title: Allopregnanolone alters the gene expression profile of human glioblastoma cells

status: Public on Feb 11 2018

city: CDMX

first: Ignacio

last: Camacho-Arroyo

address: AV. UNIVERSIDAD Nº 3000, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, C.U., DISTRITO FEDERAL

department: Biology

institute: Universidad Nacional Autónoma de México

summary:
Glioblastomas (GBM) are one of the most frequent and aggressive brain tumors. In these malignancies, progesterone (P4) promotes proliferation, migration, and invasion. The P4 metabolite allopregnanolone (3α-THP) similarly promotes cell proliferation in the U87 human GBM cell line.
Here, we evaluated global changes in gene expression of U87 cells treated with 3α-THP, P4, and the 5α-reductase inhibitor, finasteride (F).

overall_design: Human glioblastoma U87 cell line (purchased from ATCC) was treated with 3α-THP (10 nM), P4 (10 nM), F (100 nM) or vehicle (V, 0.1 %DMSO) during 72 h. Three independent experiments were performed. Total RNA was extracted and prepared for the samples hybridization with GeneChip Human Gene 1.0 ST arrays (Affymetrix microarrays).

first: Carmen

last: Zamora-Sánchez

first: Aylin

last: del Moral-Morales

first: Ana

last: Hernández-Vega

first: Valeria

last: Hansberg-Pastor

first: Ivan

last: Salido-Guadarrama

first: Mauricio

last: Rodríguez-Dorantes


title: Distinct gene expression profile between ARID1Ahigh and good prognosis and ARID1Alow and poor prognosis groups

status: Public on Feb 06 2018

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

country: Japan

institute: Gifu University School of Medcine

summary: Cancer tissue specimens from ARID1Ahigh and good prognosis and ARID1Alow and poor prognosis of patients with advanced gastric cancer were extracted and analyzed.

overall_design: We first immunohistochemically evaluated the ARID1A protein expression in advanced gastric cancer. We scored ARID1A immunoreactivity based on the sum of the percentage score in invasive cancer cells (on a scale of 0 to 5) and the intensity score (on a scale of 0 to 3), for a possible total score of 0 to 8. mRNAs extracted from two specimens, Low ARID1A expression, less that total score 2, with poor prognosis and two patients with ARID1Ahigh and good prognosis was analyzed.

first: Chiemi

last: Saigo


title: Efficacy of the highly selective focal adhesion kinase inhibitor BI 853520 in adenocarcinoma xenograft models is linked to a mesenchymal tumor phenotype

status: Public on Feb 27 2018

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Effect of PDGF-Ddstimulation on human tonsil ILC1

status: Public on Feb 01 2018

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

summary: The effect of PDGF-DD on the gene expression of human tonsil ILC1 is unknown. We used microarray to determine the transcriptional differences between unstimulated and PDGF-DD-stimulated human tonsil ILC1.

overall_design: Human ILC1 cells from tonsil were sorted to high purity for RNA extraction and hybridization on Affymetrix microarrays.

first: Cella

last: Marina

first: Barrow

last: Alexander


title: Transcriptome analysis of the microalgae Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions

status: Public on Mar 06 2018

city: Suita

first: Kenichi

last: Ogawa

state: Osaka

address: 1-5, Yamadaoka

institute: Osaka University

summary:
To investigate acclimation mechanisms employed under extreme high light conditions, gene expression analysis was performed using the model microalgae Synechocystis sp. PCC 6803 (PCC 6803) cultured under various light intensities.
From the low to the mid light conditions, the expression of genes related to light harvesting systems was repressed, whereas that of CO2 fixation and of D1 protein turnover-related genes was induced. Gene expression data also revealed that the down-regulation of genes related to flagellum synthesis (pilA2), pyridine nucleotide transhydrogenase (pntA and pntB), and sigma factor (sigA and sigF) represents acclimation mechanisms of PCC 6803 under excessive high light conditions.

overall_design: The gene expression in Synechocystis sp. PCC 6803 was analyzed following culture at 30, 50, 300, 1000, 1100, and 1300 μmol m-2 s-1. Three independent experiments were performed under each light intensity. To check the repeatability, some RNA samples are analyzed in three microarraies.

first: Katsunori

last: Yoshikawa

first: Hiroshi

last: Shimizu


title: Disruption of autophagic degradation with ROC-325 antagonizes renal cell carcinoma pathogenesis

status: Public on Feb 16 2018

city: Tucson

first: Jennifer

last: Carew

state: Arizona

address: University of Arizona Cancer Center, 1515 N. Campbell Ave

institute: USA

summary:
Autophagy plays important roles in malignant pathogenesis and drug resistance. We used medicinal chemistry approaches to generate a series of novel agents that inhibit autophagic degradation. ROC-325 was selected as a lead compound for further evaluation. Comprehensive in vitro and in vivo studies were conducted to evaluate the selectivity, tolerability, and efficacy of ROC-325 in preclinical models of renal cell carcinoma (RCC). ROC-325 exhibited superior in vitro anticancer effects than the existing autophagy inhibitor hydroxychloroquine in 12 different tumor models with diverse genetic backgrounds. Focused studies of the mechanism of action and efficacy of ROC-325 in RCC cells showed that drug treatment induced hallmark characteristics of autophagy inhibition including accumulation of autophagosomes with undegraded cargo, lysosomal deacidification, p62 stabilization, and disruption of autophagic flux. Subsequent experiments showed that ROC-325 antagonized RCC growth and survival in an ATG5/7-dependent manner, induced apoptosis, and exhibited favorable selectivity. Oral administration of ROC-325 to mice bearing 786-0 RCC xenografts was well tolerated, significantly more effective at inhibiting tumor progression than HCQ, and inhibited autophagy in vivo.
We used microarrays to determine gene expression changes following 24 h treatment with ROC-325 in RCC cell lines and identified differentially expressed genes.

overall_design: Microarray analyses were performed on two RCC cell lines, 786-O and A498. Cells were wither untreated (Control) or treated with 5 uM ROC-325 for 24 hours. Each sample was run in triplicate for a total of 6 samples per cell lines.

first: Steffan

middle: T

last: Nawrocki

middle: S


title: Expression data for human chronic myeloid leukemia K562 cell line (KS) and adriamycin induced multidrug-resistant K562/ADR (KA) cell line before and after treatment with hypomethylating agent decitabine

status: Public on Mar 01 2018

city: Shenyang

first: Huihan

last: Wang

address: No. 36 Sanhao Street

country: China

institute: China Medical University

summary: To explore the mechanisim and signaling pathway of hypomethylating agent decitabine in reversing P-glycoprotein(P-gp) induced multidrug resistance, we used adriamycin to treat drug sensitive human chronic myeloid leukemia K562 cells(KS) and successfully induced multidrug-resistant K562/ADR (KA) cells that higher expression of drug efflux pump P-gp. Gene expression profile was used to analysis the difference gene expression before and after treated with decitabine in both KS and KA cells.

overall_design: human chronic myeloid leukemia K562 cells (KS) and adriamycin induced multidrug-resistant K562/ADR (KA) cells were separately treated with hypomethylating agent decitabine, and then cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the difference expression gene in order to explore the signaling pathway and mechanism of decitabine in revering the multidrug resistance induced by drug efflux pump P-glycoprotein(P-gp).

first: Xiaobin

first: Zhuogang

last: Liu


title: Genome-wide transcriptional analysis of metabolism-related genes and pathways regulated by FAH in melanoma A375 cells

status: Public on Feb 14 2018

city: Wuhan

first: chao

middle: zhi

last: gu

state: Hubei

address: Liberation Road No. 1095

department: Department of Dermatology, Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Reprogramming metabolism plays an important role in tumor cells for maintaining their abnormal biologic behaviors. Therefore, special factors could regulate metabolic processes and influence the overall status of tumor cells. This phenomenon was obviously found in melanoma. Fumarylacetoacetate hydrolase (fumarylacetoacetase, FAH) is an enzyme encoded by the FAH gene located on the chromosome 15q25.1 region and contains 14 exons. FAH enzyme catalyzes the hydrolysis of 4- fumarylacetoacetase into fumarate and acetoacetate. It is the last enzyme in the subpathway from L-phenylalanine and tyrosine degradation. Mutations in the FAH gene cause type I tyrosinemia, which is a hereditary error of metabolism that is characterized by increased tyrosine levels in the blood and urine of patients. In the present study, we will explore whether FAH is an essential enzyme to promote multiple metabolic processes and elucidate the functions of FAH in melanoma. Gene microarrays and bioinformatics analysis of the differentially expressed genes (DEGs) were performed using A375 cells, and we concentrated on the biologic functions of FAH. In general, our work revealed several functional mechanisms of FAH in melanoma, which indicated FAH might be a potentially therapeutic target and an independent prognostic indicator for this disease.

overall_design: We used two groups of A375 cells for microarray assay and each group included three biological replicates.  A375 cells transfected with siFAH for 72 hours were regarded as experimental group compared to the control group cells were transfected with negative control siRNA. The silence efficiency was verified by real-time PCR. Total RNA of two group cells were extracted using TRIzol Reagent and further purification with an RNeasy kit (Qiagen). Then total RNA quality was assessed by agarose gel electrophoresis. Subsequently, cDNA of each sample was created using One-Cycle Target Labeling and Control Reagents (Affymetrix). Then cRNA was generated using a GeneChip IVT Labeling Kit (Affymetrix). Each product was biotin-labeled, fragmented and hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array (Affymetrix) and washed, and stained with the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). We performed three biological replicates for each sample. Then all arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix). Data were analyzed using GeneChip Operating Software 1.4.

first: Zhichao

last: Gu

first: Yuchun

last: Cao


title: Host response to the different pathologic conditions

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: The experiment adresses primary material from pneumonia, malaria, COPD and healthy patients. The transcriptome anaylsis shall shed light on the host response to the different pathologic conditions and hightlight key differences. Investigated cells (PBMCs) were obtained from patient blood by gradient centrifugation.

overall_design: RNA from peripheral blood mononuclear cells was isolated from human subjects from four groups: heathly, pneumonia, COPD, and with Malaria infection, and subjected to one-color microarray analysis.

first: Wilhelm

last: Bertrams


title: Comparison between steady-state fibroblasts and myofibroblasts in mouse lungs

status: Public on Feb 24 2018

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

summary: This analysis aimed to identify significantly up-regulated genes in myofibroblasts, compared with steady-state fibroblasts.

overall_design: Microarray comparison of mouse lung cells sorted by FACS, including steady-state fibroblasts, myofibroblasts, and lung homogenates (as controls). Each group has two sets of 50000 cells.

first: Toshihide

last: Iwashita


title: Expression data from mouse embryonic fibroblasts (MEFs) mdmxER-Cre;C463A/WT cells, with or without 4-Hydroxytamoxifen (4OHT) treatment.

status: Public on Jan 20 2018

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

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 MEFs. We used mdmxER-Cre;C463A/WTMEFs with EtOH treatment as control group, and same cells with 4OHT treatment as experimental group for gene chip analysis.

overall_design: Duplicates 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 MTA 1.0 chip (Affymetrix).

first: Weiqi

last: Zeng


title: Expression data from TCF7L1 siRNA knockdown in H9 human embryonic stem cells

city: Irvine

first: Peter

middle: J

last: Donovan

address: Gross Hall, Rm 3006, 845 Health Sciences Road

institute: University of California, Irvine

summary: We used microarray analysis to profile the function of TCF7L1 in human embryonic stem cells.

overall_design: To identify putative TCF7L1 target genes in human embryonic stem cells, we performed a loss-of-function siRNA knockdown experiment in the H9 human embryonic stem cells line.

first: Robert

middle: A

last: Sierra

first: Marian

middle: L

last: Waterman


title: Deciphering the mammary gland transcriptome during the dry period in dairy cows under heat stress

status: Public on Jan 08 2018

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

summary: The bovine dry period is a dynamic non-lactating phase where the mammary gland undergoes extensive tissue remodeling. Utilizing RNA Sequencing, this study characterized novel genes and pathways involved in this process and determined the impact of dry period heat stress. Mammary tissues were collected before and during the dry period (-3, 3, 7, 14, and 25 days relative to dry-off) from twelve heat-stressed (HT, n=6) or cooled (CL, n=6) pregnant Holstein cows.

overall_design: Twelve multiparous Holstein cows were dried off at 46 d before expected calving. Cows were randomly assigned to two treatments for the duration of the dry period: heat-stressed (HT, n=6; access to shade) or cooled (CL, n=6; access to shade, fans and soakers). Mammary biopsies were collected from the same cow at day 3 before dry-off and at day 3, 7, 14, and 25 after dry-off. Mammary tissue samples (12 cows x 5 time points = 60 samples) were subjected to RNA extraction, library generation, and subsequent sequencing.

first: Jimena

last: Laporta


title: Expression data from TCF7L1 Over-expression during primitive streak-like differentiation in H9 human embryonic stem cells

overall_design: To identify putative TCF7L1 target genes in human embryonic stem cells, we performed a gain-of-function over-expression experiment in the transgenic H9-TCF7L1 human embryonic stem cell line.


title: Identification of genes associated with breast cancer micrometastatic disease in bone marrow using a Patient Derived Xenograft mouse model

status: Public on Jan 12 2018

city: Saint Louis

first: Sreeraj

last: Pillai

state: MO

address: 660 S Euclid Avenue, CB 8109

department: Surgery

institute: Washington University School of Medicine

summary:
In this study, using a Patient Derived Xenograft (PDX) system established by transplanting primary tumors from pre-metastatic breast cancer patients we demonstrate that development of distant organ metastases correlates with the presence of Bone Marrow Disseminated Tumor Cells (BM DTCs) in the PDX mice. Comparative gene expression analysis of bone marrow (BM) from tumor bearing PDX mice which developed metastatic disease was carried out with BM from non-tumor bearing controls.
In this dataset, BM from seven tumor bearing mice with metastatic tumors, two control mice, a primary tumor and a spleen metastatic tumor from one of the tumor bearing mice were included in this analysis. This study allowed the identification of novel gene expression patterns associated with DTCs present in the BM and supports the concept that DTCs present in the BM undergo epithelial to mesenchymal transition (EMT). Analysis of the gene array data identified  several genes which are known oncogenes (ETS1, GNL3), metastatic regulators (MALAT1, ALCAM, CD44), or associated with EMT (SIP 1) expressed at significantly higher levels in the BM of PDX mice as compared to BM from control animals.

overall_design: DTC-enriched BM from seven WHIM17 mice, one primary WHIM17 tumor, and a solid organ metastasis from the WHIM17 mouse was performed to evaluate the molecular differences between primary tumor xenograft cells and their DTC counterparts, as well as to identify unique genes associated with the DTCs themselves using human-based microarrays. Control BM samples from non-tumor bearing NOD-SCID mice with and without humanized mammary fat pads were included to account for cross-hybridization and detection of transcripts emanating from mouse BM cells.

middle: G

first: Shunqiang

last: Li

first: Chidananda

middle: M

last: Siddappa

first: Nupur

last: Dasgupta

first: Mark

last: Watson

first: Timothy

middle: P

last: Fleming

first: Matthew

last: Ellis

first: Rebecca

last: Aft


title: Roles of Cdc42 and Rac in Bergmann glia during cerebellar corticogenesis

status: Public on Jan 01 2018

city: Kobe

first: Takehiko

last: Ueyama

state: Hyogo

address: Rokkodai-cho 1-1, Nada-ku

department: Biosignal Research Center

institute: Kobe university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Regulators of Human Androgen Biosynthesis

city: Bern

first: Christa

middle: E.

last: Flück

address: Freiburgstrasse 15 / C845

department: Pediatric Endocrinology and Diabetology of the Department of Pediatrics and Department of Clinical Research

country: Switzerland

institute: University of Children's Hospital, Bern

type: Expression profiling by genome tiling array

summary:
Androgens are essential for sexual development and reproduction. However, androgen regulation in health and disease is poorly understood. Previously, we showed that human adrenocortical H295R cells grown under starvation conditions acquire a hyperandrogenic steroid profile with changes in steroid metabolizing enzymes HSD3B2 and CYP17A1 essential for androgen production. Furthermore, we have shown that metformin inhibits androgen production of steroidogenic H295R cells and inhibits  complex I activity of the respriatory chain. Therefore, to search for underlying mechanisms regulting androgen production and to understand the basic biology of androgens, we have characterized the gene expression profile of H295R cells grown under normal growth conditions, serum starvation (hyperandrogenic) growth conditions as well as after metformin treatment (hypoandrogenic).
In this dataset, we first characterized the gene expression profile of H295R cells cultured under nromal growth vs serum-starved (hypernadrogenic) growth conditions. Expression profiling of starved H295R cells revealed alterations in genes involved in steroid and energy metabolism and signal transduction. We discovered two new gene networks around RARB and ANGPTL1, and show how they regulate androgen biosynthesis (Udhane SS et al.,2015).  In a second part, we compared the gene expression profile of  H295R cells grown under serum starvation (hyperandrogenic) conditions to metformin treated (hypoandrogenic) cells in search for the underlying androgen regulating network. (Udhane et al., manuscript in preparation).

overall_design: Total RNA was isolated and purified with an RNeasy Micro kit (Qiagen GmbH, Hilden, Germany) from cultured H295R cells under normal growth, serum starvation and metformin treated condition. Microarray experiments were carried out from three independent experiments with GeneChip Human Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) at the Genomic Technologies Facility (GTF) of the University of Lausanne, Switzerland.

first: Sameer

last: Udhane

middle: E


title: Roles of Cdc42 and Rac in Bergmann glia during cerebellar corticogenesis (U87_CDC42RAC1-DKD)

summary: Bergmann glia (BG) are important in the inward type of radial migration of cerebellar granule neurons (CGNs). However, details regarding the functions of Cdc42 and Rac in BG for radial migration of CGN are unknown. To examine the roles of Cdc42 and Rac in BG during cerebellar corticogenesis, mice with a single deletion of Cdc42 or Rac1 and those with double deletions of Cdc42 and Rac1 under control of the glial fibrillary acidic protein (GFAP) promoter: GFAP-Cre;Cdc42flox/flox (Cdc42-KO), GFAP–Cre;Rac1flox/flox (Rac1-KO), and GFAP-Cre;Cdc42 flox/flox;Rac1flox/flox (Cdc42/Rac1-DKO) mice, were generated. Both Cdc42-KO and Rac1-KO mice, but more obviously Cdc42-KO mice, had disturbed alignment of BG in the Purkinje cell layer (PCL). We found that Cdc42-KO, but not Rac1-KO, induced impaired radial migration of CGNs in the late phase of radial migration, leading to retention of CGNs in the inferior half of the molecular layer (ML). Cdc42-KO, but not Rac1-KO, mice also showed aberrantly aligned Purkinje cells (PCs). These phenotypes were exacerbated in Cdc42/Rac1-DKO mice. Alignment of BG radial fibers in the ML and BG endfeet at the pial surface of the cerebellum evaluated by GFAP staining was disturbed and weak in Cdc42/Rac1-DKO mice, respectively. Our data indicate that that Cdc42 and Rac, but predominantly Cdc42, in BG play important roles during the late phase of radial migration of CGNs. We also report here that Cdc42 is involved in gliophilic migration of CGNs, in contrast to Rac, which is more closely connected to regulating neurophilic migration.

overall_design: To examine the mRNA levels affected by double knockdown (KD) of CDC42 and RAC1, siRNA-mediated KD of CDC42 and RAC1 was performed in U87MG astrocytic cells.


title: Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution

status: Public on Feb 19 2018

city: San Francisco

first: Jordan

middle: Emily

last: Burke

address: N374 Genentech Hall, 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Tools to understand how the spliceosome functions in vivo have lagged behind advances in its structural biology. We describe methods to globally profile spliceosome-bound precursor, intermediates and products at nucleotide resolution. We apply these tools to three divergent yeast species that span 600 million years of evolution. The sensitivity of the approach enables detection of novel cases of non- canonical catalysis including interrupted, recursive and nested splicing. Employing statistical modeling to understand the quantitative relationships between RNA features and the data, we uncover independent roles for intron size, position and number in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal ATP-dependent discard of numerous endogenous substrates at both the precursor and lariat-intermediate stages and connect discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology to investigate an RNP central to eukaryotic gene expression.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Cryptococcus neoformans

overall_design: Spliceosome profiling of samples from S. cerevisiae, S. pombe and C. neoformans. Detailed description of the method can be found in the supplementary PDF file. 2 replicates of each sample type are analyzed (3' end profiling, spliceosome-bound RNA-seq, polyA RNA-seq, junction profiling and branch profiling.

first: Hiten

middle: D

last: Madhani


title: Expression data from human iNKT cells with or without interaction with human airway epithelium

status: Public on Dec 29 2017

first: Kambez

last: Hajipouran Benam

state: MA

address: Center for Life Science Boston, 3 Blackfan Circle

institute: Wyss Insstitute, Harvard Medical School

summary: Recent studies showing involvement of iNKT cells in lung viral infections and airway inflammation suggest that these cells are key players in both prevention and generation of immune-pathology in the lungs. It is not fully understood how iNKT cells are activated in the lungs and if this relied solely on lung dendritic cells. We recently showed that CD1d is expressed on airway epithelium, and now demonstrate that iNKT cells can be activated by primary airway epithelial cells, via both CD1d dependent and independent processes. Transcriptional analysis of human iNKT cells reveals that direct contact with lipid-pulsed primary human airway epithelial cells results in initiation of a programme of activation comprising rapid and concomitant induction of cytokine genes and genes to switch off this response. These findings establish a new mode of activation within the lungs for iNKT cells, and further enhance the role of airway epithelium in innate lung immunity.

overall_design: Human iNKT cells (an in vitro expanded clone [LH22]; Ho et al, 2004) were selected at three conditions for RNA extraction and hybridization on Affymetrix Gene ST 1.0 microarrays. For baseline, we used iNKT cells which had not been exposed to airway epithelium ('untouched' - iNKT_0h). Then, we studied the biological processes that occur in iNKT cells after interaction with human airway epithelium. For this, we pulsed normal human bronchial epithelial (NHBE) cells with αGC for 24 hours, then co-cultured these with iNKT cells directly (‘Direct’ - iNKT_Direct_4h) or separated by Transwell™ inserts (‘Transwell’ - iNKT_Transwell_4h). Three biological replicates were studied at each condition.

middle: H

last: Benam

first: Sharon

last: Sanderson

first: Wai-Ling

last: Kok

first: Helen

last: Lockstone

first: Andrew

last: McMichael

first: Ling-Pei

last: Ho


title: ODZ1 supports glioblastoma progression by enhancing proliferation and migration of cancer stem-like cells

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

summary: The invasion capacity is one of the hallmarks of glioblastoma (GBM) cells. We found that ODZ1 which is mainly expressed in fetal brain, plays a crucial role in the migration and proliferation of GBM stem-like cells (GSCs). Introduction of the entire ODZ1 or its intracellular fragment in ODZ1-deficient cells promotes migration and invasion in 2D and 3D substrates and in chicken embryo and mouse xenograft models. Moreover, ODZ1 increases the proliferation of GSCs in culture and generates bigger tumor masses in the brain of xenografted mice. Consistently, higher levels of ODZ1 are correlated with lower survival both in patients and in xenograft models. On note, ODZ1 promotes the transcriptional activation of RhoA and ODZ1-induced proliferation and invasion activities were blocked by inhibiting RhoA-ROCK axis. Overall, we describe a novel cancer-associated gene involved in the progression of glioblastoma, providing a putative prognostic marker and a new target for therapeutic strategies.

overall_design: Three samples each for icODZ1-transfected cells and empty vector-transfected cells were included

first: Jose

last: Fernández Luna


title: Whole transcript expression profiling of umbilical cord- and bone marrow-derived stem cells

status: Public on Dec 28 2017

city: Diepenbeek

first: Raf

last: Donders

address: Agoralaan Building C

department: Biomedical Research Institute

country: Belgium

institute: Hasselt University

summary:
Mesenchymal stromal cells (MSCs) are multipotent stem cells with potent immunosuppressive and trophic support functions. Although bone marrow is considered the golden standard to isolate classical MSCs (BM-MSC), MSC-like cells are currently also derived from other, more easily accessible extra-embryonic tissues such as the umbilical cord. In this study we compared the gene expression profile of human Wharton's jelly explant-derived MSC cultures with two adult MSC populations derived from bone marrow, namely BM-MSC and multipotent adult progenitor cells (MAPC).
Here we demonstrate, by using genome wide gene expression analysis, that WJ-MSCs intrinsically have a differential gene expression profile compared to the adult MSCs. Gene ontology analysis revealed an increased expression of genes associated with cell-adhesion, proliferation, and immune system functioning. Furthermore, in comparison to adult MSC, stem cells from the Wharton’s jelly highly express genes involved in neurotrophic support (e.g. LIF, BDNF, NTF3). Such enhanced signatures make WJ-MSC an attractive candidate for cell-based therapy in neurodegenerative and immune-mediated CNS disorders such as multiple sclerosis or amyotrophic lateral sclerosis.

overall_design: Umbilical cord Wharton's jelly-derived MSCs (n=5) were obtained after explant tissue culturing and harvested after 3 passages. Bone marrow-derived MSCs (n=5) were monolayer cultured until their third passage and harvested. MAPC (n=5) were cultured as previously described [Reading et al. J Immunol 2013; 190:4542-4552].


title: An epigenetic panel of NEFH and HS3ST2 relates to overall survival in human ovarian cancer .

status: Public on Dec 31 2017

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

summary: We used methylation DNA arrays to observe the genomic wild methylation profiles in 31 malignant ovarian tumors. After validations, we selected, NEFH and HS3ST2. We used bisulfite pyrosequencing to expose methylation status for 84 independent samples. Kaplan–Meier survival and Cox regression analysis estimates the association with ovarian cancer outcome. We discovered patients with high methyatlion of two genes, had a shorter median 5-years overall survival. We also evaluated the high-methylation of a panel genes in patients, that presented as an independat factor for associated with poor outcomes. High-methylation of NEFH and HS3ST2 are provided the prognostic index for the poor outcome of overall survival in ovarian cancers.

overall_design: Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Rui-Lan

last: Huang


title: Next Generation Sequencing analysis of Lhx6 heterozygote and null forebrain transcriptomes at post natal day 15

status: Public on Dec 16 2017

city: London

first: Guilherme

last: Neves

address: New Hunt's House, 4th Floor, Guy's Hospital Campus

department: MRC - Center for Neurodevelopmental Disorders

country: United Kingdom

institute: King's College London

summary: Here we characterize the changes in the forebrain transcriptome resulting from the deletion of the transcription factor Lhx6, generated by RNA-seq technology with biologic replication. Lhx6 is an essential regulatory gene in the development of cortical interneurons generated in the medial ganglionic eminences of the embryonic brain. This data contains insights into gene networks important for the development of medial ganglionic eminence derived interneurons.

overall_design: Forebrain total RNA profiles of 15-day old Lhx6 heterozygote (Het) and Lhx6 null mice were generated by deep sequencing, using Illumina GAIIx. Mutant allele used was Lhx6tm2Vpa (MGI:3702518). Each individual sample was comprised of two animals. Four samples for Lhx6 Het and three samples for Lhx6 null mice were generated and analysed in parallel.

first: Adam

last: Rabinowitz

first: Vassilis

last: Pachnis

first: Myrto

last: Denaxa


title: Effects of brain-derived neurotrophic factor on microRNA expression profile in human endothelial progenitor cells

status: Public on Dec 05 2017

city: Rochester

first: Zvonimir

last: Katusic

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary:
The mechanisms underlying proangiogenic function of brain-derived neurotrophic factor (BDNF) are not fully understood.
Current study was designed to explore the miRNA profile in human early endothelial progenitor cells (EPCs, also referred to as CFU-Hill cells) in response to BDNF treatment.

overall_design: Affymetrix GeneChip miRNA-3.0 array was used to examine miRNA expression profile in early EPCs derived from 4 subjects under control culture and BDNF treatment conditions

first: Tongrong

last: He


title: siRNA knockdown of C1GALT1 in MIA PaCa-2 cells

status: Public on Dec 04 2017

first: Min-Chuan

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

institute: National Taiwan University

summary: To determine the C1GALT1 regulated gene expression profile in MIA PaCa-2 cells.

overall_design: MIA PaCa-2 cells were transfected with non-targeting or C1GALT1-specific siRNAs for 48 hours and total RNA were extracted.

first: Min

last: CHuang


title: Global gene expression profiling of FOP- or resFOP-iMSCs after chondrogenic differentiation

status: Public on Dec 01 2017

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: Comparison of gene expressions among  FOP- or resFOP-iMSCs after chondrogenic differentiation with Activin-A, BMP-7 or TGF-B3

first: J

first: M

last: Ikeya


title: Maternal Stress and Genomic Variation

status: Public on Nov 30 2017

city: Gainesville

first: Christopher

middle: Jordan

last: Clukay

state: Florida

department: Anthropology

institute: University of Florida

summary:
Custom Affymetrix SNP used to assay 24 mothers for desired variants.
Data processed using the Affymetrix SNP Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).

overall_design: 24 samples analyzed for genetic variants. The associated DNA methylation data is GSE54399.

first: David

last: Hughes

first: Nicole

middle: C

last: Rodney

first: Darlene

last: Kertes

first: Connie

last: Mulligan


title: Expression profiling of epidermolysis bullosa associated squamous carcinoma cells

status: Public on Dec 07 2017

city: Salzburg

first: Christina

last: Guttmann-Gruber

address: Muellner Hauptstrasse 48

institute: EB House Austria

summary: Patients with the genetic skin blistering disease recessive dystrophic epidermolysis bullosa (RDEB) develop aggressive and metastatic cutaneous squamous cell carcinoma which is the principal cause of premature mortality in this patient group. We performed gene expression profiling of RDEB-SCC cells compared to RDEB keratinocytes in order to identify tumor-specific molecules that could potentially be exploited for detection, diagnosis, and therapy of this devastating disease.

overall_design: Total RNA was isolated from RDEB-SCC cells (n = 3), as well as RDEB keratinocyte (n = 3) and normal human keratinocyte (n = 1) cell lines. Gene expression profiling was performed by microarray.

first: Josefina

last: Hofbauer


title: Gene expression alterations by the mTORC1-FOXK1 pathway

status: Public on Nov 28 2017

city: Higashi-ku

first: Hirokazu

last: Nakatsumi

state: Fukuoka

address: 3-1-1, Maidashi

department: Department of Molecular and Cellular Biology

institute: Medical Institute of Bioregulation, Kyushu University

summary: C-C chemokine ligand 2 (CCL2) plays pivotal roles in tumor formation, progression, and metastasis. Although CCL2 expression has been found to be dependent on the nuclear factor (NF)–κB signaling pathway, the regulation of CCL2 production in tumor cells has remained unclear. We have identified a noncanonical pathway for regulation of CCL2 production that is mediated by mammalian target of rapamycin complex 1 (mTORC1) but independent of NF-κB. Multiple phosphoproteomics approaches identified the transcription factor forkhead box K1 (FOXK1) as a downstream target of mTORC1. Activation of mTORC1 induces dephosphorylation of FOXK1 resulting in transactivation of the CCL2 gene. Inhibition of the mTORC1-FOXK1 axis attenuated insulin-induced CCL2 production as well as the accumulation of tumor-associated monocytes-macrophages and tumor progression in mice. Our results suggest that FOXK1 directly links mTORC1 signaling and CCL2 expression in a manner independent of NF-κB, and that CCL2 produced by this pathway contributes to tumor progression.

overall_design: Two biological replicates of FOXK1 depleted, RhebCA expressing, and Rapamycin treated HeLa cells were processed for gene expression array analyses using an Affymetrix platform.

first: Masaki

last: Matsumoto

first: Keiichi

middle: I

last: Nakayama


title: Noncanonical Pathway for Regulation of CCL2 Expression by an mTORC1-FOXK1 Axis Promotes Recruitment of Tumor-Associated Macrophages

summary:
C-C chemokine ligand 2 (CCL2) plays pivotal roles in tumor formation, progression, and metastasis. Although CCL2 expression has been found to be dependent on the nuclear factor (NF)–κB signaling pathway, the regulation of CCL2 production in tumor cells has remained unclear. We have identified a noncanonical pathway for regulation of CCL2 production that is mediated by mammalian target of rapamycin complex 1 (mTORC1) but independent of NF-κB. Multiple phosphoproteomics approaches identified the transcription factor forkhead box K1 (FOXK1) as a downstream target of mTORC1. Activation of mTORC1 induces dephosphorylation of FOXK1 resulting in transactivation of the CCL2 gene. Inhibition of the mTORC1-FOXK1 axis attenuated insulin-induced CCL2 production as well as the accumulation of tumor-associated monocytes-macrophages and tumor progression in mice. Our results suggest that FOXK1 directly links mTORC1 signaling and CCL2 expression in a manner independent of NF-κB, and that CCL2 produced by this pathway contributes to tumor progression.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: MicroRNA expression data from CIE-vapor treated mice

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: We examined microRNA expression profiles in amygdala (AMY), nucleus accumbens (NAC) and prefrontal cortex (PFC) of male C57BL/6J mice exposed to 4 cycles of chronic intermittent ethanol (CIE) vapor. Animals were sacrificed at 0, 8, and 120 hr following the last ethanol exposure.

overall_design:
Mice were exposed to 4 cycles of intermittent vapor [4 days of 16 hours vapor/ 8 hours air] with a week between each cycle.
Before entry into the vapor chambers, animals were injected with pyrazole (1 mMol/kg) and either ethanol (1.6 g/kg) or saline (controls).
Animals were sacrificed at 0, 8, and 120 hr following the last ethanol exposure.
All groups contained 8 animals except: AMY 120hr control (7 animals), NAC 0hr CIE-treated (7 animals), NAC 8hr control (6 animals), PFC 0hr control (7 animals)

first: Gayatri

middle: R

last: Tiwari

first: R

last: Mayfield

last: Harris

first: Howard

last: Becker

first: Marcelo

middle: F

last: Lopez


title: De novo and rare inherited copy-number variations in the hemiplegic form of cerebral palsy

status: Public on Nov 23 2017

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

type: Genome variation profiling by genome tiling array

summary: The Affymetrix CytoScan HD array is a high resolution SNP platform for studying copy number variations in the human genome.  It is widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed this platform to investigate the risk factor CNVs in trios diagnosed with hemiplegic cerebral palsy. We genotyped 101 unrelated probands and their both parents and compared their genotypes to those of 9,611 population controls, in order to identify rare CNVs (<0.1% frequency) of at least 10 kb in size that might contribute to CP. We uncovered de novo CNVs and Decipher Syndromes in probands. We have identified additional potentially risk factor CNVs impacting the coding sequencing of genes involved in brain functions.

overall_design: We employed Affymetrix Chromsome Analysis Suite (ChAS), iPattern, Nexus, and Partek algorithms to call CNVs from the CytoScan HD array data. We defined a stringent set of variants when each variant was called by at least by two algorithms. We defined the ancestry and relatedness of the samples using PLINK.

first: Mehdi

last: Zarrei


title: In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (30 PCL miRNA data sets)

status: Public on Nov 09 2017

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: The identification of deregulated microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In addition, the cross-regulation between lncRNAs and miRNAs has begun to emerge, and theoretical and experimental studies have demonstrated the competing endogenous RNAs (ceRNAs) activity of lncRNAs as natural miRNA decoys in pathophysiological conditions, including cancer. Currently, information concerning lncRNA and miRNA interplay in MM is virtually absent. Herein, we investigated in silico the lncRNA and miRNA relationship in a representative datasets encompassing 95 MM and 30 plasma cell leukemia patients at diagnosis and in four normal controls, whose expression profiles were generated by a custom annotation pipeline to detect specific lncRNAs. We applied target prediction analysis based on miRanda and RNA22 algorithms to 235 lncRNAs and 459 miRNAs selected with a potential pivotal role in the pathology of MM. Among pairs that showed significant correlation between lncRNA and miRNA expression levels, we identified 10 lncRNA-miRNA relationships suggestive of novel ceRNA network with relevance in MM.

overall_design: We searched for putative significant correlation between lncRNAs and miRNAs expression level in paired samples, with the support of target prediction analysis. Wilcoxon rank-sum test was applied using standard functions in R base package. The Benjamini-Hochberg method was applied for multiple testing correction. miRNA targets custom predictions were obtained for lncRNA sequences by merging the results of two different algorithms: RNA-22 version 2.0 prediction algorithm and miRanda, which both allow customizing input sequences and parameters. The RNA-22 perl script was run on the combination of the 459 miRNA and 1546 (number of different transcripts corresponding to 235 lncRNAs) lncRNA FASTA sequences selected as relevant among all the miRNAs and lncRNAs respectively detected by the arrays. Default sensitivity/specificity ratio of 1.032 was chosen, provided a minimum seed size of 7 bases with only one mismatch exception, a minimum number of 12 paired-up bases in heteroduplex with -12 Kcal/mol maximum folding energy, and no more than one G-U wobble in the seed region. The miRanda algorithm has been run under default conditions, without any a-priori restrictions on score, energy and trimming parameters.

first: Domenica

last: Ronchetti

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Antonino

last: Neri


title: In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (30 PCL lncRNA data sets)


title: Profiling gene expression of HeLa cells transfected with FOXK1

overall_design: Two biological replicates of FOXK1-expressing and control HeLa cells were processed for gene expression array analyses using an Affymetrix platform.


title: Expression data from CTCL patient skin lesion [Affymetrix]

status: Public on Nov 08 2017

city: Shanghai

first: Jie

last: Zheng

address: 197 Ruijin Er Rd

department: Dermatology

institute: Ruijin Hospital

summary:
Cutaneous T cell lymphoma (CTCL) can have clinical and histological features resembling benign inflammatory dermatosis (BID) and can be difficult to diagnose especially at the early stage of CTCL.
We used microarrays to detail the global alteration of miRNA transcriptome and generate a diagnosis and prognosis signature.

overall_design: Patient skin biopsy samples were collected for RNA extraction and hybridization on Affymetrix microarrays. We pooled 3 samples per group into one Affeymetrix sample.

first: Xiaoyan

last: Shen


title: A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

status: Public on Nov 17 2017

city: CUERNAVACA

first: ADRIAN

last: OCHOA-LEYVA

state: Morelos

address: Av. Universidad #2001, Col. Chamilpa

department: Microbiología Molecular

country: Mexico

institute: Instituto de Biotecnología, UNAM

summary:
Background. Although the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under the specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays.
Methods. We extracted the RNA from 16 children leukocyte samples (9 males and 7 females, ages 6 to 10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of the 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold.  After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR).
Results.
From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and their expression level were confirmed by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEEG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell-mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment.
Discussion. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.

overall_design: Blood tissues were obtained from volunteers recruited from Hospital Infantil de México Federico Gomez. Parents or guardians of each child signed the consent form for participation in the project. The study was approved by the Ethics Committee of Hospital Infantil de México Federico Gomez.

first: Adrián

last: Ochoa-Leyva

first: Fernanda

last: Cornejo-Granados


title: Transcriptome analyses of Colletotrichum orbiculare during appressorium formation in vitro and in planta

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Elucidation of the involvement of MOR (morphogenesis-related NDR kinase network) pathway in the gene expression during appressorium development in planta, transcriptome analyses at the stage of appressorium formation (4 hours post inoculation) in vitro and in planta were performed and revealed that MOR is responsible for the expression of a subset of the plant signal induced genes with potential roles in pathogenicity.

overall_design: We collected samples from germinating conidia incubated on the polystyrene petri dishes (in vitro) for 4 h of the wild type strain 104-T or Cbk1-CA strain, and incubated on cucumber cotyledons (in planta) for 4 h of the wild type or pag1Δ. Three replicates were performed for each experiment.

first: Sayo

last: Kodama

first: Yasuyuki

last: Kubo


title: AltitudeOmics microRNA expression data

status: Public on Nov 03 2017

city: Aurora

first: Robert

last: Roach

state: CO

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

institute: University of Colorado

summary: Acclimatization to high altitude over 21 days, and upon re-ascent 7 and 21 days post-descent. See Subudhi et al. (2014) PLoS One 9(3):e92191, PMCID PMC3962396, PMID 24658407 for experiment details.

overall_design: 98 total samples representing 21 subjects at 6 time points (not all subjects represented at all time points) were taken. Significance was determined by change vs. baseline (sea level).

first: Daniel

last: Dvorkin


title: miRNA expression data in MCF-7 breast cancer Cell line post BCAS2 and FST knockdown

status: Public on Oct 31 2017

city: Bhubaneswar

first: Sandeep

last: Mishra

state: Odisha

address: Nalco Nagar Road, NALCO Nagar, Chandrasekharpur

country: India

institute: ILS

summary: Previously, we have confirmed the tumor suppressive role of Estrogen Related Receptor β (ERRβ) in breast cancer by modulation of ER transcriptional activities on Breast Cancer Amplified Sequence 2 (BCAS2) and Follistatin(FST).In the mentioned study, we proved downregulation of Cyclin D1 by BCAS2.In the previous report, we have also proved downregulation of FST by BCAS2 through inhibition of β-catenin/TCF-4 complex recruitment on FST promoter. Interestingly, Cyclin D1 induction by FST has been also reported by a different group.Recently, Cyclin D1 expression has been found to be associated with DICER1 induction. Hence it may be speculated, that a part of miRNA population, which involves Dicer for processing, is regulated by BCAS2. And it is also possible, that FST may oppose the effect of BCAS2 on those Dicer-processed miRNAs.This Dicer-regulation by Cyclin D1was reported in Luminal A type of breast cancer. Hence, we chose MCF-7 breast cancer cells for miRNA profiling post knocking down BCAS2 and FST.

overall_design:
We used affymetrix miRNA expression profile of the two transcriptional targets of Estrogen Related Receptor β (ERRβ) post BCAS2 and FST knockdown to identify the downstream signaling of ERR β in Breast Cancer.
The total RNA from control siRNA (triplicate), BCAS2 (triplicate) and FST (triplicate) knock-down samples were run in Affymetrix miRNA 3.0 platform and hybridized with miRNA-specific probes for 16hr at 60 rpm and at 48°C. Microarray scanner 3000 7G was used for signal detection. Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analysed using Affymetrix Expression Console and GeneSpring GX12.1 software followed by differential miRNA expression, fold change and cluster analysis. All the original microarray data (CEL files-) for the control & test experiment were pre-processed using RMA (Robust Multichip Average) algorithm that consists of three steps: a background adjustment, quantile normalization and finally summarization. All the above procedures were done by selecting default RMA algorithm, data adjustment and background correction (GABG) in Affymetrix Expression Console 1.2.1.20. The normalized intensity files were exported from Expression Consoles tool. In the next step, miRNA probesets representing Homo sapiens were filtered from the normalized intensity file. After generating Homo sapiens miRNA probesets intensity files, these files were imported in GeneSpring GX 12.1 software for differential miRNAs expression study followed by statistical analysis. Furthermore, differentially expressed miRNAs were preceded for fold change analysis and cluster analysis for the identification of co expressed miRNAs or similar type of experiment profiles. The total number of Homo sapiens miRNA probesets detected for the experiment is 5,617. After data processing and quality control only 2288 probesets left out of 5,617. Then, all normalized data were imported in Gene Spring 12.1 for the differential expression and cluster analysis. After normalization, experimental grouping was done according to the experiment conditions. The averages over the replicate sets were taken during the experimental grouping. Differential miRNA expression analysis was performed by comparing experiment conditions with control. One-way ANOVA method was applied for assessing the statistically significant and differentially expressed miRNAs. The cut off for significant p-value was 0.05. Next, cluster analysis was performed for the identification of co-expressed miRNA sets across the samples. miRNA expression alteration was illustrated using heat map image of hierarchical clustering. Hierarcheal clustering (hcl) was performed for the miRNAs expressed with fold change>=2.0.

first: Dharmendra

middle: K

last: Bhargava

first: Debomita

last: Sengupta

first: Ashish

last: Trivedi

first: Sandip


title: mTOR and HDAC inhibitors converge on the TXNIP/thioredoxin pathway to cause catastrophic oxidative stress and regression of RAS-driven tumors

status: Public on Oct 23 2017

city: Boston

first: Clare

last: Malone

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School -  Brigham Women's Hospital

summary:
mTOR and HDAC inhibitors induce cell death of malignant peripheral nerve sheath tumors (MPNSTs) in vitro, and in vivo
We performed microarray analysis of mTOR and HDAC inhibition alone and in combination 24 hours after treatment, prior to induction of cell death, to identify transcriptional changes that might be mechanistic drivers of the therapeutic efficacy

overall_design: 12 samples, in triplicate, 3X vehicle, 3X INK-128, 3X Vorinostat, 3X INK-128 + Vorinostat

first: Karen

last: Cichowski


title: A mutation in the viral sensor 2’-5’-oligoadenylate synthetase 2 causes failure of lactation.

status: Public on Oct 18 2017

city: Sydney

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

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


title: Expression data from CTCL patient skin lesion

first: Jie

last: Zheng


title: Regulation of microRNA in myositis skeletal muscle after exercise (microRNA)

city: Washington

first: Kanneboyina

last: Nagaraju

state: District of Columbia

address: 111 Michigan Ave NW

institute: Children's National Health System

summary: To identify changes in skeletal muscle microRNA expression after exercise and associate the identified microRNAs with mRNA and protein expression to disease-specific pathways in polymyositis and dermatomyositis

overall_design: Total RNA obtained from vastus lateralis before and after 12 weeks of endurance exercise (n = 3) compared to before and after nonexercise, control group (n = 3)

first: Jessica

last: Boehler

first: Marshall

last: W Hogarth

first: Matthew

last: Barberio

first: James

last: Novak

first: Svetlana

last: Ghimbovschi

first: Kristy

middle: J

last: Brown

first: Li

middle: A

last: Munters

first: Ingela

last: Loell

first: Yi-Wen

last: Chen

first: Helene

last: Alexanderson

first: Ingrid

last: Lundberg


title: Niche targeting enhances endogenous healthy hematopoiesis in acute myeloid leukemia

status: Public on Oct 10 2017

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Global gene expression comparison between mesenchymal stem cells (MSCs) purified from the BM of AML patients versus healthy donors.

overall_design: MSCs were purified from BM aspirate collections of healthy donors (3) and AML patients (3), using plastic adherence followed by immunomagnetic selection.

first: Allison

last: Boyd

first: Kyle

last: Salci

first: Jennifer

last: Reid

first: Zoya

last: Shapovalova


title: Mouse embryonic stem cells can differentiate via multiple paths to the same state [array]

status: Public on Oct 17 2017

middle: Alexander

last: Briggs

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

summary: In embryonic development, cells must differentiate through stereotypical sequences of intermediate states to generate mature states of a particular fate. By contrast, direct programming can generate similar fates through alternative routes, by directly expressing terminal transcription factors. Yet the cell state transitions defining these new routes are unclear. We applied single-cell RNA sequencing to compare two mouse motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both undergo similar early neural commitment. Then, rather than transitioning through spinal intermediates like the standard protocol, the direct programming path diverges into a novel transitional state. This state has specific and abnormal gene expression. It opens a 'loop' or 'worm hole' in gene expression that converges separately onto the final motor neuron state of the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons from embryos.

overall_design: Comparison of specific transitional progenitor states from each of two motor neuron differentiation protocols. This was a validation of the single-cell RNA sequencing analysis in this manuscript.

first: Victor

last: Li

first: Seungkyu

last: Lee

first: Clifford

last: Woolf

first: Allon

last: Klein

first: Marc

last: Kirschner


title: MicroRNA expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli in vitro

status: Public on Sep 14 2017

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: MicroRNA expression patterns indicating immune competence of PMEC

overall_design: miRNAs of E. coli-challenged mammary epithelial cells from lactating sows were hybridized to Affymetrix miRNA-3 Array

first: Alexandra

last: Jaeger


title: A mutation in the viral sensor 2’-5’-oligoadenylate synthetase 2 causes failure of lactation. [mouse]

first: Daniel

last: Roden

summary: We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse. The mutation activates the OAS2 pathway, demonstrated by a 100-fold increase in RNase L activity, and its effects were dependent on expression of RNase L and IRF7, proximal and distal pathway members. This is the first report of a viral recognition pathway regulating lactation.

overall_design: Gene expression analysis of mouse mammary gland with wild-type or mutant Oas2at 18 days post-coitum (18dpc) and 2 days post-partum (2dpp).

first: Samantha

last: Oakes

first: David

last: GallegoOrtega

first: Prudence

middle: M

last: Stanford

first: Simon

last: Junankar

first: Wendy

last: Au

last: Kikhtyak

first: Anita

last: von Korff

first: Marcelo

last: Sergio

first: Andrew

last: Law

first: Stephanie

middle: L

last: Allerdice

first: Adelaide

last: Young

first: Catherine

last: Piggin

first: Belinda

last: Whittle

first: Edward

last: Bertram

first: Matthew

last: Naylor

first: Jesse

last: Donovan

first: Alexei

last: Korennykh

first: Christopher

last: Goodnow

first: Moira

last: O'Bryan

last: Ormandy


title: Microarray gene expression analysis after THZ1 treatment in TL-Om1 cells

status: Public on Oct 05 2017

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: Microarray gene expression profiling was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze genes regulated by the THZ1 CDK7 inhibitor.

overall_design: TL-Om1 cells were treated with control DMSO or THZ1 for 6 hours in biological triplicates. Total RNA was harvested and microarray gene expression analysis was performed.

first: Regina

last: Wong

last: Ngoc

first: Wei

middle: Z

last: Leong

first: Alice

last: Yam

first: Takaomi

last: Sanda


title: Mucosal gene expression profiling in patients with inflammatory bowel disease study

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

institute: KULeuven

summary: Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel diseas (IBD) and controls

overall_design: Mucosal biopsies were obtained at endoscopy  from the colon of 97 ulcerative colitis (UC), 8 Crohn's disease (CD) patients and 11 controls and from the (neo-)terminal ileum of 67 CD patients and 11 controls. The biopsies were taken at the most affected sites but at a distance of ulcerations. Disease activity was endoscopically assessed. Total RNA extracted from mucosal biopsies was used to analyze mRNA expression via Affymetrix Human Gene 1.0 ST arrays

first: Maaike

last: Vancamelbeke

first: Wiebe

last: Vanhove

first: Gert

last: De Hertogh

first: Frans

last: Schuit

first: Paul

last: Rutgeerts

first: Séverine

last: Vemeire


title: DNA microarray analysis of HCT116 cells transfected with control or MYC siRNAs

status: Public on Sep 08 2017

city: Tsuruoka

first: Kiyotoshi

last: Satoh

state: Yamagata

address: Mizukami 246-2, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

summary: Cancer cells alter their metabolism for the production of precursors of macromolecules. However, the control mechanisms underlying this reprogramming are poorly understood. Here, we show that metabolic reprogramming of colorectal cancer is caused chiefly by aberrant MYC expression. Multi-omics-based analyses of paired normal and tumor tissues from 275 patients with colorectal cancer revealed that metabolic alterations occur at the adenoma stage of carcinogenesis, in a manner not associated with specific gene mutations involved in colorectal carcinogenesis. MYC expression induced at least 215 metabolic reactions by changing the expression levels of 121 metabolic genes and 39 transporter genes. Further, MYC negatively regulated the expression of genes involved in mitochondrial biogenesis and maintenance but positively regulated genes involved in DNA and histone methylation. Knockdown of MYC in colorectal cancer cells reset the altered metabolism and suppressed cell growth. Moreover, inhibition of MYC target pyrimidine synthesis genes such as CAD, UMPS and CTPS blocked cell growth, and thus they are potential targets for colorectal cancer therapy.

overall_design: Gene expression in HCT116 cells transfected with control or MYC siRNAs was measured.  Four independent experiments were performed at each siRNA.

first: Tomoyoshi

last: Soga


title: siRNA knockdown of GalNT6 in Es-2 cells

status: Public on Sep 06 2017

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

institute: National Taiwan University

summary: To determine the GalNT6 regulated gene expression profile in ES-2 cells

overall_design: ES-2 cells were transfected with non-targeting or GalNT6 specific siRNAs for 72 hours and total RNA were extracted


title: Gene expression profiling of laser capture microdissected prostate specimens

status: Public on Sep 12 2017

first: Svitlana

last: Tyekucheva

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: We performed gene expression profiling of laser capture microdissected normal non-neoplastic prostate (cystoprostatectomies) epithelial tissue and compared it to non-transformed and neoplastic low and high grade prostate epithelial tissue from radical prostatectomies, each with its immediately surrounding stroma.

overall_design: We performed gene expression profiling of laser capture microdissected tissue specimens from 12 low grade (Gleason 3+3) and 13 high grade (Gleason 8 and higher) radical prostatectomy (RP) and 5 cystoprostatectomy cases. For each RP case we took 6 regions of interest: tumor (T), PIN (P) and benign (B) epithelium each with its adjacent stroma (sT, sP, sB). For cystoprostatectomy we studied benign epithelium and adjacent stroma (H.B and H.sB).


title: Expression data from lung SCC treated with DMSO and PXD101

status: Public on Aug 31 2017

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: We used microarrays to detail the global programme of gene expression in lung SCC cells treated with belinostat, a pan-HDAC inhibitor. The primary focus of this work is to investigate the efficacy of belinostat on lung SCC cells. Our phosphoproteomic profiling analyses revealed the downregulation of MAPK signaling pathway upon drug treatment, together with the induction of apoptosis. While HDAC inhibition generally affects transcription, the mechanism of SOS/MAPK downregulation was therefore proposed to be affected at the transcriptomic level. However, genes related to MAPK pathway were not significantly regulated upon belinostat treatment, whereas ubiquitin-proteasome gene signature was affected. This supports an indirect mechanism of epigenetic regulation on MAPK signaling that should be explored further.

overall_design: Lung SCC cell lines treated with DMSO and PXD101 were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to investigate the initial transcriptomic changes impacted by belinostat at early time point. Cells were treated with belinostat for 8 hours.

first: Boon

last: Goh

first: Li

last: Kong

first: Chonglei

last: Bi

first: Tuan


title: Systemic disease signature of human cutaneous leishmaniasis

status: Public on Sep 15 2017

first: Tim

last: Dierckx

state: Vlaams Brabant

address: Herestraat 49 - 1040

department: Microbiology and Immunology

institute: KU Leuven

summary: In addition to the recently published in situ transcriptomics of LCL skin lesions (Novais et al., Khouri et al.), we herein present the first systemic disease signature of localized cutaneous leishmaniasis (LCL), using Affymetrix microarrays (HuGene 1.0) followed by systems biology analysis of the PBMC transciptome of LCL patients (n=18), as compared to healthy controls (n=12).

overall_design: We used microarrays to identify differentially expressed genes between PBMCs of healthy controls and localized cutaneous leishmaniasis (LCL) patients.

first: Johan

last: Van Weyenbergh

first: Wouter

last: Van Delm


title: Impact of disseminated neuroblastoma cells on the identification of the relapse seeding clone

city: Vienna

first: Peter. F.

last: Ambros

address: Zimmermannplatz 10

department: Tumor Biology

institute: Children's Cancer Research Institute

summary:
Background: Since the high relapse rate is considered to be responsible for the poor survival of stage M neuroblastoma patients, we tested whether the genomic information of bone marrow-derived disseminated tumor cells (DTCs) would help to better understand tumor evolution and to characterize the relapse-seeding clone.
Methods: Seven samples from different regions of a primary tumor of a stage M neuroblastoma patient, corresponding DTCs at diagnosis, and DTCs and a metastatic tumor at relapse were analyzed by a high-density SNP array. Relapse-associated chromosomal aberrations found in this case were then validated in DTCs and tumor samples of 154 stage M neuroblastoma patients.
Findings: In this case study, unique aberrations were evident in certain tissue/time points aside from a high concordance of genomic aberrations between all analyzed samples. Surprisingly, DTCs at diagnosis, and DTCs and the metastatic tumor at relapse all displayed a terminal deletion in 1q which was not detected in any of the primary tumor samples.
In the validation cohort, 1q terminal deletions were found with a higher frequency in DTCs at diagnosis (17.8%) and at relapse (27.5%) compared to primary tumors (11%). 1q deletions were significantly associated with 19q and ATRX deletions. The presence of each individual aberration in the diagnostic DTCs was associated with an increased likelihood of an adverse event and in case of 19q deletion with a decreased overall survival. Moreover, PTPRD deletion and loss of chromosome Y had significantly higher frequencies in the relapse samples compared to the diagnostic samples.
Interpretation: These data strongly suggest a branched clonal evolution and a parallel progression of primary and metastatic tumor cells. In addition, the higher frequency of relapse-associated genomic aberrations in the diagnostic DTCs compared to the primary tumors and their effect on the event-free survival rate indicate that analysis of DTCs at diagnosis may provide a higher probability for detecting the relapse-seeding clone compared to the primary tumor.
Background: Since the high relapse rate is considered to be responsible for the poor survival of stage M neuroblastoma patients, we tested whether the genomic information of bone marrow-derived disseminated tumor cells (DTCs) would help to better understand tumor evolution and to characterize the relapse-seeding clone.
Methods: Seven samples from different regions of a primary tumor of a stage M neuroblastoma patient, corresponding DTCs at diagnosis, and DTCs and a metastatic tumor at relapse were analyzed by a high-density SNP array. Relapse-associated chromosomal aberrations found in this case were then validated in DTCs and tumor samples of 154 stage M neuroblastoma patients.
Findings: In this case study, unique aberrations were evident in certain tissue/time points aside from a high concordance of genomic aberrations between all analyzed samples. Surprisingly, DTCs at diagnosis, and DTCs and the metastatic tumor at relapse all displayed a terminal deletion in 1q which was not detected in any of the primary tumor samples.
In the validation cohort, 1q terminal deletions were found with a higher frequency in DTCs at diagnosis (17.8%) and at relapse (27.5%) compared to primary tumors (11%). 1q deletions were significantly associated with 19q and ATRX deletions. The presence of each individual aberration in the diagnostic DTCs was associated with an increased likelihood of an adverse event and in case of 19q deletion with a decreased overall survival. Moreover, PTPRD deletion and loss of chromosome Y had significantly higher frequencies in the relapse samples compared to the diagnostic samples.
Interpretation: These data strongly suggest a branched clonal evolution and a parallel progression of primary and metastatic tumor cells. In addition, the higher frequency of relapse-associated genomic aberrations in the diagnostic DTCs compared to the primary tumors and their effect on the event-free survival rate indicate that analysis of DTCs at diagnosis may provide a higher probability for detecting the relapse-seeding clone compared to the primary tumor.

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from bone marrow or tumor samples.

first: M

last: Abbasi

first: Fikret

last: Rifatbegovic

first: Clemens

last: Brunner

first: Georg

last: Mann

first: Andrea

last: Ziegler

first: Ulrike

last: Pötschger

first: Roman

last: Crazzolara

first: Marek

last: Ussowicz

first: Martin

last: Benesch

last: Ebetsberger-Dachs

first: Holger

last: Lode

first: Godfrey

last: Chan

first: Neil

last: Jones

first: Ruth

last: Ladenstein

first: Inge

first: Peter


title: Global heart transcript data from fasted male BXD strains on chow or high fat diet

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: École Polytechnique Fédérale de Lausanne

summary:
Transcript data from heart tissue from fasted-state male BXD strains on chow or high fat diet
We used microarrays to compare the heart expression differences across the BXD strain family and across two diverse diets

overall_design: 29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then hearts were snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Evan

middle: G

last: Williams


title: Vitamin D regulates expression of multiple genes including CD14 and CD180 to modulate the syncytiotrophoblast response to lipopolysaccharide

status: Public on Sep 05 2017

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

institute: Medical University of Graz

summary:
We assessed the response of primary cultures of human trophoblasts to bioactive 1,25 (OH)2D3 and used whole genome microarray to identify innovative hypotheses.
Data indicate that bioactive vitamin D has wide-spread effects on villous gene expression in general, and a specific affect effect on the immune response.

overall_design: Primary human villous cytotrophoblasts were isolated as described {Chen et al., 2010, Am J Physiol Cell Physiol, 299, C968-76; Chen et al., 2015, Placenta, 36, 847-53} and washed thoroughly 4 h after plating, to eliminate villous fragments and nonviable cells.

first: Mark

middle: S

last: Longtine

last: Cvitic

first: Bryanne

middle: N

last: Colvin

first: Baosheng

last: Chen

first: Gernot

last: Desoye

first: Michael

last: Nelson


title: Dengue virus type-3 isolated from a fatal case with visceral complications induces potent inflammatory responses associated with apoptosis in human monocyte-derived dendritic cells

status: Public on Aug 25 2017

city: Curitiba

first: Guilherme

middle: Ferreira

last: Silveira

address: Prof Algacyr Munhoz Máder

country: Brazil

institute: Instituto Carlos Chagas

summary: Dengue virus (DENV) infection is one of the most serious public health problems worldwide. A recent dengue outbreak in Paraguay (2007-2009) presented unusual manifestations such as hepatitis, encephalitis, pulmonary as well as cardiac disorders associated with 50% of deaths caused by dengue in the country. Despite the knowledge on inflammatory responses observed during the course of disease, the role of innate immune cells in the control of virus replication influencing clinical outcome is poorly defined. Using two clinical isolates of the virus, a non-fatal case of classical DF (DENV3/290) and a fatal case of DF with visceral complications (DENV3/5532), we sought to determine the profile of dengue infection in human dendritic cell, a major innate immune cell population. Compared to classical DENV3/290, the strain DENV3/5532 displayed higher replicative ability in mdDCs. In addition, DENV3/5532 was found to induce elevated production of pro-inflammatory cytokines associated with higher rates of programmed cell death. The observed phenotype was due to viral replication in mdDCs and TNF appeared to display a protective effect on virus-induced mdDCs apoptosis. These results suggest that the fatal case DENV3/5532 isolate modulates dendritic cell survival as well as inflammatory mediator’s synthesis.

overall_design:
In this study we analyzed the mRNA pool of 10 cultures. Each culture was infected with MOI of 5.0, and the cells were extracted at the times points of 06, 12, 24, and 48 hours after infection.
As infection control, the same 10 cultures were mock-infected. This mRNA pool is used to hibridizated 8 chips, with no replicates.

first: Florencia

last: Meyer

first: Adriana

last: Delfraro

first: Ana

middle: P

last: Mosimann

first: Norma

last: Coluch

first: Cyntia

last: Vasquez

first: Christian

last: Probst

first: André

last: Báfica

first: Juliano

last: Bordignon

first: Claudia

last: Santos


title: DENV1-NS3hell single point mutations enhance viral replication and bypass Type I IFN anti-virus function in human dendritic cells

status: Public on Aug 29 2017

summary:
Dengue is one of the most important arboviruses in the world, with 2.5 billion people living in areas under risk to contagious. Mosquitos from Aedes genus is the transmission vector of viral particles.
The virus genome inserted in these particles is formed by a single strain of RNA molecule which codifies three structural (C, prM, and E proteins) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5).
The NS3 protein is involved in viral replication, with helicase (NS3hell) and protease functions. Once inoculated, the primary target for dengue virus (DV) infection is the Dendritic Cells (DC) in the site of mosquitos bit.
The Dendritic Cells is the most efficient antigen-presenting cell holding the connection of innate immune system with adaptive immune system. In this study we examined the response of human monocyte-derived DC (mdDCs) DV-infected with two different strains how contain a single point mutation in L435S or L480S position of NS3hell protein, named vBAC-NS3435 and vBAC-NS3480 respectively.
The analysis of these results demonstrated that the mutated strains can infect more efficiently the mdDCs compared with parental virus (vBACDV1) with more percentage of cells infected, replication and virus progeny.
Infections of mdDCs with mutated DV can induce a differentiated response in gene profile of theses cells, with up-regulation of IFN Signaling and PRR canonical pathways. In the PRR pathway the expression of TLR3 and TLR7 was determined and these seem to be the route of sensing of the ssRNA-virus for the infected mdDCs. These sensing of the DV by mdDCs is translated in production of Type I IFN.
The Type I IFN production was more important in mdDC DV-infected with mutated strains compared with parental strain. However, the enhanced levels of Type I IFN production were unable to prevent mdDCs infection by mutated strains.
A18:J192replication. In the absence of Type I IFN action, the percentage of mdDCs infected by mutated strains was significantly incremented compared with DV-infection in the presence of Type I IFN, demonstrating that the Type I IFN action was effective but not sufficient to prevent viral replication of mutated strains. The single point mutation in NS3hell protein of vBAC-NS3435 and vBAC-NS3480 are sufficient to enhance the replication and bypass the Type I IFN action. All these results together can demonstrated that the single point mutation in a NS3hel protein of DV can subvert the normal replication pathway of the virus and these change can’t by controlled by human mdDC production of Type I IFN.

overall_design:
In this study we analyzed the mRNA pool of 10 cultures. Each culture was infected with MOI of 5.0, and the cells were extracted at the times points of 8, 24, and 48 hours after infection.
As infection control, the same 10 cultures were mock-infected. This mRNA pool is used to hybridized chips, with no replicates.

first: Daisy

last: Strottmann

first: Luana

last: de Borba

first: Daniel

last: Mansur


title: microRNA data from atrophied rat gastrocnemius of 5 days post denervation versus sham control

status: Public on Aug 11 2017

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

summary:
microRNAs responsible for skeletal muscle atrophy are largely unclear.
We used microarrays to examine microRNA profiles in rat gastrocnemius muscle of 5 days after denervation of sciatic nerve versus sham control.

overall_design: Muscle atrophy was induced by denervation of right hind sciatic nerve. Rat gastrocnemius muscle samples 5 days after denervation injury (n=4) versus sham control (n=4) were used for RNA extraction and hybridization on Affymetrix miRNA 3.0.

first: Jin

last: Li

first: Junjie

last: Xiao


title: Antitumor effect of FOXO1 inhibitor AS1842856 on B-cell precursor acute lymphoblastic leukemia (BCP-ALL).

status: Public on Aug 01 2017

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary: We found that small moleculal weight FOXO1 inhibitor has antitumor affect  against BCP-ALL cell lines RS4;11 and UoCB6

overall_design: BCP-ALL cell lines RS4;11 and UoCB6  were treated with  AS1842856 at concentations of 40 and 80 nM, respectively.24 h later total RNA was isolated with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng of total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The  chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.

first: Fan

last: Wang

first: Thomas

last: Wirth


title: FOXO1 knockdown is toxic for BCP-ALL cell lines

summary: We found that FOXO1 knock-down  inhibits cell cycle progression and induces apoptosis in BCP-ALL cell lines RS4;11 and 018Z.

overall_design: BCP-ALL cell lines RS4;11 and 018Z  were transduced with sh_hFOXO1.H-10381 in pRSI12-U6-sh-UbiC-TagRFP-2A-Puro lentiviral vector (DECIPHER shRNA Library, Human Module I (Cellecta, https://www.cellecta.com/) obtained from BioCat, Heidelberg, Germany).   On Day 5 after transduction total RNA was isolated with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng of total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The  chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.


title: Impaired B-lymphocyte immunity in acute myeloid leukemia patients after chemotherapy

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

summary: We analyzed via microarray gene expression profiles in de-identified, clinically annotated samples from Ficoll-purified peripheral blood samples from 10 acute myeloid leukemia (AML) patients in remission and 10 healthy donors collected under IRB-approved protocols.

overall_design: Microarray gene expression profiles in de-identified, clinically annotated samples from Ficoll-purified peripheral blood samples from 10 AML patients in remission and 10 healthy donors collected under IRB-approved protocols.

first: C

last: Hourigan

first: M

last: Goswami


title: Expression data from human hepatocellular carcinoma (HCC), Cirrhosis, and non-tumor liver tissues.

city: Philadelphia

first: Moses

middle: Morakortoi

last: Darpolor

state: PA

address: 423 Guardian Drive

department: Radiology

institute: University of Pennsylvania

summary:
There are significant differences in the expression of genes that regulate metabolic pathways in HCC as compared to Cirrhosis or non-tumor liver tissues. These charcteristic pathways can be exploited for metabolic imaging biomarkers of HCC.
We used microarrays to perform genome-wide association study expression in human Grade III hepatocellular carcinoma and surrounding tissues.

overall_design: Human tissues were obtained from as matched paired (HCC vs Cirrhosis or HCC vs non-tumor) or individually, and total RNA was exracted from these tissues. Quality control was performed on the total RNA to assess the quality and integrity of the sample. Affymetrix genechip for microarray gene analysis in two separate experiment. Statistical comparisons were made between groups and between paired samples of the same patient.

first: D

middle: E

last: Kaplan


title: miRNA expression during early, mid and late breast cancer disease progression in mammary glands from MMTV-PyMT transgenic mice

status: Public on Aug 23 2017

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary:
MicroRNAs (miRNAs) are small noncoding RNAs that typically inhibit the translation and stability of messenger RNAs (mRNAs), controlling genes involved in a variety of cellular processes. miRNA dysregulation is recognized to play an essential role in the development and progression of cancer. MMTV-PyMT mice (Jax Strain: FVB/N-Tg(MMTV-PyVT)634Mul/J) are a well-characterized transgenic mouse model of breast cancer. Upon activation of the MMTV-PyVT transgene (mouse mammary tumor virus (MMTV) long terminal repeat upstream of a cDNA sequence encoding the Polyoma Virus middle T antigen (PyVT)) female carriers develop palpable mammary tumors as early as 5 weeks of age.
We performed miRNA microarrays on samples from the MMTV-PyMT transgenic mouse model to investigate the differential expression of miRNAs during development of malignant disease in this model.

overall_design: Mammary glands from MMTV-PyMT +/- mice were selected at successive stages of breast cancer progression for RNA extraction and hybridization on Affymatrix miRNA microarrays. Samples in biological triplicate were analyzed from time points representing early (4 weeks), mid (8 weeks) and late (13 weeks) stage breast cancer disease progression.

first: Gillian

last: Browne

first: Jane

middle: B

last: Lian


title: Genomic alterations in MPT patients with multiple primary tumors

status: Public on Aug 14 2017

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

institute: University of Brasília - UnB

summary: Multiple primary tumors (MPT) usually develop in MPT patients with hereditary cancer syndromes. Nonetheless, the genetic etiology of a large proportion of MPT cases remains unclear. In this study, germline copy number variations (CNVs) and cnLOH (copy-neutral loss of heterozygosity) were investigated in 22 MPT MPT patients having no mutations in the main cancer predisposition genes. Our main goal was to uncover new genes potentially related to a high risk of developing MPT. Twenty MPT patients have family history of cancer and 12 met criteria for hereditary cancer syndromes. Seventeen rare germline CNVs covering 40 genes were identified in 11 MPT patients, including an EPCAM/MSH2 deletion in one Lynch Syndrome MPT patient. An enrichment analysis with the genes mapped in the rare CNVs revealed a significant number of genes associated with carcinogenesis and/or related to functions implicated with tumor development, such as proliferation and cell survival. A network analysis emphasized the relevance of TP53 pathway in carcinogenesis.  A high number of germline cnLOH was detected in nine MPT patients, especially in two cases. Eighteen genes were covered both by rare CNVs and cnLOH, seven of them (ABCC1, KDM4C, KIAA0430, MYH11, NDE1, PIWIL2 and ULK2) were directly related to cellular growth and proliferation. These genes may represent interesting candidates for further studies in MPT risk.

overall_design: Microarray experiments were conducted following the manufacturer's instructions (CytoScan HD, Affymetrix) on DNA extracted from peripheral blood of 22 MPT MPT patients.


title: Loss of the tumor suppressor gene AIP mediates the browning of human brown fat tumors

status: Public on Aug 10 2017

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

summary: Human brown fat tumors (hibernomas) display concomitant loss of the tumor suppressor genes MEN1 and AIP. In the present study, we hypothesized that the brown fat phenotype is attributed to these mutations. Accordingly, we demonstrate that silencing of AIP in human brown preadipocytic and white fat cell lines results in the induction of the brown fat marker UCP1. In human adipocytic tumors, loss of MEN1 was found both in white (one out of 51 lipomas) and brown fat tumors. In contrast, concurrent loss of AIP was always accompanied by a brown fat morphology. We conclude that this white-to-brown phenotype switch in brown fat tumors is mediated by the loss of AIP.

overall_design: Array-based global gene expression analysis of hibernoma (n=14), white benign (n=49) and malignant (n=23) adipocytic tumors. RNA was extracted from frozen tumor biopsies and hybridized onto Affymetrix Human Gene 1.0 ST arrays.

first: Linda

last: Magnusson

first: Nils

last: Hansen

first: Karim

last: Saba

first: Jenny

last: Nilsson

first: Thoas

last: Fioretos

first: Pehr

last: Rissler


title: Expression profiling in hiPSC-derived liver sinusoidal endothelial cells and hepatic stellate cells

status: Public on Jul 27 2017

city: Bunkyo-ku

first: Taketomo

last: Kido

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

summary: We have established culture systems to generate liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs) from hiPSCs. To characterize gene expression profiling in hiPSC-derived LSECs and HSCs, transcriptome analysis was performed.

overall_design: Liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs) were generated from human iPS cells. Human umbilical vein endothelial cells (HUVECs) and mesenchymal stem cell (MSCs) were used as controls.

first: Yuta

last: Koui


title: Nonalcoholic steatohepatitis in adolescents undergoing bariatric surgery

status: Public on Jul 21 2017

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary:
The genomic landscape of hepatic tissue affected by nonalcoholic steatohepatitis (NASH) in severely obese adolescents undergoing bariatric surgery is unknown.  Our purpose here was to uncover genomic profiles of obese controls, and obese cases with nonalcoholic fatty liver disease (NAFLD), borderline nonalcoholic steatohepatitis, and definite nonalcoholic steatohepatitis, in order to clarify molecular functions, biological processes, and pathways that are dysregulated in nonalcoholic steatohepatitis in the severely obese adolescent.
In a prospective observational cohort study, we have intra-operatively obtained 165 liver samples; of these 67 were submited for microarray analysis.  Through ANOVA, we found 8648 genes with differential regulation between the four histologies; from these, we uncovered gene signatures shared between borderline and definite nonalcoholic steatohepatitis, and gene sets with differential effects between borderline and definite.

overall_design: Prospective observational cohort study, where liver biopsies were obtain intra-operatively and submitted for Human Gene St 1 microarray.

first: Stavra

last: Xanthakos

first: Thomas

last: Inge


title: Up- and downregulation of genes during ex vivo differentiation of human NK cells

status: Public on Jul 09 2017

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
Cord blood stem cells were expanded and differentiated to NK cells. Samples taken at different days after induction of differentiation were analyzed and compared to undifferentiated expanded stem cells. The most highly upregulated genes were further analyzed.
Results based on the analyses have been published in Lehmann et al., Stem Cells Develop 21, 2926-38 (2012), Lehmann et al., PloS One 9, e87131 (2014) and Post et al., submitted (2017).

overall_design: Human umbilical cord blood stem cells were  expanded for 10 days and then differentiation was induced by addition of IL15. At various days up to day 35 samples were taken and Affymetrix microarray performed.

first: Dorit

last: Lehmann

first: Erhard

last: Hofer


title: Human male and female GBM cells stably transfected with shRNA targeting CDCA7L

status: Public on Jul 31 2017

city: Frederick

first: Karlyne

last: Reilly

state: MD

address: West 7th St at Fort Detrick, PO Box B

department: Mouse Cancer Genetics Program

institute: National Cancer Institute, Center for Cancer Research

summary: CDCA7L is expressed higher in male astrocytoma/GBM than female tumors or normal cells, and knockdown of CDCA7L blocks growth of male tumor cells, but not female tumor cells. We stably depleted CDCA7L in human GBM cells and compared gene expression to control GBM cells expressing non-trageting scrambled shRNA in male and female cells to identify gene expression differences between male and female cells and between CDCA7L-depleted and scrambled shRNA control cells.

overall_design: Independent established cell lines taken from human male and female patients with malignant gliomas were stably transfected with either shRNA targeting CDCA7L or non-targeting scrambled shRNA control. Two independent human male GBM cell lines and two independent human female GBM cell lines were used: male LN18 GBM cells, male U118MG GBM cells, female U87MG GBM cells, and female SF539 GBM cells (2 technical replicates per each cell line except for SF539).

first: Min-Hyung

last: Lee


title: Prediction of biomarkers for coping styles according to the Mainz Coping Inventory

status: Public on Jul 01 2017

first: Georg

last: Mair

address: Veterinaerplatz 1

institute: University for Veterinary Medicine Vienna

summary: According to the Mainz Coping Inventory (MCI) (Krohne & Egloff, 1999)  people use four main strategies for coping (i.e. Non-defensive, Repressing, High-Anxious and Sensitizing). To bridge the gap between psychology and genetics, the Affymetrix GeneChip miRNA 3.0 Array (Affymetrix, Santa Clara, USA) was used to analyze blood plasma of healthy male individuals with differing MCI coping styles to gain miRNA profiles associated with the MCI assessment and to predict biomarkers for the MCI coping modes.

overall_design: Plasma Samples of 20 healthy male humans with different coping strategies according to the MCI were (either pooled or as standalone samples) analyzed using the Affymetrix GeneChip miRNA 3.0 Array (Affymetrix, Santa Clara, USA). Written informed consent was obtained from every participant. Ethics approval was provided by the ethics commitee at the Karl-Franzens-University (Graz, Austria): GZ. 39/3/63 ex 2011/12.

first: Eva

last: Rathner

first: Andreas

last: Schwerdtfeger