title: DNA methylation profiles in the uterus during subclinical endometritis

status: Public on May 07 2015

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

summary: Post-partum uterine inflammation (endometritis) is associated with lower fertility at both the time of infection and after the inflammation has resolved. It was hypothesized that aberrant DNA methylation may be involved in the sub-fertility associated with post-partum uterine inflammation. The objective of this study was to characterize genome-wide DNA methylation and gene expression in the endometrium of dairy cows with sub-clinical endometritis. Endometrial tissues were obtained at 29 days post-partum (n=12) and Agilent two-colour microarrays were used to characterize transcription and DNA methylation profiles. Analyses revealed 1,856 probes to be differentially expressed in animals with subclinical endometritis (SUI, n=6) compared with control cows (NUI, n=6, P<0.05, Storey Multiple testing correction). No significant associations among DNA methylation and gene expression were detected. Further analysis of gene expression data using GeneGo Metacore and Gene Set Enrichment Analysis identified several pathways and processes enriched in the comparison. Several pathways that are involved in the innate immune response were enriched in SUI cows. Consistent with the presence of microorganisms in the uterus, there was enrichment for the Toll-like receptor (TLR) signaling pathway, including increased expression of the transcription factor NFKB1, the pro-inflammatory cytokines IL1A and IL1B, downstream chemokines, cytokines, and acute phase and antimicrobial proteins in the endometrium of SUI cows. Furthermore, the chemokine signaling pathway was enriched in SUI cows, with increased expression of genes that attract cells of the innate immune system. Increased expression of IL-8 and CXCL6, chemotactic factors for recruitment of neutrophils along with the immune cell surface marker PTPRC in SUI cows is consistent with the greater number of polymorphonuclear cells present in the uterus of these cows. Several antimicrobial peptides (LAP, TAP, DEFB1, DEFB10, DEFB103B, DEFB7) and acute phase proteins, including SAA3, LBP, and the complement gene CFB, had greater expression in SUI cows. Gene expression profiles in cows with subclinical endometritis in this study indicate that the immune response is activated, potentially resulting in a local pro-inflammatory environment in the uterus. If this period of inflammation is prolonged, it could result in tissue damage or failure to complete involution of the uterus, which may create a sub-optimal environment for future pregnancy.

overall_design: Agilent two-colour microarrays were used to characterize DNA methylation profiles in cows with subclinical endometritis (SUI, n=6) compared to control cows (NUI, n=6). Endometrial tissues (caruncular, intercaruncular) were obtained at 29 days post-partum.

first: Murray

middle: D

last: Mitchell


title: Microarray analysis of human gene expression in metronomic cyclophosphamide-treated human glioma U251 xenografts implanted in scid mice

status: Public on May 04 2015

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

summary: Cyclophosphamide (CPA) treatment on a six-day repeating metronomic schedule induces a dramatic, innate immune cell-dependent regression of implanted gliomas. However, little is known about the underlying mechanisms of innate immune cell mobilization and recruitment, or about the role of DNA damage and cell stress response pathways in eliciting the anti-tumor immune responses linked to tumor regression. To address these questions, we compared untreated and 6-day metronomic cyclophosphamide-treated human U251 glioblastoma xenografts by human microarray analysis to identify responsive tumor cell-specific factors.

overall_design: Human glioma U251 tumors were implanted sc in scid immunodeficient mice then treated with cyclophosphamide at 140 mg/kg every 6 days. Tumors were collected 6 days after the second cyclophosphamide treatment and also 6 days after the third cyclophosphamide treatment. Tumor RNA was then analyzed on two color Agilent human expression microarrays comparing cyclophosphamide-treated RNA to untreated control tumor RNA.

first: Joshua

middle: C

last: Doloff

middle: J


title: Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies

status: Public on May 08 2015

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

summary:
Arctic Mesorhizobium strain N33 was isolated from nodules of the Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow from 0 to 30°C, is one of the best known cold-adapted rhizobia, and can fix nitrogen at ~10°C.
Here, the key molecular mechanisms of cold adaptation were investigated by determining changes in transcript profiles when cells were treated under eight different temperature conditions, including both sustained and transient cold treatments compared with cells grown at room temperature.

overall_design: The analysis used Arctic strain N33 (growth at room temperature) RNA as control (reference) samples for comparison to the experimental samples collected under constant growth at 4°C and 10°C, and five different cold treatment conditions at 2, 4, 8, 60, and 240 min (three biological replicates for each treatment). Dual-dye hybridizations were performed including three biological replicates and two technical replicates (dye flip, Cy5/Cy3) for each treatment for a total of 42 array hybridizations and 84 labelling reactions

first: Abdollah-Fardin

last: Ghobakhlou

first: Hani

last: Antoun

first: Anne

last: Johnston

first: Serge

last: Laberge


title: Radiation dose-rate effects on gene expression for human biodosimetry

status: Public on Apr 28 2015

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
Background: The effects of dose-rate and its implications on radiation biodosimetry methods are not well studied in the context of large-scale radiological scenarios. There are significant health risks to individuals exposed to an acute dose in such an event, but the most realistic scenario would be a combination of exposure to both high and low dose-rates, from both external and internal radioactivity. It is important therefore, to understand the biological response to prolonged exposure; and further, discover biomarkers that can be used to estimate the extent of damage from low-dose rate exposure and propose appropriate clinical treatment.
Methods: We irradiated human whole blood ex vivo to three doses, 0.56 Gy, 2.25 Gy and 4.45 Gy, using two dose rates: 1.1Gy/min and 3.1mGy/min. After 24 hours, we isolated RNA from blood cells and hybridized these to Agilent Whole Human genome microarrays. We validated the microarray results using qRT-PCR.
Results: Microarray results showed that there were 454 significantly differentially expressed genes after prolonged exposure to all doses. After acute exposure, 598 genes were differentially expressed to all doses combined. Gene ontology terms enriched in both sets of genes were related to immune processes and B cell mediated immunity. Genes responding to acute exposure was also enriched in functions related to natural killer cell activation and cell-to-cell signaling. As expected, p53 pathway was found to be significantly enriched at all doses and by both dose-rates of radiation. Prediction algorithms were able to distinguish between low dose-rate and acute exposures, on the basis of a group of genes. These maybe candidates for preliminary testing as markers for differences in gene expression based on dose-rate.

overall_design: Radiation induced gene expression was measured in ex vivo irradiated human blood, at the 24hr time point after irradiation. Doses (0.56 Gy, 2.2 Gy and 4.45 Gy) were delivered by two dose rates, acute dose rate of 1Gy/min and low dose rate of 3.1 mGy/min.

middle: A

first: Sally

last: Amundson


title: crpD1 mutant vs Shewanella piezotolerans WP3 wild-type strain

status: Public on Apr 10 2015

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

summary: The cAMP binding domain of crp gene was deleted from WP3 genome to construct the WP3ΔcrpD1 strain. The two strains were cultured at 20°C and the transcriptional profiles were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Jing

last: Hu

first: Fengping

last: Wang


title: Differential gene expression profiling by LSD1 inhibition using novel LSD1 inhibitors (NCD25 and NCD38)

status: Public on Apr 29 2015

city: Kyoto

first: Masahiro

last: Kawahara

state: State...

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

department: Hematology Oncology

country: Japan

institute: Kyoto University

summary: LSD1 is a demethylase of histone modification H3k4me1 and H3K4me2. We have developed novel LSD1 inhibitors (NCD25 and NCD38) and found that they are effective to myelodysplastic syndromes and leukemia cells. To understand what mechanisms are affected by these compounds, we employed gene expression profiling analyses. Gene expression profiling data were obtained from HEL, MDS-L, or CMK11-5 cells treated with DMSO (control), NCD25, or NCD38 and compared each other. Expression of eleven transcriptional factors (GFI1, CEBPA, SPI1, MNDA, TAL1, GATA1, NFE2, RXRA, HOXA9, GATA2, and PBX1) was reconfirmed by q-PCR with the same samples.

overall_design: Gene expression of leukemia cells was measured after 48 hours incubation with or without LSD1 inhibitors. Five independent experiments were performed using 3 cell lines (HEL, MDS-L and CMK11-5) and 2 drugs (NCD38 and NCD25).

first: Noriko

last: Sugino


title: Characterization of IGF1 effects on the transcriptome of normal and irradiated Sox9-EGFP cell populations

status: Public on Apr 14 2015

city: Chapel Hill

first: P. Kay

last: Lund

state: NC

address: 6336 MBRB CB 7545 111 Mason Farm Road

department: Cell and Molecular Physiology

institute: UNC at Chapel Hill

summary: Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation. In both groups, mice were treated for 5 consecutive days with either IGF1 or vehicle via mini-pumps (Alzet 1007D, IGF1 at 10mg/ml) implanted subcutaneously immediately following radiation.

overall_design:
4 distinct cell populations FACS-isolated based on levels of expression of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells).
4 conditions: Non-irradiated/vehicle vs Non-irradiated/IGF1 vs Irradiated/vehicle vs Irradiated/IGF1.
Biological replicates: 7 independent non-irradiated mice treated with vehicle - 3 independent non-irradiated mice treated for 5 days with IGF1 - 3 independent irradiated mice studied at day 5 post-irradiation treated with vehicle - 3 independent irradiated mice studied at day 5 post-irradiation treated for 5 days with IGF1.

first: P

middle: K

first: Laurianne

last: Van Landeghem

first: Amanda

middle: T

last: Mah


status: Public on Apr 06 2015

city: Yufu-shi

first: Kaei

last: Nasu

state: Oita

address: Idaigaoka 1-1, Hasama-machi

department: Obstetrics and Gynecology

institute: Oita University, Faculty of Medicine

summary:
Compulsory expression of miR-210 in normal endometrial stromal cells directed the induction of cell proliferation and vascular endothelial growth factor production, and the inhibition of apoptosis in through signal transducer and activator of transcription 3 (STAT3) activation.
Accumulating evidence suggests that microRNAs play definite roles in the pathogenesis of endometriosis. The objective of the study was to determine the role of miR-210, one of the upregulated microRNA in endometriotic cyst stromal cells, in the pathogenesis of endometriosis. Downstream targets of miR-210 were identified by Compulsory expression of miR-210 in normal eutopic endometrial stromal cells, a global mRNA microarray technique, and Ingenuity pathways analysis.

overall_design: NESCs were transfected with precursor hsa-miR-210 (Pre-miRTM miRNA precursor- hsa-miR-210, Ambion, Austin, TX, USA) or negative control precursor miRNA (Pre-miRTM miRNA precursor-negative control #1 Ambion) at a final concentration of 10 nM, using LipofectamineTM RNAiMAX (Invitrogen, Carlsbad, CA, USA). Forty-eight hours after transfection, total RNA from cultured NESCs transfected with precursor hsa-miR-210 (n=4) and NESCs (n=4) transfected with negative control precursor miRNA was extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA). Then, the samples were subjected to a gene expression microarray analysis with a commercially available human mRNA microarray (G4845A, Human Gene Expression 4x44K v2, Agilent Technologies, Santa Clara, CA, USA).

first: Mamiko

last: Okamoto


title: Gene expression profile in Caco-2 cells treated with carnosine

status: Public on Mar 31 2015

city: Fukuoka

first: Yoshinori

last: KATAKURA

state: Fukuoka

address: 6-10-1, Hakozaaaki, Higashi-ku

department: Graduate School of Systems Life Sciences

institute: Kyushu University

summary: To reveal the effects of carnosine on Caco-2 cells, we have employed whole genome microarray to detect genes that showed significantly different expression when exposed to carnosine. Caco-2 cells were treated with 1 mM carnosine for 3 days.

overall_design: Caco-2 cells were treated with 1 mM carnosine for 3 days. Three independent experiments were performed.

last: Katakura

first: Keishi

last: Kadoka


title: Identification of axonal regeneration-associated genes after spinal cord injury in adult zebrafish

status: Public on Apr 17 2015

city: Pitsburgh

first: Katarina

last: Vajn

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Adult zebrafish regenerate about half of cerebrospinal axons by six weeks after a complete spinal cord transection. We isolated the two populations of neurons that successfully regenerated their axons versus those that did not and isolated the total RNA. Cerebrospinal neurons from unlesioned animals were also collected to serve as controls. Whole transcriptome microarray was performed to determine axonal regeneration-associated genes. For each condition (regenerated, non-regenerated and control neurons) we had 3 biological replicates that consisted of neurons pooled from 3 to 9 zebrafish.

overall_design: A complete spinal cord transection with Fluororuby retrograde tracing was performed at the 8th vertebra level in adult zebrafish. Fluororuby labeled all the neurons in the brain that project their axons to the 8th vertebra. Three weeks later Fluoroemerald was injected 4mm distally from the spinal cord transection site, thereby labeling all neurons that regenerated their axons to this level. The zebrafish were sacrificed 1 week after Fluoroemerald tracing, brain enzymatically dissociated and cells sorted using fluorescence-activated cell sorter. After sorting the total RNA was extracted, amplified and labeled with biotin and then hybridized to Affymetrix 3' IVT gene expression microarray. Unlesioned fish were traced with Fluororuby at the 8th vertebra level and labeled neurons isolated 1 week after to serve as control for gene expression microarray.

first: Jadranka

last: Milosevic

first: Alexis

last: Tapanes-Castillo

first: Jeffery

last: Plunkett

first: Martin

last: Oudega


title: Naïve-like Yellow-Fever specific CD8 T cells and reference CD8 T cell subsets in humans

status: Public on Apr 08 2015

city: Lausanne

first: Silvia

last: Fuertes Marraco

address: Avenue Pierre-Decker 4

department: Ludwig Center for Cancer Research

country: Switzerland

institute: University of Lausanne

summary:
Human Naïve-like CD8 T cells induced by the Yellow Fever Vaccine 17D were compared to the conventional subsets in total CD8 T cells
Samples originate from peripheral blood mononuclear cells (PBMC) from 8 different donors vaccinated with the YF-17D vaccine

overall_design: 1'000 cells from various CD8 T cells subsets were purified by flow cytometry, from 8 vaccinees (donors d1 to d8); the subsets (cell types) include: A2/NS4b tetramer positive CCR7+ CD45RA+ CD8 T cells (A2_NS4b Naïve-like), Total Naive (CCR7+ CD45RA+), Total Tscm (CCR7+ CD45RA+ CD58+ CD95+), Total CM (CCR7+ CD45RA-) and Total Effectors (CCR7 negative).

last: Fuertes

first: Daniel

middle: E

last: Speiser


title: crpD2 mutant vs Shewanella piezotolerans WP3 wild-type strain

first: Huahua

last: Jian

summary: The DNA binding domain of crp gene was deleted from WP3 genome to construct the WP3ΔcrpD2 strain. The two strains were cultured at 20°C and the transcriptional profiles were compared.

first: Jing

last: Hu

first: Fengping

last: Wang


title: Microarray analysis of gene expression profiles in human neuroblastoma SH-SY5Y cells exposed to norephedrine

city: bunkyou-ku

first: Takeshi

last: Funakoshi

state: Tokyo

address: 1-5-45 yushima

department: forensic medicine

institute: Tokyo medical and dental university

summary: To reveal the molecular mechanism underling necrotic neuronal cell death caused by norephedrine, we examined alteration of gene expression profile during norephedrine exposure in human neuroblastoma SH-SY5Y cells.

overall_design: The alteration of gene expression during norephedrine exposure (3 mM, 0,2 and 6 hours) in differentiated SH-SY5Y cells was examined.


title: Expression of genes in hepatic progenitor-like cells derived from human iPS cells

status: Public on Mar 04 2015

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

summary: To analyze stem/progenitor cell function, we purified hepatic progenitor-like cells in human iPS cell culture stimulated with cytokines.

overall_design: Gene expression in CD13+CD133+ cells derived from human iPS cell culture


title: Translatome and transcriptome profiling of FK866 response in Jurkat cells

status: Public on Apr 01 2015

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
We treated Jurkat cells for 48 hr with a sublethal dose of FK866 (5 nM) and DMSO (Mock, control treatment).  RNA samples for microarrays derived from fractionated samples by sucrose gradient (sub-polysomes, polysomes), giving us the chance to perform an analysis among polysomal/subpolysomal distribution in treated or untreated cells and the possibility to identify the multi-level gene expression regulation effects of FK866. We are interested to find differentially expressed genes, in the early phase of cell response to FK866, and genes that account for a specific post-transcriptional regulation exerted by the cell in response to the drug.
Keywords: polysomal profiling, translatome profiling, polysomal RNA, subpolysomal RNA,  translational profiling, polysome profiling, post-transcriptional regulation, FK866, translational efficiency.

overall_design: Gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from total RNAs (derived from the sum of all the fractions in the polysomal gradient). Polysomal RNA, subpolysomal RNA and total RNA were isolated from Jurkat cells treated with FK866 5 nM  or DMSO (mock, control treatment) for 48 hr. Cells lysates were collected from control cells (mock) and from treated cells (FK866). All experiments were run in biological quadruplicates.

first: Chiara

last: Zucal

first: Vito

middle: G

last: D'Agostino

first: Valentina

last: Adami

first: Alessandro

last: Provenzani


title: Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a

status: Public on Mar 01 2015

city: Philadelphia

first: Kyoko

last: Hayakawa

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

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

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

overall_design: Refer to individual Series


title: Gene expression data from human oral squamous cell carcinoma cell-lines; OSC19 and OSC20

status: Public on Mar 14 2015

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

institute: The Nippon Dental University

summary: Oral squamous cell carcinoma cell lines, OSC19 and OSC20, presented aggressive proliferation in vitro but displayed discrete cellular phenotypes and lymphangiogenic activity when transplanted into tongues of nude mice. We thus aimed to explore the molecular factors responsible for their malignant properties.

overall_design: To overview the genetic diversity in relation to the cellular behavior and susceptibility to a stromal impact upon transplantation, genes differentially expressed between pre-transplantation (culture cells in vitro) and post-transplantation (developed tumor in vivo) were analyzed by microarray.

first: Kaori

last: Sato

first: Yuji

last: Taya

first: Takaaki

last: Aoba


title: Effects of polyamidoamine dendrimer on neuronal differentiation from human neural progenitor cells using the neurosphere assay

status: Public on Feb 13 2015

city: tsukuba

first: Yang

last: Zeng

state: ibaraki

address: Onogawa 16-2

institute: NIES

summary: Polyamidoamine (PAMAM) dendrimers have been investigated for the development of engineered nanomaterial drug delivery systems and other industrial uses. However, the major concern for their potential adverse effects on human neural progenitor cells remains unclear. In the present study, we employed human neural progenitor cells (hNPCs) to study the effects of G4-PAMAM dendrimers on neuronal differentiation.

overall_design: Neurospheres were treated with PAMAM dendrimer-NH2 (10 μg/mL) for 72 h. Four neurospheres from the treatment and control groups were pooled together, and RNAs were isolated from each group.


title: Reproduction of reset cell

status: Public on Mar 10 2015

city: Minato-ku

first: Hideki

last: Masaki

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

summary: Functional-assay limitations are an emerging issue in characterizing human pluripotent stem cells (hPSCs).  With rodent PSCs, chimera formation, using pre-implantation embryos, is the gold-standard assay of pluripotency.  In hPSCs, this can only be monitored via teratoma formation or in vitro differentiation, as ethical concerns preclude generation of human-animal chimera.  To circumvent this issue, we established a functional assay utilizing interspecific blastocyst injection and in vitro culture (interspecies in vitro chimera assay).  The assay uses mouse pre-implantation embryos and human PSCs to make interspecies chimeras cultured in vitro to the early egg cylinder stage. When hiPSCs, both conventional and naive type, which called “reset cell”, were injected into mouse embryos and cultured. The cells were never integrated into the epiblast of egg cylinder stage-embryo.  These results suggest that hPSCs, including naïve type, are unable to form chimera with mouse embryo.

overall_design: Reset cells were converted from conventional human iPSC line PB004, and then compared their gene expression profile with or without transgene overexpression induced by doxycyclin treatment.

first: Hiromitsu

last: Nakauchi


title: KSHV-infected invasive bladder cancer cell: Control vs. KSHV-infected

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

summary: Transcriptional profiling of bladder cancer cell lines comparing control uninfected cells with KSHV-infected cells.

first: Jisu


title: Gene expression profiles of uhrf1 mutant zebrafish

status: Public on Feb 09 2015

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: UHRF1 (Ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication, is essential for maintaining DNA methylation patterns during cell division and is suggested to direct additional repressive epigenetic marks. Uhrf1 mutation in zebrafish results in multiple embryonic defects including failed hepatic outgrowth, but the epigenetic basis of these phenotypes is not known. We find that DNA methylation is the only epigenetic mark that is depleted in uhrf1 mutants and make the surprising finding that despite the reduced organ size in uhrf1 mutants, genes regulating DNA replication and S-phase progression were highly upregulated. Further, there is a striking increase in BrdU incorporation in uhrf1 mutant cells, and they retained BrdU labeling over several days, indicating they are arrested in S-phase. Moreover, some of the label retaining nuclei co-localized with TUNEL positive nuclei, suggesting that arrested cells are responsible for apoptosis.  Importantly, dnmt1 mutation phenocopies the S-phase arrest and hepatic outgrowth defects in uhrf1 mutants and Dnmt1 knock-down enhances the uhrf1 hepatic phenotype. Together, these data indicate that DNA hypomethylation is sufficient to generate the uhrf1 mutant phenotype by promoting an S-phase arrest.  We thus propose that cell cycle arrest is a mechanism to restrict propagation of epigenetically deranged cells during embryogenesis.

overall_design: Genome-wide expression profiling was performed on 2 uhrf1 mutant and 2 wildtype zebrafish larvae (120 hours post fertilization) by using Zebrafish Genome Array (Affymetrix) according to manufacturer's instruction.

first: Vinitha

last: Jacob

first: Yelena

last: Chernyavskaya

first: Xintong

last: Chen

first: Poh Seng

middle: S

last: Tan

first: Kirsten

last: Sadler


title: Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a [Lin28b & Let7 transduction]

summary:
Mouse B cell precursors from fetal liver and adult bone marrow generate distinctive B cell progeny when transplanted into immunodeficient recipients, supporting a two-pathway model for B lymphopoiesis, fetal “B-1” and adult “B-2”. Recently Lin28b was shown to be important for the switch between fetal and adult pathways; however, neither the mechanism of Lin28b action nor the importance of BCR signaling in this process was addressed. Here we report important advances in our understanding of the regulation of B 1/B-2 development.
First, modulation of Let-7 in fetal Pro-B cells is sufficient to alter fetal B-1 development to produce B cells resembling the progeny of adult B-2 development. Second, intact BCR signaling is required for generation of B1a B cells from Lin28b-transduced bone marrow progenitors, supporting a requirement for ligand-dependent selection, as is the case for normal B1a B cells. Third, the VH repertore of Lin28b-induced bone marrow B1a B cells differs from that of normal B1a. Finally we identify the Arid3a transcription factor as a key target of Let-7, whose ectopic expression is sufficient to induce B-1 development in adult Pro-B cells and whose knockdown blocks B-1 development in fetal Pro-B cells.

overall_design: 2 individual sorts of bone marrow Pro-B cells 4 days after  Lin28b retroviral transduction (and 2 sorts of empty vector control) and 2 individual sorts of fetal liver Pro-B cells 4 days after Let-7b retroviral transduction (and 2 sorts of empty vector controls).

first: Yan

last: Zhou

first: Yue-Sheng

last: Li

first: Srinivasa

last: Bandi

first: Lingjuan

last: Tang

first: Susan

last: Shinton

first: Richard

middle: R

last: Hardy


title: Integrative genomic analysis identifies clinically relevant subtypes of head and neck cancer characterized by hypoxia, T-cell infiltration, and EMT

city: chicago

first: Tanguy

last: Seiwert

state: IL

address: 900 E. 57th street

institute: University of Chicago

summary: Current classification of head and neck squamous cell carcinomas (HNSCC) based on anatomic site and clinical stage fails to capture biologic heterogeneity or adequately inform treatment. Here we use consensus clustering on 371 HNSCC in three cohorts, including a new cohort of 134 patients with locoregionally advanced HNSCC and 43% HPV(+) tumors to identify five HNSCC subtypes. Subtypes closely correlate with biologic processes (hypoxia, cytotoxic T-cell infiltration, copy number changes, EGFR/HER-ligand phenotype), survival, and HPV-status. Two biologically distinct HPV-associated subtypes are identified. Gene modules of candidate drivers characterize each subtype using the CONEXIC algorithm. The proposed 5-subtype classification provides a biologic basis for future clinical and preclinical studies and lays the groundwork for improved prognostication and therapy development in HNSCC.

overall_design: We use consensus clustering on 371 HNSCC in three cohorts, including a new cohort of 134 patients with locoregionally advanced HNSCC and 43% HPV(+) tumors to identify five HNSCC subtypes.

middle: Y

first: Michaela-Kristina

last: Keck

first: Zhixiang

last: Zuo

first: Arun

last: Khattri


title: Tetraspanin CD63 acts as a pro-metastatic factor via β-catenin stabilization

status: Public on Jan 23 2015

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The tetraspanin CD63 is implicated in pro-metastatic signaling pathways, but so far, it is unclear how CD63 levels affect the tumor cell phenotype. Here, we investigated the effect of CD63 modulation in different metastatic tumor cell lines. In vitro, knock down of CD63 induced a more epithelial-like phenotype concomitant with increased E-cadherin expression, downregulation of its repressors Slug and Zeb1, and decreased N-cadherin. In addition, β-catenin protein was markedly reduced, negatively affecting expression of the target genes MMP-2 and PAI-1. β-catenin inhibitors mimicked the epithelial phenotype induced by CD63 knock down. Inhibition of β-catenin upstream regulators PI3K/AKT or GSK3β could rescue the mesenchymal phenotype underlining the importance of the β-catenin pathway in CD63-regulated cell plasticity. CD63 knock down-induced phenotypical changes correlated with a decrease of experimental metastasis, while CD63 overexpression enhanced the tumor cell-intrinsic metastatic potential. Taken together, our data show that CD63 is a crucial player in the regulation of the tumor cell-intrinsic metastatic potential by affecting cell plasticity.

overall_design: Stable knock down of CD63 was performed in SKOV3ipL ovarian carcinoma cell line using 2 shRNAs lentiviral constructs (sh49 and sh51), and as a negative control, a shNT construct. Parental cells, control shNT and the 2 shCD63 cell lines were seeded 24 hours prior to RNA isolation on a 10 cm dish, labelling and hybridization on microarrays. One color experiment with 2 biological replicates of the 4 experimental conditions: SKOV3ipL, SKOV3ipL_shNT, SKOV3ipL_sh49 and SKOV3ipL_sh51.

first: A

last: Krüger

first: B

last: Mari

first: K

first: P

last: Barbry


title: Aberrant chromatin acetylation in MLL-AF9 leukemia mediates the response to HDAC inhibition (microarray)

city: Madrid

first: Sara

last: Alvarez

state: Madrid

address: C/Faraday 7

country: Spain

institute: NIMGenetics

summary:
We investigated the response of acute myeloid cells (AML) expressing MLL-AF9 fusion gene to the pan-HDACi panobinostat (LBH589), and found that low conentrations of panobinostat lead to MLL-AF9 cell toxicity and rapid changes in gene expression.
Human hematopoietic stem/progenitor cells (HSPC) expressing MLL-AF9 fusion protein (Wei et al, Cancer Cell 2008) were cultured with 30 nM panobinostat during 6 and 24 hours. The different gene expression between cells treated and untreated was studied by gene expression analysis.

overall_design: Three independent HSPC-MA9 clones were used, for each two replicates of cells after culture with 30 nM panobinostat for 6 and 24 hours and one untreated were used.  A total of 16 samples were analyzed.

first: Alba

last: Maiques-Diaz

first: Alvaro

last: Eguileor

first: Mahesh

last: Shrestha

first: Gonzalo

last: Gómez López

first: Mark

last: Wunderlich

first: Ana

last: del Rio-Machin

first: Javier

last: Santoyo-Lopez

first: Xabier

last: Agirre

first: James

last: Mulloy

first: Juan

last: Cigudosa


title: Transcription profiling of cutaneous lesions caused by Leishmania braziliensis and normal skin.

status: Public on Feb 01 2015

city: Marseille

first: Pablo

last: Oliveira

state: PACA

address: 27, bd Jean Moulin

institute: INSERM

summary: This study was carried out to evaluate the changes that occur in the skin after the development of cutaneous leishmaniasis, aiming at a comprehensive understanding of immune pathways and biological functions activated in lesions caused by L. braziliensis.

overall_design: This analysis was conducted on 8 skin ulcers from patients infected with L. braziliensis. The patients selected for the gene expression analysis had recent L. braziliensis infection that had not yet been treated. 8 controls samples are skin biopsies from healthy donors (non-infected).

first: Dessein

last: Alain

first: Oliveira

last: Pablo


title: Targeted inhibition of the JAK/STAT3 pathway inhibits ovarian carcinoma growth

first: Denise

last: Connolly

summary: Ovarian carcinoma (OC) is the fifth leading cause of death among women in the United States. Persistent activation of signal transducer and activator of transcription (STAT3) is frequently detected in OC. STAT3 is activated by Janus family kinases (JAK) via cytokine receptors, growth factor receptor and non-growth factor receptor tyrosine kinases. Activation of STAT3 mediates tumor cell proliferation, survival, motility, invasion, and angiogenesis, and recent work demonstrates that STAT3 activation suppresses anti-tumor immune responses and supports tumor-promoting inflammation. We hypothesized that therapeutic targeting of the JAK/STAT3 pathway would inhibit tumor growth by direct effects on OC cells and by inhibition of cells in the tumor microenvironment (TME). To test this, we evaluated the effects of a small molecule JAK inhibitor, AZD1480, on cell viability, apoptosis, proliferation, migration and adhesion of OC cells in vitro. We then evaluated the effects of AZD1480 on in vivo tumor growth and progression, gene expression, tumor-associated matrix metalloproteinase (MMP) activity and immune cell populations in a transgenic mouse model of OC. AZD1480-treatment inhibited STAT3 phosphorylation and DNA binding, and migration and adhesion of cultured OC cells and ovarian tumor growth rate, volume and ascites production in mice. In addition, drug treatment led to altered gene expression, decreased tumor-associated MMP activity, and fewer suppressor T cells in the peritoneal tumor microenvironment of tumor-bearing mice than control mice. Taken together, our results show pharmacological inhibition of the JAK2/STAT3 pathway leads to disruption of functions essential for ovarian tumor growth and progression and represents a promising therapeutic strategy.

overall_design: 8 female C57BL/6JTgMISIIR-TAg mice with ovarian tumors of ~500 mm3 were used. 4 vehicle-treated mice (0.5% hypermellose/0.1%Tween 80);4 drug-treated mice (30 mg/kg AZD1480 in 0.5% hypermellose/0.1%Tween 80).

first: Galina

last: Gritsina

first: Fang

last: Xiao

first: Shane

middle: W

last: O’Brien

first: Rashid

last: Gabbasov

first: Marisa

last: Maglaty

first: Ren-Huan

last: Xu

first: Roshan

last: Thapa

first: Yan

last: Zhou

first: Samuel

last: Litwin

first: Siddharth

last: Balachandran

first: Luis

last: Sigal

first: Dennis

last: Huszar


title: Epigenetic modification and antibody-dependent expansion of memory-like NK cells in human cytomegalovirus-infected individuals

status: Public on Feb 20 2015

city: East Lansing

first: Sungjin

last: Kim

state: MI

address: 567 Wilson Rd

department: Department of Microbiology and Molecular Genetics

institute: Michigan State University

summary: As a starting point for exploring potential differences in gene expression between conventional NK and FcRγ-NK cells, and to screen for genes that might contribute to the enhanced CD16 responsiveness of g-NK cells, we performed gene expression profiling studies on sorted samples of NK cells. NKG2C, NCR, and KIR surface receptors were used to separate FcRγ- NK and conventional NK cells.

overall_design: Indicated subsets of NK cells were sorted from 4 individual donors using a two-way sorter. RNA extracted from the sorted enriched samples were treated with Dnase and analyzed by DNA microarray (Agilent).

first: Jaewon

last: Lee

first: Ilwoon

last: Hwang


title: Gene expression profiling of human prostate tumors identifies chromatin remodeling as a molecular link between obesity and lethal prostate cancer

status: Public on Mar 01 2017

city: Boston

first: Ericka

last: Ebot

state: MA

address: 677 Huntington Avenue

department: Epidemiology

institute: Harvard T.H. Chan School of Public Health

type:
Expression profiling by array
Third-party reanalysis

summary: Obese men are at higher risk of developing advanced prostate cancer and have higher rates of cancer-specific mortality. However, the biological mechanisms explaining these associations are unknown. Using gene expression data, we aimed to identify molecular alterations in prostate cancer tissue associated with obesity. Gene Set Enrichment Analysis identified fifteen gene sets up-regulated in the tumor tissue of obese prostate cancer patients (N=84) compared to healthy weight patients (N=192), five of which were related to chromatin remodeling. These gene sets were not identified in an analysis of adjacent normal tissue. Patients with tumors with high expression of chromatin remodeling genes had worse clinical characteristics (Gleason grade >7, 41% versus 17%, p-trend = 3.21 x 10-4) and poorer prostate cancer-specific survival independent of Gleason grade (lethal outcome, OR = 5.01, 95% CI = 2.31 to 11.38). Mediation analysis further supported a role for chromatin remodeling in the obesity-lethal prostate cancer relationship.

overall_design: Gene expression profiling was performed on 602 prostate tissue samples (402 tumor and 200 normal) from the Health Professionals Follow-up Study and Physicians' Health Study Prostate Tumor Cohort. This study includes analysis of 400 samples in GSE62872.

middle: M

first: Lorelei

last: Mucci


title: Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function [Agilent expression]

status: Public on Jan 07 2015

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

summary: The epithelium lining the epididymis in the male reproductive tract maintains a luminal environment that promotes sperm cell maturation. This process is dependent on the coordinated expression of many genes that encode proteins with a role in epithelial transport. We previously generated genome-wide maps of open chromatin in primary human fetal epididymis epithelial cells to identify potential regulatory elements controlling coordinated gene expression in the epididymis epithelium. Subsequent in silico analysis identified transcription factor binding sites (TFBS) that were over-represented in the HEE open chromatin, include the motif for paired box 2 (PAX2). PAX2 is a critical transcriptional regulator of urogenital tract development, which is well studied in the kidney but is unexplored in the epididymis. Due to the limited lifespan of primary HEE cells in culture we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cells were evaluated by DNase-seq and their open chromatin map overlapped that of primary HEE cells at ~ 65% of sites. Moreover, the PAX2-binding motif was again identified as an overrepresented TFBS within intergenic open chromatin, though on fewer chromosomes than in the primary HEE cells. To identify PAX2-target genes in REP cells, RNA-seq analysis was performed after siRNA-mediated depletion of PAX2 in comparison to a non-targeting siRNA. In response to PAX2-represssion, 3142 transcripts were differentially expressed (1334 up-regulated and 1808 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with a predicted function in the epididymis epithelium.

overall_design: Gene expression in REP cells was measured at 16 hours after exposure to 1nM R1881 or vehicle control.

first: James

last: Browne

first: Rui

last: Yang


title: Gene expression profiling of prefrontal cortices of mice subjected to acute and chronic social stress

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary:
In order to better understand the effects of social stress on the prefrontal cortex, we investigated gene expression in mice subjected to acute and repeated social encounters of different duration using microarrays. The observed up-regulation of genes associated with vascular system and brain injury suggests that stressful social encounters may affect brain function through the stress-induced dysfunction of the vascular system.

The study was supported by Grant N N311 604938, 2011/03/N/NZ29/05222 and partially by IP2011 030371. Statistical analysis of microarray data was supported with Grant N N519 657940.

overall_design: We studied gene expression profiles of prefrontal cortices of male mice subjected to social stress of different durations: Comparisons included: acute stress (24 hours after single social stress episode) vs. acute control (unstressed), stress-8 days vs. control-8 days, stress-13 days vs. control-13 days, stress-13 days+5 days of rest vs. control-13 days+5 days of rest.  For each comparison, we analyzed 3 biological replicates per group. Two of out of three biological replicates were further replicated in dye swap (final dye swap failed due to problem during microarray hybridization). Each biological replicate consisted of equal amounts of total RNA from 3 mice subjected to the same experimental condition.

first: Joanna

last: Goscik

first: Artur

middle: H

last: Swiergiel

first: Alicja

last: Majewska

first: Marek

last: Wieczorek

first: Grzegorz

last: Juszczak

first: Pawel

last: Lisowski


title: The identification of differentially downregulated genes in hypoxia or G9a overexpression

city: Daegu

first: You Mie

address: 80, Daehak-ro

institute: Kyungpook National University

summary: To identify differentially downregulated genes in hypoxia or G9a overexpression, we have employed whole genome microarray expression profiling.

overall_design: SNU484 cells expressing GFP, GFP-G9a or G9a-∆SET vector under normoxic or hypoxic conditions were used to identify differentially downregulated genes.

first: You

first: Sun


title: A Long Noncoding RNA Acts as a Tumor Suppressor in Esophageal Squamous Cell Carcinoma

status: Public on Jan 09 2015

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the KYSE30 cells overexpressing an empty vector and Epist, thus identified 95 and 99 down-regulated and up-regulated genes, respectively. Expression levels of several previously reported genes implicated in cancer development and progression were altered, such as DDIT3, GATA6, UPP1, FAT3. These genes are involved in tumorigenesis through diverse mechanisms. The present study reveals that Epist functions as a tumor suppressor in Esophageal Squamous Cell Carcinoma.

overall_design: KYSE30 cells overexpressing an empty vector were compared to KYSE30 cells overexpressing Epist. Three biological replicates of each condition were analysed on Agilent microarray.

first: G

first: H

last: Luo

first: Y

last: Sun

first: J

last: Li

first: L

last: Tian

first: W

last: Liu

last: He

first: R

last: Chen


title: Effect of fatty acids from CLA-enriched egg yolk on MCF-7 adenocarcinoma cells

status: Public on Jan 30 2015

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

institute: Warsaw University of Life Sciences

summary: It was analyzed whole genome microarray data to describe the changes in gene transcription profile in human MCF-7 cancer cells under the influence of fatty acid extracts from CLA-enriched and non-enriched egg yolks.Those results might be found useful in assessing the application of CLA-enriched egg as a nutraceutics in cancer prevention.

overall_design: Six-condition experiment: CLA, KT, cis9,trans11-CLA, trans10,cis12-CLA, KT+cis9,trans11-CLA and KT+trans10,cis12-CLA vs MCF-7 adenocarcinoma cell line. Two control of expreriment.  Three biological replicates and three technical replicates.

first: Aneta

last: Koronowicz

first: Dominik

last: Domagała

first: Paula

last: Banks

first: Teresa

last: Leszczyńska

first: Adam

last: Master

first: Piotr

last: Laidler


title: Gene expression profile of osteogenically differentiated human adipose-derived stem cells

status: Public on Jan 11 2015

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

summary: Adipose tissue harbours a significant number of multipotent adult stem cells of mesenchymal origin known as adipose-derived stem cells (ADSCs). Broad differentiation potential and convenient accessibility of ADSCs make them an attractive source of adult mesenchymal stem cell for regenerative medicine and cell developmental plasticity research. Genome-wide microarray expression profiling was performed to identify genes deregulated during osteogenic differentiation of ADSCs to evaluate developmental plasticity of these cells. Dynamics of epigenetic modifications were analyzed in parallel and associated with the gene expression profile.

overall_design: Gene expression profile was analyzed in adipose-derived stem cells (ADSCs) differentiated into osteogenic lineage from 3 donors and compared to undifferentiated cells from the same donors.

first: Sonata

last: Jarmalaite


title: Effects of dexamethasone for primary trabecular meshwork cell gene expression

status: Public on Jan 24 2015

city: Tokyo

first: Akira

last: Matsuda

address: 2-1-1 Hongo

department: Ophthalmology

institute: Juntendo University School of Medicine

summary: To clarify the effects of dexamethasone treatment for primary trabecular meshwork cell gene expression, which may relates to the pathophysiology of glucocorticoid-induced glaucoma

overall_design: Three lots (lot #2584, 3423 and 4973) of primary culture human trabecular meshwork (TM) cells were purchased from ScienCell Research Laboratories (Carlsbad, CA). The TM cells were treated with and  without 100nM dexamethasone (DEX) for 14 days. Genomewide gene expression analysis was carried out using Agilent 8X60K array.


title: Maternal peripheral blood natural killer cells incorporate placenta-associated microRNAs during pregnancy

status: Public on Jan 13 2015

city: Bunkyo

first: Yoichi

last: Ishida

address: Nippon Medical School

department: Molecular Anatomy

institute: Nippon Medical School

summary: Although recent studies have revealed that microRNAs (miRNAs) regulate fundamental Natural Killer (NK) cell processes including cytotoxicity and cytokine production, little is known about the miRNA-gene regulatory relationships in maternal peripheral blood NK (pNK) cells during pregnancy. To predict the role of miRNAs within gene regulatory networks of maternal pNK cells during pregnancy, we performed comprehensive miRNA and gene expression profiling of maternal pNK cells using a combination of real-time PCR-based array and DNA microarray analyses and analyzed these differential expression levels between first- and third-trimester pNK cells. Furthermore, we constructed regulatory networks for miRNA-mediated gene expression in pNK cells during pregnancy by Ingenuity Pathway Analysis. By PCR-based array analysis of miRNAs, 12 miRNAs including 6 placenta-derived miRNAs [chromosome 19 microRNA cluster (C19MC) miRNAs] were significantly upregulated in third-trimester pNK cells compared to first-trimester pNK cells. pNK cells incorporated C19MC miRNAs, whose interaction would be mediated via exosomes. Rapid clearance of C19MC miRNAs also occurred in NK cells after delivery. By DNA microarray analysis, 13 NK cell function-related genes were significantly downregulated between first- and third-trimester pNK cells. By pathway and network analysis, 9 downregulated NK-function-associated genes were in silico target candidates of 12 upregulated miRNAs including C19MC miRNA miR-512-3p. The results suggest that transfer of placental C19MC-miRNAs into maternal pNK cells occurs during pregnancy. The present study provides clues to understand maternal NK cell functions

overall_design: Gene expressions in human maternal peripheral blood NK cells were measured at 1st-trimester, 3rd-trimester.  Five independent experiments were performed at each term (1st-trimester or 3rd-trimester) using different donors for each experiment.

first: Toshihiro

last: Takizawa


title: Identification of markers of early dementia in adults with Down syndrome

status: Public on Dec 05 2014

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

institute: Jagiellonian University

summary: We aimed at identification of variations of genome expression in white blood cells, which could serve as blood markers of early dementia in adults with Down syndrome

overall_design: Whole genome expression analysis was compared between groups of younger and older patients with or without severe cognitive disability


title: p63+/Krt5+ Distal Airway Stem Cells are Essential for Lung Regeneration (transplanted and damaged)

status: Public on Nov 20 2014

city: Houston

first: Frank

last: McKeon

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: The possibility of lung regeneration has been long discounted due to the irreversible nature of chronic lung diseases.  However, patients who sustain massive loss of lung tissue during acute infections often recover full pulmonary function.  Correspondingly, we previously demonstrated lung regeneration in mice following H1N1 influenza virus infection and implicated p63+Krt5+ distal airway stem cells, or DASCp63/Krt5, in this process.  We show here that rare, preexisting DASCp63/K5 undergo a proliferative expansion in response to influenza and lineage-trace to nascent alveoli assembled at sites of interstitial inflammation.  We also show that the ablation of DASCp63/Krt5 in vivo prevents the regeneration of lung tissue following influenza leading to pre-fibrotic lesions and deficient oxygen exchange.  Finally, we demonstrate that exogenously cloned and propagated DASCp63/Krt5 readily contribute to lung regeneration following transplantation.  The transplanted DASC ameliorated influenza-induced lung injury. These data suggest that DASCp63/K5 are required for lung regeneration and may have therapeutic utility in acute and chronic lung diseases.

overall_design: Transplanted DASC cells incorporated into damaged host lung were laser capture microdissected and analyzed. Duplicate mice were included. We used the Affymetrix Mouse Exon 1.0 ST platform

first: Wei

last: Zuo

first: Ting

last: Zhang

first: Daniel

middle: Z

last: Wu

first: Shouping

last: Guan

first: Audrey

last: Liew

first: Yusuke

last: Yamamoto

first: Tiffany

last: Lim

first: Matthew

last: Vicent

first: Mark

last: Lessard

first: Christopher

middle: P

last: Crum

first: Wa

last: Xian


title: Transcriptomic analysis of Mtb H37Rv on treatment with ATD-3169 (Redox generating compound)

status: Public on Nov 30 2014

city: Bangalore

first: Amit

last: Singh

state: Karnatka

address: CIDR,Near CAF,

department: MCBL

country: India

institute: Indian Institute of Sciences (IISc)

summary: Mtb H37Rv was found to be highly susceptible to ATD-3169 (Redox generating compound). To further understand the mechanism of ATD-3169 action, we performed microarray analysis of Mtb H37Rv exposed to 3µM, 30 µM and 150µM of ATD-3169 for 4h.

overall_design: Mtb H37Rv was grown till early log phase and treated with ATD-3169 concentrations (3uM, 30uM, 150uM) for 4 hours at 37 degrees at 180rpm. Three independent experiments were done for each of the strain.

first: Priyanka

last: Tyagi


title: Yarrowia lipolytica biolipid production during D-stat setup.

status: Public on Jan 01 2015

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

institute: INRA

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

overall_design: Refer to individual Series


title: Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease

city: Stony Brook

first: Bassem

last: Allam

state: NY

address: School of Marine and Atmospheric Sciences

institute: Stony Brook University

summary:
Transcriptional profiling of different clam tissues (hemolymph, extrapallial fluid and mantle) in response to brown ring disease;
Brown ring disease (BRD) is a bacterial infection affecting the economically-important clam Ruditapes philippinarum. The disease is caused by a bacterium, Vibrio tapetis, that colonizes the edge of the mantle, altering the biomineralization process and normal shell growth. Altered organic shell matrices accumulate on the inner face of the shell leading to the formation of the typical brown ring in the extrapallial space (between the mantle and the shell). Even though structural and functional changes have been described in solid (mantle) and fluid (hemolymph and extrapallial fluids) tissues from infected clams, the underlying molecular alterations and responses remain largely unknown. This study was designed to gather information on clam molecular responses to the disease and to compare focal responses at the site of the infection (mantle and extrapallial fluid) with systemic (hemolymph) responses. To do so, we designed and produced a Manila clam expression oligoarray (15K Agilent) using transcriptomic data available in public databases and used this platform to comparatively assess transcriptomic changes in mantle, hemolymph and extrapallial fluid of infected clams. Results showed significant regulation in diseased clams of molecules involved in pathogen recognition (e.g. lectins, C1q domain-containing proteins) and killing (defensin), apoptosis regulation (death-associated protein, bcl-2) and in biomineralization (shell matrix proteins, perlucin, galaxin, chitin- and calcium-binding proteins). While most changes in response to the disease were tissue-specific, systemic alterations included co-regulation in all 3 tested tissues of molecules involved in microbe recognition and killing (complement-related factors, defensin). These results provide a first glance at molecular alterations and responses caused by BRD and identify targets for future functional investigations.

overall_design:
Two-condition experiment (healthy/diseased), 3 tissues, 6 biological replicates/tissue/condition

Please note that mantle tissues from this study were labelled with Cy3 and hybridized against a set of reference samples that are not part of this study. Thus, the Cy5 data from the associated raw data files were excluded in the analysis.

Please note that hemocytes are collected from hemolymph or extrapallial fluid and hybridized on the same array (i.e. technically as dual channel) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated). The hemocytes from extrapallial fluid were labelled with Cy3, while hemocytes from hemolymph were labelled with Cy5.  The raw data files that are associated with two sample records are linked as series supplementary files and are indicated in the sample description field.

first: Emmanuelle

last: Pales Espinosa

first: Arnaud

last: Tanguy

first: Fanny

last: Jeffroy

first: Cedric

last: Le Bris

first: Christine

last: Paillard


title: Global transcriptome analysis identifies shade avoidance-related genes regulated by BBX24 in Arabidopsis thaliana

status: Public on Jan 08 2015

city: Buenos Aires

first: Carlos

middle: Daniel

last: Crocco

state: Buenos Aires

address: Av. San Martín 4453

country: Argentina

institute: University of Buenos Aires - IFEVA - CONICET

summary: In seedlings, the induction of shade avoidance syndrome (SAS) involves a rapid up-regulation for known shade marker genes and subsequently activates an interacting network of various hormones that will eventually lead to cell elongation. We found that the B-box protein AtBBX24 have positive effects on the SAS (positive regulators). Global expression analysis of col and bbx24 seedlings reveals that a large number of genes involved in hormonal signaling pathways are positively regulated by BBX24 in response to simulated shade.

overall_design: The microarray experiment consisted in a factorial design comprising two genotypes (col and bbx24-1) and two light treatments (white light and simulated shade).  RNA material was extracted from 7-day-old seedlings. Two replicates per treatment were performed using Affymetrix Arabidopsis ATH1 GeneChips. RNA was prepared, labeled and hybridized in accordance with the manufacturer’s instructions. Data were normalized and genes with ‘absent’ calls and a signal of <50 units in all replicate experiments were filtered out. Significantly differentially expressed genes were identified by performing profile analysis using Significance Analysis of Microarrays (SAM; Tusher et al., 2001).

first: Javier

middle: F

last: Botto

middle: D


title: p63+/Krt5+ Distal Airway Stem Cells are Essential for Lung Regeneration (Dtox treatment)

first: Frank

last: McKeon

overall_design: DASC stem cells were ablated by Dtox treatment in Krt6:DTR mouse model. Control and stem cell ablated lungs were analyzed. We used the Affymetrix Mouse Exon 1.0 ST platform

first: Wei

last: Zuo

first: Ting

last: Zhang

first: Daniel

last: Wu

first: Shouping

last: Guan

first: Audrey

middle: A

last: Liew

first: Yusuke

last: Yamamoto


title: Yarrowia lipolytica biolipid production during D-stat setup. [Part 1]

summary: First part of the time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, obtained during a controlled decellerostat (D-stat) setup. A nitrogen limitation was applied during the course of the D-stat to initiate and control de novo biolipid synthesis.

overall_design: Yarrowia lipolytica Agilent microarray, one-color staining.  Each time sample was spotted in triplicate. A reference condition was spotted in quadruplicate, based on a RNA pool from three samples obtained during the biomass production phase.

first: Abril

last: Ochoa-Estopier

first: Jérome

last: Bouscaut

first: Lidwine

last: Trouilh

first: Véronique

last: Le Berre

first: Valentin

last: Loux

first: Stéphane

last: Guillouet

first: Jean-Marc

last: Nicaud


title: Differential Gene Expression in PARP13 Knockdown

status: Public on Nov 13 2014

city: Cambridge

first: Paul

last: Chang

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: Massachusetts Institute of Technology

summary: Poly(ADP-ribose) Polymerase-13 (PARP13/ZAP/ZC3HAV1) is an antiviral factor, active against specific RNA viruses such as MLV, SINV and HIV. During infection PARP13 binds viral RNA via its 4 CCCH-type zinc finger domains and targets it for degradation by recruiting cellular mRNA decay factors such as the exosome complex and XRN1. Here we show that PARP13 binds to and regulates cellular mRNA under physiological conditions. Knock-down of PARP13 via RNAi results in the misregulation of hundreds of transcripts with an enrichment in signal peptide containing proteins. Among the most upregulated transcripts is TRILR4

overall_design: 2 replicates of Control siRNA knock-down vs  PARP13 siRNA knock-down


title: siRNA knockdown of GALNT1 in hepatocellular carcinoma HA22T and PLC5 cells

status: Public on Jan 03 2015

city: Taipei

first: Min-Chuan

last: Huang

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

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

summary: To determine the whole genome profile of GALNT1 silenced HA22T and PLC5 cells

overall_design: HA22T and PLC5 cells were transfected with non-targeting and GALNT1 specific siRNA with Lipofectamine RNAiMAX for 48 hours and extracted for total RNA

first: Huang

last: Min-Chuan


title: p63+/Krt5+ Distal Airway Stem Cells are Essential for Lung Regeneration (before and after in vitro differentiation)

first: Frank

last: McKeon

overall_design: Stem cells before and after in vitro differentiation were subjected to whole genome microarray analysis. Duplicates were included for each sample. We used the Affymetrix Mouse Exon 1.0 ST platform

first: Tiffany

last: Lim

first: Matthew

last: Vicent

first: Mark

last: Lessard

first: Christopher

last: Crum

first: Wa

last: Xian


title: THOC5 controls 3´end-processing of immediate early genes via interaction with CPSF100

status: Public on Nov 03 2014

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

summary: Transcription of immediate early genes (IEGs) in response to extrinsic and intrinsic signals is tightly regulated at multiple stages. THOC5, a member of the TREX (transcription/export) complex plays a role in expression of only a subset of constitutively active genes. In this report, we show that THOC5 plays a role in the 3´end-processing of more than 90% of IEGs induced by serum stimulation, however THOC5 depletion does not influence the expression of the most rapidly induced IEGs, such as Fos or Jun. One group of THOC5 target genes, including Id1, Id3 and Wnt11 transcripts were not released from chromatin in THOC5 depleted cells. Another group of genes, such as Myc, and Smad7 transcripts, were released with shortening of 3´UTR by alternative cleavage, and were spliced but were exported to a lesser extent in THOC5 depleted cells. Furthermore, upon stimulation with serum THOC5 forms a complex with polyadenylation specific factor 100 (CPSF100). THOC5 is required for recruitment of CPSF100 to 3´UTR of THOC5 target genes, but not for THOC5 independent genes. These data suggest the presence of a novel mechanism for the control of immediate early genes response via 3´end-processing.

overall_design: In 2 dual-color microarray hybridizations, mRNA expression changes after 1h of FCS treatment were examined. MEF(Rosa26ERT2 Cre: THOC5 (flox/flox)) cells in which a THOC5 knockdown is inducible upon Tamoxifen treatment were analyzed. M4040 represents cells without Taxoxifen pre-treatment (wildtype reference) whereas M4041 represents the same celltype pre-treated for 2 days with Tamoxifen to induce a THOC5 knockdown.

first: Doan

last: Tran

first: Shashank

last: Saran

first: Andrew

middle: J

last: Williamson

last: Pierce

first: Lutz

last: Wiehlmann

first: Alexandra

last: Koch

first: Anthony

last: Whetton

first: Teruko

last: Tamura


title: Yarrowia lipolytica biolipid production during D-stat setup. [Part 2]

first: Nicolas

last: Morin

summary: Second part of the time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, obtained during a controlled decellerostat (D-stat) setup. A nitrogen limitation was applied during the course of the D-stat to initiate and control de novo biolipid synthesis.

overall_design: Yarrowia lipolytica Agilent microarray, one-color staining. Each time sample was spotted in triplicate (except for sample 26, for which a technical replicate of replicate r1 was performed).

first: Abril

last: Ochoa-Estopier

first: Jérome

last: Bouscaut

first: Lidwine

last: Trouilh

first: Véronique

last: Le Berre

first: Valentin

last: Loux

first: Stéphane

last: Guillouet

first: Jean-Marc

last: Nicaud


title: miRNA profiling of Macaca mulatta intact colon samples during chronic SIV infection

status: Public on Dec 01 2014

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: This study describes differential miRNA expression in intact colon tissue during chronic SIV infection of rhesus macaques. Ten miRNAs were found to be significantly affected by infection, with 7 down-regulated and 3 up-regulated miRNAs. The expression of one upregulated miRNA was further characterized and found to be upregulated in both colonic epithelium and lamain propria cells. Further, its expression positively correlated with colonic inflammation scores and viral loads. Additional studies suggested that its expression was driven in response to oxidative stress induced double stranded DNA damage response  and may play a role in chronic activation of colonic plasma cells.

overall_design: We performed TaqMan Low Density Array based high throughput miRNA analysis on intact colon tissue from 12 chronically SIV-infected and 4 uninfected control macaques. All SIV-infected animals were inoculated intravenously with 100TCID50 of SIV. Out of the ten, one animal each was at 7, 8 and 10DPI (days post infection), 3 each at 13 and 21DPI, and 1 at 29DPI. microRNA reverse transcription and preamplification was performed according to the manufacturer’s recommendation. Data analysis was performed using RQ Manager 1.2.2 and DataAssist v3.01 software. Data was normalized using Global normalization method and multiple comparisons correction was performed using Benjamini-Hochberg method.

first: M


title: Characterization of FOXL2 and 17beta-estradiol transcriptional function in mouse granulosa cells

status: Public on Oct 29 2014

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

institute: CNRS

summary: FOXL2 is a lineage determining transcription factor in the ovary, but its direct targets and modes of action are not fully characterized. Interaction of FOXL2 with several members of the nuclear receptor familly of transcription factors has been described, and many nuclear receptors play a key role in ovarian biology. Here, we explore the effect of FOXL2 on estrogen signaling in murine primary follicular cells.

overall_design: siRNA targeting FOXL2 or control siRNA were used in conjunction with 17beta-estradiol or vehicle (2x2=4 conditions). Each condition was analysed in completely independent biological duplicates (i.e. cell from different animals grown independently)

first: David

last: L'Hôte

first: Anne

middle: L

last: Todeschini

first: Aurélie

last: Auguste

first: Bérangère

last: Legois

first: Alain

last: Zider

first: Reiner

last: Veitia


title: Identification of microRNAs involved in acute rejection and spontaneous tolerance in murine hepatic allografts

status: Public on Oct 21 2014

first: Masayuki

last: Fujino

address: Toyama, Shinjuku-ku, 1-23-1

institute: NIID

summary: Graft acceptance without the need for immunosuppressive drugs is the ultimate goal of transplantation therapy. In murine liver transplantation, allografts are accepted across major histocompatibility antigen complex barriers without the use of immunosuppressive drugs and constitute a suitable model for research on immunological rejection and tolerance. MicroRNA (miRNA) has been known to be involved in the immunological responses. In order to identify mRNAs in spontaneous liver allograft tolerance, miRNA expression in hepatic allografts was examined using this transplantation model. According to the graft pathological score and function, miR-146a, 15b, 223, 23a, 27a, 34a and 451 were upregulated compared with the expression observed in the syngeneic grafts. In contrast, miR-101a, 101b and 148a were downregulated. Our results demonstrated the alteration of miRNAs in the allografts and may indicate the role of miRNAs in the induction of tolerance after transplantation. Furthermore, our data suggest that monitoring the graft expression of novel miRNAs may allow clinicians to differentiate between rejection and tolerance. A better understanding of the tolerance inducing mechanism observed in murine hepatic allografts may provide a therapeutic strategy for attenuating allograft rejection.

overall_design: B10.BR mice were used as donors and B10.D2 mice were used as recipients. Liver allo-transplantation surgery on the mice was performed in this combination. Three mice from each group were sacrificed, and the liver grafts were removed on days 5, 8, 14 and 100 after transplantation. Total RNA, including miRNA was isolated. 100ng of total RNA was labeled by Cy3 and used as probe for hybridization to the microarray.

first: Miwa

last: Morita

first: Jiajie

last: Chen

first: Yusuke

last: Kitazawa

first: Atsushi

last: Sugioka

first: Liang

last: Zhong

first: Xiao-Kang

last: Li


title: Radiation-induced bystander effects and gene expression in cells deficient for RAD9

status: Public on Oct 07 2014

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary: Background: The radiation bystander response is an important component of the overall response of cells to radiation and critical to understanding health risks of radiation exposure to humans. The mechanism of radiation response includes inter-cellular signaling and intra-cellular communication by which the bystander signal is propagated.  Methods: We measured the bystander response to 1Gy a-particle radiation in Mrad9-/- mouse stem cells and H1299shRAD9 cells, using chromosomal aberration and micronucleus formation as DNA damage endpoints. In the H1299 model we used whole genome microarray analyses to profile the transcriptome of irradiated and bystander cells.  Results: We investigated the role of RAD9 in the bystander response and showed that depletion or mutation of RAD9 had an effect of increasing chromosomal structural damage as well as micronucleus formation in bystander cells. The enhancement of the damage effect correlated strongly with a transcriptomic response in critical pathways. RAD9 depletion affected many pathways in the cell, including the UV-MAPK pathway, involving p38MAPK members, STAT1 and PARP1 at the mRNA levels. There was an overall reduction of RNA biogenesis of gene members of this pathway suggesting that perhaps these signaling pathways do not function optimally after RAD9 depletion. Using network analysis we found there may be differential activation of transcriptional regulators between the irradiated and bystander cells involving the SP1 and NUPR1 transcription factors. Network analysis also suggested that HIF1a (Hypoxia induced factor 1a) activation could be a negative predictor of the bystander effect and perhaps that local hypoxic stress observed by cells that are directly exposed to radiation may predict whether or not they will elicit a bystander response.

overall_design: Gene expression in H1299 cells was measured at 4 hours after exposure to 1 Gy a-particles. There were two groups based on RAD9 status, RAD9 normal and RAD9 depleted by siRNA. In each of these groups, sham irradiated, direct irradiated cells for positive bystanders, positive bystanders, direct irradiated cells for negative bystanders and negative bystanders; were identified based on micronucleus responses.  Five biological replicates were analyzed for each experimental group.

first: Sally

last: Amundson

first: Howard

middle: B

last: Lieberman


title: Characterization of FOXL2 and five nuclear receptors transcriptional function in mouse granulosa cells

first: Adrien

last: Georges

summary: FOXL2 is a lineage determining transcription factor in the ovary, but its direct targets and modes of action are not fully characterized. Interaction of FOXL2 with several members of the nuclear receptor familly of transcription factors has been described, and many nuclear receptors play a key role in ovarian biology. Here, we explore the targets of FOXL2 and five nuclear receptors in murine primary follicular cells.

overall_design: siRNA targeting FOXL2 or control siRNA were used in conjunction with siRNAs targeting five different nuclear receptors or control siRNAs (2x6=12 conditions). Each condition was analysed in completely independent biological duplicates (i.e. cell from different animals grown independently)


title: Inflammatory signaling regulates fetal hematopoiesis

status: Public on Nov 12 2014

city: Philadelphia

first: Nancy

last: Speck

state: United States

address: 3451 Walnut St

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Multiple signaling pathways contribute to blood cell formation in the fetus, but a role for innate immune/inflammatory signaling has not been described. Here we show that mouse fetuses deficient for either interferon gamma 1 (IFNg) or its receptor have decreased numbers of lymphoid progenitors and hematopoietic stem cells (HSCs) in the aorta/gonad/mesonephros region and placenta. The role of IFNg signaling was evolutionarily conserved, as morpholino knockdown of IFNg and its receptor reduced the number of hematopoietic stem and progenitor cells in the dorsal aorta and caudal hematopoietic territory of zebrafish embryos, and rag2 expressing cells in the thymus. ChIP-Seq analysis demonstrated that interferon regulatory factor 2 occupied genes in human fetal liver CD34+ hematopoietic stem/progenitor cells, and Gene Ontology analysis identified innate immunity and interferon signaling as enriched processes. Thus inflammatory signaling in the fetus, in the absence of pathogenic challenge, regulates the production of lymphoid progenitors and HSCs.

overall_design:
Tg(Ly6a-GFP) conceptuses were generated by crossing C57BL/6 x 129S1/SVImJ F1 females with Tg(Ly6a-GFP) males.
The AGM region, umbilical and vitelline arteries (A+U+V) from 100 E10.5 Tg(Ly6a-GFP) embryos were dissected, and 30,000  Ly6a-GFP+ hematopoietic cluster cells (CD31+ VEC+ ESAM+ Kit+), 130,000 Ly6a-GFP- hematopoietic cluster cells, 70,000 Ly6a-GFP+ endothelial cells (CD31+ VEC+ ESAM+ Kit-), and 300,000 Ly6a-GFP- endothelial cells sorted into TRIzol-LS (Invitrogen). The cells were lysed in TRIzol-LS and the aqueous phase was collected after adding chloroform. The aqueous phase was homogenized by 70% ethanol and RNA was isolated using Qiagen RNeasy mini kit. Four samples and two replicates for each sample.

first: Yan


title: Transcriptional Changes in the Aging Mouse Hippocampus (expression)

status: Public on Sep 23 2014

city: Cork

first: Roman

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

summary: We sequenced mRNA from three age groups (3months (3M), 24 months (24M) and 29 months (29M)) from the full hippocampus and compared this to microarray analysis.

overall_design: Young (3 months (3M)) mice were compared to aged mice (29 months (29M)), n=4

first: Vincenzo

last: Capece

first: Stefan

last: Bonn

first: Andre

last: Fischer

first: Eva

last: Benito


title: Activating c-KIT mutations confer oncogenic cooperativity and rescue RUNX1-ETO-induced DNA damage in human cells

status: Public on Sep 30 2014

city: Munich

first: Christian

last: Wichmann

address: Marchioninistr. 15

institute: LMU

summary: REtr causes genomic instability in human CD34+ cells. Activated forms of c-KIT, like c-KIT(N822K), rescue the REtr-induced genomic instability by increasing the rate of DNA repair by homologous recombination.

overall_design: Human CD34+ hematopoietic progenitor cells were transduced with retroviral vectors encoding c-KIT(N822K) or mock control vectors, expanded in culture and FACS selected prior to molecular analysis.

first: Manuel

last: Grez


title: Expression data from HTR-8/Svneo side population (SP) and non-side population (NSP) cells

status: Public on Sep 18 2014

city: Tokyo

first: Tetsunori

last: Inagaki

address: Hongo 2-1-1, Bunkyo-ku,

department: Obstetrics and gynecology

institute: Juntendo University

summary: Immature cell populations, including stem cells and progenitor cells, can be found in “side-population (SP)” cells. Although SP cells isolated from some adult tissues have been reported elsewhere, isolation and characterization of human trophoblast SP cells remained to be reported. We used microarrays to detail the global program of gene expression underlying cell differentiation and identified up-regulated genes of SP

overall_design: HTR-8/SVneo SP cells or NSP cells were isolated using a FACS Vantage fluorescence-activated cell sorter (BD Bioscience, San Jose, California) using dual wavelength analysis (blue, 424 - 444nm; red 675 nm) after excitation with 350 nm UV light. PI-positive dead cells were excluded from the analysis. Sorted SP and NSP cells'  RNA had been analyzed by microarray analysis.

first: K

last: Kato

first: T


title: Whole-genome expression profile in zebrafish embryos after chronic exposure to morphine

status: Public on Sep 04 2014

city: Salamanca

first: Raquel

middle: E.

last: Rodriguez

state: Salamanca

address: C/ Pintor Fernando Gallego, 1

institute: Institute of Neurosciences of Castilla y León

summary:
A great number of studies have investigated changes induced by morphine exposure in gene expression using several experimental models. In this study, we examined gene expression changes during chronic exposure to morphine during maturation and differentiation of zebrafish CNS.
Our study identified different functional classes of genes and individual candidates involved in the mechanisms underlying susceptibility to morphine actions related to CNS development. These results open new lines to study the treatment of pain and the molecular mechanisms involved in addiction. We also found a set of zebrafish-specific morphine-induced genes, which may be putative targets in human models for addiction and pain processes.

overall_design: Zebrafish embryos were divided into two experimental groups: control embryos and embryos at 5 hpf exposed to 10 nM morphine and collected at 24 hpf (covering the complete embryogenesis). Morphine was administered to the embryos in their water environment, i.e., diluted in E3 embryonic medium. The exposition to begun at the stage of 5 hpf (end of blastula) is continuous, in order to study the chronic effects of the exposure to drug. Microarray experiments were performed using six replicates for each condition, which contained the RNA of approximately one hundred embryos to minimize the influence of potential individual differences between the animals and technical variation introduced by tissue preparation. We previously reported that a concentration of 10 nM morphine is the highest concentration that can be used without a toxic effect on the embryos, and close to 5% of the morphine diluted in the E3 medium is detected in the embryo.

first: M

last: Herrero-Turrion

middle: E


title: Identification of transcripts regulated by CEBPA in K562

status: Public on Sep 01 2014

city: Rome

first: Alessandro

last: Fatica

address: P.le Aldo Moro 5

department: Biology and Biotechnology "C. Darwin"

institute: Sapienza University of Rome

summary: To investigate the effect of CEBPA on the expression of mRNAs and long non-coding RNAs ( lncRNAs), we utilized the K562 AML cell line carrying a stable and Tet-on inducible CEBPA allele. K562 cells lack endogenous CEBPA and restoration of its expression induces proliferation arrest and granulocytic differentiation .

overall_design: Based on the expression of known CEBPA transcriptional targets, we selected RNA extracted from 48 hours of induction (CEBPA) together with RNA extracted from control-induced cells (CTR). 4 biological replicates for each sample have been utilized.

first: James

last: Hughes

first: Beatrice

last: Salvatori


title: Identification of gene expression signature of LILRA3 stimulation

status: Public on Sep 12 2014

first: Hui Zhi

last: Low

department: Department of Clinical Immunology and Rheumatology

institute: Hannover Medical School

summary: To determine the functional role that LILRA3 plays in the immune system, we used a gene expression microarray as a discovery platform to identify genes and pathways regulated by LILRA3

overall_design: LILRA3 induced gene expression in PBMCs was measured at 24 hours, comparing 1 µg/mL LILRA3 to unstimulated control

first: Hui

first: Torsten

last: Witte


title: Effects of acute prenatal exposure to ethanol on microRNA expression are ameliorated by environmental manipulation.

status: Public on Aug 28 2014

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: In this study, we tested if miRNAs are altered in amygdala and ventral striatum as a consequence of prenatal ethanol exposure and/or social enrichment. miRNA samples from 72 male and female adolescent rats were analyzed by RNA-Seq analysis and Affymetrix miRNA arrays. Several miRNAs showed significant changes due to prenatal ethanol exposure or social enrichment in one or both brain regions. Some of the miRNA changes caused by ethanol were reversed by social enrichment. The top predicted gene targets of these miRNAs were mapped and subjected to pathway enrichment analysis. We also directly examined the evidence for modulation of target mRNAs in whole transcriptome microarray data from the same rats. Among the pathways most strongly affected were p53, CREB, Glutamate and GABA signaling. Together, our data suggest a number of novel epigenetic mechanisms for social enrichment to reverse the effects of ethanol exposure.

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: A total of 48 Rat ST Gene 1.0 GeneChips and 48 miRNA 2.0 GeneChips were run on RNA purified from 2 brain regions (amygdala and ventral striatum) of postnatal day 42 Long Evans rats. 3 replicate arrays were run for each gender within 4 different treatment groups (prenatal ethanol or prenatal saline exposed; postnatal socially-enriched or non-enriched environment)

first: Sandra

last: Mooney

first: Cherry

last: Ignacio


status: Public on Aug 27 2014

city: Shanghai

first: Yang

last: Sun

address: Yueyang Road 320

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

summary: To analysis TCR induced Med23-dependent gene expression programs in T cells, we have employed microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by Med23 in unstimulated or stimulated T cells. Mice CD4 T cells from wildtype and Med23 knockout mice were left unstimulated or stimulated for 6 hr, and gene expression difference was identified among four samples. Expression of seven genes (Med23, IFNg, IL2, Egr2, c-Fos, c-Jun and Foxp1) was validated in the same RNA samples by real-time PCR.

overall_design: TCR induced Med23-dependent gene expression was measured after unstimulation or stimulation for 6 hr in wildtype and Med23 knockout CD4 T cells.

first: Xiaolong

last: Liu

first: Xiaoyan

last: Zhu


title: Epigenetic silencing of SFRP4 contributes to epidermal hyperplasia in psoriasis

first: Hong

middle: Lin

last: Wang

address: 280 Chongqing South Road

institute: Shanghai Jiao Tong University

summary: To investigate the gene expression of imiquimod induced psoriasis-like mouse model, we have employed whole genome microarray as a discovery platform  to identify genes differentially expressed compared with wild type C57BL6 mouse exposed to the vehicle of imiquimod.

overall_design: C57BL/6J mice at 6 to 8 weeks of age were applied to a daily topical dose of 62.5 mg of IMQ cream (5%) on the shaved back for 7 consecutive days. Control mice were treated with a same dose of vehicle cream.The total RNA was extracted by using TRIzol.

first: Honglin

first: Jing

last: Bai


title: Cells and exosomes after cell-free culture

city: Houston

first: RAGHU

last: KALLURI

address: 1881 East Rd.

department: CANCER BIOLOGY

institute: MDACC

summary: The goal of this study is to report that breast cancer associated exosomes contain microRNAs (miRNAs) associated with the RISC Loading Complex  (RLC) and display cell-independent capacity to process precursor microRNAs (pre-miRNAs) into mature miRNAs. Pre-miRNAs, along with Dicer, AGO2, and TRBP, are present in exosomes of cancer cells. CD43 mediates the accumulation of Dicer specifically in cancer exosomes. Cancer exosomes mediate an efficient and rapid silencing of mRNAs to reprogram the target cell transcriptome. Exosomes derived from cells and sera of patients with breast cancer instigate non-tumorigenic epithelial cells to form tumors in a Dicer-dependent manner. These findings offer opportunities for the development of exosomes based biomarkers and therapies.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Exosomes from cancer cells and non-tumorigenic cells were isolated using established ultracentrifugation methods. The global miRNA content of cancer exosomes [MCF7 exos, MDA-MB-231 exos and 4T1 exos] and normosomes [NmuMG exos and MCF10A exos]  was investigated before and after exosomes were cultured in cell-free media to study the microRNA biogenesis in exosomes. Samples 1 and 2 are samples with different times of culture [72hr and 24hrs, respectively].

first: Sonia

last: Melo

first: Raghu

last: Kalluri


title: Gene expression comparison between Mycobacterium tuberculosis infected monocytes from tuberculous and healthy elders

status: Public on Aug 29 2014

city: Leon

first: Octavio

middle: Miguel

last: Rivero-Lezcano

state: Leon

address: Altos de Nava, s/n

department: Unidad de Investigación

institute: Hospital de Leon

summary: Differences in the activity of monocytes/macrophages, important target cells of Mycobacterium tuberculosis, might influence tuberculosis progression. With the purpose of identifying candidate genes for tuberculosis susceptibility we infected with M. tuberculosis monocytes from both, healthy elders (a tuberculosis susceptibility group) and elderly tuberculosis patients, and performed a microarray experiment. We detected 78 differentially expressed transcripts and confirmed these results by quantitative PCR of selected genes. We found that monocytes from tuberculosis patients showed similar expression patterns of these genes regardless of whether they were obtained from younger or elder patients. Only one of the detected genes corresponded to a cytokine: IL-26, a member of the IL-10 cytokine family that we found downregulated in infected monocytes from tuberculosis patients.

overall_design: We have analyzed total RNA from Mycobacterium tuberculosis infected monocytes. We have isolated CD14+ cells (monocytes) from peripheral blood mononuclear cells by magnetic separation, and infected them for 4 days with 1 bacterium per monocyte. Blood donors were 7 elderly patients with pulmonary tuberculosis (average age: 83 years; sex: 3 men and 4 women) and 8 non-tuberculous volunteers (81 years, 6 men and 2 women).


title: Gene expression in blood of mice with internal exposure to Cs-137

status: Public on Aug 31 2014

first: Sally

last: Amundson

institute: Columbia University

summary: Cesium-137 is a radionuclide of concern in fallout from reactor accidents or nuclear detonations.  When ingested or inhaled, it can expose the entire body for an extended period of time, potentially contributing to serious health consequences ranging from acute radiation syndrome to increased cancer risks.  In order to identify changes in gene expression that may be informative for detecting such exposure, and to begin examining the molecular responses involved, we have profiled global gene expression in mice injected with 137CsCl.  We extracted RNA from the blood of control or 137CsCl-injected mice at 2, 3, 5, 20 or 30 days after exposure.  Gene expression was measured using Agilent Whole Mouse Genome Microarrays, and the data was analyzed using BRB-ArrayTools.

overall_design: Three-month old male C57Bl/6 mice were injected intraperitoneally with 8.0 ± 0.3 MBq 137CsCl solution in a volume of 50 μL, or left as controls.  Groups of treated and control mice were sacrificed at intervals during the first 2-30 days after exposure, and total blood was collected using cardiac puncture.  RNA was extracted from the blood, globin-transcript reduced, and subjected to whole genome expression microarray analysis.

first: Sunirmal

last: Paul

first: Waylon

last: Weber

first: Melanie

last: Doyle-Eisele

first: Raymond

last: Guilmette


title: Notch2 over expression in urinary bladder RT4V6 cell line

status: Public on Aug 21 2014

city: Vancouver

first: Peter

last: Black

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: Notch2 in promotion of bladder cancer growth and metastasis through epithelial to mesenchymal transition (EMT), cell cycle progression and maintenance of stemness.

overall_design: Notch2 induced gene expression in human urinary bladder cancer was measured at three independent experiments.

first: Tetsutaro

last: Hayashi

first: Kilian

middle: M

last: Gust

first: Wolfgang

last: Jaeger

first: Shannon

last: Awrey

last: Li

first: Anne

last: Haegert

first: Manuel

last: Altamirano-Dimas

first: Ralph

last: Buttyan

first: Ladan

last: Fazli

first: Akio

last: Matsubara

middle: C


title: The mRNA expression of FaDu-Ctrl, FaDu-Snail, FaDu-Snail2R cells

status: Public on Aug 16 2014

first: Dennis

middle: Shin-Shian

last: Hsu

state: Taiwan

address: No.155, Sec.2, Linong Street

department: Clinical medicine

institute: National Yang Ming University

summary:
To screen the genes regulated by wt-Snail and non-acetylated Snail
The successful development of cancer metastasis requires two major events: the reprogramming of cancer cells to increase their migration and tumor-initiation capabilities; and the remodeling of the tumor microenvironment to facilitate invasion and colonization of cancer cells. Epithelial-mesenchymal transition (EMT) is a crucial mechanism for reprogramming cancer cells to possess tumor initiation and migration capabilities1,2. However, the role of EMT in the interplay between tumor and host cells is largely unknown. The EMT regulator Snail is mainly known as a transcriptional repressor of the adhesion protein E-cadherin, whose repression is considered to be a key step in initiating metastasis3,4. We previously found that Snail can also act as an activator that induces the transcription of ERCC15 and IL86. Here we show that Snail is acetylated by CREB-binding protein (CBP) and that Snail and CBP co-occupy the promoters of target genes to activate transcription of the target genes. Furthermore, Snail activates the expression of a panel of cytokine genes, including TNFa (which forms a positive feedback loop with Snail to amplify the signal) and CCL2 and CCL5 (which facilitate the recruitment of macrophages by cancer cells). Our results demonstrate a novel function for Snail, providing new understanding of the recruitment of host cells to tumor sites during metastatic evolution.

overall_design: Establish stable transfectants of pCDH-Snail and  pCDH-Snail2R in FaDu cells and analyze the mRNA expression level of  by cDNA microarray. FaDu transfected with pCDH vector was used as a control experiment.

first: Muh-Hwa

last: Yang

middle: S


title: A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression (array)

status: Public on Aug 25 2014

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Mitotic genes are one of the most strongly oscillating groups of genes in the eukaryotic cell cycle. Understanding the regulation of mitotic gene expression is a key issue in cell cycle control but is poorly understood in most organisms. Here, we find a new mitotic transcription factor, Sak1, in the fission yeast S. pombe.  Sak1 belongs to the RFX family of transcription factors, which have not previously been connected to cell cycle control.  Sak1 binds upstream of mitotic genes in close proximity to Fkh2, a forkhead transcription factor previously implicated in regulation of mitotic genes. We show that Sak1 is the major activator of mitotic gene expression and also confirm the role of Fkh2 as the opposing repressor. Sep1, another forkhead transcription factor, is an activator for a small subset of mitotic genes involved in septation. From yeasts to humans, forkhead transcription factors are involved in mitotic gene expression, and it will be interesting to see whether RFX transcription factors may also be involved in other organisms.

overall_design: 24 samples were analyzed. Control for all experiments was the same. The samples are representative of selective spore germination in S. pombe (time course arrays for the WT as well as the mentioned mutants) or the sak1-891 ts strain restrictive temperature time course (WT and ts strain)

first: Bruce

last: Futcher

first: Janet

last: Leatherwood


title: MicroRNA profile of cells and exosomes

first: RAGHU

last: KALLURI

overall_design:
Exosomes from cancer cells and non-tumorigenic cells were isolated using established ultracentrifugation methods. The global miRNA content of cancer exosomes and normosomes was investigated. Profiling of cells themselves was also used as a control.
Exosomes with Dicer down regulation (MCF10AshDicer and MDA-MB-231shDicer exosomes), as well as MDA-MB-231 exosomes that contain a Dicer antibody inside were used to study the function  Dicer protein in the microRNA biogenesis in exosomes.

first: Sonia

last: Melo

first: Raghu

last: Kalluri


title: Real-time quantitative PCR analysis of mouse lungs

status: Public on Aug 26 2014

city: Galveston

first: Istvan

last: Boldogh

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary: Balb/cJ mouse received control RNAi or RNAi to 8-oxoguanine DNA glycosylase (Ogg1) intranasally prior to the exposure for 1 h to a) glucose oxidase (1 mU) to induce OGG1-BER or  b) OGG1-BER product 8-oxoguanine (1 μM). We used SABiosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011A) to quantitate inflammatory gene expression dependent on OGG1 and its product 8-oxoguanine.

overall_design: After intranasal challenge with glucose oxidase or 8-oxoguanine, mice were sacrificed and lungs were collected and processed to obtain RNA. Total pooled (n=5) RNA (1 μg) was reverse transcribed into cDNA using Superscript® III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X SYBR Green Supermix (Qiagen) and 20 μl of reaction mixture was added to each well of the PAM-011A array. The reaction was evaluated using an ABI PRISM® 7000 Sequence Detection System using recommended settings by SABiosciences.

first: Leopoldo

last: Aguilera-Aguirre


title: Kidney toxicity in miR-155-/- mice

status: Public on Aug 05 2014

city: Jefferson

first: Tao

last: Han

state: Arkansas

address: 3900 NCTR Road

department: Division of Systems Biology

institute: National Center for Toxicological Research

summary: The development of nephrotoxicity limits the maximum achievable dosage and treatment intervals for cisplatin chemotherapy. Therefore, identifying mechanisms that regulate this toxicity could offer novel methods to optimize cisplatin delivery. MicroRNAs are capable of regulating many different genes, and can influence diverse cellular processes, including cell death and apoptosis. We previously observed miR-155 to be highly increased following ischemic or toxic injury to the kidneys and, therefore, sought to determine whether mice deficient in miR-155 would respond differently to kidney injury.

overall_design: miR-155-/- mice (B6.Cg-Mir155tm1.1Rsky/J originally purchased from The Jackson Laboratory) and age- and weight-matched C57BL/6 (wild type) mice (Charles River Laboratories) were used in this study. Mice were injected with one single 20mg/kg dose of cisplatin. Kidney tissues were collected at 0, 24, 48, and 72 hours i.p. with saline-injected mice as control. Total RNA extracted from the kidney tissues were used for gene expression analysis with Agilent Mouse whole genome 4x44k v2 array.

first: Kathryn

last: Pellegrini