are associated, as well as the molecular mechanisms involved.
Material and methods: Mutation and copy-number variation in PIK3CA, and whole-genome expression profiles, were analyzed in primary HNSCC tumors from The Cancer Genome Atlas (TCGA) cohort (n=243). The results were validated in an independent cohort form the University Hospital of A Coruña (UHAC, n=62). Expression of the PIK3CA gene protein product (PI3K p110α) and nuclear YAP were assessed in tissue microarrays in a cohort from the University Hospital 12 de Octubre (UH12O, n=91).
Results: Only high expression of the PIK3CA gene was associated with poor clinical outcome. The study of gene expression, transcription factor and protein signatures suggested that the activation of the Hippo-YAP pathway, involved in organ size, stem cell maintenance and tumorigenesis, could underlie tumor progression in PI3KCA overexpressing tumors. Tissue arrays showed that PI3K p110α levels correlated with YAP nuclear localization in HNSCC tumors.
Conclusions: High expression of PIK3CA in HNSCC primary tumors identifies patients at high risk for recurrence. In these tumors, progression could rely on the Hippo-YAP pathway instead of the canonical Akt/mTOR pathway. This observation could have important implications in the therapeutic options for patients.

overall_design: Gene expression was studied in primary tumors from patients diagnosed with HNSCC

first: Carmen

last: Segrelles

first: Marta

last: Duenas

first: Pombo

last: Maria

first: Claudio

last: Ballestín

first: Marina

last: Alonso-Riaño

first: Pablo

last: Nenclares

first: Roberto

last: Álvarez-Rodríguez

first: Gregorio

last: Sánchez-Aniceto

first: Ana

last: Ruíz-Alonso

first: Jose

middle: L

last: López-Cedrún

first: Jesus

middle: M

last: Paramio

first: Corina

last: Lorz


title: NANOG is required for the long-term establishment of avian somatic reprogrammed cells [duck]

status: Public on Apr 08 2018

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

summary:
Purpose: the goal of this study is to analyse various duck stem cell lines and to compare them with both primary somatic fibroblasts and blastodermal cells derived from pre-gastrulating embryos.
Methods: NGS RNA-sequencing was performed on duck primary embryonic fibroblasts (DEF), on blastodermal cells from EGK-X to EG XV embryos (BCs) and reprogrammed cells (R71-2 and R71-5) derived from DEF by somatic reprogramming process. The libraries were prepared using the TruSeq R Stranded mRNA sample preparation kit (Illumina). The paired-end sequencing was performed either on NextSeq 500 or Hiseq 2500 illumina sequencers and controlled by the SeqencingAnalysis viewer software (Illumina). The quality control of the `Sample-ID.fastq' files was performed with the FasQC software (Babraham Institute).
Results: the total number of reads ranges was from 30 millions to 40 millions.

overall_design: Duck stem cells and somatic cells mRNA profiles were generated by next-generation sequencing (NGS) using Illumina kits.

first: Valérie

last: Sylvain

first: Véronique

last: Vidal

first: Christian

last: Jean

last: Pain


title: Reprograming of Glucose Metabolism by Zerumbone Suppresses Hepatocarcinogenesis

status: Public on Apr 01 2018

first: Lianbo

last: Yu

address: 1800 Cannon Drive

department: Center for Biostatistics

summary: Hepatocellular carcinoma (HCC) is the most prevalent and highly aggressive liver malignancy with limited therapeutic options. Here, the therapeutic potential of zerumbone, a sesquiterpene derived from the ginger plant Zingiber zerumbet, against HCC was explored. Zerumbone inhibited proliferation and clonogenic survival of HCC cells in a dose-dependent manner by arresting cell at the G2/M phase, and inducing apoptosis. To elucidate the underlying molecular mechanisms, a phosphokinase array was performed that showed significant inhibition of the PI3K/AKT/mTOR and STAT3 signaling pathways in zerumbone treated HCC cells. Gene expression profiling using microarray and analysis of microarray data using Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) revealed that zerumbone treatment resulted in significant deregulation of genes regulating apoptotic, cell cycle and metabolism. Indeed, tracing glucose metabolic pathways by growing HCC cells with 13C-glucose and measuring extracellular and intracellular metabolites by 2D-NMR showed a reduction in glucose consumption and reduced lactate production, suggesting glycolytic inhibition. Additionally, zerumbone impeded shunting of glucose-6-phosphate through the pentose-phosphate-pathway, thereby forcing tumor cells to undergo cell cycle arrest and apoptosis. Importantly, zerumbone treatment suppressed subcutaneous and orthotopic growth and lung metastasis of HCC xenografts in immune-compromised mice. In conclusion, these findings reveal a novel and potentially effective therapeutic strategy for HCC using a natural product that targets cancer cell metabolism.

overall_design: MHCC-LM3 cells were treated with Zerumbone or DMSO as a control. Total RNA from the MHCC-LM3 cells was isolated using TRIzol (Invitrogen) and purified using RNeasy Mini columns (QIAGEN), and the integrity and quantity of the RNA were assessed using an Agilent Bioanalyzer and Nanodrop RNA 6000, respectively. Total RNA was labeled using the Affymetrix Whole Transcript Sense Target Labeling kit and hybridized to the Affymetrix human Exon 2.0 ST array following the manufacturer’s protocol at the Microarray Shared Resource Facility at the Ohio State University Comprehensive Cancer Center.

first: Nissar

middle: A

last: Wani

first: Juan

last: Barajas

first: Kalpana

last: Ghoshal

first: Samson

last: Jacob


title: Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: implications for disease suppression

status: Public on Mar 30 2018

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

summary: Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives.

platform_organism: Bacteria Archaea Eukaryota

overall_design: The genomic DNA was extracted from 50 pastoral fields (1 replicate per soil) varying in management intensity. The DNA from each sample was hybridised to GeoChip 5.0 mciroarrays and processed. The genes associated with the biosynthesis of a suite of secondary metabolites were then investigated

first: Bryony

last: Dignam

first: Steve

last: Wakelin


title: Rheb1-mTORC1 maintains macrophage differentiation and phagocytosis in mice

status: Public on Mar 23 2018

city: Tianjin

first: wang

last: xiaomin

state: Tianjin

address: Institute of Hematology and Blood Diseases Hospital, Tianjin 300020, China.

institute: Institute of Hematology and Blood Diseases Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Ras homolog enriched in brain (Rheb1) is a small GTPase and is known to be a direct activator of mTORC1. Dysregulation of Rheb1 has been shown to impair the cellular-energetic state and cell homeostasis. However, the role of Rheb1 in monocytes/macrophages differentiation and maturation is not clear. Here, we investigate the role of Rheb1 in mouse myelopoiesis using a Rheb1 conditional deletion murine model. We found that the absolute number of macrophages decreased in the bone marrow (BM) of Rheb1-deficient mice. Loss of Rheb1 inhibited the monocyte-to-macrophage differentiation process. Additionally, Rheb1 deletion reduced phagocytosis ability of macrophages by inhibiting the mTORC1 signaling pathway. Furthermore, 3BDO (an activator of mTORC1) rescued the phagocytosis ability of Rheb1-deficient macrophages. Thus, Rheb1 is critical for macrophage production and phagocytosis and executes these activities possibly via mTORC1-dependent pathway.

overall_design: Gene expression in myeloid progenitor, hematopoietic stem cells and myeloid cells isolated from the Rheb1fl/fl mice and the wildtype mice was measured.  Three independent experiments were performed using three different cells for each experiment.

first: Xiaomin

last: Wang

first: Minghao

last: Li

first: Yanan

last: Gao

first: Wanzhu

last: Yang

first: Honghai

last: Liang

first: Qing

last: Ji

first: Yanxin

first: Hanzhi

last: Liu

first: Tao

last: Cheng

first: Weiping

last: Yuan

first: Jian

last: Huang


title: Ex-vivo screening platform to identify tumor-specific therapies

status: Public on Apr 07 2018

city: Houston

first: Geoffrey

middle: Arthur

last: Bartholomeusz

state: Texas

address: 1901 East Road

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

summary:
We report the generation of a preclinical IBC patient-derived xenograft (PDX)-derived ex vivo tumor tissue model and show that it closely replicates the tissue architecture of the original PDX tumor harvested from mice and show that its genetic signature highly correlates with that of the original tumor.
We used microarrays to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.

overall_design: We chronicle the development of an IBC PDX-derived ex vivo tumor tissue model generated from the cellular milieu released from a PDX tumor harvested from a mouse and demonstrated its predictive value in identifying tumor-specific therapies in a time and cost effective manner.


title: Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented With Ammonium Derived From Glutamine

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

summary: Algal biofuel production requires an input of synthetic nitrogen fertilizer. Fertilizer synthesized via the Haber-Bosch process produces CO2 as a waste by-product and represents a substantial financial and energy investment. Reliance on synthetic fertilizer attenuates the environmental significance and economic viability of algae production systems. To lower fertilizer input, the waste streams of algal production systems can be recycled to provide alternative sources of nitrogen such as amino acids to the algae. The halophytic green alga Dunaliella viridis can use ammonium (NH4+) derived from the abiotic degradation of amino acids, and previously, supplementation of NH4+ from glutamine (GLN) degradation was shown to support acceptable levels of growth and increased neutral lipid production compared to nitrate. To understand the effect of glutamine-released NH4+ on algae growth and physiology, metabolite levels, growth parameters, and transcript profiles of D. viridis cultures were observed in a time course after transition from media containing nitrate as a sole N source to medium containing GLN, glutamate (GLU), or a N-depleted medium. Growth parameters were similar between GLN (NH4+) and nitrate supplemented cultures, however, metabolite data showed that the GLN supplemented cultures (NH4+) more closely resembled cultures under nitrogen starvation (N-depleted and GLU supplementation). Neutral lipid accumulation was the same in nitrate and glutamine-derived NH4+ cultures. However, glutamine-derived NH4+ caused a transcriptional response in the immediate hours after inoculation of the culture. The strong initial response of cultures to NH4+ changed over the course of days to closely resemble that of nitrogen starvation. These observations suggest that release of NH4+ from glutamine was sufficient to maintain growth, but not high enough to trigger a cell transition to a nitrogen replete state. Comparative transcript profiling of the nitrogen-starved and nitrate-supplied cultures show an overall downregulation of fatty acid synthesis and a shift to starch synthesis and accumulation. The results indicate that a continuous, amino acid derived slow release of NH4+ to algae cultures could reduce the amount of synthetic nitrogen needed for growth, but optimization is needed to balance nitrogen starvation and cell division.

overall_design: Dunaliella viridis cells were grown on 3 different nitrogen sources, glutamate, glutamine, nitrate, and no nitrogen over a course of 51 hours with triplicate sequencing samples taken at 3hr, 27hr, and 51hrs.

first: Jacob

last: Dums

first: Colin

last: Murphree

first: Naresh

last: Vasani


title: Endometrial Tissue RNA expression in Recurrent Implantation Failure vs. Conrol

status: Public on Mar 18 2018

city: Istanbul

first: Tuba

last: Günel

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü Vezneciler

department: Department of Molecular Biology and Genetics

country: Turkey

institute: Istanbul University

summary: We aimed to identify altered biological processes in the endometrium that may be potential markers of receptive endometrium. RNA expression profiling of the endometrium during the window of implantation was performed in patients with Recurrent Implantation Failure (RIF) versus fertile controls.

overall_design: 24 patients with RIF treated at the IVF clinic and 24 fertile control patients recruited from the gynecology clinic of Istanbul University School of Medicine during 2014-2015 were involved in this prospective cohort study. RIF was determined as failure of pregnancy in ≥ 3 consecutive IVF cycles with ≥1 transfer(s) of good quality embryo in each cycle. Exclusion criteria for this group were active pelvic infections, undiagnosed vaginal bleeding, uterine anomalies, endometriosis, karyotype anomalies in one or both partners. Fertile control patients had a history of at least one live birth with no associated comorbidities.

first: Ugur

middle: O

last: Sezerman

first: Ege

last: Ulgen


title: Comparison of expression data from DLD-1 subpopulations II

status: Public on Mar 14 2018

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
The function of cell-cell contact for radiochemosensitivity is unclear. Here, we investigate the role of the E-cadherin/catenin complex proteins under more physiological three-dimensional (3D) cell culture conditions in a panel of CRC cell lines.
To gain further insights, differential gene expression was investigated in DLD-1 subpopulations showing distinct morphology and invasion in 3D collagen type I.

overall_design: RNA extracted from DLD-1 subpopulations grown in 3D collagen type I (n=3 per subpopulation) was used for Affymetrix microarrays.

first: Nils

last: Cordes


title: Blood and skeletal muscle gene signatures of exercise training in men (PBMC data set)

status: Public on Mar 13 2018

city: São Paulo

first: Michelle Sabrina

last: Moreira Silva

state: SP

address: Av. Dr. Enéas de Carvalho Aguiar

country: Brazil

institute: Heart Institute - InCor

summary: Accounting for transcriptional features of endurance adaptations to training is important and could help elucidate the high variability in oxygen uptake (VO2) response. We aimed to identify whole-transcriptome signatures of an endurance training protocol in whole-blood (leukocytes), PBMCs and skeletal muscle tissue of the same group of individuals in a controlled environment.

overall_design: Two groups of healthy untrained policemen recruits (G1, n=20, 26±4 yrs; G2, n= 21, 27±3 yrs) were selected. Blood (PAXgene and EDTA tubes) and muscle tissueforgene expression assays and peak VO2peak measures by cardiopulmonary exercise test were taken before and after 18 weeks of running (3 times/wk; 60min). RNA was extracted from whole-blood (leukocytes), PBMCs and muscle and was used for whole-genome expression analysis using AffymetrixGene Chip Human Transcriptome Array 2.0.   Differentially expressed transcriptswere identified in muscle (547; p<0.01), PBMCs (876; p<0.000001) and leukocytes (175; p<0.0005). We identified significant correlation among muscle and blood tissues, as well as between repeated measures of transcriptomes from the same individual. Using sPLS analysis we derived a leukocyte gene-based classifier that was predictive of VO2peak status (pre and post-training) in G1 and was later validated in G2. Enrichment analysis of the genes present in the final classifier was concordant with previous, per-tissue, analysis and a clear enrichment of mitochondrial oxidative process was evident.

first: Michelle

last: Silva

first: Alexandre

last: Pereira


title: Blood and skeletal muscle gene signatures of exercise training in men (Total blood data set G2)


title: Blood and skeletal muscle gene signatures of exercise training in men (Muscle data set)


title: Blood and skeletal muscle gene signatures of exercise training in men

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

overall_design: Refer to individual Series


title: PLAG1 and USF2 Co-regulate Expression of Musashi-2 in Human Hematopoietic Stem and Progenitor Cells

status: Public on Mar 15 2018

city: Hamilton

first: Sonam

last: Bhatia

state: ON

address: 1280 Main Street West

country: Canada

institute: McMaster University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MSI2, which is expressed predominantly in hematopoietic stem and progenitor cells (HSPCs), enforces HSPC expansion when overexpressed and is upregulated in myeloid leukemias indicating its regulated transcription is critical to balanced self-renewal and leukemia restraint. Despite this, little is understood of the factors that enforce appropriate physiological levels of MSI2 in the blood system. Here we define a promoter region that reports on endogenous expression of MSI2 and identify USF2 and PLAG1 as transcription factors whose promoter binding drives reporter activity. We show that these factors co-regulate, and are required for, efficient transactivation of endogenous MSI2. Coincident overexpression of USF2 and PLAG1 in primitive cord blood cells enhanced MSI2 transcription and yielded cellular phenotypes, including expansion of CD34+ cells in vitro, consistent with that achieved by direct MSI2 overexpression. Global ChIP-seq analyses confirm a preferential co-binding of PLAG1 and USF2 at the promoter of MSI2, as well as regulatory regions corresponding to genes with roles in HSPC homeostasis. PLAG1 and USF2 cooperation is thus an important contributor to stem cell-specific expression of MSI2 and represents novel HSPC-specific transcriptional circuitry.

overall_design: Examination of chromatin binding sites for two different transcription factors, PLAG1 and USF2, in K562 cells (n=2 per transcription factor) by chromatin immunoprecipitation followed by sequencing

first: Kristin

middle: J

last: Hope

first: Muluken

last: Belew

first: Ava

middle: K

last: Chahi

first: Stefan

last: Rentas

first: Jonathan

last: Draper


title: LncRNA expression profiling of hepatocellular carcinoma cell line BEL-7402 treated with baicalein

status: Public on Mar 01 2018

city: Xi'an

first: Zongfang

last: Li

state: Shaanxi

address: 157 W 5th RD

department: the second affiliated hospital

institute: Xi’ an Jiaotong University

summary:
Baicalein, a purified flavonoid compound with defined chemical structure extracted from the dry roots of Scutellaria radix that is a broadly used herb in China, has been proved to possess significant anti-hepatoma activity by inhibiting cell proliferation, invasion, metastasis and inducing apoptosis, autophagy via several cancer-related signaling molecules. In recent years, emerging studies have demonstrated that Chinese medicinal herbs can exert their anti-tumor effects through targeting lncRNAs，such as curcumin, camptothecin, resveratrol，paclitaxel. However, there is still no related report about the effects of baicalein on lncRNA expression profile when it exerts its inhibition on hepatoma tumor growth. To investigate whether the antitumor effect of baicalein is related to its modulation of lncRNA expression in hepatocellular carcinoma (HCC), we profiled the lncRNA expression in HCC cell line Bel-7402 treated with baicalein (0, 40, 80μM) for 24 hours using lncRNA microarray and detected the changes by comparing the lncRNA expression profile of HCC cell line Bel-7402 treated with baicalein (40 and 80 μM) and its DMSO control (0 μM). These findings suggest that modulation of lncRNA expression may be an important mechanism underlying the anti-hepatoma effects of baicalein and lay the groundwork for further investigations.
To investigate whether the antitumor effect of baicalein is related to its modulation of lncRNA expression in hepatocellular carcinoma (HCC), we profiled the miRNA expression in HCC cell line Bel-7402 treated with baicalein (0, 40, 80μM) for 24 hours using miRNA microarray and detected the changes by comparing the lncRNA expression profile of HCC cell line Bel-7402 treated with baicalein (40 and 80 μM) and its DMSO control (0  μM). These findings suggest that modulation of lncRNA expression may be an important mechanism underlying the anti-hepatoma effects of baicalein and lay the groundwork for further investigations.

overall_design: In this study, we profiled the lncRNA expression in hepatocellular carcinoma cell line Bel-7402 treated with baicalein (40 μM), baicalein (80 μM) and and DMSO control (0 μM) for 24 hours using miRNA microarray, and each of three groups have three biological replicates.

first: Jin

last: Sun


title: Effect of Lipiodol on Dendritic Cell

status: Public on Feb 28 2018

city: Adachi

first: Gentaro

last: Izumi

state: Tokyo

address: Senju-kotobukicho 6-15-1203

country: Japan

institute: The University of Tokyo

summary:
Hysterosalpingography with Lipiodol is known to enhance fertility.  Frequency of mature dendritic cell of pertitoneal cavity is higher in the patients after hysterosalpingography with Lipiodol than control.
In order to elucidate the mechanism of fertility enhancing effect of Lipiodl, we used microarray to clarify the effect of Lipiodol on dendritic cells.

overall_design: Monocyte derived dendritic cells from monocytes obtained from healthy doner were cultured with or without 1% Lipiodol.

first: Kaori

last: Koga


title: Next generation sequencing establishes the differentially expression profiles of transgenic rainbow trout bearing cecropin P1 transgene

status: Public on Mar 03 2018

city: Storrs

first: Yueh-chiang

last: Han

state: CT

address: 92 N. Eagleville Rd., Unit 3125, TLS 415

department: Molecular and cell biology

institute: University of Connecticut

summary:
Purpose: mRNA-Seq to reveal the differentially expression pattern of genes in innate/adaptive immune relevant pathways, and combining to the previous DNA microarray analysis to address the immunomodulatory effects of cecropin P1 transgene in rainbow trout.
Methods: Total RNA were isolated from three tissues, spleen, liver  and kidney, from two individuals of two families of transgenic and one family of non-transgenic fish. The sequencing was conducted by Illumina HiSeqTM 2000 followed by Trinity de novo assembly into unigenes (the reference library constructed by non-trasngenic control fish), and, finally, been normalized to RPKM to represent the expression levels.
Results: By sorting the RPKM ratio among transgenic and non-transgenic with threshold > two fold, DEGs can be defined. By RT-qPCR analysis with random selected DEGs (n=36), the reliability of RNA-Seq was comfirmed with high linear correlation (R square= 0.81). By the enrichment analysis via GeneCodis and pathway analyses via customized pathway editor tool, the functional perturbed immune relevant pathway can be determined in tissue specific manner.
Conclusion: By combining the results of RNA-Seq and previous DNA microarray, the immunomodulatory effects of cecropin P1 transgene were estalished in the host, i.e. rainbow trout. By combining the direct eliminating pathogens ability and indirect immunomodulatory stimulating host immune responces of cecropin P1, the host elevates its disease resistance to pathogenic infections.

overall_design:
To generate expressoin profiles of transgenic rainbow trout bearing cecropin P1 transgene in spleen, liver and kidney, mRNA sequencing was done by Illumina HiSeqTM 2000.

Please note that the de novo assembly via Trinity (used for aligning reference) was done by RNA sample from pool three tissues (spleen, liver and kidney) of non-transgenic fish samples.

last: Chen


title: Comprehensive molecular profiling of children with recurrent cancer I

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

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

summary:
to explore possible treatment targets and reasons for agressive children cacners by comprehensive molecular profiling on several platforms
to explore copy number aberrations related to cancers

overall_design: diagnostics of children meeting the oncologist with recurrent or agressive cancers where treatment options have been exhausted

first: Olga

last: Østrup

first: Karsten

last: Nysom

first: David

last: Scheie

first: Ane

middle: Y

last: Schmidt

first: Rene

last: Mathiasen

first: Lisa

last: Hjalgrim

first: Tina

middle: E

last: Olsen

first: Jane

last: Skjøth-Rasmussen

first: Birthe

last: Henriksen

first: Finn

last: Nielsen

first: Peder

last: Wehner

first: Henrik

last: Schrøder

first: Astrid

last: Sehested

first: Catherine

last: Rechnitzer

first: Maria

last: Rossing


title: Gene expression and alternative splicing profiles of BEZ235 treated Ewing Sarcoma cells

status: Public on Feb 14 2018

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: TC71 cells treated either with BEZ235 or DMSO

overall_design: Three biological replicates were labeled (biotinylated) and hybridized with Affymetrix Gene ChIP Scanner 3000 7G

first: Paronetto

last: Paola


title: Blood and skeletal muscle gene signatures of exercise training in men (Total blood data set G1)

first: Michelle Sabrina

last: Moreira Silva

first: Michelle

last: Silva

first: Alexandre

last: Pereira


title: Gene Expression Changes in the Duodenal Adenoma-Carcinoma Sequence in Familial Adenomatous Polyposis (FAP)

status: Public on Feb 27 2018

city: Stanford

first: Sushrut

middle: Sujan

last: Thiruvengadam

state: CA

address: 300 Pasteur Drive

department: Internal Medicine

institute: Stanford University Hospitals and Clinics

summary: Duodenal cancer is a leading cause of death in patients with FAP after colectomy. While cancer risk is up to 36% in Spigelman Stage IV patients, a significant proportion of cases occur in lower stage patients. Genome wide interrogation of APC-deficient mice revealed candidate biomarkers whose altered expression accompanied the evolution of small intestinal neoplasia. To date, no similar investigations have been pursued in FAP patients. In this study, a genome-wide transcriptional analysis of duodenal specimens from FAP patients was performed in order to describe changes occurring in the duodenal adenoma-carcinoma sequence in FAP

overall_design: Gene expression analysis was performed on duodenal samples of 12 FAP patients diagnosed with duodenal cancer (cases) between 1988-2014 and 12 FAP patients without duodenal cancer (controls). RNA was extracted from archived normal, adenoma and cancer tissue from cases and from archived adenoma tissue from controls. Gene expression profiling and analysis was performed using the Affymetrix Human Transcriptome Array 2.0. Three pairwise comparisons were conducted to describe the adenoma-carcinoma sequence: normal-adenoma (No-Ad), adenoma-cancer (Ad-Ca) and normal-cancer (No-Ca). To determine genes differentially expressed in FAP patients with duodenal cancer, adenoma from cases was compared with adenoma from controls (Ad-Ad). In total, 48 samples were analyzed, 36 from cases (normal, adenoma, cancer) and 12 from controls (adenoma).

first: Carol

last: Burke

first: Jill

last: Barnholtz-Sloan

first: Yanwen

last: Chen

first: Chunbiao

last: Li

first: Martina

last: Veigl

first: Bonnie

last: Shadrach


title: Expression data from human endothelial cells co-cultured with cancer associated fibroblasts

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Cancer associated fibroblasts (CAFs) have been shown to plays crucial roles in cancer progression. Although increasing evidence demonstrates that CAFs have important roles in modulating the aggressive phenotypes of cancer cells, their effects on the tumor vasculature remain underexplored. We co-cultured TIME human microvascular endothelial cells (MECs) with either primary human ovarian CAFs or normal ovarian fibroblasts (NFs) to evaluate the effects of CAFs on phenotypes of endothelial cells.

overall_design: RNA samples isolated from TIME cells that had been co-cultured with CAFs or NFs was analyzed using Affymetrix Clariom D human gene expression assays.

first: Tsz

first: Sze

last: Leung

first: Samuel

last: Mok


title: Identification of a novel role of MTF2 in the regulation of H3K27me3 by PRC2 (ChIP-Seq)

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: The epigentic mechnism establised by PRC2 silece the target genes by H3K27me3. H3K27me3 ChIP-seq was performed in the core PRC2 components knockded down cells.

overall_design: Examination of the H3K27me3 changes in the PRC2 knocked down cells.

first: Abdul

last: Khan

first: Seokjin

last: Ham


title: Expression analysis of Bacillus anthracis Sterne wild-type and deltaClpX mutant strains

city: Fort Worth

first: Shauna

last: McGillivray

address: 2800 S. University Dr

department: Biology

institute: TCU

summary:
Investigation of whole genome expression level changes in Bacillus anthracis Sterne deltaClpX mutant compared to the wild-type strain after growth in nutrient rich media.
The deltaClpX mutant used in this study is described in McGillivray et al. 2009. ClpX Protease Contributes to Antimicrobial Peptide Resistance and Virulence Phenotypes of Bacillus anthracis. Journal of Innate Immunity 1(5): 494-506.

overall_design: A six chip study using total RNA recovered from three separate cultures of the wild-type Bacillus anthracis Sterne strain and three separate cultures of the deltaClpX mutant strain.  Each chip measures the expression level of 5287 chromosomal genes from Bacillus anthracis Sterne.


title: Expression Profile of Noncoding RNAs and mRNA in Children with Systemic Lupus Erythematosus

status: Public on Feb 10 2018

city: beijng

first: shipeng

address: Nan Li Shi Road No. 56,Beijing

institute: Beijing children's hospital

summary:
noncoding RNAs (ncRNAs) are reported to play crucial roles in many physiological and biological processes. However, knowledge of ncRNAs in children with systemic lupus erythematosus (cSLE) remains limited. Therefore, we investigate the ncRNA expression profile of cSLE.
Microarrays were performed to identify changes in ncRNA and mRNA expression between children with SLE and paired healthy children.

overall_design: All samples from patients with SLE were obtained from the Department of Rheumatology of Beijing Children’s Hospital (Beijing, China). All patients with SLE fulfilled at least four of the revised criteria for SLE by the American College of Rheumatology (ACR). The control group included healthy volunteers with no history of autoimmune disease or immunosuppressive therapy. Four children first diagnosed with untreated SLE and four ‘control’ children were used for microarray analysis.

first: Shipeng

first: Caifeng


title: Expression data from stimulated NK cells

status: Public on Feb 11 2018

city: Silver Spring

first: Michael

last: Eller

state: MD

address: 503 Robert Grant Ave. 1N11

department: U.S. Military HIV Research Program

institute: Henry Jackson Foundation

summary:
In an effort to define unique and common signatures of NK cell activity that is non-detected at the protein level, we studied the entire transcriptome of NK cells.
We used Human Transcriptome Array (HTA) technology to investigate expression profiles of responding NK cells across the three stimulations in six donors.

overall_design: Due to down regulation of CD16 within the CD56dimCD16bright compartment, healthy donor CD56dimCD16dim/neg cells, post-stimulation are stained and sorted for gene expression analysis.

first: Margaret

last: Costanzo

first: Dohoon

last: Kim

first: Karen

last: Gentile


title: PEST-domain-enriched tyrosine phosphatase and glucocorticoids as regulators of mast cell signalling

status: Public on Jan 31 2018

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

institute: Centre de recherche en transplantation et immunologie

summary: PEST-domain-enriched tyrosine phosphatase (PEP) is a cytoplasmic protein tyrosine phosphatase that regulates immune cell functions, including mast cell functions. Using bone marrow derived mast cells (BMMCs) from PEP+/+ and PEP-/- mice, RNA-seq data showed that dinitrophenol (DNP) - activated PEP-/- BMMCs have misregulated gene expression, with some  cytokine/chemokine genes (eg.TNFα, IL13, CSF2) showing reduced gene expression in the dinitrophenol (DNP) - activated PEP-/- BMMCs compared to (DNP)-activated PEP+/+ BMMCs. Also, the ability of the glucocorticoid dexamethasone (Dex) to negatively regulate DNP - induced COX-2 gene expression in PEP-/- BMMCs was inhibited  compared to the  PEP+/+ BMMCs.

overall_design: Biological replicates are sequenced and analyzed. The samples are either wild-type or mutant for PEP and cells were sensitized with Ig-E, activated with Dinitrophenol and glucocorticoid treatment done with Dexamethasone.

first: George

last: Ainooson

last: Gourain

first: Andrew

last: Cato


title: Expression data from Mesenchymal stem cells

status: Public on Feb 09 2018

city: beijing

first: yu

middle: qian

last: zhuang

state: beijing

address: Peking Union Medical College Hospital, 1 Shuai Fu Yuan

department: Orthopedics

institute: Peking Union Medical College Hospital

summary:
Abnormal osteogenic differentiation of mesenchymal stem cells (MSCs) is implicated in the pathogenesis of Adolescent idiopathic scoliosis(AIS). However, the biological roles of long noncoding RNAs (lncRNAs) in the regulation of osteogenic differentiation of MSCs are unknown.
We used LncRNA microarray analyses of bone marrow (BM) MSCs from non-AIS patients and AIS patients and identified significant differentially expressed lncRNAs in AIS BM-MSCs.

overall_design: Bone marrow (BM) aspirates were obtained from 12 AIS patients, and5 healthy donors)  for RNA extraction and hybridization on Affymetrix microarrays. In the AIS group, all of the patients underwent full clinical and radiological examinations to rule out other causes of scoliosis and to ascertain the diagnosis of AIS. In the control group, each of the 25 age- and gender-matched subjects had a straight spine and a normal forward bending test on the physical examination. They were confirmed to be free of any associated medical diseases or spinal deformities when entered to the study. The study was approved by the Ethics Committee of Peking Union Medical College Hospital. Written informed consents were obtained from all subjects and their parents before entering the study.

first: Jianguo

last: Zhang

first: Qianyu

last: Zhuang

first: Guixing

last: Qiu


title: A tissue-engineered mimic of the ovarian cancer microenvironment of increases cell proliferation and tumor growth.

status: Public on Jan 25 2018

city: London

first: Daniela

last: Loessner

address: Mile End Rd

country: United Kingdom

institute: Queen Mary University of London

summary: Using tissue engineering technologies, we aimed to engineer the ovarian tumor microenvironment to study disease progression by combining biomimetic hydrogels with melt electrospun written scaffolds. 3D co-cultures were constructed by assembling ovarian cancer cell-laden hydrogels with mesothelial cell-layered scaffolds. 3D constructs were characterised by proliferation and transcriptomic analyses and applied to an intraperitoneal xenograft model. Increased cancer cell proliferation upon 3D co-cultures was validated using patient-derived cells and linked to greater tumor burden in vivo. Genome-wide microarray analysis identified IGFBP7, PTGS2, VEGFC and FGF2 as being upregulated in 3D co-cultures compared to 3D mono-cultures. Protein expression of these differentially regulated factors was confirmed by immunohistochemistry in xenograft and patient-derived tumor tissues and correlated with overall and progression-free survival. This pre-clinical cancer model harbors the complexity of the disease seen in patients and advances our understanding of the underlying cell biology and the contribution of the tumor microenvironment to cancer growth.

overall_design: The dataset was derived from three biological repeats of each of the sample groups after 14 days in 3D mono- or culture.

first: Anja

last: Rockstroh

first: Ali

last: Shokoohmand

first: Boris

last: Holzapfel

first: Ferdinand

last: Wagner

first: Jeremy

last: Baldwin

first: Melanie

last: Straub

first: Barbara

last: Schmalfeldt

first: Ernst

last: Lengyel

first: Judith

last: Clements

first: Dietmar

middle: W

last: Hutmacher


title: Gene Expression during Panobinostat Dosing

status: Public on Jan 30 2018

city: Aarhus

first: Martin

last: Tolstrup

state: DK

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

institute: Aarhus University

summary:
A clinical study evaluating the dosing of an oral HDACi panobinostat in patient infected with HIV-1. Dosing was  20 mg orally, 3 times weekly, every other week for a total of 8 weeks.
Gene expression was evaluated in whole PBMCs at baseline (Visit 2), after 3 doses (Visit 4), 4 weeks after dosing (Visit 12) and 6 months after dosing (Visit 13) using the Affymetrix HTA 2.0 gene expression chip

overall_design: PBMC's were isolated from EDTA blood tubes by Ficoll separation on the indicated visits. Five million cells were lysed directly in PAX-tubes as recommended by manufacturer. Cell lysate was stored at -80C until RNA extraction was performed

first: Jesper

last: Falkesgaard


title: Localization of dimethylated histone three lysine four in the Rattus norvegicus sperm genome

status: Public on Feb 01 2018

city: Berkeley

first: Shelby

last: Wilson

address: 16 Barker Hall # 3204

institute: University of California, Berkeley

type: Genome variation profiling by high throughput sequencing

summary: We examined the precise localization of dimethylated histone three lysine four (H3K4me2) in mature rat sperm.

overall_design: Four paired H3K4me2 immunoprecipitated and genomic control libraries constructed from four biological replicates of 10 million rat sperm

first: Kim

last: Boekleheide


title: A toxicogenomics approach to screen chlorinated flame retardants tris(2-chloroethyl) phosphate and tris(2-chloroisopropyl) phosphate for potential health effects

status: Public on Jan 20 2018

city: Antwerp

last: Krivoshiev

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

summary: Tris(2-chloroethyl) phosphate (TCEP) is a pervasive flame retardant that has been identified as a chemical of concern given its health effects and therefore its use has since been tightly regulated. Tris(2-chloroisopropyl) phosphate (TCIPP), an analogue of TCEP, is believed to be its replacement. However, compared to TCEP, little is known of the toxicological impacts of TCIPP. We used RNA sequencing as unbiased and sensitive tool to identify and compare effects on a transcriptome level of TCEP and TCIPP in the human hepatocellular carcinoma cell line, HepG2. We identified that compared to other flame retardants, TCEP and TCIPP had little cytotoxicity. Treatment with sub-cytotoxic concentrations of the two compounds revealed that both chemicals elicited similar effects; both compounds were found to affect genes involved in immune responses and steroid hormone biosynthesis, while also affecting xenobiotic metabolism pathways in a similar manner. Specifically for effects on immune responses, both compounds were shown to alter the expression of the receptor of the potent and pleiotropic complement component, C5a. Additionally, expression of genes encoding for effector proteins involved in the complement cascade along with other potent inflammatory regulators were found altered in response to TCEP and TCIPP, further emphasizing their potential effects on immune function. Taken together, given that TCIPP elicited similar effects compared to TCEP, and at lower concentrations, the potential health effects of TCIPP need to be further studied for a complete risk assessment of the compound.

overall_design: HepG2 cells were treated with low (25 uM) or high (250 uM) concentrations of tris(2-chloroethyl) phosphate (TCEP), low (2.5 uM) or high (25 uM) concentrations of tris(2-chloroisopropyl) phosphate (TCIPP). For control purposes, cells were exposed to 0.1% DMSO alone. Treatment lasted for 72 hours. Treatments were done in triplicate for each condition involving separate cell seeding, cell growth, treatments and RNA extractions per triplicate. RNA was isolated with Trizol (Invitrogen, USA) and RNeasy Kit (Qiagen, GER). Libraries were prepared with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, USA). 50bp long paired-ends reads were sequenced using the HiSeq(R) 1500 platform (Illumina, USA). Alignment, mapping and annotation of sequenced reads were performed using the CLC Genomics Workbench (CLC Bio, Aarhus, Denmark). Samples were normalized by quantile normalization before being mapped and annotated using the human reference hg19 genome.

middle: V

first: Gerrit

last: Beemster

first: Katrien

last: Sprangers

first: Ronny

last: Blust

first: Steven

last: Husson


title: Transcriptional Profiling of the Chicken Liver during the Embryo-to-Hatchling Metabolic Transition

city: Newark

first: Chuming

last: Chen

state: DE

address: 15 Innovation Way, Suite 205

department: Computer and Information Sciences

institute: University of Delaware

summary: In the present study, we examined the hepatic transcriptome of chickens during the peri-hatch period—or the metabolic jump from chorioallantoic (embryo) to pulmonary (hatchling) respiration. Although our major interest was comparison of differentially-expressed genes between embryos and hatchlings, we made pairwise contrasts across six developmental ages. We collected the liver from four embryos at three ages (e16, e18 and e20) and four hatchling chicks at three ages (1, 3 and 9 days) post hatching.  Liver samples (N=24) were used for extraction of total RNA which was then used for hybridization to 24 Affymetrix Chicken Genome Arrays. Ingenuity Pathways Analysis was used for functional annotation and mapping of differentially expressed (FDR≤0.05) genes to canonical pathways and gene interaction networks. We identified 1274 hepatic genes that were differentially expressed between embryos and hatchling chicks and of these, 284 genes are involved in lipid metabolism. The three most abundant found in liver of embryos were (MOGAT1, DIO3 and PDK4), whereas THRSP, FASN and DIO2 were greatly expressed in liver of hatchlings. Two functionally-distinct clusters of hepatic genes have emerged from our time-course transcriptional scans in the peri-hatch chicken. Cluster A genes are largely lipolytic with higher expression in the embryo, while Cluster B genes are mainly lipogenic and thermogenic with greater expression in liver of hatchlings. The present study describes the innate chorography of transcriptional responses of liver to the abrupt metabolic switch from aquatic ectothermy (embryos) to free-living endothermy (hatchling chicks).

overall_design: This study of the chicken liver transcriptome included 24 liver samples: four biological replicates (i.e., individual liver samples) at six developmental ages (e16, e18 and e20 embryos; and day 1, day 3 and day 9 hatchling chicks)

first: Larry

last: Cogburn

first: Nares

last: Trakooljul

first: Hongzhan

last: Huang

first: Cathy

middle: H

last: Wu

first: Wilfrid

last: Carre

first: Xiaofei

last: Wang

first: Harold

middle: B

last: White III


title: Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq.

status: Public on Jan 12 2018

first: Boris

summary: Tris (2-butoxyethyl) phosphate (TBOEP) is a compound produced at high volume that is used as both a flame retardant and a plasticizer. It is persistent and bioaccumulative, yet little is known of its toxicological modes of action. Such insight may aid risk assessment in a weight-of-evidence approach supplementing current testing strategies. We used an RNA sequencing approach as an unbiased and sensitive tool to explore potential negative health effects of sub-cytotoxic concentrations of TBOEP on the transcriptome of the human liver hepatocellular carcinoma cell line, HepG2, with the lowest concentration used potentially holding relevance to human physiological levels. Over-representation and gene set enrichment analysis corresponded well and revealed that TBOEP treatments resulted in an upregulation of genes involved in protein and energy metabolism, along with DNA replication. Such increases in cell and macromolecule metabolism could explain the increase in mitochondrial activity at lower TBOEP concentrations. In addition, TBOEP affected a wide variety of biological processes, the most notable one being the general stress response, wound healing. Finally, TBOEP showed effects on steroid hormone biosynthesis and activation, regulation, and potentiation of immune responses, in agreement with other studies. As such, this study is the first study investigating genome-wide changes in gene transcription in response to TBOEP in human cells.

overall_design: HepG2 cells were treated with low (2.5 uM) or high (125 uM) concentrations of Tris (2-butoxyethyl) phosphate (TBOEP) in 0.1% DMSO. For control purposes cells were exposed to 0.1% DMSO alone. Treatment lasted for 72 hours. All treatments were conducted in triplicates, involving separate seeding of cells. RNA was isolated with Trizol (Invitrogen, USA) and RNeasy Kit (Qiagen, GER). Libraries were prepared with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, USA). 50bp long paired-ends reads were sequenced using the HiSeq(R) 1500 platform (Illumina, USA). Alignement to the UCSC hg19 assembly of the human genome, mapping and annotation was performed with CLC Genomics Workbench (CLC Bio, DEN). Samples were normalised by quantile normalisation. Differential expression p-values were generated using Baggerly's test statistic. These p-values were subsequently corrected with the Benjamini-Hochberg procedure to limit the false discovery rate (FDR) to 5% of the significant genes .

middle: T

first: Bart

last: Cuypers

first: Kris

last: Laukens


title: Effect of BORIS depletion on transcriptome of breast cancer cell line MCF7

status: Public on Sep 25 2017

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

summary:
Transcriptome analysis of BORIS depleted MCF7 cells
To delineate the alternative pre-mRNA splicing program mediated by BORIS in breast cancer cells, BORIS was depleted in MCF7 using shRNA, and the resultant changes in alternative pre-mRNA splicing and mRNA expression pattern was profiled using Affymetrix Human Transcriptome 2.0 Array

overall_design: We analyzed shContol and shBORIS transfected MCF7 cell line using the Affymetrix Human Transcriptome 2.0 platform. Array data was processed by Affymetrix transcriptome console Computational Tool. Biological replicates were performed.

first: Smriti

last: Singh

first: Sathiya

middle: P

last: Narayanan

first: Kajal

last: Biswas

first: Amit

last: Gupta

first: Neha

last: Ahuja

first: Sandhya

last: Yadav

first: Rajendra

last: Panday

first: Samaiya

last: Atul

first: Shyam

last: Sharan


title: Neurons generated by mouse ES cell with hippocampal or cortical identity display distinct projection patterns when co-transplanted in the adult brain

status: Public on Dec 23 2017

city: Pisa

first: Marco

last: Terrigno

address: Via Giuseppe Moruzzi, 1

country: Italy

institute: Scuola Normale Superiore

summary: The capability of generating neural precursor cells with distinct types of regional identity in vitro has recently opened new opportunities of cell replacement in animal models of neurodegenerative diseases. By manipulating Wnt and BMP signaling, we steered the differentiation of mouse ES cells towards isocortical or hippocampal molecular identity. These two types of cells showed different degrees of axonal outgrowth and targeted different regions when co-transplanted in the healthy or lesioned isocortex, or in hippocampus. In hippocampus, only precursor cells with hippocampal molecular identity were able to extend projections, contacting CA3. Conversely, isocortical-like cells were capable of extending long-range axonal projections only when transplanted in motor cortex, sending fibers toward both intra- and extra-cortical targets. Ischemic damage induced by photothrombosis greatly enhanced the capability of isocortical-like cells to extend far-reaching projections. Our results indicate that neural precursors generated by ES cells carry intrinsic signals specifying axonal extension in different environments.

overall_design: Gene expression was evaluated in ESC-derived neurons at 16 days of in vitro differentiation upon treatment at different times with Wnt and BMP inhibitors or WNT; agonist  global gene expression profiles were compared to E15 mouse embryo cortex, hippocampus, ventral telencephalon and midbrain.

first: Irene

last: Busti

first: Claudia

last: Alia

first: Marta

last: Pietrasanta

first: Ivan

last: Arisi

first: Mara

last: D'Onofrio

first: Matteo

last: Caleo

first: Federico

last: Cremisi


title: Gene expression microarray analysis of NCK1-AS1 knockdown in CaSki cells

status: Public on Jan 01 2018

city: chongqing

first: haiyu

last: li

address: Yixueyuan Road1#, Yuzhong District, Chongqing

country: China

institute: chongqing medical university

summary: To further explore the potential molecular mechanisms of NCK1-AS1 in CC cells，Human Transcriptome Array 2.0 analysis was performed to investigate the differential gene expression profiles between NCK1-AS1 knockdown group and control group in CaSki cells.

overall_design: To investigate the differential gene expression profiles between NCK1-AS1 knockdown group and control group in CaSki cells.

first: Haiyu

last: Li

first: Fangzhou

last: Song


title: Expression data from MCF7 wildtype and MCF7 MDMXC463A/WT cells

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

country: USA

institute: Harvard University

summary:
MDMX C463A mutation disrupts its binding with MDM2, and leads insufficient of MDM2 E3 ligase activity. With that, p53 degradation would be slower. In this case, p53 remaining its tumor suppressor function without transactivation.
To figure out the whole map of transcripts change in MDMX C463A mutation cells. We used MCF7 parental cells as control group, and MCF7 MDMXC463A/WT mutation cells as experimental group for gene chip analysis.

overall_design: Triplicates of each group were cultured until log phase and subjected to RNeasy MinElute Cleanup kit (QIAGEN). Purified RNA were send to Danar-Faber core for gene-chip analysis with HTA 2.0 chip (Affymetrix).

first: Weiqi

last: Zeng


title: Dysregulated mRNA and miRNA expression networks in Helicobacter pylori infected gastric epithelial cell line,  AGS (miRNA)

status: Public on Dec 20 2017

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

institute: Bose Institute

summary: We performed genome-wide mRNA and miRNA expression analysis in gastric epithelial cell line AGS infected with Helicobacter pylori at 100 Multiplicity of Infection (MOI), comparing the expression profile of infected cells with uninfected cells. Differentially expressed mRNAs and miRNAs were identified, which showed a 1.5 fold change in expression in infected cells compared to uninfected cells. We performed in silico analysis of miRNA-mRNA target interactions among the inversely correlated differentially expressed miRNAs and mRNAs, and performed functional enrichment analysis of the target genes, to identify important cellular pathways that reflect the patho-biology of H. pylori infected cells. Among the important miRNA-mRNA target pairs, PHLPP1, reported to be associated with poor prognosis in cancer, was predicted to be a putative target of miR-29b-1-5p. Therefore, we focused on the miR-29b-1-5p/PHLPP1 miRNA/target pair for detailed investigation into their role in H. pylori-mediated signalling in gastric epithelial cells. This study demonstrates that an integrated analysis of global mRNA and miRNA expression patterns, combined with miRNA-mRNA target prediction and functional analysis of miRNA target genes can yield an understanding of the critical pathways regulating the behaviour of gastric epithelial cells challenged with H. pylori.

overall_design: AGS cells (human gastric epithelial cell line) were infected with H. pylori 26695 at 100 MOI for 4 h.Total RNAs were isolated from both AGS cells infected with H. pylori (2 samples) and uninfected AGS cells (2 samples).Total RNA for each sample was sent to Genotypic for further processing.

first: Zhumur

last: Ghosh


title: Dysregulated mRNA and miRNA expression networks in Helicobacter pylori infected gastric epithelial cell line,  AGS

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: In vitro Exon Level Expression Profiling of dermal fibroblast

status: Public on Dec 31 2017

city: Columbus

first: Chandan

last: Sen

state: Ohio

address: 473W. 12th Avenue,

department: Surgery

institute: Ohio State University Wexner Medical Center

summary:
Transcriptome analysis of of control inhibitor and miR200b inhibitor transfected Human Dermal Adult Fibroblasts (HDAF) compared with Human Dermal Microvascular Endothelial Cells (HMEC).
Injury induced inhibition of miR200b induces angiogenesis at the wound edges which help in the healing process. We have characterised the effect of miR200b suppression in Human Adult Dermal Fibroblasts converts to endothelial cells through transcriptional profiling. In this dataset, we include the expression data obtained from control inhibitor and miR200b inhibitor transfected Human Dermal Adult Fibroblasts, as well as Human Dermal Microvascular Endothelial Cells (HMEC) as positive control.

overall_design: 9 total samples were analyzed by using the Affymetrix GeneChip®   Human Transcriptome Array 2.0

first: Pal

last: Durba

first: Ghatak

last: Subhadip

first: Singh

last: Kanhaiya

first: Roy

last: Sashwati

first: Castro

last: Natalia

first: Khanna

last: Savita

first: Perez

middle: G

last: Daniel

first: Sen

last: Chandan


title: A 29-Gene and Cytogenetic Score for the Prediction of Resistance to Induction Treatment in Acute Myeloid Leukemia

status: Public on Dec 16 2017

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model. The final predictor (PS29MRC) consisted of 29 gene expression markers and a cytogenetic risk classification. A continuous predictor is calculated as a weighted linear sum of the individual variables. Additionally, a cut off was defined to divide patients into a high-risk and a low-risk group for resistant disease. PS29MRC was highly significant in the validation set, both as a continuous score (OR=2.39; p=8.63·10-9, AUC=0.76) and as a dichotomous classifier (OR=8.03; p=4.29·10-9). The accuracy was 77%. In multivariable models, only TP53 mutation, age and PS29MRC (continuous: OR=1.75; p=0.0011; dichotomous: OR=4.44, p=0.00021) were left as significant variables. PS29MRC dominated all models when compared with currently used predictors and also predicted overall survival independently of established markers. When integrated in the European LeukemiaNet 2017 genetic risk stratification, four groups (median survival [months] of 8, 18, 41, not reached) could be defined (p=4.01·10-10). PS29MRC will make it possible to design trials which stratify induction treatment according to the probability of response and refines the ELN 2017 classification.

overall_design: The set consists of all patients with available material treated in the AMLCG-2008 study (NCT01382147, n=210) and additional 40 patients with resistant disease that were treated in the AMLG-1999 trial (NCT00266136). RNAseq libraries were prepared using the Sense mRNA Seq Library Prep Kit V2 (Lexogen, n=238) and the TruSeq RNA Library Preparation V2 Kit (Illumina, n=12). Between 500-1000 ng total RNA (RNA integrity number [RIN] >7) were used as input material. All sequencing was paired end and performed using polyadenylated-selected and, in case of the Lexogen libraries, stranded RNA sequencing. Samples were sequenced on a HiSeq 1500 instrument (Illumina) as 100 bp reads to a targeted depth of 20 million mappable paired reads per sample.

first: Vindi

last: Jurinovic

first: Aarif

middle: M

last: Batcha

first: Stefanos

last: Bamopoulos

first: Maja

last: Rothenberg-Thurley

first: Bianka

last: Ksienzyk

first: Luise

last: Hartmann

first: Philipp

last: Greif

first: Julia

last: Phillippou-Massier

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Susanne

last: Amler

first: Maria

middle: C

last: Sauerland

first: Dennis

last: Görlich

first: Wolfgang

last: Berdel

first: Bernhard

last: Woermann

first: Jan

last: Braess

last: Hiddemann

first: Klaus

last: Metzeler

first: Ulrich

last: Mansmann

first: Karsten

last: Spiekermann


title: MAPK pathway activation abrogates CCR7-mediated migration and prolongs survival to trap dendritic cells in LCH lesions

status: Public on Nov 23 2017

city: Houston

first: Carl

last: Allen

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

summary:
Patient  lesion and control sorted cells were used, treatment with different inhibitors for MAPK pathways for desired amount of time and then was sorted for CD207
and was used for RNA followed by Cdna amplification and was subjected for gene expression analysis using Affy Chips

overall_design: Gene expression analysis from inhibitor treated and sorted LCH lesion cells to understand how the treatment can change gene regulation

first: Rikhia

last: Chakraborty

first: Karen

last: Har Lim


title: Whole transcriptome profiling reveals major cell types in the cellular immune response against acute and chronic active Epstein-Barr virus infection

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Epstein–Barr virus (EBV) is a common human pathogen that infects over 95% of the population worldwide. In the present study, the whole transcriptome microarray data were generated from peripheral blood mononuclear cells from Chinese children with acute infectious mononucleosis (AIM) and chronic active EBV infection (CAEBV) that were also compared with a publicly available microarray dataset from a study of American college students with AIM. Our study characterized for the first time a broad spectrum of molecular signatures in AIM and CAEBV. The key findings from the transcriptome profiling were validated with qPCR and flow cytometry assays. The most important finding in our study is the discovery of predominant γδ TCR expression and γδ T cell expansion in AIM. This finding, in combination with the striking up-regulation of CD3, CD8 and CD94, suggests that CD8+ T cells and CD94+ NK cells may play a major role in AIM. Moreover, the unique up-regulation of CD64A/B and its significant correlation with the monocyte marker CD14 was observed in CAEBV and that implies an important role of monocytes in CAEBV. In conclusion, our study reveals major cell types (particularly γδ T cells) in the host cellular immune response against AIM and CAEBV.

overall_design: Total RNAs were extracted from peripheral blood mononulear cells from 6 acute infectious mononucleosis (AIM), 5 chronic active EBV infection (CAEBV) and 6 healthy controls. Differential expression was assessed using the R package "limma", and pathway enrichment was performed using the R package "GAGE". Expression signal correlation with 36 blood cell markers was defined by Pearson correlation analysis.

first: Huaqing

last: Zhong

first: Jin

last: Xu

first: Xinran

last: Hu


title: Differences of gene expression profiling of breast cancer cells with stable SREBP1 knockdown and the control cells [MDA-MB-231]

status: Public on Oct 24 2017

city: Jinan

first: Qifeng

last: Yang

state: Shandong

address: Wenhua West Road No.44

department: Department of Breast Surgery

institute: Qilu Hospital

summary: SREBP1 is a master regulator of lipogenic gene expression. However, the underlying mechanisms of SREBP1-mediated metastasis has not been thoroughly elucidated.We involved microarray to analyze the differences of gene expression profiling between breast cancer cells with stable SREBP1 knockdown and the control cells.

overall_design: We established stable SREBP1 knockdown breast cancer cells (MDA-MB-231) and used microarray to compare differential gene expression profiling between the stable SREBP1 knockdown cell lines and the control cells.

first: Ning

last: Zhang


title: Nanotopography guides morphology and spatial patterning of induced pluripotent stem cell colonies

status: Public on Sep 18 2017

city: Aachen

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: The role of topographic cues in controlling commitment of induced pluripotent stem cells (iPSCs) is largely unknown. Here we demonstrate that groove-ridge nanostructures induce the elongation of iPSC colonies, guide the orientation of apical actin fibers and direct the polarity of cell division. Elongation of iPSC colonies impacts also on the intrinsic molecular patterning which seems to be orchestrated starting from the rim of the colonies. We followed the hypothesis that nanotopography directly modulates the transcriptional program of iPSC, further to guiding the overall spatial organization of the colonies.  Single iPSC were seeded on flat (PI flat) and nanostructured polyimide (PI 650) and gene expression profiles were analyzed after three days. No significant differences were observed when cells were kept under culture conditions that sustained pluripotency. Then, we analyzed gene expression changes upon two weeks of multi-lineage differentiation. Many genes revealed significant expression changes in the course of differentiation and this was more pronounced on PI flat as compared to PI 650. Comparison of iPSC that were either differentiated on flat or nanostructured biomaterials revealed differential expression of several genes. Noteworthy, among significantly regulated genes, the biggest fold change on PI 650 versus PI flat after differentiation was observed in ANKRD1, which is one of the best readouts of YAP/TAZ activity. Our study suggests that nanotopography impacts on orientation and organization of iPSC colonies and highlight a possible interaction between mechanosensors and mechanotransducers.

overall_design: 12 samples were hybridized to the Human Transcriptome Array 2.0 (Affymetrix)

first: Giulio

last: Abagnale

first: Antonio

last: Sechi

first: Michael

last: Steger

first: Joseph

last: Kuo

first: Gülcan

last: Aydin

first: Carmen

last: Schalla

first: Gerhard

last: Müllern-Newen

first: Martin

last: Zenke

first: Ivan

last: Costa

first: Arnold

last: Gillner


title: Transcript levels in the normal epithelium and adenomas of the colon of Min mice

status: Public on Nov 21 2017

city: Madison

first: Jennifer

last: Pleiman

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

summary: We sought to identify gene transcripts altered in level between the normal epithelium and adenomas in colon of the Apc-Min/+ mouse.  These differences in level can be compared to those observed for the colons of the Apc-Pirc/+ rat and the human.

overall_design: Male (BTBR/Pas x C57BL/6J)F1-Min mice, were housed under conditions of 12 hour light:12 dark, and provided feed  and water ad lib.  Normal epithelial tissue and adenomas were harvested from the colon at 100 days of age.  RNA was extracted, purified and hybridized according to Agilent protocols.

first: William

middle: F

last: Dove


title: The gene expression profile of rat hepatocytes grown on decelllularized liver

status: Public on Dec 26 2017

first: Doris

middle: A

last: Taylor

state: Texas

address: 6770 Bertner Ave MC2-255

department: Regenerative Medicine Research Laboratories

institute: Texas Heart Institute

summary: The objective of this study was to determine the gene expression profile of rat hepatocytes grown on decellularized rat liver matrices as a function of time.

overall_design: Recellularized matrices were harvested 2, 15 and 28 days after cell seeding for gene expression analysis. Three or four matrices were collected at each time point. Four normal cadaveric rat livers were collected as reference, and four separate isolations of hepatocytes were also collected as an additional reference.

first: Matthew

last: Robertson


title: Expression data of human clear cell renal cell carcinoma

status: Public on Nov 04 2017

city: Beijing

first: Hailiang

last: Feng

address: dong dan 3 tiao 5 hao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary:
Human tumor cell lines are important tools in tumor biological studies, here the authors report the establishment and characterization of 7 new ccRCC stable cell lines with complete clinical data. Gene expression and methylation were profiled with microarrays between the new cells and those had a finite in vitro life span, and the results prompt that genes such as SLC34A2 and VHL play key roles in the continuous in vitro growth and development of ccRCC.
In order to find out what genetic features are related to the successful establishment of stable cell lines, early stage cells of 5 stable cell lines (UT14(P2), UT16(P2), UT33a(P3), UT48(P2), UT56(P1) ), named as P group and 5 finite cell lines (UT13a(P3), UT27(P3), UT37(P2), UT41(P2), UT54(P3) ) which could not be cultured more than 10 generations named as N group were chosen to do gene expression chip. Features such as age, gender, tumor size and Fuhrman nuclear grading were matched in these two groups.

overall_design: Early stage cells of 5 stable cell lines (>20 generations in vitro)(UT14(P2), UT16(P2), UT33a(P3), UT48(P2), UT56(P1) ), named as P group and 5 finite cell lines (UT13a(P3), UT27(P3), UT37(P2), UT41(P2), UT54(P3) ) which could not be cultured more than 10 generations named as N group were chosen to do gene expression chip. Features such as age, gender, tumor size and Fuhrman nuclear grading were matched in these two groups

first: Yu


title: Different expression of inflammation-related proteins in human heart failure

status: Public on Sep 01 2017

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background: Heart failure (HF) causes various inflammatory responses. It remains unclear whether the inflammation the cause or effect of HF. Therefore, we wished to characterize the transcript profiles in the left ventricle (LV) of preserved and failed hearts respectively.
Results: Twenty inflammatory genes were differentially expressed between the preserved and failed LV respectively.

first: Shang-Hung

last: Chang

first: Yung-Hsin

last: Yeh

first: Wei-Jan

last: Chen

first: Chi-Tai

first: Feng-Chun

last: Tsai


title: Expression data from human cell lines before and after treated with drugs.

status: Public on Oct 01 2017

city: Osaka

first: Kazuko

last: Sakai

address: 377-2, Osaka-sayama

department: Dept. of Genome Biology

institute: Kindai University Faculty of Medicine

summary:
Analysis of HER2-amplified NCI-N87 gastric cancer cell line exposed to 0.1 µg/mL T-DM1 and subsequently cultured in the presence of gradually increasing doses, up to a maximum of 4 µg/mL. The resultant cell lines that grew exponentially in the presence of T-DM1 were designated as drug resistant gastric cancer cell lines, and named  N87-TDMR.
We used microarrays to detail the gene expression in N87-TDMR and N87-parent cells to screen for transcripts correlated with T-DM1 resistance.

overall_design: Total RNA was purified using RNeasy Mini Kit (Qiagen), including a DNase digestion treatment. RNA concentrations were determined by NanoDrop 2000 (Thermo Scientific). RNA was labeled using the GeneChip® WT Terminal Labeling and Controls Kit combined with the Ambion® WT Expression Kit. Labeled cRNA was hybridized to GeneChip® Human Transcriptome Array 2.0 arrays (Affymetrix).

first: Naoki

last: Takegawa

first: Yoshikane

last: Nonagase

first: Kimio

last: Yonesaka


title: Expression data of HBV positive cells

status: Public on Sep 07 2017

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

summary:
To determine host factors that regulate HBV, cells positive for and negative for HBV were compared.
We identified three transcription regulators (HNF4A1, HNFA2, HNFA3) that support HBV replication

overall_design: 14 cell lines were analyzed, including 4 liver cells  (2 HBV positive; 2 HBV negative) and 10 non-liver cell lines (all HBV negative)

first: Tze

first: HuiLing

last: Ko

first: Ee

last: Ren


title: Serine/Threonine kinase MLK4 determines Mesenchymal identify in glioma stem cells in an NFkB-dependent manner

city: Birmingham

first: Ichiro

last: Nakano

state: AL

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

summary:
Activation of NF-kB induces MES trans-differentiation and radio-resistance in glioma stem cells (GSCs), but molecular mechanisms for NF-kB activation in GSCs are currently unknown. Here we report that Mixed Lineage Kinase 4 (MLK4) is overexpressed in MES but not PN GSCs. Silencing MLK4 suppresses self-renewal, motility, tumorigenesis, and radio-resistance of MES GSCs via a loss of the MES signature. MLK4 binds and phosphorylates the NF-κB regulator IKKα, leading to activation of NF-κB signaling in GSCs. MLK4 expression is inversely correlated with patient prognosis in MES, but not PN high-grade gliomas. Collectively, our results uncover MLK4 as an upstream regulator of NF-kB signaling and a potential molecular target for the MES subtype of GBMs.
We used microarrays to validate MLK4 target gene expression.

overall_design: GSCs were treated with shNT (control), shMLK4_1. Total RNA was isolated using the Qiagen RNeasy kit(Qiagen).

first: Sunghak

last: Kim


title: Expression data from SKOV3.ip cells by knockdown RAD51-AS1 expression.

status: Public on Aug 17 2017

city: Shanghai

first: Xiaodan

last: Zhang

address: Room 208, 413 Zhaozhou Road

department: Department of Gynecology

institute: Obstetrics and Gynecology Hospital of Fudan University

summary:
Long non-coding RNAs (lncRNA) have been shown to play crucial roles in tumorigenesis. Little is known about lncRNA RAD51-AS1 in diseases. Here, we investigated the role of RAD51-AS1 in Epithelial ovarian cancer. Silencing RAD51-AS1 inhibited proliferation through cell cycle arrest and promotion in apoptosis, both in vitro and in vivo. But the mechanism of RAD51-AS1 downstream regulation remains unclear.
In order to identify the downstream regulation of RAD51-AS1 in epithelial ovarian cancer, we used antisene oligotides targeting RAD51-AS1 / negative control to transfect Skov3.ip cells. Then, we used microarrays to identified differential expression genes and to look for possible target genes by knockdown RAD51-AS1 expression.

overall_design: SKOV3.ip cells transfected with antisene oligotides targeting RAD51-AS1 or negative control siRNA were analyzed. There are three samples in each group.

first: Guoping

last: Liu


title: Genome-wide analysis of the regulatory function mediated by the small regulatory psm-mec RNA of methicillin-resistant Staphylococcus aureus

status: Public on Aug 29 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Several methicillin resistance (SCCmec) clusters characteristic of hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) strains harbor the psm-mec locus. In addition to encoding the cytolysin, phenol-soluble modulin (PSM) mec, this locus has been attributed gene regulatory functions. Here we employed genome-wide transcriptional profiling to define the regulatory function of the psm-mec locus. The immune evasion factor protein A emerged as the primary conserved and strongly regulated target of psm-mec, an effect we show is mediated by the psm-mec RNA. Furthermore, the psm-mec locus exerted regulatory effects that were more moderate in extent and possibly mediated by the PSM-mec peptide. For example, expression of PSM-mec limited expression of mecA, thereby decreasing methicillin resistance. Our study shows that the psm-mec locus has a rare dual regulatory RNA and encoded cytolysin function, both with the potential to enhance MRSA virulence. Furthermore, our findings reveal a specific mechanism underscoring the recently emerging concept that S. aureus strains balance pronounced virulence and high expression of antibiotic resistance.

platform_organism:
Borreliella burgdorferi
Yersinia pestis
Coxiella burnetii
Chlamydia trachomatis
Staphylococcus aureus
Streptococcus pyogenes

overall_design: wild type vs. mutant

first: Gordon

last: Cheung

first: Amer

last: Villaruz

first: Hwang-Soo

last: Joo

first: Anthony

last: Duong

first: Thuan

last: Nguyen

first: Daniel

first: S

last: Queck

first: M

last: Otto


title: Heterogeneous tumor-immune microenvironments among differentially growing metastases in an ovarian cancer patient

status: Public on Jul 14 2017

city: Cambridge

first: Martin

middle: Lee

last: Miller

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

summary:
We present an exceptional responder case of a patient with high-grade serous ovarian cancer, treated with multiple chemotherapy regimens, who exhibited regression of some metastatic lesions with concomitant progression of other lesion during a treatment-free period. Using an immunogenomics approach, we found that progressing metastases were infiltrated by CD8+ and CD4+ T cells, exhibited oligoclonal expansion of specific T-cell subsets, and showed indications of neoepitope depletion. These findings imply that multiple distinct tumor immune microenvironments co-exist within a single individual and may explain in part the heterogenous fates of metastatic lesions often observed in the clinic post therapy.
The goal of this particular experiment was quantify RNA expression using microarrays, and then evaluate differentially expressed genes and pathways between the different tumor samples.

overall_design: Samples analyzed:1) Primary high-grade serous ovarian cancer, 2) Growing spleen metastasis, 3) Shrinking right upper quadrant metastasis, 4) Stable liver metastasis, 5) Growing vaginal cuff metastasis. No control healthy tissues were availabl.e

first: Alejandro

last: Jimenez-Sanchez

first: Tyler

last: Walther

first: Alexandra

last: Snyder

middle: L


title: Gene expression of mesenchymal stromal cells in platelet lysate versus fetal calf serum

status: Public on Aug 11 2017

first: Wolfgang

last: Wagner

summary: Culture medium of mesenchymal stromal cells (MSCs) is usually supplemented with either human platelet lysate (HPL) or fetal calf serum (FCS). Many studies have demonstrated that proliferation and cellular morphology is influenced by these additives – hence they may favor outgrowth of specific subpopulations, thereby affecting the heterogeneous composition of MSCs. We have isolated and expanded human bone marrow derived MSCs in parallel with HPL or FCS for two passages. In HPL the proliferation was significantly higher and cells reflected more spindle-shaped morphology. Pairwise comparisons of gene expression profiles (Affymetrix HTA 2.0) revealed only moderate differences. When we apply a fold change >1.5 and limma-adjusted P-value of <0.05, only 69 transcripts were differentially expressed. These results indicate that there is no systematic bias for specific subpopulations of MSCs by using either HPL or FCS.

overall_design: Affymetrix Human Transcriptome 2.0 arrays analysis of Mesenchymal stromal cells after 2 passages under HPL or FCS supplementation.

first: Eduardo

last: Fernandez-Rebollo

first: Birgit

last: Mentrup

first: Regina

last: Ebert

first: Julia

last: Franzen

first: Giulio

last: Abagnale

first: Torsten

last: Sieben

first: Pierre-François

last: Roux

first: Björn

last: Rath

first: Oliver

last: Bischof

first: Franz

last: Jakob


title: miRNA analysis to identify common targets for GSK3

status: Public on Jul 06 2017

city: Miami

first: Eléonore

last: Beurel

state: FL

address: 1011 NW 15th Street

department: Departments of Psychiatry and Biochemistry

institute: University of Miami

summary: common targets with different GSK3 inhibition approaches

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: mice were treated with siRNA forGSK3b or GSK3 inhibitors, and sacrificed 24 h later, RNA were extracted from hippocampus and sequenced

first: Richard

last: Jope

first: Eleonore