title: Study of the function of COX17 by transcriptional profiling of Arabidopsis thaliana cox17-2 mutant plants with COX17-1 silenced by amiRNA (amiCOX17-1/cox17-2 plants)

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

address: Ciudad Universitaria

institute: Instituto de Agrobiotecnología del Litoral

summary: COX17 is a soluble protein from the mitochondrial intermembrane space that participates in the transfer of copper for cytochrome c oxidase (COX) assembly in eukaryotic organisms. The function of both Arabidopsis thaliana AtCOX17 genes were studied using plants with altered expression levels of these genes. Silencing of AtCOX17-1 in a cox17-2 knockout background generates plants with smaller rosettes and decreased expression of genes involved in the response of plants to different stress conditions, including several genes that are induced by mitochondrial dysfunctions. These results together with other experiments indicate that AtCOX17 is required for optimal expression of a group of stress-responsive genes, probably as a component of signalling pathways that link stress conditions to gene expression responses.

overall_design: Two-condition experiment, Control vs. Silenced Plants. Biological replicates: 2 control, 2 silenced.

first: Daniel

last: Gonzalez

first: Lucila

last: García

first: Elina

last: Welchen

first: Agustín


title: Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells [Microarray Expression]

status: Public on Feb 13 2018

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

summary: The host innate immune response to influenza virus is a key determinant of pathogenic outcomes and long-term protective responses against subsequent exposures. Comparison of the transcriptional profiles obtained 24 and 36 hrs post-infection showed that the magnitude of gene expression was greater in LAIV infected cells relative to that observed in WT infected cells. Functional enrichment analysis revealed that the antiviral and inflammatory responses was largely driven by type III IFN induction in both WT and LAIV infected cells. However, the enrichment of biological pathways involved in the recruitment of mononuclear leukocytes, antigen presenting cells, and T lymphocytes was uniquely observed in LAIV infected cells. These findings indicate that cell-intrinsic type III IFN-mediated innate immune responses in the nasal epithelium are not only crucial for viral clearance and attenuation, but may also play an important role in the immunogenicity of live-attenuated vaccines

overall_design: Differentiated hNECs were infected at a multiplicity of infection (MOI) of 5 50% tissue culture infectious dose per cell.  Prior to infection, cells were apically washed and the basolateral media was refreshed with 500 μl of fresh LHC Basal Medium.  The virus inoculum was added to the apical compartment and incubated for 2 hours, after which the inoculum was aspirated and the apical chamber was washed three times.  The plates were then returned to the incubator. RNA was isolated from Trizol homogenates from samples harvested at 24hpi and 36hpi.  Gene expression microarray analysis was conducted on these samples.

first: Adriana

last: Forero

first: Nicholas

last: Wohlgemuth

first: Katherine

last: Fenstermacher

first: Juliet

last: Morrison

first: Andrew

last: Nishida

first: Victoria

last: Carter

first: Elise

last: Smith

first: Xinxia

last: Peng

first: Melissa

last: Hayes

first: John

last: Treanor

last: Lane

last: Pekosz


title: Gene expression profile of SoNar-high and SoNar-low B-cell acute lymphoblastic leukemia (B-ALL) cells

status: Public on Feb 06 2018

city: Shanghai

first: Hao

last: Gu

address: 280 South Chongqing Road, Shanghai

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: To dissect the metabolic state of B-ALL cells, we have developed a genetically encoded fluorescent sensor (SoNar) for tracking cytosolic NADH and NAD+ redox states and constructed the transgenic mouse. Based on the NADH/NAD+ ratio, we have sorted SoNar-high and SoNar-low B-ALL cells to employ whole genome microarray expression profiling as a discovery platform to identify genes with the potential to regulate the metabolism of B-ALL cells.

overall_design: SoNar-high and SoNar-low two population B-ALL cells from bone marrow were sorted to measure gene expression.

first: Junke

last: Zheng

first: Chiqi

last: Chen


title: Expression profile of cultured CD4 T cells

city: Fukuoka

first: Mitsuhiro

last: Kanamori

state: Fukuoka

address: Higashi-ku Maidashi 3-1-1

department: Allergy and Immunology

country: Japan

institute: Kyushu University

summary: After activation via TCR, naïve CD4 T cells differentiate into several subsets including effector helper T cells and TGF-b-dependent inducible regulatory T (Treg) cells. These differentiated CD4 T cell subsets are more plastic than have previously been assumed to be, and some transdifferentiations among subsets have been reported. However, Th1 cells are one of the most stable subsets, and reprogramming of Th1 to Treg cells, especially underlining mechanism(s) of such conversion, has not been investigated in depth. Here we established a culture method of inducing Foxp3 expression from differentiated Th1 cells. This is achieved simply by resting Th1 cells in the absence of TCR ligation before stimulation in the presence of TGF-b. We named these Th1-derived Foxp3+ cells Th1reg cells. Th1reg cells showed an iTreg-like phenotype and suppressive ability. Th1reg cells induced with vitamin C showed high stability of Foxp3 expression in vitro and in vivo. Th1reg cells could also be induced from in vivo-developed Th1 cells prepared from mice with graft versus host disease. Surprisingly, the resting process did not induce appreciable change in epigenetic modifications at the Foxp3 locus, but down-regulated the mTORC1 activity of Th1 cells. Shift from glycolysis, downstream of the mTORC1 pathway, to oxidative phosphorylation-dependent metabolism was important for the induction of Th1reg cells. Both expression and TGF-b-induced phosphorylation of Smad2/3 were impaired in Th1 cells, and inhibition of mTORC1 restored the phosphorylation. Our study would lead to the development of a novel therapy for Th1-type aberrant inflammation.

overall_design: CD4 T cells cultured under different conditions are profiled for mRNA expression

first: Hiroko

last: Nakatsukasa

first: Minako

last: Ito

first: Shunsuke

last: Chikuma

first: Akihiko

last: Yoshimura


title: MHOR002 expression: Forkhead box O transcription factors both suppress and support breast cancer progression.

status: Public on Feb 11 2018

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: FOXOs are regulators of cellular homeostasis and putative tumor suppressors. The role of FOXOs in cancer progression remains to be determined however as the data on FOXO function in cancer are fragmentary and come from studies that focused on isolated aspects of cancer, especially for epithelial cancers. To clarify the role of FOXOs in epithelial cancer progression we characterized the effects of inducible FOXO activation and loss in a mouse model of metastatic invasive lobular carcinoma. Strikingly, either activation or loss of FOXO function suppresses tumor growth and metastasis. We show that the multitude of cellular processes critically affected by FOXO function including proliferation, survival, redox homeostasis and PI3K-signaling need to be carefully balanced for tumor cells to thrive.

overall_design: Mouse invasive lobular carcinoma cells mILC1 were derived from tumors that developed in female K14cre;Cdh1F/F;Trp53F/F mice.  In these cells Foxo1 and Foxo3  knockdown was done using the lentiviral FH1tUTG doxycycline inducible vector. Resulting mILC1-shFOXOs  cells were treated with and without Doxycyclin for 48hr and 72hr. pINDUCER20-GFP-FOXO3mt was used for induction of mutant FOXO3.A3 in the same parental cells. mILC1-iFOXO3.A3 cells were induced with and without Doxycyclin for 8hr and 16hr.    Four independent samples for each condition were hybridized against a common-reference sample of the parental mILC1 cells in balanced dye-swap design. Microarrays used were Agilent Mouse WHole Genome Expression arrays V1 (44K).

first: M

last: Hornsveld

first: A

middle: M

last: Smits

last: Meerlo

last: van Amersfoort

middle: J

first: D

last: van Leenen

middle: E

last: Kloet

first: F

middle: C

last: Holstege

first: P

middle: W

last: Derksen

first: B

last: Burgering

first: T

middle: B

last: Dansen


title: Characterization of nucleolus-associated domains in mus musculus and their dynamics after inactivation of the Upstream binding factor protein

status: Public on Feb 02 2018

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

country: Germany

institute: University Regensburg

type: Genome variation profiling by genome tiling array

summary:
Nucleolus-associated DNA was isolated from MEF cells before and after conditional knock-out of UBF and hybridized against genomic DNA in biological replicates.
Two different types of immortalized MEF cells were used. MEFs were immortalized by genetic depletion of p53, iMEFs were immortalized by transfection of the SV40 Tt antigen.

overall_design: Two biological replicates of wild-type vs flox cells of MEF and iMEF cells before and three days after UBF knock-out.

first: Attila

last: Németh


title: 3D cultivation of NSCLC cell lines alters gene expression of key cancer-associated signalling pathways

status: Public on Feb 07 2018

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Background: The main focus of the work was the evaluation of gene expression differences between our established NSCLC 3D cell culture model and the 2D cell culture in regard to the use of our model for drug screening applications.
Methods: The non-small cell lung cancer (NSCLC) cell lines Colo699 and A549 were cultivated as monolayer (2D) on cell culture plates for five days or as microtissues (3D) in a hanging-drop system for five and ten days, respectively. Cells and microtissues were harvested and Affymetrix chip analyses were performed with the prior isolated RNA. This was repeated in three independent experiments. Subsequent biostatistical data analyses tested for reproducibility, comparability and significant differences in gene expression profiles between cell lines, experiments and culture methods.
Results: The analyses revealed a high interassay correlation within the distinct culture systems, thus proving a high validity of our data. The comparison of 3D versus 2D cell cultures revealed significant differences in RNA expression (979 genes for A549; 1106 genes for Colo699), but the overlap of changes in RNA profiles between the cell lines at the individual gene level was small (149 genes), potentially reflecting overall heterogeneity and their origin, i.e. primary vs pleural effusion. Nevertheless, these RNA expression changes affected most relevant cancer-associated pathways as DNA methylation, cell cycle, rRNA expression and meiosis pathways. Furthermore, the expression differences between 2D and 3D were more evident after longer cultivation time, which supports the hypothesis of cultivation related mechanisms and the usage of long-time cultivation systems.
Conclusion: In summary, our data support the need of innovative 3D drug testing systems to close the gap between in-vitro drug screening and in-vivo data. Thus, our 3D NSCLC model might provide a model to address the challenge of microenviroment associated resistance mechanisms, as well as cell-cell interaction related effects.

overall_design: Cancer cell lines A549 and Colo699 were cultivated in 2D and 3D cell culture conditions. Differential gene expression between 3D and 2D cell cultures was determined for each cell line.

first: Gabriele

last: Gamerith

first: Arno

last: Amann

last: Koeck

first: Edith

last: Lorenz

first: Jens

last: Kelm

last: Schmidt

first: Heinz

last: Zwierzina

first: Julia

last: Huber


title: Essential role of Arid1a in intestinal stem cell maintenance and homeostasis through Sox9 regulation

city: Kyoto

first: Yukiko

last: Hiramatsu

state: Kyoto

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

department: Department of Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

summary: Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, have been reported in multiple human cancers, however, its functional role in intestinal homeostasis remains unclear. To investigate the role of Arid1a in murine intestine, we have employed whole genome microarray expression profiling of Arid1a conditional knock out mouse intestines. We found that Wnt signaling is downregulated in Arid1a conditional knock out mouse intestines compared to that of wild type mouse intestines.

overall_design: We used the isolated crypts of Arid1a conditional knock out muse intestines as samples and compared to that of wild type mouse intestine.

first: Akihisa

last: Fukuda


title: Differential gene expression analysis in cold tolerant and cold sensitive D. ananassae strains

status: Public on Feb 01 2018

city: Planegg-Martinsried

first: Annabella

last: Königer

address: Großhaderner Straße 2

department: Biology II

institute: LMU Munich

type: Expression profiling by high throughput sequencing

summary: We analyzed differential gene expression before and after a cold shock in D. ananassae strains from Bangkok to identify candidate genes involved in cold tolerance.

overall_design: We performed RNA-sequencing of 4 cold tolerant and 4 cold sensitive fly strains before and at two time points after a cold shock.

first: Sonja

last: Grath


title: Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma

city: Birmingham

first: Rebecca

last: Arend

state: Alabama

address: 619 19th Street South 176F Rm 10250

institute: University of Alabama at Birmingham

summary:
While high-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants (by DNA next-generation sequencing [NGS] using a 50 gene Ion Torrent panel) and gene expression (using the NanoString® PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT). NGS was performed on plasma cell free DNA (cfDNA) on a select group of patients (n=14) in order to assess the utility of using cfDNA to monitor these changes.
A total of 86 genes had significant changes in RNA expression after NACT. Thirty-eight genetic variants (including SNPs) from 6 genes were identified in tumors pre-NACT, while 59 variants from 19 genes were detected in the cfDNA. The number of DNA variants were similar after NACT. Of the 59 variants in the plasma pre-NACT, only 6 persisted; whereas 33 of 38 specific variants in the tumor DNA remained unchanged. Pathway analysis showed the most significant alterations in the cell cycle and DNA damage pathways.

overall_design: We compared genetic variants (by DNA next-generation sequencing [NGS] using a 50 gene Ion Torrent panel) and gene expression (using the NanoString® PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT). NGS was performed on plasma cell free DNA (cfDNA) on a select group of patients (n=14) in order to assess the utility of using cfDNA to monitor these changes.  This series contains only the gene expression data using the NanoString platform.


title: Gene expression in the colon from IL10 KO mice

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary:
That commensal bacteria can influence intestinal inflammation has been observed using other models of chronic colitis. Loss of IL-10, a major immunosuppressive cytokine, induces spontaneous colitis in mice. The incidence of spontaneous polyp formation in IL-10-deficient mice was also completely eliminated in the absence of STING
We used microarrays to evaluate the inflammatory cytokine expression in the colon from IL10 KO mice and IL10/STING KO mice.

overall_design: We generated the IL10KO, IL10/STINGKO mice to compare the gene expression profile in the colon from those mice.

first: Glen

middle: N

last: Barber

first: Jeonghyun

last: Ahn

first: Sehee

last: Son


title: CART-19 Responses in Human CD19 Transgenic Mice

city: Minneapolis

first: Christopher

middle: A

last: Pennell

state: Minnesota

address: 420 Delaware St SE

department: Laboratory Medicine & Pathology

institute: University of Minnesota

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

overall_design: Refer to individual Series


title: CART-19 Responses in Human CD19 Transgenic Mice [inflammationv2 platform]

summary: The clinical success of chimeric antigen receptor (CAR) T-cell therapy for CD19+ B-cell malignancies may come at the expense of acute and chronic morbidities. Some patients suffer from significant, acute toxicities and those with persistent CAR T-cells require immunoglobulin therapy due to CAR-induced B-cell aplasia. Life-threatening effects include cytokine release syndrome, the exact etiology of which is unclear. To elucidate the underlying mechanisms of CAR-induced toxicities, we developed a mouse model in which human CD19 (hCD19)-specific mouse CAR T-cells were adoptively transferred into mice whose normal B-cells express a hCD19 transgene at hemizygous levels. In contrast to homozygous mice, hemizygous mice have higher B cell frequencies, providing a greater target antigen load to drive CAR-T cell activation. Hemizygous mice given a lethal dose of hCD19 transgene-expressing lymphoma cells and treated with CAR-T cells had undetectable levels of tumor. However, recipients experienced acute B-cell aplasia, morbidities and mortality in an antigen- and dose-dependent manner. IL-6, INF-g, and inflammatory pathway transcripts were enriched in affected tissues. As in patients, antibody-mediated neutralization of IL-6 blunted toxicity. This new model will prove useful in testing strategies designed to improve CD19-specific CAR T-cell therapy by reducing acute toxicities and reversing B-cell aplasia.

overall_design: mRNA was extracted from colons and spleens from human CD19 transgenic mice 2 and 5 days after adoptive transfer of 3E+06 human CD19-specific CAR T-cells (or control hEGFRT-cells). mRNA for 268 unique genes were quantitated on the nanoString mouse inflammation codeset.  48 samples/codeset= 40 unique samples (8 groups x 5 biological replicates/group) + 8 technical replicates (1 for each of 8 samples).

first: Jessie

middle: L

last: Barnum

first: Cameron

middle: S

last: McDonald-Hyman

first: Angela

last: Panoskaltsis-Mortari

first: Megan

last: Riddle

first: Zhengming

last: Xiong

first: Michael

last: Loschi

first: Govindaragjan

last: Thangavelu

first: Heather

last: Campbell

first: Yosef

last: Refaeli

first: Scott

last: Furlan

last: Jensen

first: Leslie

last: Kean

first: Jeffrey

last: Miller

first: Jakub

last: Tolar

first: Mark

last: Osborn

first: Bruce

middle: R

last: Blazar


title: STING-Dependent Signaling Manifests IL-10 Controlled Inflammatory Colitis

first: Anthony

last: Griswold


title: In planta transcriptome analysis of Pseudomonas syringae pv. tomato DC3000 during early infection and early exposure to pattern-triggered immunity in Arabidopsis thaliana

status: Public on Feb 03 2018

city: Athens

first: Brian

middle: H

last: Kvitko

state: GA - Georgia

address: 120 Carlton St

department: Plant Pathology

institute: University of Georgia

summary: We develop a protocol for extracting P. syringae transcriptome from infected A. thaliana tissue through physical separation by low speed centrifugation. We use this protocol to compare the RNASeq transcriptome profiles of DC3000 during naïve host infection and exposure to pattern triggered immunity at 1, 3, and 5 hours post inoculation

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: Bacteria extracted from naïve mock-treated leaves at 1, 3, and 5 hours post inoculation. Bacteria extracted from immune-induced leaves at 1, 3, and 5 hours post inoculation. Bacterial initial inoculum as in vitro media-based sample. Samples collected in triplicate on different days for each time and treatment

first: Amelia

last: Lovelace


title: Identification of target genes in human lung tissue of COPD patients

status: Public on Feb 08 2018

city: Borstel

first: Lena

last: Heinbockel

address: Parkallee 3

department: Pathology

institute: Research Center Borstel

summary: Lung tissue of COPD patients and tissue of non-smokers was investigated in transcriptome analysis with regard to differences in RNA expression levels to identify target genes for COPD treatment.

overall_design: 5 tumor-free tissue samples of non-smoking patients and 14 tumor-free lung tissue samples (6 smokers and 8 ex-smokers) were used for transcriptome analysis.

first: Sebastian

last: Marwitz


title: Functional impact of the H2A.Z histone variant during meiosis in Saccharomyces cerevisiae

city: Salamanca

first: Pedro

last: San Segundo

state: Salamanca

address: Instituto de Biología Funcional y Genómica. Zacarías González 2.

department: Unidad II. Dinámica del genoma y epigenética.

country: Spain

institute: University of Salamanca

summary: Among the collection of chromatin modifications that influence its function and structure, the substitution of canonical histones by the so-called histone variants is one of the most prominent actions. Since crucial meiotic transactions are modulated by chromatin, here we investigate the functional contribution of the H2A.Z histone variant during both unperturbed meiosis and upon challenging conditions where the meiotic recombination checkpoint is triggered in budding yeast by the absence of the synaptonemal complex component Zip1. We have found that H2A.Z localizes to meiotic chromosomes in an SWR1-dependent manner. Although meiotic recombination is not substantially altered, the htz1 mutant (lacking H2A.Z) shows slower meiotic progression, impaired sporulation and reduced spore viability. These phenotypes are likely accounted for by the misregulation of meiotic gene expression landscape observed in htz1. In the zip1 mutant, the absence of H2A.Z results in a tighter meiotic arrest imposed by the meiotic recombination checkpoint. We have found that Mec1-dependent Hop1-T318 phosphorylation and the ensuing Mek1 activation are not significantly altered in zip1 htz1; however, downstream checkpoint targets, such as the meiosis I-promoting factors Ndt80, Cdc5 and Clb1, are drastically down-regulated. The study of the checkpoint response in zip1 htz1 has also allowed us to reveal the existence of an additional function of the Swe1 kinase, independent of CDK inhibitory phosphorylation, which is relevant to restrain meiotic cell cycle progression. In summary, our study shows that the H2A.Z histone variant impacts various aspects of meiotic development adding further insight into the relevance of chromatin dynamics for accurate gametogenesis.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three biological independient replicates were use for each strain

first: Sara

last: González-Arranz

first: Santiago

last: Cavero

first: Macarena

last: Morillo-Huesca

first: Eloísa

last: Andújar

first: Mónica

last: Pérez-Alegre

first: Félix

last: Prado

last: San-Segundo


title: Expression data from mouse hematopoietic stem cells

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Hematopoietic stem cells (HSCs) are a specialized group of cells with the ability to self-renew and differentiate into distinct lineages of the entire hematopoietic system throughout lifetime. The maintenance of a quiescent state is essential for sustaining the normal function of HSCs. Many regulatory factors involved in HSC quiescence maintenance have been found. However the role steroid receptor coactivator 3 (SRC-3) in the regulation of HSC maintenance remains unexplored.
We used microarrays to detail the global programme of gene expression in lineage- Sca1+ c-Kit+ cells (LSKs) from wild-type (WT) and SRC-3 knockout (KO) mice and identified distinct classes of altered genes after SRC-3 knockout.

overall_design: To obtain differentially expressed genes in LSKs after SRC-3 knockout. Total RNA was extracted from sorted WT or SRC-3-deficient LSKs. Then, cDNA was generated and hybridized on Affymetrix microarrays in duplicate.

first: Mengjia

last: Hu

first: Shilei

last: Chen


title: CART-19 Responses in Human CD19 Transgenic Mice [immunology platform]

first: Christopher

last: Pennell

overall_design: mRNA was extracted from colons and spleens from human CD19 transgenic mice 2 and 5 days after adoptive transfer of 3E+06 human CD19-specific CAR T-cells (or control hEGFRT-cells). mRNA for 561 unique genes were quantitated on the nanoString mouse immunology codeset.  48 samples/codeset= 40 unique samples (8 groups x 5 biological replicates/group) + 8 technical replicates (1 for each of 8 samples).

first: Jessie

last: Barnum

first: Cameron

last: McDonald-Hyman

first: Angela

last: Panoskaltsis-Mortari

first: Megan

last: Riddle

first: Zhengming

last: Xiong

first: Michael

last: Loschi

first: Govindaragjan

last: Thangavelu

first: Heather

last: Campbell

first: Yosef

last: Refaeli

first: Scott

last: Furlan

last: Jensen

first: Leslie

last: Kean

first: Jeffrey

last: Miller

first: Jakub

last: Tolar

first: Mark

last: Osborn

last: Blazar


title: Gene expression in murine embryonic fibroblasts stimulated with DNA or LPS

first: Anthony

last: Griswold

summary:
MyD88 may play a direct role in STING-dependent signaling, or alternatively that STING-dependent pro-inflammatory cytokines may require downstream MyD88-dependent signaling to exert their effect.
To determine this, we treated STING or MyD88-deficient murine embryonic fibroblasts (MEFs), bone marrow derived macrophages (BMDM) or dendritic cells (BMDC) with exogenous CDN’s or cytosolic dsDNA (ISD) which triggers STING-signaling and type I IFN production.

overall_design: To evalulate the gene expression profiling, we isolated mouse embryonic fibroblast from WT, SKO, or MyD99KO mice and treated with dsDNA or LPS for 6 hours.

first: Glen

last: Barber

first: Jeonghyun

last: Ahn

first: Sehee

last: Son


title: Characterization of 5-aminolevulinic acid and radiation dose effects on radiotherapy using mouse tumor model.

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

summary: B16-BL6 mouse melanoma that had been maintained in C57BL/6J mice were used to evaluate the 5-aminolevulinic acid (ALA) and radiation dose effects on radiotherapy. Mice were divided into 6 groups after implantation of B16-BL6 cells; (1) no treatment (NT) ;  (2) 5-ALA treatment (ALAT); (3) 10 session of fractionated irradiation (2Gy/day) (20XT); (4) 10 sessions of 5-ALA treatment followed by fractionated irradiation (2Gy/day) (ALA-20XT); (5) 10 session of fractionated irradiation (3Gy/day) (30XT); (6) 10 sessions of 5-ALA treatment followed by fractionated irradiation (3Gy/day) (ALA-30XT).

overall_design: B16-BL6 mouse melanoma tumor gene expressions in 6 groups were measured after fractionated doses of radiation with local administration of 50mg/kg ALA prior to fractional irradiation.

first: Hitoshi

last: Iwahashi


title: CHD6 transcriptome

status: Public on Jan 31 2018

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

summary: HEK293T cells were transfected with plasmids expressing a control siRNA or a siRNA especific for CHD6 protein. 48H post-transfection, total RNA was isolated and used for transcriptome analysis. Four biological replicates carried out by triplicate were used.

overall_design: 4 replicates each of HEK293T cells transfected with siRNA especific for CHD6 protein (siRNAm) and with a control siRNA (Contr) were analyzed

first: Juan

middle: P

last: Chavez


title: Systematic Identification of Genes Involved in Feather Regeneration in Wanxi-White Goose

city: Hefei

first: Xing young

last: Chen

address: 130, Changjiang Xi Road

institute: Anhui Agricultural University

summary: Regeneration is one of the key factors affecting downy feather production. However, the signals and molecular controlling the progression of feather regeneration was poorly understood. We used a high density microarray to profile the temporal transcriptome dynamics during the regeneration periods. A total of 3540 genes expressed differentially with significant fold changes during feather regeneration. Cluster analysis revealed event specific dynamic expression of genes related to cell cycling, cell migration, cell proliferation, follicle re-growth and fiber elongation. These clusters involved functional clusters like regulation of actin cytoskeleton, focal adhesion and sphingolipid metabolism, and enriched signaling pathways like Wnt signaling pathway, MAPK pathway and TGFβ signaling pathway. In cell cycling, mainly involved genes were cyclin B3, cyclin Y. In  TGFβ signaling pathway, mainly involved genes were TGFβ3, BMP7, NOG and BMP2. While Wnt5a, Wnt10a, FZD2, and FZD10 were involved in canonical Wnt/β-catenin pathway. Our study provides a comprehensive genetic blue print of diverse cellular responses during regeneraton of goose feather. The data provide an initial step towards a better understanding of molecular mechanisms underlying feather regeneration process and also suggest that signals or molecular participated in feather regeneration was quite different from the generation of hair in mammals.

overall_design: Six separately reared geese were selected for skin sample collection before molting, 1.5 day after molting, 5 day after molting and 10 day after molting. 1.5×1.5 cm2 rhombic skin samples from ventral were excised in each time and placed in tubes containing RNALater for RNA extraction.

first: Zhaoyu

last: Geng

first: Xingyong


title: Expression data of plasma microRNA from the healthy children and children who diagnosed with acute lymphoblastic leukemia

first: Qian

last: Jiang

state: Beijing

address: No.56 Nanlishi Road Xicheng District Beijing

department: Hematology Oncology Centre

institute: Beijing Childrens' Hospital Capital Medical University

summary: According to the status of children acute lymphoblastic leukemia,we collected samples from the new dignosed, complete remmission and relapsed.

overall_design: Twelve plasma samples from healthy children (H) and pediatric ALL were collected, including 3 samples from the healthy children, 3 pairedof samples from newly diagnosed (ND), complete remission (CR), and relapsed (RE) patinets , respectively. The miRNA expression profiles were detected by Taqman miRNA Array. Unsupervised hierarchical clustering was performed based on the expression of miRNAs toidentify differentially expressed miRNAs among the groups

first: Huyong

last: Zheng

first: Xiaojing

last: Lu


title: Genetic variants associated with development of pseudoexfoliation syndrome

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Pseudoexfoliation syndrome (PEXS) is a late-onset disorder in which fibrillar material accumulates at abnormally high concentrations mainly in the anterior segment of the eye. PEXS is the most common cause of secondary glaucoma, which can ultimately lead to blindness and is associated with a higher risk of cataract and serious complications following different types of intraocular surgery. Although PEXS clearly has a genetic component, it remains poorly explored. In our genome-wide association study, we searched for an association of genetic variants with this disorder among older Poles with PEXS without glaucoma.

overall_design:
A total of 209 individuals including 103 PEXS patients without glaucoma and 106 perfectly (age- and gender-) matched controls were recruited for the study. Genomic DNA was extracted from whole blood treated with EDTA. DNA samples that passed quality control tests were combined according to diagnosis and gender at equimolar concentrations to obtain 10-DNA sample pools. A total of 10 DNA pools were prepared for each of the two groups (control and PEXS), seven for women and three for men.

Please note that no data processing was applied and thus only theta values from unprocessed file were provided in the 'Matrix_signal_intensities.txt' file.

The main reason for not normalizing the data was that it was derived from pooled samples. Data normalization algorithms were in general optimized for genotype calling (which is impossible for these samples), and thus may introduce possible artifact introduction. Thus "the less the better" approach was made with the data analysis. PCA hasn't revealed any considerable stratification. Raw theta values were used as an input for Student's t-test. Clusters of significant probes were selected for validation in individual patients.

first: Katarzyna

last: Zagajewska

first: Magdalena

last: Piątkowska

first: Aneta

last: Bałabas

first: Anna

last: Kluska

first: Agnieszka

last: Paziewska

first: Ewelina

last: Pośpiech

first: Iwona

last: Grabska-Liberek

first: Ewa

last: Hennig


title: Gene expression analysis of the inflorescence of 35S::SUP-GR after Mock and DEX treatment

city: Singapore

first: Yifeng

last: XU

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Identification of putative downstream genes of SUP with the functional inducible line 35S::SUP-GR

overall_design: The 35S::SUP-GR seeds in Ler WT were  grown at 22°C under continuous light conditions. The inflorescences with flower buds earlier than stage 10 were collected 4 hours after the Mock and DEX treatment .Three independent sets of Mock and DEX-treated inflorescence mRNA samples were used for this array.

last: Xu

first: Eng

last: Gan

first: Wanyi

last: Wee

first: Toshiro

last: Ito


title: Implication of VSMC heterogeneity among arterial beds in vascular calcification

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

summary: Transcriptome analysis of human primary smooth muscle cells from different arterial beds (abdominal and thoracic aorta, carotid and femoral and infrapopliteal arteries).

overall_design: Smooth muscle cells were isolated from non atheromatous peripheral arteries from deceased organ donors. Allografts were obtained from the following arterial locations; carotid artery, thoracic aorta, abdominal aorta, common femoral aorta, infrapopliteal artery. RNA was extracted from 2 samples for each arterial bed and hybridized to microarrays.


title: Expression data from rice stem bases in two different genotypes

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

summary:
Crown roots differentiate from stem base in rice. In this study, we followed gene expression in stem base of two Vietnamese indica rice varieties that belong to two haplotypes defining a QTL associated with crown root number.
We used microarrays to look for the gene differentially expressed in stem base of two varieties.

overall_design: Stem bases were collected from 22 days old plantlets of the two cultivars for RNA extraction and hybridization on Affymetrix microarrays. Two independent repetitions of the experiment were done.

first: Le

middle: K

last: Nguyen

first: Brigitte

last: Courtois

first: Thi

last: To


title: Domestication of flor yeast: Rewiring the map kinase signaling pathway for lifestyle switching

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

summary: The yeast Saccharomyces cerevisiae is a model for biology and is also one of the most important microorganisms for food and drink production. Surprisingly, only a few genes involved in the adaptation to anthropic niches have been described until now. Wine fermentation and flor aging, which are performed by strains from two closely related groups of yeast, are two technologies that have opposite approaches toward oxygen, which results in contrasting lifestyles for yeast: fermentation growth on grape for wine yeast, and biofilm aerobic growth on ethanol and glycerol contained in wine for flor strains. This pair of environments and the associated yeast populations can be a model for studying adaptation to anthropic environments. In this project, we have obtained high-quality genome sequences of 20 yeast strains from 9 flor yeast, 9 wine yeast as well as EC1118 and haploid derivative 59A. Phylogeny and population structure analysis, based on GATK genotyping, enable us to characterize a group of flor yeast that is clearly different from wine yeast. A comparison of the genomes of wine and flor yeasts using various methods (PCA, nucleotidic diversity, McDonald Kreitman test, potentially impacted genes according to SIFT) enabled us to note divergent regions, or genes, with potential non-neutral evolution, and highly variant genes. The results of these genomic comparisons are echoed by the comparison of a wine and a flor yeast transcriptome. These methods, as expected, highlight key genes that are involved in FLO11 regulation as well as in biofilm growth, but they also revealed the presence of many allelic variations in genes that are involved in the sensing and regulation of osmotic pressure (such as SLN1, HKR1, SSK22, AQY2) and specific metabolic traits, such as the fructophily of flor yeast, which carry a fructophile allele of HXT3. More remarkable is the accumulation of mutations in multiple genes, which creates a pattern of convergent mutations in regulatory networks, as seen in FLO11 regulation or the HOG MAP kinase pathway. The rewiring of these regulatory networks is clearly one of the hallmarks of domestication for the flor yeast genome. Data presented here correspond to the comparison of Flor yeast P3-D5 and wine yeast K1-280-2B transcriptomes under conditions potentially enabling the production of a biofilm.

overall_design: 2 strains with 3 biological replicates compared

first: Anna-Lisa

last: Coi


title: DNA methylation patterns separate senescence from malignant transformation potential in human cells [gene expression]

city: Baltimore

first: Wenbing

last: Xie

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Department of Oncology

institute: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine

summary: Replicative senescent cells reportedly share similar DNA methylation changes with cancer cells, which are purported to facilitate tumorigenesis in cells bypassing senescence. However, we now report biologically critical and distinct patterns of DNA methylation evolution between replicative and oncogene-induced senescence and transformation in a classic human cell transformation model. While overall DNA methylation losses and gains occur in both replicative senescent and transformed cells, the patterns evolve more programmatically for the former and stochastically for the latter. Oncogene-induced senescence is an acute process involving minimal changes to DNA methylation. The stochastic DNA methylation alterations in transformation mainly involve a set of pro-survival promoter CpG-island methylation events targeting genes controlling development and differentiation processes, while the senescence-specific promoter changes occur in genes involved in positive regulation of cellular biosynthesis and macromolecular metabolism. The above set of pro-survival promoter CpG-island hypermethylation events, but not the senescence-specific events, are prone to occur in primary tumors and aging tissues. Importantly, cells manifest senescence-specific epigenomic patterns very early during commitment to senescence, and while these “near-senescent” cells can be immortalized, they are refractory to transformation by H-Ras oncoprotein (H-rasV12). The senescence-specific methylation is retained during immortalization and transformation attempts, suggesting it does not function to promote tumorigenesis. Thus, abnormalities in cancer-related methylation has their origins in aging and not replicative senescence, and senescence-associated methylation potentially prevents malignant transformation.

overall_design: Examination of the gene expression alterations when early passage (EP) human fibroblast BJ cells become senescent (Sen) and transformed (HRAS and HRAS_X). At least two biological replicates are performed.

first: Lixia

last: Pan

first: Yang

last: Zhang

first: Lauren

last: Murphy

first: Xiangqian

last: Kong

first: Limin

last: Xia

first: Fillipe

last: Carvlho

first: Stephen

last: Baylin

first: Hariharan

last: Easwaran


title: Transcriptomics effects of ingestion of food additive titanium dioxide (E171) in the colon of BALB/c mice

status: Public on Jan 24 2018

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

institute: Maastricht University

summary: Colorectal cancer is one of the most common cancers worldwide. Factors that could influence the increase or reduction of the risks, including dietary pattern, are under investigation. Previous studies showed the capacity of food additive titanium dioxide (E171) to induce DNA damage in vitro and facilitate growth of colorectal tumors in vivo. The aim of this study is to understand the molecular mechanisms behind these effects of E171 exposure. BALB/c mice were exposed by gavage to 5 mg/kgbw/day of E171 for 2, 7, 14 and 21 days. Transcriptome changes of the response to E171 exposure were studied by whole genome mRNA microarray analysis on the distal colons of the mice. The results showed significant changes in the transcriptome, mainly gene expression changes of the olfactory/GPCR receptor family, oxidative stress, immune responses and of cancer related genes. These pathways may represent the underlying molecular mechanisms by which E171 facilitates tumor formation in the colon of these mice.

overall_design: Total of 32 samples of colon of mice, every sample is in duplicate for the microarray analysis. Two different type of exposure; non exposed (sterile water) (Ctrl), exposed to 5mg/kg bw/day of E171 (E171). Four time points: 2, 7, 14, and 21 days. At each time point 4 mice are euthanised (2 males, 2 females).

first: Marlon

last: Jetten

first: Marloes

last: Jonkhout

first: Luis

middle: G

last: Garduño-Balderas

first: Jacob

last: Briedé

first: Theo

last: de Kok

first: Yolanda

middle: I

last: Chirino

first: Henk

last: van Loveren


title: Gender differences of gene expression profiles in brain cardiovascular centers of WKY rats [hypothalamus]

status: Public on Jan 30 2018

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

institute: International Christian University

summary: Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the hypothalmus is strongly functionnaly connected to the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP, we hypothesized that a different neuronal functions at the level of hypothalamus between men and women could contribute to the gender difference in cardiovascular homeostasis. Females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age and their hypothalamus is characterized by a specific gene expression profile. This gender dependence of AP level is less marked in the normotensive strain, Wistar Kyoto rats (WKY). In this study, we investigated the gender-dependent gene expression profile of the hypothalamus of WKY rats by using microarray technique.

overall_design: 2 groups of adult WKY rats (9 weeks old) were formed : males (n=5) and females(n=5). For each rat, the whole hypothalamus was dissected and total RNAs were extracted. For each group, 100ng of total RNAs from each rats were pooled together before being processed in the microarray experiment.

first: Makiko

last: Onishi

first: Ko

last: Yamanaka

first: Yasunori

last: Miyamoto

first: Hidefumi

last: Waki


title: Neuronal activity, TGFβ signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo [Affymetrix]

status: Public on Dec 31 2017

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

institute: University Freiburg

summary: Neuronal activity is altered in several neurological and psychiatric diseases. Upon depolarization not only neurotransmitters are released but also cytokines and other activators of signaling cascades. Unraveling their complex implication in transcriptional control in receiving cells will contribute to understand specific central nervous system (CNS) pathologies and will be of therapeutical interest. In this study we depolarized mature hippocampal neurons in vitro using KCl and revealed increased release not only of Brain-derived neurotrophic factor (BDNF), but also of Transforming growth factor beta (TGFB). Neuronal activity together with BDNF and TGFB controls transcription of DNA modifying enzymes specifically members of the DNA-damage-inducible (Gadd) family, Gadd45a, Gadd45b, and Gadd45g. MeDIP followed by massive parallel sequencing and transcriptome analyses revealed less DNA methylation upon KCl treatment. Thereby, psychiatric disorder-related genes, namely Tshz1, Foxn3, Jarid2, Per1, Map3k5, and Arc are transcriptionally activated and demethylated upon neuronal activation. To analyze whether misexpression of Gadd45 family members can be associated with psychiatric diseases, we applied unpredictable chronic mild stress (UCMS) as established model for depression to mice.UCMS lead to a reduced expression of Gadd45 family members. Taken together, our data demonstrate that Gadd45 family members are new putative targets for UCMS treatments.

overall_design: Definition of activity dependent targets on transcriptional and DNA methylation level

first: Patrick

last: Bovio

first: Daniela

last: Grassi

first: Tanja

last: Vogel

first: Riccardo

last: Vezzali


title: Cancer-related epigenome changes among induced pluripotent stem cell lines

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

summary: To identify hypermethylated genes in induced pluripotent stem cell lines, human embryonic stem cell lines, and non-nucleofected CD34+ CB cells, indicated cell lines were treated with 5-aza-2′-deoxycytidine (DAC) or trichostatin A (TSA), and drug-induced changes in gene expression vs control treatment (PBS) were identified using Agilent two-color arrays, using the experimental methods of Ohm et al. (Cancer Res 70:7662-7673 2010).

overall_design: Total RNA was harvested from indicated conditions. A single sample of each cell line was used for this analysis.

first: Kurinji

last: Pandiyan

first: Leander

last: Van Neste

first: Tea

last: Park

first: Wayne

last: Yu

first: Ann

last: Peters

first: Renee

last: Reijo-Pera

first: Stephen

last: Baylin

middle: T


title: Comparative profiling of cortical gene expression in Alzheimer's disease patients and mouse models demonstrates a link between amyloidosis and neuroinflammation

status: Public on Dec 21 2017

city: Fukuoka

first: Yusaku

last: Nakabeppu

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary: Alzheimer's disease (AD) is the most common form of dementia, characterized by accumulation of amyloid beta (Abeta) and neurofibrillary tangles. Oxidative stress and inflammation are considered to play an important role in the development and progression of AD. However, the extent to which these events contribute to the Abeta pathologies remains unclear. We performed inter-species comparative gene expression profiling between AD patient brains and the App (NL-G-F/NL-G-F) and 3xTg-AD-H mouse models. Genes commonly altered in App (NL-G-F/NL-G-F) and human AD cortices correlated with the inflammatory response or immunological disease. Among them, expression of AD-related genes (C4a/C4b, Cd74, Ctss, Gfap, Nfe2l2, Phyhd1, S100b, Tf, Tgfbr2, and Vim) was increased in the App (NL-G-F/NL-G-F) cortex as Abeta amyloidosis progressed with exacerbated gliosis, while genes commonly altered in the 3xTg-AD-H and human AD cortices correlated with neurological disease. The App (NL-G-F/NL-G-F) cortex also had altered expression of genes (Abi3, Apoe, Bin2, Cd33, Ctsc, Dock2, Fcer1g, Frmd6, Hck, Inpp5D, Ly86, Plcg2, Trem2, Tyrobp) defined as risk factors for AD by genome-wide association study or identified as genetic nodes in late-onset AD. These results suggest a strong correlation between cortical Abeta amyloidosis and the neuroinflammatory response and provide a better understanding of the involvement of gender effects in the development of AD.

overall_design: 12-months old mice from two mouse model were used in this study: AppNL-G-F/NL-G-F mice, harboring three pathogenic App-knock-in mutations that promote aggressive amyloidosis by increasing total Aβ production (Swedish mutation KM670/671NL), increasing the Aβ42/Aβ40 ratio (Iberian mutation I716F), and promoting Aβ aggregation through facilitating oligomerization and reducing proteolytic degradation (Arctic mutation E693G), under the control of the endogenous APP promoter; and 3xTg-AD-H mouse carrying two mutated human overexpressed transgenes, APP (Swedish KM670/671NL) and MAPT (P301L), driven by exogenous Thy1.2 promoter with a knock-in mutation of Psen1 (M146V), together with their correspondent controls (male, n=3 for each group). RNA samples prepared from total cortex were subjected to microarray analysis using the Affymetrix Mouse Gene 2.0 ST platform.

first: Erika

last: Castillo


title: Gender differences of gene expression profiles in brain cardiovascular centers of WKY rats

first: Sabine

last: Gouraud

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

overall_design: Refer to individual Series


title: Genomic Circuitry Underlying Immunological Response to Pediatric Acute Respiratory Infection

status: Public on Jan 09 2018

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary:
Acute respiratory tract viral infections (ARTI) cause significant morbidity and mortality. While CD8 T cells are fundamental to the host response, the transcriptional alterations underlying anti-viral mechanisms within these cells, and the links to clinical characteristics, remain unclear. The transcriptional circuitry in CD8 T cells from acutely ill pediatric patients with influenza-like illness was distinct for different viral pathogens.
We used microarray analysis to profile sorted CD8 T cells from PBMCs of various influenza-like illness patients.

overall_design: Sorted CD8 T cells from PBMCs of 29 patients with a subset of viral infections (influenza (IFV), human rhinovirus (HRV), respiratory syncytial virus (RSV) and each of these with coinfections and 18 healthy control (HC) patients were subjected to transcriptional profiling group and the transcriptional profiles were studied using Affymetrix microarrays.

first: Sarah

last: Henrickson

first: Douglas

middle: V

last: Dolfi

middle: J

last: Wherry


title: Inhibiting the mammalian target of rapamycin (mTOR) as an adjunctive therapy for cerebral malaria

status: Public on Jan 06 2018

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Malaria is an infectious disease caused by parasites of the Plasmodium spp. In endemic areas, in approximately 1% of cases, almost exclusively in young children, malaria becomes severe resulting in nearly seven hundred thousand deaths each year in Africa alone. Cerebral malaria (CM) is a common form of severe malaria and one for which we have no effective adjunctive therapy. Although the cellular and molecular mechanisms underlying the pathogenesis of CM are incompletely understood, it is likely that both intrinsic features of the parasite and the human host’s immune response contribute to disease. Indeed, two hallmarks of CM are the sequestration of infected red blood cells in the brain vasculature and severe immune inflammation. The kinase, mammalian target of rapamycin (mTOR), through its regulation of cellular metabolism, is a central regulator of immune responses and drugs that inhibit the mTOR pathway have been shown to be antiparasitic, raising the possibility that mTOR inhibitors could be effective adjunctive therapies for CM. Here we show in a mouse model of CM, experimental CM (ECM), that the mTOR inhibitor rapamycin protects against ECM when administered within the first four days of infection. Treatment with rapamycin increased survival, blocked breakdown of the blood brain barrier and brain hemorrhaging, decreased the influx of both CD4+ and CD8+ T cells into the brain and the accumulation of parasitized red blood cells in the brain. Remarkably, animals were protected against ECM even though rapamycin treatment significantly increased the inflammatory response induced by infection in both the brain and spleen and elevated the levels of peripheral parasitemia. These results open a new avenue for the development of highly selective adjunctive therapies for CM, by targeting pathways that regulate host and parasite metabolism

overall_design: various tissues of mice infected with P. berghei or saline and treated with Rapamycin or saline

first: Emile

last: Gordon

first: Michael

last: Waisberg

first: Geoffrey

last: Hart

first: Tuan

middle: M

last: Tran

first: Munir

last: Akkaya

first: Jeff

last: Skinner

first: Severin

last: Zinöcker

first: Mirna

last: Pena

first: Takele

last: Yazew

first: Chen-Feng

last: Qi

first: Louis

last: Miller

first: Susan

last: Pierce


title: Diferential Gene Expression of CAR T cell Derived from Naïve mice vs Tumor Bearing mice

city: Bethesda

first: Stefano

last: Marenco

address: Building 10, Room 4N306

institute: National Institute of Mental Health

summary: CAR T cell derived from tumor bearing mice show positive correlation with T cell exhausion, TH17 penotype and T cell activation, and upregulated in Cholesterol, carbohydrate matabolism, over expression in hypoxia, deminished in IL12-family cytokines, IFN signalling

overall_design: We used microarrays to detail the global differeential gene expression of these CAR T cells derived from Naïve or Tumor Bearing mouse.

first: Haiying

last: Qin

first: Terry

last: Fry


title: Gender differences of gene expression profiles in brain cardiovascular centers of WKY rats [nucleus of solitarii tract]

first: Sabine

last: Gouraud

summary: Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP is strongly associated with the AP level, we hypothesized that a different neuronal functions at the level of the NTS between men and women could contribute to the gender difference in cardiovascular homeostasis. Females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age and their NTS is characterized by a specific gene expression profile. This gender dependence of AP level is less marked in the normotensive strain, Wistar Kyoto rats (WKY). In this study, we investigated the gender-dependent gene expression profile of the NTS of WKY by using microarray technique.

overall_design: 2 groups of adult WKY rats (9 weeks old) were formed : males (n=5) and females(n=5). NTS was dissected and total RNAs were extracted from each rat. For each group, 100ng of total RNAs from each rats were pooled together before being processed in the microarray experiment.

first: Makiko

last: Onishi

first: Ko

last: Yamanaka

first: Yasunori

last: Miyamoto

first: Hidefumi

last: Waki


title: The transcriptome analysis of cucumber ovaries and pericarps from numerous-spine and few-spine inbred lines

status: Public on Jan 27 2018

city: Beijing

first: Qing

last: Xie

address: No.12 Zhongguancun South St.,Haidian District

institute: Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences

summary:
Purpose: Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, and cucumber fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation.In this study, the transcriptome analyses of ovaries and pericarps from numerous-spine parent and few-spine parent were conducted to identify the gene regulatory networks involved in the formation and development of numerous fruit spines in cucumber.
Methods: Cucumber mRNA profiles of ovaries and pericarps from numerous-spine parent and few-spine parent were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Then, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data. Simultaneously, the Q20, Q30 and GC contents of the clean data were calculated. All of the downstream analyses were based on the high-quality clean data. Clean paired-end reads were mapped to the reference genome using TopHat v2.0.12 (Trapnell et al. 2012). Then, the FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) value of each gene was calculated to estimate gene expression levels (Trapnell et al. 2010). Genes with an adjusted P-value < 0.05 identified by DESeq were assigned as differentially expressed genes(DEGs).
Results: We generated 42.96-57.53 million raw reads from each library, and 39.85-54.02 million clean reads were obtained after the removal of low-quality reads and adapter sequences. Among the clean reads, 79.03-80.94% were mapped to the gene database .  Based on the KEGG database, pathway enrichment analysis was performed to identify significantly enriched metabolic pathways or signal transduction pathways in DEGs. Plant hormone signal transduction was significantly enriched in up-regulated genes in both F_6DBF compared with M_6DBF and F_0DAA compared with M_0DAA.
Conclusions: Based on the transcriptome analysis, we excavated possible biological regulatory networks involved in the formation and development of numerous fruit spines in cucumber. This work will promote the exploration of molecular mechanisms that regulate cucumber fruit spine density.

first: Panna

last: Liu


title: Genetic characterization of different tumor cell lines isolated from lung tumors of c-myc and c-raf transgenic mice

status: Public on Dec 26 2017

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

institute: Medizinische Hochschule Hannover

summary: We recently reported isolation of various cancer progenitor cells of transgenic c-Myc and c-Raf mouse lung tumors [Reamon-Buettner SM and Borlak J, 2008].  As lung tumors can arise following dysregulation of signalling pathways normally activated during lung development we were particularly interested in investigating the genetic heterogeneity of these cancer cell lines. By whole genome expression analysis we identified two cell lines (A2C12, cRAF_cMYC) to be very different from the remaining tumor cells. Specifically the A2C12 and cRAF_cMYC cell lines expressed various stem cell markers, most notably CD34, CD44, Pdpn and Dlg7. Likewise, the A2C12 and cRAF_cMYC expressed the ATP-binding cassette (ABC) transporters Abcc1 and Abcg2 at different level when compared to other established cell lines. Furthermore, a genome wide expression profiling displayed differential gene expression pattern between and within progenitor cell lines. That provided important clues on heterogeneity in the signalling pathways amongst the cancer cell lines. We also knock down CD44 using a retroviral delivery system and observed an increased G1 peak and apoptosis as determined by flow cytometry.  Finally, we analyzed promoters of regulated genes and identified overrepresented 18 transcription factor binding sites (TFBS) in common regulated genes, 10 unique TFBS in A2C12 and 9 unique TFBS in cRaf_cMyc.  These data indicates that our tumor cell lines are suitable models to study the biology of lung cancer progenitor cell. Most importantly, we show that our tumor cell lines do not represent a homogeneous population of tumor-initiating cells. Understanding heterogeneity in tumors will lead to new diagnostic and therapeutic approaches.

overall_design: We analyzed 11 cancer cell lines from c-Myc and c-Raf transgenic mice. Cells were isolated from lung tumors of 8-month-old transgenic mice according to our protocol described in detail previously [Hansen T, Blickwede M, Borlak J; 2006]. Non transgenic alveolar epithelial cells isolated from healthy animals were used as control.

first: Jürgen

last: Borlak


title: Differential Expression Data from Lipopolysaccharide (LPS) Injected Mice

status: Public on Dec 13 2017

city: Québec

first: Hejer

last: Boutej

state: Québec

address: 2601, de la Canardière

department: NEUROBIOLOGY

country: Canada

institute: LAVAL University

summary: Uncontrolled microglial activation may lead to development of inflammation-induced brain damage. Here we uncover a ribosome-based mechanism/check point involved in control of the innate immune response and microglial activation. Using an in vivo model-system for analysis of the dynamic translational state of microglial ribosomes with mRNAs as input and newly synthesized peptides as an output, we find a marked dissociation of microglia mRNA and protein networks following innate immune challenge. Highly up-regulated and ribosome-associated mRNAs were not translated resulting in two distinct microglial molecular signatures, a highly specialized pro-inflammatory mRNA and immunomodulatory/homeostatic protein signature. We find that this is due to specific translational suppression of highly expressed mRNAs through a 3’UTR-mediated mechanism involving the RNA binding protein SRSF3. This discovery suggests avenues for therapeutic modulation of innate immune response in resident microglia.

overall_design: Transgenic mice expressing Flag/EGFP-RPL10a under the control of CD11b promoter were used to perform transcriptomic analysis in the baseline and following Lipopolysaccharide (LPS) injection (5mg/kg; for 24 hrs). RNA was extracted according to the TRAP protocol and hybridized on Affymetrix microarrays (MoGene-2_0-st). The mice were used at the age of 2-3 months with an equal ratio of male/female. Array data was processed by Transcriptome Analysis Console 3.0 (TAC). Three biological replicates were performed for each condition.

first: Reza

last: Rahimian

first: Sai Sampath

last: Thammisetty

first: Louis-Charles

last: Béland

first: Mélanie

last: Lalancette-Hébert

first: Jasna

last: Kriz


title: Microarray analysis to identify miRNA targetome of primary Burkitt lymphoma tumors in comparison to normal CD19+ B cells

status: Public on Jan 19 2018

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: MicroRNAs (miRNAs) are small non-coding RNAs involved in the posttranscriptional regulation of gene expression. Deregulated miRNA levels have been reported in Burkitt lymphoma (BL) compared to normal B cells and a number of miRNA target genes have been identified in BL cell lines. Here, we determined for the first time the miRNA targetomes of primary BL tumors in comparison with normal B cells. AGO2-RNA immunoprecipitation (AGO2-RIP) in two frozen diagnostic BL tissue samples and three CD19+ B-cell samples isolated from routinely removed tonsils revealed distinct miRNA targetomes of BL and normal B cells. Targets of the miR-17~92 cluster were significantly more frequently AGO2-IP enriched in BL while targets of miR-29 and miR-150 were more frequently AGO2-IP enriched in normal B cells. Furthermore, we showed that miRNA target genes in BL are mainly involved in cell cycle and cell death. Immunohistochemistry on BL tumor samples and tonsil tissues confirmed altered protein levels for two out of six selected miRNA targets, in line with the differential AGO2-IP enrichment between BL and normal B cells. A comparison of AGO2-IP enriched genes in primary BL cases with BL cell lines indicated that approximately half of the miRNA targets may be missed in studies using BL cell lines, while almost 60% of miRNA target genes identified in cell lines were not AGO2-IP enriched in primary BL cases. Our results demonstrate both the necessity and feasibility of studying miRNA-target interactions in primary tumors.

overall_design: AGO2 RNA immunoprecipitation was performed on two primary BL tumor tissues and three samples of CD19+ B cells isolated from tonsils of healthy controls, followed by microarray analysis of all known mRNAs and >15 000 lncRNAs (based on lncpedia) to identify miRNA target genes in BL and normal B cells.

first: Bea

last: Rutgers

first: Gertrud

last: Kortman

first: Debora

last: de Jong

first: Jasper

last: Koerts

first: Marian

last: Bulthuis

first: Tineke

last: van der Sluis

first: Annika

last: Seitz

first: Lydia

last: Visser

first: Arjan

last: Diepstra

first: Klaas

last: Kok

first: Joost

last: Kluiver

first: Anke

last: van den Berg


title: Highly multiplexed single-cell quantitative PCR

city: Utrecht

first: Michael

last: VanInsberghe

address: Uppsalalaan 8

institute: Hubrecht Institute

type:
Expression profiling by RT-PCR
Other

summary: We present a microfluidic device for rapid gene expression profiling in single cells using multiplexed quantitative polymerase chain reaction (qPCR). This device integrates all processing steps, including cell isolation and lysis, complementary DNA synthesis, pre-amplification, sample splitting, and measurement in twenty separate qPCR reactions. Each of these steps is performed in parallel on up to 200 single cells per run. Experiments performed on dilutions of purified RNA establish assay linearity over a dynamic range of at least 104, a qPCR precision of 15 %, and detection sensitivity down to a single cDNA molecule. We demonstrate the application of our device for rapid profiling of microRNA expression in single cells. Measurements performed on a panel of twenty miRNA in two types of cells revealed clear cell-to-cell heterogeneity, with evidence of spontaneous differentiation manifest as distinct expression signatures. Highly multiplexed microfluidic RT-qPCR fills a gap in current capabilities for single-cell analysis, providing a rapid and cost-effective approach for profiling panels of marker genes, thereby complementing single-cell genomics methods that are best suited for global analysis and discovery. We expect this approach to enable new studies requiring fast, cost-effective, and precise measurements across hundreds of single cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We analyzed 1454 samples in order to validate the performance of our device for performing single-cell RT-qPCR, and 362 samples in order to demonstrate it's efficacy on single-cells. For the validation experiments, 208 samples were in order to determine the lower sensitivity; 208, 207, and 208 samples were to determine amplification uniformity and mRNA-assay linearity, from each of three technical replicates; and 208, 208, and 207 samples were to determine amplification uniformity and microRNA-assay linearity, from each of three technical replicates. For the single-cell mRNA expression experiments, 175 single cells and 4 no cell controls (NCC) were measured using an assay panel designed to interrogate genes that spanned a wide range of abundance, and included i) three genes typically used as endogenous controls in bulk gene expression experiments (human GAPDH, RPPH1, and TBP), ii) a fusion transcript associated with CML (BCR-ABL), iii) a heterogeneously expressed gene (GGCX), and iv) a negative control (murine Gapdh). For the single-cell microRNA expression experiments, we measured 95 single K562 cells, 81 BaF3 cells, and 7 no cell controls against a panel of miRNA.

first: Hans

last: Zahn

first: Adam

last: White

first: Oleh

last: Petriv

first: Carl

last: Hansen


title: Early gene expression in mouse hematopoietic stem cells induced by Thrombopoietin stimulation and irradiation

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: Thrombopoietin (TPO) was shown to prevent irradaition-induced hematopoietic stem cells (HSCs) loss of function. A single injection of TPO to mice 45-60 min prior to irradiation is sufficient to reverse the long-lasting  accumulation of persistent DNA damage. We used microarrays to analyze whether this effet can relie on TPO-induced specific transcriptional changes during this early time.

overall_design: 10,000 HSCs (Lin-Sca+Kit+-CD34-Flk2-) from pools of 8 to 10 C57BL/6 mice were FACS sorted and cultured in vitro for 45 min in medium containing or not TPO before irradiation. Microarrays were performed 45 min later.

first: Françoise

last: Porteu

first: Bérengère

last: de Laval


title: Effect of cardiomyocyte and vascular smooth muscle cell specific KO of p38 MAPKα on gene expression profile of the heart

status: Public on Nov 30 2017

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: p38MAPKα KO mice develop in response to Angiotensin II treatment a dilative cardiomyopathy. Gene expression profile of KO hearts was compared to equally treated control heart under baseline conditions and after 48 hours of Angiotensin II treatment via osmotic mini pumps.

overall_design: Gene expression of mouse hearts of conditional p38 KO mice. Mice express a cre recombinase under control of SM22α promotor and a p38 MAPKα gene, which has loxPside-flanked exons 2 and 3. This expression lead to a specific KO of p38 MAPKα in vascular smooth muscle cells and cardiomyocytes. Control mice only express the floxed p38MAPKα gene. For RNA isolation four hearts of control and KO mice were harvested from untreated 3 month old male mice (Basal) and after 48 hours treatment with Angiotensin II  (AngII) (1.5mg/kg/d). RNA was isolated from heart apex.

first: Katharina

last: Bottermann

first: Lucia

last: Leitner

first: Mirjam

last: Pfeffer

first: Jana

last: Nemmer

first: René

last: Deenen

last: Köhrer

first: Johannes

last: Stegbauer

first: Axel

last: Gödecke


title: Gene expression analysis in primary murine Alveolar type II cells under Normoxia 21% O2 and Hyperoxia 85% O2 after 6 hours and 24 hours

status: Public on Dec 16 2017

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

summary: In this study the gene expression of primary murine (C57BL/6) lung alveolar type II cells belonging to four different conditions was analyzed. Effects of hyperoxia 24 hours group (group 2) were compared to the normoxia 24 hours (group 1) and effects of the hyperoxia 6 hours group (group 4) were compared to the normoxia 6 hours (group 3)

first: Tatiana

last: Likhoshvay

middle: E


title: Oncogenic Kras synergizes with enhanced TGF-beta-Foxd4 signaling to maintain leukemia-initiating cells in acute myeloid leukemia

status: Public on Nov 25 2017

city: Tianjin

first: Feifei

last: Liu

address: 94 Weijin Road

department: School of Medicine

institute: Nankai University

summary: In this study, the expression profiles of the granulocyte-macrophage progenitor cells (GMP) in bone marrow from KrasG12D/+; CD2Cre mice and wild-type mice were utilized as the in vivo model of acute-myeloid leukemic initiating cells for comparison. We compared the microarray data for transcriptional analysis of the GMP cells from KrasG12D/+; CD2Cre+ mice and littermate control.

overall_design: Gene expression profiling was performed on GMP cells sorted from leukemic KrasG12D/+; CD2Cre+ mice and littermate control.

first: Yinghui

last: Li


title: Effect of cardiac specific KO of p38 MAPKα on gene expression profile of the heart

summary: The gene expression profile of cardiomyocyte specific KO hearts was compared to equally treated control hearts after 48 hours of Angiotensin II-treatment via osmotic mini pumps. KO hearts develop during this treatment a dilative cardiomyopathy.

overall_design: Gene expression of mouse hearts of conditional p38 KO mice. Mice express tamoxifen inducible cre recombinase mercremer under control of α-MHC promotor and a p38 MAPKα gene, which has loxPside-flanked exons 2 and 3. At age of 6 weeks mice were treated with 500µg hydroxytamoxifen (OH-Tx) per day for 10 days to induce the specific KO of p38 MAPKα in cardiomyocytes. Control mice express the floxed p38MAPKα gene and were treated with OH-Tx equally. For RNA isolation four hearts of control and KO mice were harvested from 3 month old male mice after 48 hours treatment with Angiotensin II  (AngII) (1.5mg/kg/d). RNA was isolated from heart apex.


title: Cecum gene expression signatures in germ-free WT mice colonized with microbiota from WT or Card9-/-  mice and infected with Citrobacter rodentium induced colitis

city: Paris

first: Bruno

last: LAMAS

address: 27 rue Chaligny

department: CHU St Antoine

institute: Unité INSERM 1157/UMR 7203

summary: It is crucial to decipher the host-microbiota interactions as they are involved in intestinal homeostasis and diseases. Caspase Recruitment Domain 9 (Card9) is an inflammatory bowel disease (IBD) susceptibility gene coding for an adapter protein for innate immunity toward many microorganisms. Card9-/- mice are more susceptible to colitis induced by Citrobacter rodentium as a result of impaired of the IL-22 pathway. C. rodentium is a natural mouse pathogen widely used to model human infections with Enteropathogenic Escherichia coli and Enterohaemorrhagic E. coli. To explore the role of the gut microbiota in the susceptibility of Card9-/- mice to C. rodentium infection, we colonized WT germ-free (GF) mice with the microbiota of WT (WT-->GF) or Card9-/- (Card9-/- -->GF) mice and challenged them with C. rodentium. Card9-/- -->GF mice were more susceptible than WT-->GF mice to C. rodentium. To examine the mechanisms responsible for this defect, we compared the cecum transcriptomes of WT -->GF and Card9-/- -->GF mice before and during C. rodentium-induced colitis. The number of down-regulated and up-regulated genes on day 12 after C. rodentium infection was lower in Card9-/- -->GF mice than WT-->GF mice. Card9-/- -->GF mice showed a significant down-regulation of gut morphogenesis and wound healing pathways suggesting that recovery is impaired in Card9-/- -->GF mice after C. rodentium infection. Immune response and cell division pathways were up-regulated in WT-->GF mice but not in Card9-/- -->GF confirming the defect of global response to infection when only the Card9-/- microbiota was transferred. The most induced and differentially expressed genes between Card9-/- -->GF and WT-->GF mice on day 4 after C. rodentium infection were Reg3g (encoding REGIIIγ) and Reg3b (encoding REGIIIβ).

overall_design: Germ-free (GF) C57BL/6 wild-type (WT) mice were inoculated by oral gavage with fresh stools from conventional WT (WT-->GF) or Card9-/- (Card9-/- -->GF) mice. Three weeks after the colonization, WT-->GF and Card9-/- -->GF mice were infected by oral gavage with 1x10^9 CFU of C. rodentium strain DBS100. 5 mice of each groups (WT-->GF and Card9-/- -->GF) were sacrified before infection. 6 mice of each group were sacrified 4 days after infection, 5 mice of each group were sacrified at day 12 and 3 WT-->GF mice and 5 Card9-/- -->GF mice were sacrified at day 22.

last: Lamas

first: Hang-Phuong

last: Pham

first: Harry

last: Sokol


title: Acute treatment with kynurenic acid in inguinal primary adipocytes

city: Stockholm

first: Leandro

middle: Z.

last: Agudelo

state: Stockholm

address: von eulers väg 8, plan 3

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
Tryptophan-kynurenine metabolism plays an important role in the pathogenesis of several psychiatric diseases but its physiological function in peripheral tissues remains unclear. Physical exercise training activates a biochemical pathway in skeletal muscle that protects from neuroinflammation and, as a byproduct, leads to kynurenic acid accumulation in the periphery. We therefore investigated the effects of kynurenic acid in murine white adipose tissue.
We used microarrays to detail  global programme of gene expression underlying Kynurenic acid mediated effects on inguinal primary adipocytes.

overall_design: Fully differentiated inguinal primary fat cells were treated for 12h with 50μM of kynurenic acid or PBS (control), in triplicate. RNA was extracted and used for global gene expression analyses.

middle: Z

first: Jorge

last: Ruas


title: Expression data from RAW-264.7 cells transfected with empty vector and mouse FoxQ1 expression construct

status: Public on Nov 23 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Transcription factor FoxQ1 belongs to family of Fox transcription factors containing forkhead box (winged helix) domain. This family of proteins plays an important role in cell growth, proliferation, and differentiation. Expression of FoxQ1 was found in cancer cells and was associated with increased migration and invasion. Recently, elevated FoxQ1 expression was found in IL4 stimulated macrophages.
We used microarrays to clarify the role of FoxQ1 in macrophages

overall_design: Murine macrophage/monocyte cell line RAW-264.7 was transfected with murine FoxQ1 expression construct in pEF6/V5-His TOPO vector. Five stable clones stably expressing FoxQ1 were compared with four clones expressing empty vector

first: Ilja

last: Ovsiy

first: Vladimir

last: Riabov

first: Julia

last: Kzhyshkowska

first: Alexei

last: Gratchev


title: Opposing effects of CREBBP mutations during cerebellar development govern the pathogenesis of Rubinstein-Taybi syndrome and adult SHH medulloblastoma

status: Public on Nov 22 2017

city: Boston

first: Daniel

middle: Josef

last: Merk

state: MA

address: 450 Brookline Ave, Smith 1050

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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


title: The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [murine SNP array]

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

summary: T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. To address its incomplete molecular concept, we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identified novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor / cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM towards a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.

overall_design: Murine T-cell leukemia. Sample preparation: We hybridized DNA samples (QIAamp DNA Kit, Qiagen) onto the Affymetrix MOUSEDIVm520650 chip. We compared 4 controls (DNA isolated from normal liver tissues of age- and background-matched wild-type mice) to 3 ‘chronic phase’ and 5 ‘exponential phase’ (defining features in 4.2) splenic isolates from T-cell leukemia / lymphoma bearing Lckpr-hTCL1A+/- mice.


title: Gene expression profiling of resident microglia and invading macrophages

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Microglia represent the resident immune cells of the central nervous system. However, blood-borne monocytic cells are also able to invade the ischemic brain. In this study, we aim to characterize similarities and differences between these two cell populations using gene expression profiling.

overall_design: The dataset consists of eight sorted samples, representing two groups of GFP-labeled (resident microglia) or RFP-labeled (invaded) cells isolated from mice. RNA was amplified (SuperAmpTM) prior to labeling and hybridization.

first: Golo

last: Kronenberg

first: Ria

last: Uhlemann

first: Karen

last: Gertz


title: Lymph Node Metastases in Colon Cancer are Polyclonal

city: Ann Arbor

first: Karin

last: Hardiman

state: Michigan

address: 2922F Taubman Center

department: General Surgery

institute: University of Michigan

summary: Recent studies have highlighted the role of sub-clones in tumors. Lymph nodes are generally the first location of metastasis for most solid epithelial tumors including Colorectal cancer (CRC). We sought to understand the genetic origin of lymph node metastasis in CRC by evaluating the relationship between CRC tumor sub-clones and lymph nodes.

overall_design:
A total of 33 samples from 7 CRC’s, including two or three spatially disparate regions from each colon cancer and one to four matched lymph nodes for each tumor, were subjected to next-generation whole exome DNA sequencing, Affymetrix OncoScan SNP arrays, and targeted deep confirmatory sequencing. We performed mapping between SNPs and copy number events from the primary tumor and matched lymph node samples, allowing us to profile heterogeneity and mutational origin of LN metastases.  The computational method PyClone was used to define sub-clones within each tumor. The method Citup was subsequently used to infer phylogenetic relationships between sub-clones.
ThermoFisher (Affymetrix) OncoScan v3 arrays were run on all samples. The assay detects copy number change by generating data at 50-100kb resolution across a set of 891 cancer genes and 300-400kb across the rest of the genome.  Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (ThermoFisher, Waltham, Massachusetts) and processed using the standard Affymetrix reference control files, based on sample type (normal or FFPE).

first: P

last: Ulintz

first: K


title: Expression (Gene) array  from AMl12-Zfp125- stably expressing  cells

city: Chicago

first: Gustavo

middle: Werpel

last: Fernandes

state: IL

address: 5841 South Maryland Av.

department: Endocrinology

institute: University of Chicago

summary: Microarray analysis obtained from RNA of AML12 cells stably expresing Zfp125 or empty vector (EV)

overall_design: We analyzed differently expressed genes from AML12-Zfp125, using MouseGene 2.0_ST array


title: Chronic Crebbp knockout in cerebellar granule neuron precursors [development]

summary:
Recurrent mutations in chromatin modifiers are specifically prevalent in adolescent or adult patients with Sonic Hedgehog-associated medulloblastoma (SHH MB). Here, we report that mutations in the acetyltransferase CREBBP have opposing effects during the development of the cerebellum, the primary site of origin of SHH MB. Our data reveal that loss of Crebbp in cerebellar granule neuron progenitors (GNPs) during embryonic development of mice compromises GNP development, in part by downregulation of brain-derived neurotrophic factor (Bdnf). Interestingly, concomitant cerebellar hypoplasia was also observed in patients with Rubinstein-Taybi syndrome, a congenital disorder caused by germline mutations of CREBBP. By contrast, loss of Crebbp in GNPs during postnatal development synergizes with oncogenic activation of SHH signaling to drive MB growth, thereby explaining the enrichment of somatic CREBBP mutations in SHH MB of adult patients. Together, our data provide novel insights into time-sensitive consequences of CREBBP mutations and corresponding associations with human diseases.
We used microarrays to detail the global programme of gene expression underlying the knockout of Crebbp in murine granule neuron precursors, chronically induced at embryonic stages of development.

overall_design: We performed RNA extraction and hybridization on Affymetrix microarrays for murine cerebellar tissue at postnatal day 7 for mice with wild type Crebbp (Math1Cre) or loss of Crebbp (Math1Cre::CrebbpFl/Fl).

first: Ulrich

last: Schüller


title: Molecular heterogeneity of NK/T-cell lymphoma (miRNA profiling)

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

institute: National University Health System, Singapore

summary: To investigate if biologically distinct subsets exists in extranodal NK/T-cell lymphoma (NKTL), we performed unsupervised integrative analyses of gene expression profiling (GEP), miRNA profiling, and copy number aberration (CNA) on 66 cases of NKTL from diverse anatomical sites. This series is the miRNA profiling of 24 cases.

overall_design: Unsupervised analysis of FFPE NKTL samples (20 test, 46 validation set)

first: Tae-Hoon

last: Chung


title: Molecular heterogeneity of NK/T-cell lymphoma [CNV]

summary: To investigate if biologically distinct subsets exists in extranodal NK/T-cell lymphoma (NKTL), we performed unsupervised integrative analyses of gene expression profiling (GEP), miRNA profiling, and copy number aberration (CNA) on 66 cases of NKTL from diverse anatomical sites. This series is the CNA data.

overall_design: Unsupervised analysis of FFPE NKTL samples.


title: Molecular heterogeneity of NK/T-cell lymphoma [CNV supplementary]

summary: To investigate if biologically distinct subsets exists in extranodal NK/T-cell lymphoma (NKTL), we performed unsupervised integrative analyses of gene expression profiling (GEP), miRNA profiling, and copy number aberration (CNA) on 66 cases of NKTL from diverse anatomical sites. This series is the CNA of 23 supplementary cases.

overall_design: Unsupervised analysis of FFPE NKTL samples (20 test, 46 validation set, 23 supplementary set)


title: Differential Role of NKG2D in Recognition and Killing of Hepatic Lineage Cells Derived from Embryonic Stem Cells and Induced Pluripotent Stem Cells

status: Public on Nov 14 2017

city: Stanford

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

summary:
Recent advances towards the efficient and reproducible differentiation of stem cells into hepatocyte-like cells (HLC) have created potential opportunities in clinical transplantation. For this approach to be successfully translated, however, it is necessary to understand the immune response to stem cell-derived cellular products. Whereas both embryonic stem cells and induced pluripotent stem cells have been utilized as cellular sources for differentiation and lineage specification, their relative ability to be recognized by immune effector cells is unclear. Here we determine the expression of immune recognition molecules on HLC generated from murine embryonic stem cells and induced pluripotent stem cells, compared to adult hepatocytes, and we evaluate the impact on recognition by NK cells. We report that HLC lack MHC class I expression, and that embryonic stem cell derived-HLC have higher expression of the NK cell activating ligands Rae1, H60, and Mult1 than induced pluripotent stem cell-derived HLC and adult hepatocytes. Moreover, the lack of MHC class I render embryonic stem cell derived-HLC, and induced pluripotent stem cell derived-HLC, susceptible to killing by syngeneic and allogeneic NK cells.  Both embryonic stem cell derived-HLC, and induced pluripotent stem cell derived-HLC, are killed by NK cells at higher levels than adult hepatocytes. Finally, we demonstrate that the NK cell activation receptor, NKG2D, plays a key role in NK cell killing of embryonic stem cell derived-HLC, but not induced pluripotent stem cell-derived HLC.
Hepatocytes were isolated from FVB/NJ mice and C57Bl/6 mice using a modification of the Seglen’s perfusion technique.

overall_design: Undifferentiated embryonic stem cells ESC (n=4), Adult Hepatocytes (AD-Hep) (n = 3), mESC differentiated into hepatocyte like cells (n =3).

first: Olivia

last: Martinez

first: Trinidad

last: Cisneros


title: Genome-wide transcriptome analysis of Fusarium fujikuroi Δset2 and Δash1 mutants

city: Freising

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary:
We performed genome-wide transcriptome analyses of the Fusarium fujikuroi wild type (WT) in comparison to deletion mutants of the histone methyltransferase genes SET2 and ASH1
The results show that the two methyltransferases control large sets of genes involved in primary and secondary metabolism due to the modifications of the chromatin structure (methylation of histone 3 lysine 36)

overall_design: The WT and mutant strains were grown for 3 days in synthetic medium with low (6 mM glutamine) and high (60 mM glutamine) amounts of nitrogen. The RNA was isolated from two biological replicates each and used for microarray analysis.

last: Güldener

first: Martin

last: Münsterkötter

first: Slavica

last: Janevska

first: Bettina

last: Tudzynski


title: Transcriptome profiling of Drosophila motor neurons with age

status: Public on Nov 08 2017

city: Stony Brook

first: Jorge

last: Azpurua

state: New York

address: 100 Nicolls Rd

department: Anesthesiology

institute: Stony Brook University

summary: The purpose of this array was to investigate age-dependent changes the transcriptome of a highly homogenous cell population (Drosophila motor neurons) in order to help understand the contribution of changes in gene expression to age-dependent motor deficiencies. Drosophila motor neurons expressing GFP (via the UAS-Gal4 binary expression system) were isolated using flow cytometry from flies that were 7, 35 or 45 days old. The microarray design was highly redundant for calcium-binding and ion channel genes as we had apriori reasons to believe changes in these genes would be important. The ages were chosen because previous work had identified a major shift in neurotransmitter release between the ages of 35 and 45 days in Drosophila motor neurons. Although no significant changes were identified in that window, several genes showed elevated expression in old (35 day and 45 day) motor neurons compared to young (7 day) including matrix metalloproteinase 1 (dMMP1).

overall_design: For each age group, 5 or 6 biologically independent replicates were performed. Replicates were microarray hybridizations of transcripts from pools of approximately 10000 Drosophila motor neurons from 5 individual flies.

first: Benjamin

middle: A

last: Eaton


title: Development of gene expression signatures on immature B cell for bursal peptide BP9

status: Public on Nov 21 2017

city: Nanjing

first: Xiu

middle: Li

last: Feng

address: No.1, Weigang

institute: Nanjing Agricultural University

summary: To further elucidate the mechanism of BP9 on immature B cell on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BP9 treatment in a mouse derived immature B cell WEHI231cells culture system. WEHI231 cells were treated ex vivo, and robust normalization of the data identified 2602 differentially expressed probe sets exhibiting minimum 2.0-fold changes that distinguished between BP9 and control sample. Four pathways were significantly impacted by BP9 treatment, and gene Ontology annotations show changes in the expression of molecules involved in immune, T cell, and autophagy related biological processes. Expression of seven genes (Sos1, Ccl6, Atg14, Atg12, Ube2b, Pias3 and Ifnb1) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns.

overall_design: BP9 induced gene expression in WEHI231 cells were measured at 4 hours after exposure to doses of 0ug/ml and 0.01ug/ml.  Two independent experiments were performed using different cells for each experiment.

middle: L


title: SIRT6 is Essential for Adipocyte Differentiation through Regulating Mitotic Clonal Expansion

status: Public on Jan 16 2018

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Preadipocytes initiate differentiation into adipocytes through a cascade of events. Mitotic clonal expansion, as one of the earliest event, is essential for adipogenesis. However, the underlying mechanisms that regulate mitotic clonal expansion remain elusive. SIRT6 is a member of the evolutionarily conserved sirtuin family of NAD+ dependent protein deacetylases and plays roles in genomic stability, aging, glucose metabolism and inflammatory response. Here, we show that SIRT6 deficiency in preadipocytes blocked their adipogenesis. Analysis of gene expression during adipogenesis reveals that KIF5C, which belongs to kinesin family, is negatively regulated by SIRT6. Furthermore, we show that KIF5C is a negative factor for adipogenesis through interacting with CK2α’, a catalytic subunit of CK2. This interaction blocks CK2α’ nuclear translocation and CK2 kinase activity, and inhibits mitotic clonal expansion during adipogenesis. Thus, SIRT6 acts as an important factor of adipogenesis through inhibiting KIF5C expression and enhancing CK2 kinase activity.

overall_design: Identification of genes expressed in WT vs. SIRT6 inhibitation under three time point (T=0, 20 40) conditions with three replications per group.

first: Qiang

first: Xiaoling

last: Xu

first: Wenhui

last: Hao

first: Huiyan

last: Lu

first: Cuiying

last: Xiao

first: Weiping

first: Ruihong

last: Wang

first: Chu-Xia

last: Deng


title: Expression data from C57BL/6 wild type and MK2-deleted lipopolysaccharide (LPS)-activated murine splenic dendritic cells

status: Public on Nov 01 2017

city: Vienna

first: Klara

last: Soukup

address: Zimmermannplatz 10

department: Tumor Immunology

country: Austria

institute: St Anna Kinderkrebsforschung (Children's Cancer Research Institute)

summary:
Upon toll-like receptor (TLR) ligation, dendritic cells (DCs) undergo an activation process referred to as maturation. Over the course of maturation, global DC gene expression is severely altered, resulting in phenotypic changes including DC morphology, migration, immune stimulatory and inhibitory receptor expression, cytokine production, etc.
We performed microarray analysis to investigate changes in gene expression patterns between wild type and MK2-deleted murine splenic DCs over time (0 - 24 hours) following TLR stimulation by LPS.

overall_design: CD11c+ DCs were isolated from whole spleens of C57BL/6 WT and CD11cCre-MK2fl/fl mice via magnetic beads, and stimulated in vitro by LPS. Cells at time points 0, 4 hours and 24 hours post-stimulation were harvested and subjected to RNA extraction and hybridization on Affymetrix 2.0 ST arrays.

first: Alexander

last: Dohnal