title: Acute Crebbp knockout in postnatally induced Shh medulloblastoma [tumor]

first: Daniel

last: Merk

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 Shh medulloblastoma, acutely induced at postnatal stages of development.

overall_design: We performed RNA extraction and hybridization on Affymetrix microarrays for mouse tumors from induced at postnatal day 5 with either wild type Crebbp (Math1CreERT2SmoM2) or loss of Crebbp (Math1CreERT2CrebbpSmoM2).

first: Ulrich

last: Schüller


title: Transcriptional profiling of murine CD4+ T cells following treatment with the supercooling compound icilin

status: Public on Nov 03 2017

city: Calgary

first: Robin

middle: M.

last: Yates

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: The synthetic supercooling drug, icilin, and its primary receptor target, the cation channel transient receptor potential (TRP) melastatin-8 (TRPM8), have been described as potent negative regulators of inflammation in the colon. The aim of this study was to determine whether the anti-inflammatory action of icilin could potentially be used to treat autoimmune neuroinflammatory disorders, such as multiple sclerosis (MS). During experimental autoimmune encephalomyelitis (EAE)—a CD4+ T cell–driven murine model of MS—we found that both wild-type (WT) and TRPM8-deficient EAE mice were protected from disease progression during icilin treatment, as evidenced by delays in clinical onset and reductions in neuroinflammation. In vitro, icilin potently inhibited the proliferation of murine and human CD4+ T cells, with the peripheral expansion of autoantigen-restricted T cells similarly diminished by the administration of icilin in mice. Attenuation of both TRPM8-/- and TRP ankyrin-1-/- T cell proliferation by icilin was consistent with the WT phenotype, which suggests a mechanism that is independent of these channels. In addition, icilin treatment altered the expressional profile of activated CD4+ T cells to one that was indicative of restricted effector function and limited neuroinflammatory potential. These findings identify a potent anti-inflammatory role for icilin in lymphocyte-mediated neuroinflammation and highlight clear pleiotropic effects of the compound beyond classic TRP channel activation.

overall_design: Purified murine WT CD4+ T cells were treated with 100 µM icilin (n=3 from n=3 mice) or the vehicle DMSO (n=3 from the same n=3 mice) for 24 h. T cells were stimulated with 10 µg/mL anti-mouse CD3 and 10 µg/mL anti-mouse CD28 monoclonal antibodies for 24 h before addition of icilin or vehicle. Total RNA was extracted by using an RNeasy Mini Kit, and RNA quality and RNA integrity number was measured with Agilent RNA Nano Chips on a 2100 Bioanalyzer. A total of 0.25 µg of RNA with an RNA integrity number of ≥8 was used for each sample. RNA was labeled by using the GeneChip Whole Transcript Express Labeling Assay and hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) at 45°C for 16 h at the SACRI Microarray and Genomics Facility (University of Calgary) (n=6 total array samples). Arrays were stained and washed by using GeneChip Fluidics 450 per manufacturer protocols and scanned with a GeneChip Scanner 3000 7G System (Affymetrix). Probe cell intensity data files were generated and summarized with GeneChip Command Console Software, and Robust Multi-Array Average was used to log 2 transform and normalize data. Altered gene expression was analyzed by Significance Analysis of Microarrays software, with genes that were differentially expressed ≥1.5-fold with a false discovery rate of <0.1 deemed significant.

first: Benjamin

middle: W

last: Ewanchuk

middle: M


title: Microarray-based transcriptomic responses of zebrafish embryos exposed to 2 µM TDCIPP from  0.75 hpf to 2 and 6 hpf

status: Public on Nov 22 2017

city: Riverside

first: David

last: Volz

state: CA

address: 900 University Ave.

department: Environmental Sciences

country: USA

institute: University of California, Riverside

summary: Tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) is a high-production volume organophosphate flame retardant widely used within the United States. Within zebrafish, initiation of TDCIPP exposure at 0.75 h post-fertilization (hpf) results in genome-wide alterations in methylation during cleavage (2 hpf) as well as epiboly delay or arrest (at higher concentrations) during late-blastula and early-gastrula (4-6 hpf). To determine whether these TDCIPP-induced effects were associated with impacts on the transcriptome, embryos were exposed to vehicle (0.1% DMSO) or 2 μM TDCIPP from 0.75 hpf to 6 hpf, and total RNA was extracted from triplicate embryo pools per treatment and hybridized onto duplicate Affymetrix Zebrafish Gene 1.0 ST Arrays per RNA sample.  Based on transcriptome-wide profiling, TDCIPP resulted in a significant impact on biological pathways involved in dorsoventral patterning and bone morphogenetic protein (BMP) signaling. Consistent with pathway-level responses, TDCIPP exposure also resulted in strongly dorsalized embryos by 24 hpf – a phenotype that mimicked the effects of dorsomorphin, a potent and selective BMP inhibitor. Moreover, the majority of dorsalized embryos were preceded by epiboly arrest at 6 hpf. Our microarray data also revealed that the expression of sizzled (szl) – a gene encoding a secreted Frizzled-related protein that limits BMP signaling – was significantly decreased by nearly 4-fold at 6 hpf. Therefore, we used a splice-blocking morpholino to test the hypothesis that knockdown of szl phenocopies TDCIPP-induced delays in epiboly progression.  Interestingly, contrary to our hypothesis, injection of szl MOs did not affect epiboly progression but, similar to chordin (chd) morphants, resulted in mildly ventralized embryos by 24 hpf. Overall, our findings suggest that TDCIPP-induced epiboly delay may be independent of szl expression and function, and that TDCIPP-induced dorsalization may – similar to dorsomorphin – be due to interference with BMP signaling during early zebrafish.

overall_design: Zebrafish embryos were exposed to 0.1% DMSO or 2 µM TDCIPP from 0.75 hpf. Embryos (25 per replicate) were collected at either 2 or 6 hpf, transferred from beakers to 2-mL cryovials, snap-frozen in liquid nitrogen, and stored at -80ºC. These experiments resulted in three independent replicate samples for each time point and treatment group, resulting a total of 12 samples for RNA extractions.  Total RNA was extracted from pooled embryos using a SV Total RNA Isolation System (Promega). After elution of RNA in 100 μL nuclease-free water, total RNA concentrations, 260/280 ratios, and 260/230 ratios were quantified using a NanoDrop ND-2000 spectrophotometer (ThermoFisher Scientific) and then stored at -80°C; total RNA quality was also confirmed using an Agilent 2100 Bioanalyzer system.  Total RNA samples were amplified and biotinylated using GeneChip WT PLUS Reagent Kit (Affymetrix).  Briefly, 100 ng of total RNA per sample was reverse-transcribed into ds-cDNA using NNN random primers containing a T7 RNA polymerase promoter sequence; cDNA quality was then confirmed using an Agilent 2100 Bioanalyzer system. T7 RNA polymerase was then added to cDNA samples to amplify RNA, and then RNA was reverse-transcribed to ss-DNA and degraded using RNase H. ss-DNA molecules were then fragmented and terminally labelled with biotin. Amplified and labeled samples were hybridized onto duplicate Zebrafish Gene 1.0 ST Arrays (Affymetrix) for 16 h at 45°C using a GeneChip Hybridization Oven 640 and a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix); these arrays were constructed by Affymetrix based on the danRer6/Zv9 genome build and contained 1,255,682 probes representing 59,302 unique genes.  Hybridized arrays were washed and stained using GeneChip Fluidics Stations 450 (Affymetrix). Arrays (24 total) were then scanned using a GeneChip Scanner 3000 7G system and computer workstation equipped with GeneChip Command Console 4.0 software (Affymetrix).

first: Subham

last: Dasgupta

first: Sara

last: Vliet

first: Allison

last: Kupsco

first: Jessica

middle: K

last: Leet

first: Diego

last: Altomare

middle: C


title: Circulating Adipose-derived Exosomal miRNAs and metabolites associated with insulin signaling are altered by gastric bypass surgery

status: Public on Oct 15 2017

city: Washington

first: Robert

last: Freishtat

state: DC

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Affymetrix miRNA 4.0 array profiling of adipocyte-derived exosomes from pre and post bariatric subjects.
We used miRNA arrays to profile FABP4+ (adipocyte-derived) exosomes isolated from serum from pre and post bariatric subjects.

overall_design: We isolated FABP4+ (adipocyte-derived) exosomes from Human bariatric patient pre and post serum and profiled them to determine insulin signaling correlations.

first: Monica

last: Hubal

first: Sarah

last: Ferrante

first: Matt

last: Barberio

first: Evan

last: Nadler

middle: J

first: Samuel

last: Epstein


title: miRNA expression data before and after TGF-β treatment and Ago2-associated transcripts in lung fibroblasts

status: Public on Nov 01 2017

city: Groningen

first: Jennie

last: Ong

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

type:
Other
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Transcriptome analysis of the Bacillus subtilis ccpA topA(S478P) strain

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

summary:
In this study the isogenic Bacillus subtilis mutant strains ccpA topA+ and ccpA topA(S478P) were analyzed. The S478P suppressor mutation occurred when the ccpA mutant was grown on minimal medium supplemented with glucose and ammonium as single sources of carbon and nitrogen, respectively.
Under these conditions, the ccpA mutant is unable to produce enough glutamate for growth, since gltAB, encoding the glutamate synthase, is not expressed. In order to get an insight how the S478P mutation in the DNA topoisomerase I affects expression on a global level, the two strains were subjected to a microarray analysis. Bacteria were cultivated in minimal medium supplemented with glucose and glutamate. The microarray data show that the topA(S478P) mutation results in a global re-direction of the central carbon metabolism that includes glutamate biosynthesis.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Cells were grown under vigorous agitation at 37 °C in minimal medium supplemented with glucose and glutamate. Samples were taken at OD600 of 1.0.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

first: Hermann

last: Rath

first: Daniel

last: Reuss

first: Jörg

last: Stülke


title: Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor

status: Public on Oct 30 2017

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

country: India

institute: CDFD

type:
Expression profiling by array
Genome variation profiling by array


title: Transcriptome expression pattern of E11.5 PGCs, P2 GSCs, and CD49f+GSCs.

status: Public on Nov 09 2017

city: Taipei

first: Yung-Che

last: Kuo

address: 250 Wuxing

country: Taiwan

institute: Taipei Medical University

summary:
The cell identities of CD49f+GSCs were further identified by comparing them with the E11.5 PGCs and P2 GSCs. The transcriptomic analysis revealed that the CD49f+GSCs had 1/3 similar genes profile to the E11.5 PGCs and P2 GSCs.
Further gene ontology (GO) analysis demonstrated that the E11.5 PGCs, P2 GSCs, and CD49f+GSCs shared the partial similar gene expression profile of pluripotency regulation signaling pathway, PI3K-AKT signaling, chemokine signaling, and HIF-1 signaling.

overall_design: Isolation of the gonadal cells from 67 E11.5 ICR embryos, and testicular cells from 80 newborn to P2 ICR mice (0- to 2-day-old postpartum), followed by stem cell colony formation under 5% O2 hypoxia for 7 days, and subjected to transcriptome analysis. Meanwhile, CD49f+GSCs from 100 newborn to P2 ICR mice were purified and subjected to transcriptome analysis.

first: Yen-Hua

last: Huang


title: R-spondin 2 is required for optic vesicle morphogenesis and neuroretina specification in vivo and in vitro

status: Public on Nov 07 2017

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Using stem cell–based therapies to treat retinal abnormalities is becoming a likely possibility; therefore, identifying the key factors and the relevant mechanisms controlling optic vesicle morphogenesis and neuroretina (NR) differentiation is important. Recent advances in self-organizing, 3-dimensional (3D) tissue cultures of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provided a valuable in vitro model for characterizing regulatory cascades and signaling pathways controlling mammalian retinal development. Using Rx-GFP expressing ESCs and Six3–/– iPSCs we identified R-spondin 2 (Rspo2)-mediated repression of Wnt signaling as a novel required step during optic vesicle morphogenesis and NR differentiation. Furthermore, we also show that transient ectopic expression of Rspo2 in the anterior neural plate of transgenic mouse embryos was sufficient to arrest NR differentiation. ChIP assays identified Six3-responsive elements in the Rspo2-promoter region, indicating that Six3-mediated repression of Rspo2 is required to restrict Wnt signaling in the developing anterior neuroectoderm and allow eye development to proceed.

overall_design: We used microarrays to measure changes in gene expression profiles in mouse embryonic stem cells after retinal differentiation for 4 or 7 days. Mouse ES cells were derived from the mouse embryonic stem cell line EB5 (129/Ola)  in which GFP gene is knocked-in under Rx promoter (Eiraku and Sasai, Nat Protocols 7:69-79, 2012; RIKEN cell line AES0145).  Expression profiles were compared at day 4 and day 7 of retinal differentiation between WT Rx-GFP ESC.

first: Deepti

last: Abbey

first: Guillermo

last: Oliver


title: Gene changes in response to asbestos and carbon nanotube exposure in the pleural cavity, measured using microarrays.

status: Public on Nov 20 2017

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

country: United Kingdom

institute: MRC Toxicology Unit

summary: Exposure to asbestos fibres causes profound pathological changes in the pleural cavity and can result in the development of a fatal tumour, malignant mesothelioma (MM). Due to their structural similarities there is concern that carbon nanotubes (CNTs) may present a similar inhalation hazard. However the underlying mechanisms leading to fibre-mediated mesothelioma development are not yet fully understood. To investigate the molecular changes which occur at the mesothelium as a consequence of direct exposure to fibres, short and long asbestos fibres (SFA and LFA) and short and long CNTs (NTS and NTL) were instilled directly into the pleural cavity in mice. After 12 weeks RNA was extracted from the diaphragm and microarray analysis was performed on all of the treatment groups compared to a 0.5% BSA/saline control. Concurrent histopatholgical investigations were performed and revealed that exposure to fibres resulted in responses that were dependent upon the length of the fibres, but not on fibre type. In response to NTL and LFA there was acute inflammation and fibrosis on the parietal pleura; no inflammatory changes were detected histologically after exposure to SFA and NTS. Furthermore, changes in the mTOR signalling pathway were observed. Thus, this study served to illustrate which pathways are involved in the development of fibre-mediated toxicity, and demonstrated that pleural lesions induced by long asbestos fibres and long CNT exhibit a common pro-oncogenic molecular signature.

overall_design: Single channel microarrays were performed on n=4 samples. There was one control (0.5% BSA/saline) group and 4 treatment groups; SFA (short asbestos fibres), LFA (long asbestos fibres), NTS (short carbon nanotubes) and NTL (long carbon nanotubes).


title: Hdac3 regulation of myogenesis

status: Public on Oct 12 2017

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Progenitor cells require coordinated expression of lineage-specific programs, and the nuclear lamina has emerged as an important scaffold for organizing chromatin in many cell types. These transcriptome profiling experiments accompany a study focused on defining nuclear organization changes during cardiac development. This dataset defines gene expression changes induced by Hdac3 deletion during early stages of cardiogenesis, modeled using ESC differentiation assays.

overall_design: Hdac3 was deleted in an ESC line harboring a CMV-ERCre and in which Hdac3 is floxed. Upon tamoxifen addition, ER-Cre is translocated to the nucleus and Cre recombinase recombines out the DNA between the loxP sites. At day 5 of ESC differentiation, either tamoxifen or vehicle was added and samples were collected on day 8 (n=3 per condition).

first: Andrey

last: Poleshko

first: Mudit

last: Gupta

first: Parisha

middle: P

last: Shah

first: Apoorva

last: Babu

first: Lauren

last: Manderfield

first: Jamie

middle: L

last: Ifkovits

first: Damelys

last: Calderon

first: Haig

last: Aghajanian

first: Javier

middle: E

last: Sierra-Pagan

first: Zheng

last: Sun

first: Qiaohong

last: Wang

first: Li

last: Li

first: Nicole

last: Dubois

first: Edward

last: Morrisey

first: Mitchell

middle: A

last: Lazar

first: Cheryl

last: Smith

first: Jonathan

first: Rajan

last: Jain


title: SVG cells infected with Zika virus for 24, 48 and 72 hr post infection

status: Public on Oct 13 2017

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

institute: Public Health Agency of Canada

summary: Transcriptional profiling of human astrocyte cells (SVG) infected with Zika virus. Goal was to identify temporal changes in gene expression post infected by Zika virus.

overall_design: Triplicates were pooled and compared between infected and control cells at each time point. A total of 3 time points were investigated (24, 48 and 72 hours post infection). Dye swaps were performed for each condition.

first: Robert

last: Kozak

first: Anna

last: Majer

first: Mia

last: Biondi

first: Babu

middle: V

last: Sajesh

first: Jessy

last: Slota

first: Vanessa

last: Lobach

first: Alberto

last: Severini

first: Daniel

last: Beniac

first: Timothy

middle: F

last: Booth

first: Stephanie

first: Gary

last: Kobinger

first: Lee

last: Goneau

first: David

last: Safronetz

first: Shannon

last: Hiebert


title: CCCTC-binding factor is essential for the mouse hematopoietic stem cell maintenance and quiescence

status: Public on Oct 31 2017

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

summary:
Hematopoiesis is a series of lineage differentiation programs initiated from hematopoietic stem cells (HSCs) in the bone marrow (BM). To maintain lifelong hematopoiesis, the pool of HSCs is precisely maintained by diverse molecular mechanisms. CCCTC-binding factor (CTCF) is a DNA-binding zinc-finger protein which regulates its target gene expression by organizing higher order chromatin structures. Currently, the role for CTCF in controlling HSC homeostasis is unknown. By using a tamoxifen-induced CTCF conditional knockout mouse system, we demonstrate that CTCF is a critical regulator for the homeostatic maintenance of adult HSCs by retaining HSC cell cycle quiescence. Acute systemic CTCF ablation leads to a severe BM failure and rapid shrinkage of multiple c-Kithi progenitor populations, including Sca-1+ HSCs in adult mice. Similarly, a hematopoietic system-confined CTCF depletion elicits an acute loss of HSCs and highly increased mortality. Mixed BM chimeras reconstituted together with the supporting BM reveal that CTCF deficiency-mediated HSC depletion is a cell-autonomous effect. Although c-Kithi myeloid progenitors were severely reduced after ablating Ctcf gene, c-Kitint common lymphoid progenitors and their progenies were less affected by the lack of CTCF. Whole transcriptome analyses show that CTCF deficiency results in an enhanced expression of the cell cycle-promoting program and CTCF-depleted HSCs express higher level of reactive oxygen species (ROS). Importantly, in vivo treatment with the antioxidant partially rescued the c-Kithi population and their quiescence. We conclude that CTCF is a pivotal player in maintaining adult HSC pool likely through regulating ROS-dependent HSC quiescence.
We used gene expression microarray to elucidate CTCF-regulated gene profiles of the Lin−Sca-1+c-Kithi (LSKs) stem/progenitor populations.

overall_design: Total mRNAs were directly extracted from the FACS-sorted bone marrow LSKs from CreER and tamoxifen-inducible Ctcf conditional knockout mice. Isolated RNA was linearly amplified, labeled and hybridized on the Affymetrix Mouse GeneChip 2.0 ST Arrays.


title: RT quantitative PCR analysis of inflammasome related genes in mice choclea after noise exposure

city: Madrid

first: Sara

last: Pulido

address: Arturo Duperier, 4.

department: Department of Endocrine and Nervous Systems Pathophysiology

country: Spain

institute: Alberto Sols Biomedical Research Institute (Spanish National Research Council - Autonomous University of Madrid)

summary: Six month-old wild type and Igf1 heterozygous mice were exposed to a violet swept sine noise (frequency range 2–20 kHz) at 110 dB SPL for 30 minutes. Cochlear samples were taken at 2 and 24 hours post-noise exposure to study the evolution of the expression of  inflammation genes by using PCR arrays and RT-qPCR. Six month-old wild type and Igf1 heterozygous mice not exposed to noise were used as control.

overall_design: qPCR gene expression profiling. Cochlea samples from 3 animals per group were analised.  The expression of genes related to inflammation was studied at 2 and 24 hours post-noise exposure.

first: Marta

last: Milo


title: Cysteine protease exposure induces upper airway rhinosinusitis through IL-33 mediated effects on innate immune and epithelial barrier function

status: Public on Nov 15 2017

city: Stanford

first: Jayakar

middle: V.

last: Nayak

address: 801 Welch Road

department: Otolaryngology

institute: Stanford University School of Medicine

summary: A hallmark of type 2 inflammation in rhinosinusitis is the presence of eosinophilic infiltrates. In the lung, the cysteine protease papain causes robust type 2 inflammation due to innate mucosal immunity triggered by interleukin-33 release from the epithelial lining. As these effects are poorly understood for the sinonasal tissues, we investigated the epithelial and inflammatory findings induced by short-term papain instillation in the upper airway. C57BL/6 mice were intranasally exposed to papain and PBS as a model for protease-induced epithelial injury inflammation. We  assessed the upper airway for changes mRNA shifts by microarray.

overall_design: For microarray analysis we combined 4 samples into a single specimen that were instilled with papain and PBS, and analyzed using GeneChip Mouse Gene 2.0 ST Array (Affymetrix).

first: Tsuguhisa

last: Nakayama

first: Wei

last: Lee

last: V. Nayak


title: miRNA expression in mature natural killer cell subsets

city: Columbus

first: Michael

last: Caligiuri

state: OH

address: 460 W 10th Ave

institute: The Ohio State University

summary: The expression of 800 miRNAs in three human matura natural killer cell subsets was measured.

overall_design: miRNA expression was measured in primary human NK cells sorted for the following three phenotypes: CD56bright/CD94high, CD56dim/CD94high, CD56dim/CD94low.

first: Aaron

last: Victor

first: Steven

last: Scoville


title: aCGH from mouse gPAK testicular teratocarcinomas

status: Public on Nov 14 2017

city: ITHACA

first: Robert

last: Weiss

state: NY

address: T2006C Veterinary Research Tower

institute: Cornell University

type: Genome variation profiling by genome tiling array

summary:
Testicular germ cell tumors are among the most responsive solid cancers to conventional chemotherapy. To elucidate the underlying mechanisms, we developed a mouse testicular germ cell tumor model in which germ cell-specific oncogenic Kras activation and tumor suppressor Pten inactivation was driven by CRE-mediated recombination. The resulting mice rapidly developed malignant, metastatic testicular cancers composed of both teratoma and embryonal carcinoma, the latter of which exhibited stem cell characteristics, including expression of the pluripotency factor OCT4.
As part of our analysis of mouse gPAK testicular tumors, as well as comparison to benign 129-Dnd1Ter/Ter testicular teratomas, we used NimbleGen Mouse CGH 3x720k Whole-Genome Tiling Arrays to assess copy number variations in this novel genetically engineered mouse model of malignant, metastatic testicular cancer.

overall_design: DNA from six mouse gPAK testicular teratocarcinomas and six mouse 129-Dnd1Ter/Ter testicular teratomas was analyzed relative to DNA from normal mouse spleen.

first: Amy

last: Lyndaker

first: Claire

last: Anderson

middle: S


title: Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [GE]

first: Murali

last: Bashyam

summary: Transcriptional profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially expressed genes between them based on global gene expression.

overall_design: Two-condition experiment, Wnt- vs. Wnt+ rectal tumors. Wnt- tumors: 28, Wnt+ tumors: 23.

first: Raju

last: Kumar

middle: D


title: Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated genes in Arabidopsis

city: Ikoma

first: Nobuo

last: Ogita

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

summary: NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify genes whose expression is regulated by SOG1 in response to double strand breaks, wild-type (WT: Col-0 ecotype) and sog1-1 mutant plants were treated with or without zeocin for 2 h and were subjected to microarray analysis using Arabidopsis custom microarrays (GEO array platform: GPL19830). We found that 432 genes exhibited altered expressions in response to zeocin-induced double strand breaks in the SOG1-dependent manner. In addition, combining them with ChIP-Seq data, we identified 146 genes as SOG1-direct target genes.

overall_design: 2 week-old WT and sog1-1 mutant plants, grown in liquid MS medium under continuous light, were transferred to liquid MS medium with or without 15 µM zeocin and treated for 2 h. Two biological repeats of WT (mock), WT (zeocin-treated), sog1-1 (mock) and sog1-1 (zeocin-treated) whole plants were harvested and were subjected to microarray analysis.

first: Yoko

last: Okushima

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Naoki

last: Takahashi

first: Masaaki

last: Umeda


title: Expression data from kidney of Grhl1wt and Grhl1 ko mice.

status: Public on Oct 10 2017

city: Warsaw

first: Tomasz

last: Wilanowski

state: Mazowieckie

address: 3 Pasteur Street

department: Department of Cell Biology

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary:
The aim of our study was to investigate the functions of Grhl transcription factor in  the kidney.
We used microarrays to detect altered expression of genes knowed to be involved in susceptibility to hypertension and/or in the regulation of blood pressure.

overall_design: We used 8 Grhl1-/- and 7 Grhl1+/+ mice of age about 6 months.

first: Jelena

last: Pistolic

first: Vladimir

last: Benes


title: Expression data from liver samples of wild type and Pfn2-/- mice

status: Public on Oct 14 2017

city: Badalona

first: Mayka

last: Sanchez

address: Ctra Can Ruti, Cami de les Escoles s/n

institute: IMPPC

summary: Affymetrix microarrays were used to characterize the differential expression profile of liver samples from wild type and Pfn2-/- mice (reference Pilo Boyl et al., EMBO J, 2007).

overall_design: 6 liver samples were analyzed in total: 3 independent biological replicas from wild type and 3 from Pfn2-/- mice. All the microarray procedures were conducted at the Affymetrix Microarrays Platform (Josep Carreras Leukaemia Research Institute, Badalona, Spain) using standard Affymetrix protocols.

first: S

last: Luscieti

first: M

first: P

last: Pilo Boyl

first: W

last: Witke

last: Mallo

first: L

last: Nonell


title: MYCN induces neuroblastoma in primary neural crest cells

status: Public on Sep 25 2017

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Neuroblastoma (NBL) is an embryonal cancer of the sympathetic nervous system (SNS) that causes 15% of pediatric cancer deaths.  High-risk neuroblastoma is characterized by N-Myc amplification and segmental chromosomal gains and losses.  Due to limited disease models, the etiology of neuroblastoma is largely unknown, including both the cell of origin and the majority of oncogenic drivers.  We have established a novel system for studying neuroblastoma based on the transformation of neural crest cells (NCCs), the progenitor cells of the SNS, isolated from mouse embryonic day 9.5 trunk neural tube explants.  Based on pathology and gene expression analysis, we report the first successful transformation of wild-type NCCs into NBL by enforced expression of N-Myc to generate phenotypically and molecularly accurate tumors that closely model human MYCN-amplified NBL.  Using comparative genomic hybridization, we found that NCC-derived neuroblastoma tumors acquired copy number gains and losses that are syntenic to those observed in human MYCN-amplified neuroblastoma including 17q gain, 2p gain and loss of 1p36.  When p53-compromised NCCs were transformed with N-Myc we generated primitive neuroectodermal tumors with divergent differentiation including osteosarcoma.  These subcutaneous tumors were metastatic to regional lymph nodes, liver and lung.  Our novel experimental approach accurately models human neuroblastoma and establishes a new system with potential to study early stages of neuroblastoma oncogenesis, to functionally assess neuroblastoma oncogenic drivers, and to characterize neuroblastoma metastasis.

overall_design: 8 neural crest cell derived N-myc amplified p53 mixed neuroblastoma mouse tumors

first: Rachelle

middle: R

last: Olsen

first: Joel

middle: H

last: Otero

first: Jesus

last: Garcia-Lopez

first: Kirby

last: Wallace

first: Jerold

last: Rehg

first: Zhirong

last: Yin

first: Michael

last: Wang

first: Kevin

middle: W

last: Freeman


title: Expression data from wild type mice and REDD1 null mice following acute aerobic exercise

status: Public on Oct 05 2017

city: SAN DIEGO

first: Alexey

middle: M

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

summary:
Regulated in DNA Damage and Development 1 (REDD1) is a stress induced protein whose expression is highly induced in skeletal muscle following a single bout of aerobic exercise.  However, the role of this induction is unknown
We used microarrays to detail the change in gene signature within skeletal muscle following a single bout of aerobic exercise in wild type and REDD1 null mice

overall_design: Wild type and REDD1 knockout mice were randomized to remain sedentary or undergo a single bout of aerobic exercise.  One hour following the completion of the exercise protocol, the plantaris from sedentary and exercised mice was extracted and frozen.

first: Bradley

last: Gordon


title: Transcriptome profile in RAW264.7 cells in response to LPS stimulation

status: Public on Oct 01 2017

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

summary: The lincRNA-Tnfaip3 is an early-primary gene controlled by the NF-κB signaling in murine macrophages. This study aims to measure the impact of lincRNA-Tnfaip3 knockdown on the transcriptome profile in cultured 264.7 macrophages in response to LPS stimulation. Cells were treated with a specific siRNA to knockdown lincRNA-Tnfaip3 and then exposed to LPS for stimulation. Cells treated with a scrambled non-specific siRNA were used as the control. Total RNA was collected for the genome-wide analysis. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A).

overall_design: The RAW264.7 mouse macrophage cells were grown to 80% confluence for four groups: the siRNA control (Group A, cells treated with a non-specific scrambied siRNA control), the LPS-stimulated (Group B, cells treated with the siRNA control plus LPS stimulation), lincRNA-Tnfaip3 siRNA (Group C, cells treated with an siRNA to lincRNA-Tnfaip3), and lincRNA-Tnfaip3 siRNA/LPS stimulated (Group D, cells treated with the lincRNA-Tnfaip3 plus LPS stimulation). Cells were treated with the siRNAs for 24h, followed by additional culture for 4h in the presence or absence of LPS (E. coli LPS, 1 µg/ml). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: mRNA expression profiling after Ago2-immunoprecipitation (IP) in unstimulated and TGF-β1-stimulated primary parenchymal lung fibroblasts of two control subjects

city: Groningen

first: Jennie

last: Ong

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: To identify the target gene repertoire of miRNAs (i.e. the miRNA-targetome) of unstimulated and TGF-β1-stimulated primary parenchymal lung fibroblasts, Ago2-IP was performed followed by mRNA expression profiling.

overall_design: The Ago2-IP was performed on the unstimulated and TGF-β1-stimulated primary parenchymal lung fibroblasts of two control subjects. The RNA of the Total (T) fraction and the immunoprecipitated (IP) fraction were isolated using miRNeasy Mini Kit and miRNeasy Micro Kit, respectively. Subsequently, the RNA was labeled with Cyanine 3 (Cy3) and Cyanine 5 (Cy5) in a dye-swap experiment and cRNA was generated which was purified using the RNeasy Mini Kit. The labeled and amplified cRNA was then used to perform the mRNA expression profiling using the G3 Human Gene Expression 8x60K v3 Microarray.

first: Wim

last: Timens

first: Vijay

last: Rajendran

first: Arjan

last: Algra

first: Avrum

last: Spira

first: Marc

last: Lenburg

first: Joshua

last: Campbell

first: Maarten

last: van den Berge

first: Dirkje

last: Postma

first: Anke

last: van den Berg

first: Joost

last: Kluiver

first: Corry-Anke

last: Brandsma


title: Effects of Pre-freeze and Thaw Times on Gene Expression Profiles Using the PAXgene® Blood RNA System

status: Public on Sep 22 2017

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

summary: Using Normal Donor Blood, the effects of pre-freeze and thaw incubation time variables on the global gene expression signature and yield from RNA extracted using the PAXgene Blood RNA System

overall_design: Blood from healthy male volunteers (n=4) was collected into EDTA tubes or PAXgene collection tubes.  PAXgene tubes were mixed and then stored at room temperature for 0, 2, 5, or 17 hours before transfer to a -80C freezer, where they remained frozen until RNA extraction.  PAXgene tubes were then thawed for 2 or 17 hours prior to RNA extraction.  Yield and gene expression profiles were assayed for all samples and analyzed for gene expression changes and different yields relative to EDTA collection tubes.

first: Chetan

last: Deshpande

first: Abraham

last: Anderson

last: Fitzpatrick

first: Michael

last: Damore

first: Daniel


title: Identification of receptors involved in hemophagocytosis

status: Public on Sep 18 2017

city: kanazawa

first: Takamasa

last: Ishidome

state: Ishikawa

department: Medical sciences

institute: Kanazawa University

summary: To identify the mediators of phagocytosis of living cells upregulated by the triple stimuli, we examined the gene expression profiles of BMDMs(Bone-marrow derived macrophages) with microarray consisting of about 40,000 mouse genes

overall_design: Stimuli induced gene expression in BMDMs was measured 20hrs after addition of CpG, IFN-g+IL-10 receptor blocker(IL-10RB) or triple(CpG+IFN-g+IL-10RB)

first: Rikinar

last: i Hanayama


title: Gene expression profiles in nineteen Kawasaki Disease (KD) patients before and after intravenous immunoglobulin (IVIG) treatment

status: Public on Sep 19 2017

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: In this study, we compared global gene expressions between pre- and post- intravenous immunoglobulin (IVIG) administration in nineteen Kawasaki disease (KD) patients. Peripheral blood mononuclear cells (PBMCs) obtained from nineteen patients before and after IVIG treatment was extracted using a PAXgene blood RNA isolation kit. Amplified cRNAs of each patient were analyzed using with Agilent Whole Human Genome Microarray 4x44K G4112F array.

overall_design: Nineteen pair of dye-swapped experiments were performed.

first: Hiroshi

last: Nojima


title: Tumor suppression via inhibition of SWI/SNF complex-dependent NF-kappaB activation

city: Chiba

first: Kazuyoshi

last: Kobayashi

address: 1-8-1 Inohana, Chuo-ku

department: Medical Mycology Research Center (MMRC)

institute: Chiba University

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

overall_design: Refer to individual Series


title: Tumor suppression via inhibition of SWI/SNF complex-dependent NF-kappaB activation [HeLaS3 subset]

summary:
The transcription factor NF-kappaB is constitutively activated in many epithelial tumors but few NF-kappaB inhibitors are suitable for cancer therapy because of the broad biological effects of NF-κB. We previously reported that the d4 family (DPF1, DPF2, DPF3a/b) function as adaptor proteins linking NF-kappaB with the SWI/SNF complex. Here, we demonstrate that in epithelial tumor cell lines, exogenous expression of the highly conserved N-terminal 84-amino acid region of either DPF2 or DPF3a/b (designated “CT1”) has stronger inhibitory effects on anchorage-independent growth than single knockdown of any d4 protein, indicating that CT1 can function as an efficient dominant-negative mutant of the entire d4 family. By proximity ligation assays, CT1 was further shown to retain full function as an adaptor. Microarray analysis categorized NF-kappaB target genes by their CT1 sensitivity. Among CT1-sensitive genes, IL-6 was shown to strongly contribute to the anchorage-independent growth. Finally, exogenous CT1 expression efficiently suppressed tumor formation in a mouse xenograft model, suggesting that the d4 protein family could be a promising cancer therapy target.
TNF-alpha induced gene expression in HeLaS3 cells was measured at 0 and 1 hour after the treatment of TNF-alpha (10 ng/ml). Beforehand, the cells were transduced with either lentivirus vector expressing a dominant-negative mutant of d4-family protein (named CT1) or with empty vector (control).

overall_design: Kazuyoshi,Kobayashi

first: Hiroaki

last: Hiramatsu

first: Shinya

last: Nakamura

first: Kyousuke

first: Takeshi

last: Haraguchi

first: Hideo

last: Iba


title: Analysis of gene expression in human LHCN-M2 cells with siControl or siZNF 148

status: Public on Sep 15 2017

city: Memphis

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: An upregulation of muscle specific genes has been identified in siZNF148 treated cells.

overall_design: Gene expression of LHCN-M2 cells treated with siZNF148 or siControl in triplicate

first: Taosheng

last: Chen

first: Jesse

last: Bakke


title: Novel data integration approaches identify concordant and discordant immune responses between mice and humans [mouse]

status: Public on Sep 21 2017

city: Berlin

first: Teresa

last: Domaszewska

state: Berlin

address: Virchovweg 12

department: Immunology

institute: Max Planck Institute for Infection Biology

summary: We have conducted experiments to compare transcriptional response to tuberculosis (TB) in whole blood in two different TB murine models (susceptible 129S2 strain and resistant C57BL/6 strain) in time points day 1, day 7, day 14 and day 21 after infection.

overall_design: We collected whole blood samples from two TB murine models (129S2 and C57BL/6 mice), uninfected and at day 1, day 7, day 14 and day 21 p.i. , extracted RNA and performed microarray experiments. There were 5 infected mice of each strain in every time point after infection, 8 control 129S2 non-infected mice and 6 control C57BL/6 non-infected mice.

first: Lisa

last: Scheuermann

first: Anca

last: Dorhoi

first: Karin

last: Hahnke

first: Hans

last: Mollenkopf

first: January

last: Weiner


title: Gene expression profiles of 16 relapsed/refractory CLL patients treated with lenalidomide in a phase II clinical trial

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

summary:
The aim of the study is to identify differentially expressed genes between chronic lymphocytic leukemia (CLL) patients who will respond to lenalidomide treatment and non responsive patients. We performed a whole genome gene-expression analysis of pre-treatment samples collected from 16 CLL patients included in a phase II clinical trial. The pre-treatment sample comprises purified CD19 cells from peripheral blood. Ten (37%) patients achieved partial responses (PR) and were classified as responders (R), 2 (7%) stable diseases (SD) and 4 (15%) progressive diseases (PD) and were classified as non responders (NR).
Supervised analysis identified 78 genes up-regulated and 119 genes down-regulated in R compared with NR (Fold change [FC]≥2, p<0.01, Figure 4). Different expression levels of genes involved in interferon (INF) and Wnt signaling pathways characterized patients who will respond to lenalidomide. In particular, R showed a 23-fold increase in Wnt inhibitor Shisa homolog 3 (SHISA3), whereas a decrease of WISP3, CDH4, HOXB7 and WNT10A. Moreover, leukemic cells collected from R down-regulated interferon-induced proteins (IFI44, -6.6; IFI44L, -9.3; IFIT2, -2) and STAT1 (-2.4 fold change). NR group up-regulated lipoprotein lipase (LPL, +7.5). The baseline expression levels of cereblon (CRBN) were not dissimilar between R and NR subsets

overall_design: Large-scale gene expression profiling (GEP) was performed on total RNA extracted from purified CD19+ CLL cells (RNeasy Mini kit Plus, QIAGEN, Valencia, CA, USA)  from 16 individual CLL patients by hybridization on 4X44K Whole Human Genome Microarray (Agilent Technologies, Palo alto, CA). Fluorescence data were analysed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3. Agglomerative two-dimensional clustering analysis and supervised analyses based on t-test were performed using Gene Spring GX (Agilent) software. Genes were defined as differentially expressed between groups at a significant level of p<0.05 and with a fold change cut off ± 2 in all the pair wise comparisons.

first: Roberto

last: Marasca


title: Tumor suppression via inhibition of SWI/SNF complex-dependent NF-kappaB activation [A549 subset]

first: Kazuyoshi

summary: The transcription factor NF-kappaB is constitutively activated in many epithelial tumors but few NF-kappaB inhibitors are suitable for cancer therapy because of the broad biological effects of NF-κB. We previously reported that the d4 family (DPF1, DPF2, DPF3a/b) function as adaptor proteins linking NF-kappaB with the SWI/SNF complex. Here, we demonstrate that in epithelial tumor cell lines, exogenous expression of the highly conserved N-terminal 84-amino acid region of either DPF2 or DPF3a/b (designated “CT1”) has stronger inhibitory effects on anchorage-independent growth than single knockdown of any d4 protein, indicating that CT1 can function as an efficient dominant-negative mutant of the entire d4 family. By proximity ligation assays, CT1 was further shown to retain full function as an adaptor. Microarray analysis categorized NF-kappaB target genes by their CT1 sensitivity. Among CT1-sensitive genes, IL-6 was shown to strongly contribute to the anchorage-independent growth. Finally, exogenous CT1 expression efficiently suppressed tumor formation in a mouse xenograft model, suggesting that the d4 protein family could be a promising cancer therapy target.

overall_design: TNF-alpha induced gene expression in A549 cells was measured at 0 and 1 hour after the treatment of TNF-alpha (10 ng/ml). Beforehand, the cells were transduced with either lentivirus vector expressing a dominant-negative mutant of d4-family protein or with empty vector (control).


title: Expression data from Men1 knockout MEFs

status: Public on Aug 22 2017

city: philadelphia

first: Xianxin

last: Hua

address: 421 Curie BLVD

department: Department of Cancer Biology

institute: University of Pennsylvania Perelman School of Medicine

summary:
Multiple endocrine neoplasia type1 (MEN1), an inherited autosomal dominant syndrome characterized by the development of endocrine tumors including NETs, results from mutation in the MEN1 gene that encodes the protein menin. In mouse models, heterozygous loss of Men1 leads to multiple endocrine tumors with loss of heterozygocity at the Men1 locus. Men1 interacts with several partners to regulate cellular processes and gene expression through regulating histone modification.
We used microarrays to detail the global gene expression change in Men1 knockout MEFs and identified up-regulated genes during this process.

overall_design: Men1 knockout mouse embryonic fibroblasts complemented with vector or Men1 were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain downstream target genes regulated by menin.

first: Zijie

last: Feng


title: Gene expression changes in the respiratory epithelium of miR-34/449 knockout mice

status: Public on Sep 12 2017

city: Boston

first: Tobias

last: Otto

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary:
MicroRNA ablation prevents multiciliogenesis via cell cycle deregulation
MicroRNAs (miRNAs) have been implicated in various biological processes but have been most frequently described to inhibit proliferation and tumorigenesis. Here we describe an essential function of the miR-34/449 family during differentiation of multiciliated cells that is mediated by their well-described suppression of cell cycle progression. Constitutive deletion of all six members of this miRNA family triggers a derepression of multiple cell cycle-promoting proteins, thereby preventing epithelial cells from exiting the cell cycle and to maintain in a quiescent state. As a result, formation of motile multicilia is strongly inhibited in several tissues including the respiratory epithelium and the fallopian tube. Consequently, mice lacking miR-34/449 genes display infertility as well as severe chronic airway disease leading to postnatal death. These results show how miRNA-mediated repression of the cell cycle is required to allow multiciliogenesis to proceed during epithelial differentiation.

overall_design: We analyzed samples from the respiratory epithelium of the nose (NRE) of 5 wild-type (WT) and 5 miR-34/449 triple knockout (TKO) embryos (at E16.5), which were isolated using Laser Capture Microdissection (LCM).

first: Michaela

last: Bowden

first: Piotr

last: Sicinski


title: Investigation of the molecular mechanism of liver regeneration by the multi-omics approach

status: Public on Sep 07 2017

city: Sendai

first: Yoshihiro

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Biochemistry

institute: Tohoku University

summary: Liver regeneration has fascinated the field of regenerative medicine due to its outstanding capacity to undergo a substantial regeneration. The capacity to regenerate is likely to be encoded as a plasticity of molecular networks within the liver. While several reports have utilized massive molecular profiling approaches, a bird-like view of the molecular processes is still lacking. Here, by applying a combination of comprehensive analysis of epigenome, transcriptome and proteome, we depict the molecular landscape of liver regeneration. We demonstrate that histone H3K4 was tri-methylated at promoter regions of many loci, among which only a fraction including cell cycle related genes were transcriptionally up-regulated. Cistrome analysis guided by the histone methylation patterns and transcriptome identified FOXM1 as the key transcription factor to promote liver regeneration, which was confirmed using hepatocytes in vitro. Conditional protein degradation was also observed. These sets of informational resources will be useful to further investigate liver regeneration.

overall_design: We ligated the left branch of the portal vein of mice (PVBL), and collected the right robe as a regenerating liver at three days after surgery.We prepared the sham-operated mice as control mice. Sham operated liver was collected at three days after surgery.

first: Kazuhiko

last: Igarashi


title: Transcription profile of WT and LKB1 (encoded by the gene Stk11)-deficient Treg cells

status: Public on Aug 29 2017

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
LKB1 deficiency in Treg cells impairs their survival, metabolism and suppressive function. To exclude the impact of excessive inflammation on LKB1-deficient Treg cells, we generated mixed bone marrow (BM) chimeras using Foxp3-Cre WT and Foxp3-Cre Stk11 fl/fl BM cells, together with CD45.1+ BM cells.
We used microarray to compare the global transcription profile of dornor-derived LKB1-deficient Tregs with WT counterparts.

overall_design: In total 10 samples; 5 sampels WT Treg cells and 5 samples of LKB1-deficient Treg cells

first: Kai

last: Yang

first: Daniel

last: Bastardo Blanco

first: Sharad

last: Shrestha

first: Hongbo

last: Chi


title: Imbalance of mitochondrial respiratory chain complexes in the epidermis induces severe skin inflammation

status: Public on Aug 16 2017

city: Cologne

first: Olivier

middle: R.

last: Baris

state: NRW

address: Robert-Koch Str. 39

department: Center for Physiology and Pathophysiology

institute: University of Cologne

summary: Accumulation of mitochondrial DNA (mtDNA) deletions to detrimental levels in few cells and chronic inflammation are concomitant during aging in many tissues, thus raising the question of a causal link between both phenomena. To approach this, we generated mice which accumulate such deletions in the epidermis by expression of a mutant TWINKLE helicase in keratinocytes. These short-lived mice showed a severe depletion of mtDNA, as well as low amounts of large-scale deletions in the epidermis. These alterations led to an imbalanced stoichiometry of mitochondrial respiratory chain complexes, inducing a unique combination of cytokine expression in the epidermis. This caused a severe inflammatory phenotype, with massive immune cell infiltrates already before birth, resulting in serous scabs at the ventral skin region and limb joints. Altogether, these data suggest that severe respiratory chain dysfunction, as observed in a few cells in aged tissues, might be involved in the development of chronic inflammation.

overall_design: Epidermal RNA was isolated from newborn mice expressing a mutant form of the mitochondrial helicase Twinkle (K320E-TwinkleEpi) under the control of the K14 promotor.  RNA isolated from the epidermis of  R26-K320E-TwinkleloxP/+ newborns was used as control. RNA was extracted and the expression profile between  the genotypes was compared.

first: Rudolf

middle: J

last: Wiesner


title: Inhibition of GGPPS1 attenuated LPS-induced acute lung injury by suppressing the NLRP3 inflammasome

status: Public on Aug 15 2017

city: Nanjing

first: wujian

last: xu

state: Jiangshu

address: 305 Esat Zhongshan Road

department: The department of respiratory disease

country: China

institute: Jinling Hospital

summary:
Rationale: Geranylgeranyl pyrophosphate synthase large subunit 1 (GGPPS1), a catalase downstream of the mevalonate pathway, regulates various pathological processes through balancing the production of farnesyl pyrophosphate and geranylgeranyl pyrophosphate. We sought to investigate whether GGPPS1 plays a role in mediating acute lung injury (ALI) using a mouse model of inflammation.
Methods: Lipopolysaccharide (LPS) was intra-tracheally instilled to induce ALI in lung specific GGPPS1 knockout and wild-type mice. Expression of GGPPS1 in lung tissues and alveolar epithelial cells (AECs) was examined at different time points. Alveolar exudate, neutrophil infiltration, lung injury and cell death were determined. Change in global gene expression in response to GGPPS1 depletion was measured using mRNA microarray and verified in vivo and in vitro.
Results: GGPPS1 levels increased significantly in lung tissues from LPS-induced ALI mice, where it showed a time- and dose-dependent increase in alveolar epithelial cells. Specific deletion of pulmonary GGPPS1 reduced the alveolar exudate and attenuated the severity of lung injury through inhibiting apoptosis of AECs. However, GGPPS1 deletion had limited effect on neutrophil counts and TNF-α levels in alveolar fluids. Deletion of GGPPS1 inhibited LPS-induced inflammasome activation, in terms of IL-1β release and pyroptosis, by down-regulating NLRP3 expression.
Conclusions: Inhibition of pulmonary GGPPS1 attenuated LPS-induced ALI, predominantly by suppressing NLRP3 inflammasome activation.

overall_design: A total of 8 samples from mice treated with LPS in lung specific GGPPS1 knockout and wild-type mice (n=4 for each group)

first: Wujian

last: Xu

first: Yong

last: Song


title: Licensing Delineates Helper and Effector NK Cell Subsets During Viral Infection

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Natural killer (NK) cells can be divided into phenotypic subsets based on the expression of receptors that bind self-MHC-I molecules with differing affinities; a concept termed licensing or education. Here we show that NK cell subsets exhibit markedly different migratory, effector, and immunoregulatory functions on dendritic cells and antigen-specific CD8+ T cell responses during influenza and murine cytomegalovirus infections. Shortly after infection, unlicensed NK cells preferentially trafficked to draining lymph nodes and produced GM-CSF, which promoted the expansion and activation of dendritic cells, and ultimately resulted in sustained antigen-specific CD8+ T cell responses. In contrast, licensed NK cells preferentially migrated to infected parenchymal tissues and produced greater levels of interferon-γ (IFN-γ). Importantly, human NK cell subsets exhibited similar phenotypic characteristics and patterns of cytokine production. Collectively, our studies demonstrate a critical demarcation between the functions of licensed and unlicensed NK cell subsets, with the former functioning as the classical effector subset in inflamed tissues and the latter as modulators of adaptive immunity helping to prime immune responses in draining lymph nodes.

overall_design: Gene expression profiling of isolated pools of unlicensed (Ly49-negative, Ly49G2/A+) and licensed (Ly49C/I+) NK cells was performed in order to confirm the unique phenotypic and functional characteristics of these subsets. For this, unlicensed (CD3-CD122+Ly49G2+Ly49A+Ly49C/I- and CD3-CD122+Ly49G2 A Ly49C/I-; referred to as Ly49G2/A+ and Ly49-negative, respectively) and licensed (CD3-CD122+Ly49G2-A-Ly49C/I+; referred to as Ly49C/I+) NK cells were isolated by fluorescence-activated cell sorting of splenocytes from 30 naïve C57BL/6 mice. Total cellular RNA was isolated and then microarray gene expression profiling performed with Affymetrix GeneChip Mouse Gene 2.0 Sense Target (ST) Arrays.

first: Anthony

last: Zamora

first: William

last: Murphy


title: A history of obesity leaves an inflammatory fingerprint in liver and adipose tissue [Liver]

status: Public on Sep 05 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Dieting is a popular yet often ineffective way to lower body weight, as the majority of people regain most of their pre-dieting weights in a relatively short time. The underlying molecular mechanisms driving weight regain and the increased risk for metabolic disease are still incompletely understood. Here we investigate the molecular alterations inherited from a history of obesity. In our model, male HFD fed obese C57BL/6J mice, were switched to a low caloric chow diet, resulting in a decline of body weight to that of lean mice. Within seven weeks after diet switch, most obesity associated phenotypes, such as body mass, glucose intolerance and blood metabolite levels were reversed. However, hepatic inflammation, hepatic steatosis as well as hypertrophy and inflammation of perigonadal, but not subcutaneous, adipocytes persisted in formerly obese mice. Transcriptional profiling of liver and perigonadal fat revealed an upregulation of pathways associated with immune function and cellularity. Thus, we show that weight reduction leaves signs of inflammation in liver and perigonadal fat, indicating that persisting proinflammatory signals in liver and adipose tissue could contribute to an increased risk of formerly obese subjects to develop the metabolic syndrome upon recurring weight gain.

overall_design: We performed gene expression microarray analysis of liver and gonadal fat from from formerly obese mice, lean mice and other mice

first: Ingrid

last: Fischer

first: Martin

last: Irmler

first: Carola

last: Meyer

first: Frauke

last: Neff

first: Matthias

last: Tschöp

first: Susanna

last: Hofmann

first: Siegfried

last: Ussar


title: A history of obesity leaves an inflammatory fingerprint in liver and adipose tissue


title: A history of obesity leaves an inflammatory fingerprint in liver and adipose tissue [gWAT]


title: Transcriptional profiling of the maturation of human in vivo-generated plasma cells

city: Cádiz

first: Antonio

last: Campos-Caro

state: Cádiz

address: Avda. Ana de Viya, 21

department: Unidad Investigación

institute: Hospital Universitario Puerta del Mar

summary: In vivo antigen (Ag)-induced differentiation of B lymphocytes into plasma cells (PCs) takes place in extra-follicular foci and germinal centers of the secondary lymphoid organs (SLOs). Most of these SLO PCs are short-living and only relatively few PCs, characterized by secreting high-affinity antibodies (Ab), travel through the circulation and finally home in specialized survival niches of the bone marrow (BM) and, at a lesser extent, in the SLOs, where they become long-living Ab-secreting PCs. Initially, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between human circulating Ag-induced PCs in comparison with tonsil and BM PCs distinctively regulate genes involved in cell proliferation. Now, moreover, to characterize further the B-cell transition into PC, transcriptomes from human naïve B lymphocytes were also included in the analysis, and genes showing significant changes in the comparison between B lymphocytes and every of the three PC subsets were selected as the PC signature.

overall_design: Gene expressions in human B-lymphocyte cells isolated from peripheral blood (3 samples) were measured. Each sample was isolated from a different donor.

first: Luis

last: Valor

first: Ana

last: Ramos-Amaya

first: Beatriz

last: Rodríguez-Bayona

first: José

last: Brieva


title: Expression data from young HSCs with or without Pot1a overexpression

city: Fukuoka

first: Kentaro

last: Hosokawa

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Stem Cell Biology and Medicine

institute: Graduate School of Medical Sciences, Kyushu University

summary:
Appropriate regulation of hematopoietic stem cell (HSC) self-renewal is critical for the maintenance of life long hematopoiesis. However, long-term repeated cell divisions induce the accumulation of DNA damage, especially at telomere, significantly compromises HSC function. Therefore, shelterin elements Pot1a is required to prevent DNA damage response at telomeres in order to maintain their function.
We used microarrays to detail the global gene expression underlying Pot1a function in Pot1a transduced HSCs during culture and identified distinct molecular signature in this process.

overall_design: 10wks-old mice LT-HSCs were sorted and cultured for 1 day. Mock control (control) and full length WT-Pot1a (Pot1a) genes were transduced into cells by using retro viral vectors. After 3 days culture, GFP+ LT-HSCs were sorted for RNA extraction and hybridization on Affymetrix microarrays.

first: Ben

last: MacArthur

first: Yoshiko

last: Ikushima

first: Hirofumi

last: Toyama

first: Yoshikazu

last: Masuhiro

first: Shigemasa

last: Hanazawa

first: Toshio

last: Suda

first: Fumio

last: Arai


title: expression changes by establishing metastasis

status: Public on Aug 31 2017

city: Tokyo

first: Mariko

last: Honda

address: 3-19-18, Nishishimbashi, Minato-ku

department: urology department

institute: The Jikei University School of Medicine

summary: Labeled PC3 were injected into male mice. 5-7 weeks later, cancer cells of metastasis site were extracted from bone marrow was compared with injected cell in vitro culture by microarray and pathway analysis.

overall_design: mRNA expression of PC3 prostate cancer cells extracted from bone marrow was compared with injected cell in vitro culture

first: Kiyotsugu

last: Yoshida


title: mRNA profiling after Inhibition of the lncRNA Ntep

status: Public on Aug 08 2017

city: Hannover

first: Julia

last: Beermann

address: Carl-Neuberg-Straße 1

department: IMTTS

institute: Hannover Medical School (MHH)

summary:
To investigate the effect of inhibition of Ntep on 3T3 cells, we treated cells for 48h with GapmeR control or Gapmer against Ntep
Afterwards total RNA was isolated and used for microarray profiling.

overall_design: Inhibition of Ntep in 3T3 for 48h

first: Oliver

last: Dittrich-Breiholz


title: Gene expression in lacrimal gland

status: Public on Aug 13 2017

first: Masatoshi

last: Hirayama

address: 35 Shinanomachi, Shinjuku

institute: Keio University

summary: To analyze the gene expression of mouse embryonic lacrimal gland and its developmental related organs such as harderian gland and eye lid. We performed microarray using them.

overall_design: To analyze the gene expression patterns of  lacrimal gland epithelium (LGE), we used mouse whole 7w LG and 7w harderian gland (HG), and separated epithelial and mesenchymal tissues from the lacrimal glands, harderian glands and eye lid (Lid), including ocular conjunctiva of embryonic day 16.5 (E16.5) of mouse embryos.

first: Tetsuya

last: Kawakita


title: Gene expression profiling in CD4+CD25+CCR4+ T-cells isolated from HAM/TSP, ATLL and healthy donor

city: Kawasaki

first: Yoshihisa

last: Yamano

address: 2-16-1 Sugao, Miyamae-ku

institute: St. Marianna University School of Medicine

summary: Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus that is the causative agent of adult T cell leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1-infected T cells have been hypothesized to contribute to the development of these disorders, although the precise mechanisms are not well understood. Recently, we and others have proposed that HTLV-1 preferentially infects CD4+CD25+CCR4+ T-cells. In this study, we used microarrays to examine the gene expression profiles of CD4+CD25+CCR4+ T-cells isolated from a HAM/TSP patient, an ATLL patient and a healthy donor to identify gene signatures that may be characteristic for these particular diseases.

overall_design: We performed microarray gene expression profiling of immune cells selected on the marker of HTLV-1 infection, CD4, CD25 and CCR4 from a HAM/TSP patient, an ATLL patient and a healthy donor. Total RNA samples from CD4+CVD25+CCR4+ T-cells were subjected to Cy-3 labeling followed by human whole genome gene expression microarray analyses.


title: Expression data from Aged HSCs cultured with or without MTM-Pot1a

summary:
Appropriate regulation of hematopoietic stem cell (HSC) self-renewal is critical for the maintenance of life long hematopoiesis. However, long-term repeated cell divisions induce the accumulation of DNA damage, especially at telomere, significantly compromises HSC function. Therefore, shelterin elements Pot1a is required to prevent DNA damage response at telomeres in order to maintain their function.
We used microarrays to detail the global gene expression underlying MTM-Pot1a function in aged HSCs during culture and identified distinct molecular signature during this process.

overall_design: 10wks-old and 60wks-old LT-HSCs were sorted after 3days culture with control-MTM (control), MTM-Pot1a (M-Pot1a) or MTM-dOB-Pot1a (dOB-Pot1a) for RNA extraction and hybridization on Affymetrix microarrays.


title: Microglia contribute to normal myelinogenesis and oligodendrocyte homeostasis during adulthood

status: Public on Jul 19 2017

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Whereas microglia involvement in virtually all brain diseases is well accepted their role for the control of homeostasis in the central nervous system (CNS) is mainly thought to maintain neuronal function through the formation, refinement and monitoring of synapses in both the developing and adult brain. Although the prenatal origin and the neuron-centered function of cortical microglia has recently been elucidated much less is known about a distinct amoeboid microglia population formerly described as “fountain of microglia” that appear only postnatally in the myelinating regions such as corpus callosum and cerebellum. Using large-scale transcriptional profiling, fate-mapping and genetic targeting approaches we identified a unique molecular signature of this microglia subset that arose from a CNS endogenous microglia pool independent from circulating myeloid cells. Microglia depletion experiments unexpectedly revealed an essential role of postnatal microglia for the proper development and homeostasis of oligodendrocytes. Our data provide new cellular and molecular insights into the myelin-supporting function of microglia in the normal CNS.

overall_design: We collected microglia samples from P7 or adult brain from the cortex or corpus callosum using FACS based cell sorting. RNA of these samples was used for Affymetrix Microarray Analyses. 3 samples per group were analyzed; all samples are from healthy mice.

first: Nora

last: Hagemeyer

first: Klara-Maria

last: Hanft

first: Maria-Anna

last: Akritidou

first: Leda

last: Dimou

first: Marco

last: Prinz


title: Differential innate immune signaling in macrophages by wild type vaccinia virus and mutant virus deleting A26 protein

status: Public on Jul 09 2017

city: Taipei

first: Wen

last: Chang

address: 128 Sec 2 Academia Rd, Nankang

institute: Institute of Molecular Biology, Academia Sinica

summary: We infected bone marrow derived macrophages (BMDM) with wild type vaccinia virus Western Reserve (WT-WR) and mutant virus deleting A26 protein (WRΔA26) and analyzed transcriptional profiling of cellular genes at 1, 2, 4 and 8 hours post-infection times (p.i.).

overall_design: Two-condition experiment, WT-WR VS WRΔA26 infected BMDM cells at 4 time points. Biological replicates: 3 infection replicates.

first: Siti

last: Khadijah


title: Pig testis extract augments the expression and secretion of adiponectin in 3T3-L1 adipocytes

status: Public on Jun 30 2017

city: Tsukuba

first: Keishi

last: Kadooka

address: 3-3 Midorigahara

department: R&D center

institute: NH Foods Ltd.

summary: Adiponectin is known as a key molecule to ameliorate symptoms of the type 2 diabetes mellitus and disorder of lipid metabolism. In this study, we investigated whether hot water extracts of some livestock by-products induced expression of adiponectin using 3T3-L1 adipocytes. Out of 11 extracts tested, pig testis extracts (PT) enhanced adiponectin mRNA expression and secretion of adiponectin protein from 3T3-L1 cells. Furthermore, simultaneous treatment with PT and daidzein, soy phytoestrogen, enhanced synergistically adiponectin secretion. Moreover, pretreatment with an estrogen receptor β (ERβ) antagonist (PHTPP) diminished adiponectin secretion in daidzein treated cell, but not in PT treated cells. Transcriptome analyses revealed that daidzein and PT commonly regulated PPAR signaling pathway, although gene expression was differently regulated in PT-treated cells and daidzein-treated cells. The expression of 476 and 380 genes significantly up-regulated in daidzein and PT treatment, although commonly regulated genes were only 86 genes. These results suggested that PT may ameliorate lipid metabolic dysfunction via promote adipocytes differentiation and enhance adiponectin secretion through different mechanism from daidzein.

overall_design: 3T3-L1 cells were induced into differentiated adipocytes and then treated with daidzein (25μM), PT (100μg/ml), daidzein+PT or PBS for 7 days.

first: Mikako

last: Sato

first: Takashi

last: Matsumoto

first: Satoru

last: Kuhara

first: Yoshinori

last: Katakura

first: Tatsuya

last: Fujimura


title: Induction of alternative proinflammatory cytokines accounts for sustained psoriasiform skin inflammation in IL-17C+IL-6KO mice [array]

status: Public on Aug 01 2017

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: IL-6 inhibition has been unsuccessful in treating psoriasis, despite high levels of tissue and serum IL-6 in patients. Additionally, de novo psoriasis onset has been reported following IL-6 blockade in rheumatoid arthritis patients. To explore mechanisms underlying these clinical observations, we backcrossed an established psoriasiform mouse model (IL-17C+ mice) with IL-6 deficient mice (IL-17C+KO) and examined the cutaneous phenotype.  IL-17C+KO mice initially exhibited decreased skin inflammation, however this decrease was transient and reversed rapidly, concomitant with increases in skin Tnf, Il36α/β/γ, Il24, epigen and S100a8/a9 to levels higher than those found in IL-17C+ mice. Comparison of IL-17C+ and IL-17C+KO mouse skin transcriptomes with that of human psoriasis skin, revealed significant correlation among transcripts of psoriasis patient skin and IL-17C+KO mouse skin, and confirmed an exacerbation of the inflammatory signature in IL-17C+KO mice that aligns closely with human psoriasis. Transcriptional analyses of IL-17C+ and IL-17C+KO primary keratinocytes confirmed increased expression of proinflammatory molecules, suggesting that in the absence of IL-6, keratinocytes increase production of numerous additional proinflammatory cytokines. These preclinical findings may provide insight into why arthritis patients being treated with IL-6 inhibitors develop new onset psoriasis and why IL-6 blockade for the treatment of psoriasis has not been clinically effective.

overall_design: 12 groups in total; with pooled samples equaling 58 mice in total; two time points, uninvolved and involved dorsal skin from male and female C57Bl/6 (WT), IL-6KO, IL-17C+, IL-17C+KO pooled as indicated

first: Nicole

last: Ward

first: Philip

last: Klenotic

first: Sarah

middle: G

last: Groft

first: Thomas

last: McCormick

first: Patrick

last: Leahy


title: Analysis of DC vaccines used for phase II clinical trial in prostate carcinoma patients

status: Public on Jul 10 2017

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

summary: Dendritic cell (DC)-based cancer vaccines are a promising immunotherapy against cancer. However, despite the vast number of clinical trials conducted so far, factors and manufacturing procedures essential for these therapeutics to induce effective anti-tumor immune responses have yet to be fully characterized. Here, we performed an extensive characterization of DCs used to vaccinate 18 prostate carcinoma patients enrolled in a pilot trial of TCR gamma alternate reading frame protein (TARP) peptide vaccination (NCT00908258) and looked for correlates with clinical and immunological responses. DCs showing lower expression of tolerogenic gene signature induced strong antigen-specific immune response and slowing in Prostate Specific Antigen (PSA) velocity, a surrogate for clinical response. These DCs were also characterized by lower surface expression of CD14, secretion of IL-10 and MCP-1; and greater secretion of MDC. When combined, these four factors were able to remarkably discriminate DCs that were sufficiently potent to induce strong immunological response. In summary, we identified DC factors essential for the activation of immune responses associated with TARP vaccination in prostate cancer patients. This study highlights the importance of in-depth characterization of DC vaccines – and other cellular therapies, to understand the critical factors that hinder potency and potential efficacy in patients.

overall_design: This study includes 93 DC vaccines that were administered to 18 prostate carcinoma patients. Each patient received multiple lots of autologous DC freshly manufactured from cryopreserved aliquots of elutriated monocytes. Vaccination regimen included 5 vaccinations (one every 3 weeks) with boost vaccinations in case of response. At least 2 vaccine per patient are included. Technical replicates were included for quality control

first: Marianna

last: Sabatino

first: Jiaqiang

last: Ren

first: Masaki

last: Terabe

first: Hanh

last: Khuu

first: Lauren

last: Wood

first: Jay

last: Berzofsky

first: David

last: Stroncek


title: Transcriptome-wide comparison of the impact of Atoh1 and miR-183 family on pluripotent stem cells and multipotent otic progenitors

status: Public on Jul 01 2017

city: Downers Grove

first: Michael

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

summary:
Hair cells (HCs) are the mechanoreceptors responsible for hearing and balance in the inner ear. Multiple factors cause HC loss including aging, noise exposure and genetic predisposition. A barrier to hearing restoration after HC loss is the inability of mammalian auditory HCs to spontaneously regenerate. Multiple factors are shown to be crucial for HC development and represent good candidates for regenerative studies. Atoh1 is widely accepted to be necessary and contextually sufficient for driving HC fate. Furthermore, the miRNA-183 family is known to be expressed at the time of HC differentiation, and mutations in miR-96 (one member of the family) can cause deafness both in mouse and human.
Our goal is to identify and compare the impact of Atoh1/miR-183 family alone and in combination on the transcriptome of two different developmental cell models; mouse embryonic stem cells (mESCs) and immortalized multipotent otic progenitors (iMOPs)

overall_design: mESCs & iMOPs were transfected with plasmid vectors carrying RFP alone (pT), Atoh1+RFP (pAT), miR-183 family+RFP (p183T) or Atoh1+miR-183 family+RFP (p183AT) for 48 hours, then RFP-positive cells were sorted using fluorescence activated cell sorting. Gene expression profiling was assessed using Affymetrix Mouse Gene ST Arrays and trancriptome analysis comparing each tranfection condition to the control pT condition was conducted. Three distinct biological samples per condition were included. Unmanipulated (untransfected control; UT) was also included.

first: Garrett

last: Soukup


title: Critical roles of mTORC1 and mTORC2 kinase signaling and glucose metabolism in follicular helper T cell differentiation

status: Public on Aug 04 2017

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

institute: St Jude Childrens Research Hospital

summary: AbstractFollicular helper T (Tfh) cells are crucial for germinal center (GC) formation and humoral adaptive immunity. Mechanisms underlying Tfh cell differentiation in peripheral and mucosal lymphoid organs are incompletely understood. We report here that mTOR kinase complexes 1 and 2 (mTORC1 and mTORC2) are essential for Tfh cell differentiation and GC reaction under steady state and after antigen immunization and viral infection. Loss of mTORC1 and mTORC2 in T cells exerted distinct effects on Tfh cell signature gene expression, whereas increased mTOR activity promoted Tfh responses. Deficiency of mTORC2 impaired CD4+ T cell accumulation and IgA production, and aberrantly induced Foxo1 transcription factor. Mechanistically, the costimulatory molecule ICOS activated mTORC1 and mTORC2 to drive glycolysis and lipogenesis, and Glut1-mediated glucose metabolism promoted Tfh cell responses. Altogether, mTOR acts as a central node in Tfh cells to link immune signals to glucose metabolism and transcriptional activity.

overall_design: We used micorarrays to compare the global transcription profile in CD4+CD25-CD44+CD62L- T cells from Peyer's patch of  WT, Raptor-/- (Cd4cre x Raptorfl/fl mice), or Rictor-/- (Cd4cre x Rictorfl/fl mice) mice.

first: Hu

last: Zeng

first: Hongbo

last: Chi


title: Astrocytoma cell lines transduced to either express GFAP isoforms or to knockdown GFAP isoforms

status: Public on Jul 03 2017

city: Utrecht

first: Elly

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

institute: University Medical Center Utrecht

summary:
Modulation of the GFAP cytoskeleton in astrocytoma cells alters processes involved in extracellular matrix remodelling and cell-cell signalling – a transcriptome analysis
Astrocytomas grade IV are malignant brain tumours with no effective treatment and a five year survival rate of only 5%. Expression of Glial Fibrillary Acidic Protein (GFAP) is lower in high astrocytoma grade, but the expression of the splice isoform GFAPδ is similar in low and high-grade astrocytomas. Thus the ratio of GFAPδ/α is increased in high-grade astrocytomas. We studied transcriptome changes in astrocytoma cell lines resulting from an induced alteration of GFAP isoform expression. GFAPα or GFAPδ were increased or decreased by recombinant expression or shRNA mediated knockdown of GFAPpan or GFAPα. We find that the most prominent effects are induced by the modulations where the GFAPδ/GFAPα ratio is increased. Gene ontology analysis revealed that the main effects of GFAP modulation take place in the extracellular matrix remodelling and cellular signalling clusters, with possible implications in astrocytoma invasive behaviour and angiogenesis.

overall_design: 2 cell lines (U251 and U373) with respectively recombinant expression or knockdown of GFAP isoforms. Biological replicates: U251 control - N=8, U251 recombinant GFAPa - N=8, U251 Recombinant GFAPdelta - N=8, U373 shRNA Non Targeting Control - N=6, U373 shRNA GFAPalpha - N=5, U373 shRNA GFAPpan - N=5

first: Oscar

last: Stassen

first: Martina

last: Moeton

first: Regina

last: Kanski

first: Willem

last: Kamphuis


title: Transcriptomic comparison of mouse Epithelial Trachea Cells

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: We isolated mouse epithelial trachea cells from FVB mice in order to identify their transcriptomic signature.

overall_design: Samples from mouse trachea epithelial cells were analyzed using Genespring 12.5 GX to obtain the  data.

first: Nikolaos

middle: I

last: Kanellakis


title: Opposite roles for astrocytes in developmental myelination and early myelin repair

city: Cleveland

first: Robert

last: Miller

state: OH

address: 10900 Euclid Avenue

department: Neurosciences

institute: Case Western Reserve University

summary:
Understanding the regulation of oligodendrocyte development and myelination in the central nervous system (CNS) is essential, not only to facilitate myelin repair but also to define the role of oligodendrocytes in maintaining axonal integrity. In vitro studies have implicated astrocytes in influencing multiple aspects of oligodendrocytes and their precursors, however the in vivo role of astrocytes in myelination and myelin repair remain poorly defined. We show that astrocyte ablation during postnatal spinal cord development resulted in a concomitant delay in myelination, demonstrating a critical role for astrocytes in promoting developmental myelination. By contrast, in the adult CNS, localized ablation of astrocytes 2 days after a demyelinating insult resulted in increased numbers of oligodendrocytes and accelerated remyelination in both the spinal cord and the corpus callosum. Microarray analysis reveals astrocytic NF-kB signaling pathway as a major contributor to pathological events occurring after demyelination. We suggest that the localized functions of astrocytes are fundamentally different during developmental myelination and myelin repair.
Astrocytes are critical for developmental myelination, however in a demyelinating environment they are detrimental to myelin repair.

overall_design: Due to potentially conflicting roles for astrocytes in demyelination and myelin repair, it becomes challenging to target astrocytes for therapeutic intervention in demyelinating diseases such as MS. Not only is there uncertainty regarding the roles of astrocytes in demyelination, but their roles in developmental myelination in-vivo remain ill defined, with much of our understanding coming from in vitro studies . In the current study, we developed a transgenic strategy that allows for the selective elimination of non-proliferative GFAP+ astrocytes through the targeted induction of physiological apoptosis that allows detailed loss of function analysis.

first: Reshmi

last: Tognatta

first: Christopher

last: Kantor

first: Molly

last: Karl

first: Sharyl

middle: L

last: Fyffe-Maricich

first: Patrick

last: Leahy

first: Rita

last: Romito-DiGiacomo


title: Expression data from innate and conventional CD8+ T cell populations from naïve CXCR3-GFP Reporter mice

status: Public on Aug 05 2017

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

summary:
Innate CD8+ T cells are a heterogeneous population with developmental pathways distinct from conventional CD8+ T cells. Their biology, classification and functions remain incompletely understood. We recently demonstrated the existence of distinct populations of innate CD8+ T cells based on CXCR3 expression.
We characterized these subsets through gene expression profiling and identified effector molecules and pathways which mediate their function.

overall_design: CXCR3+ innate CD8+, CXCR3- innate CD8+  and naïve CD8+ T cell populations were sorted from 3 to 5 CXCR3-GFP Reporter mice. RNA was prepared from these cell populations, the quantity, quality and integrity were confirmed by Nanodrop and Agilent Bioanalyzer before inclusion in the array.

first: Abhay

last: Satoskar


title: Effect of HIRA deletion on gene expression in mouse skeletal muscle at 6 weeks of age

status: Public on Jun 26 2017

city: Houston

first: M. David

last: Stewart

state: TX

address: 4800 Calhoun Rd

institute: University of Houston

summary: We performed gene expression profiling by microarray using RNA extracted from the tibialis anterior of control and Hira myofiber-specific conditional knockout mice at 6 weeks of age. Hira is a histone chaperone responsible for replication-independent incorporation of histone variant H3.3 at actively transcribed loci. Conditional knockout of Hira in myofibers caused hypertrophy, degeneration, and increased the percentage of type I fibers. These results illustrate the physiological consequences of disrupting Hira-mediated chromatin assembly in myofibers.

overall_design: 4 animals per group (control and Hira conditional knockout) hybridized in triplicate. RNA was extracted from the tibialis anterior muscle.

first: M


title: Age-Related Gene Expression in mouse liver tissues after exposure to Gamma-ray irradiation

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To identify age-related gene expression changes in infant (1-week-old) and adult (7-week-old) mouse liver tissues after Gamma-ray irradiation.

overall_design: Changes in gene expression in infant (1-week-old) and adult (7-week-old) mouse liver tissures were measured at 0, 24 and 48 hours after 4 Gy Gamma-ray irradiation. Two male and two female mice were used for each time point.

first: Yi

last: Shang

first: Yurika

last: Sawa

first: Benjamin

last: Blyth

first: Chizuru

last: Tsuruoka

first: Hiroyuki

last: Nogawa

first: Yoshiya

last: Shimada

first: Shizuko

last: Kakinuma


title: Effect of a myofiber-specific HIRA conditional knockout on gene expression in mouse skeletal muscle at 6 months of age

summary: We performed gene expression profiling by microarray using RNA extracted from the tibialis anterior of control and Hira myofiber-specific conditional knockout mice at 6 months of age.  Hira is a histone chaperone responsible for replication-independent incorporation of histone variant H3.3 at actively transcribed loci.  Conditional knockout of Hira in myofibers improved strength and endurance, caused hypertrophy and regeneration, and increased the percentage of type I fibers.  These results illustrate the physiological consequences of disrupting Hira-mediated chromatin assembly in myofibers.

overall_design: 4 animals per group (control and Hira conditional knockout) hybridized in triplicate.  RNA was extracted from the tibialis anterior muscle.


title: siRNA knockdown of GATA3 or HIF-1α in OEC-M1 cells under hypoxia

first: Min-Chuan

last: Huang

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

department: Graduate Institute of Anatomy and Cell Biology

institute: National Taiwan University

summary: To determine the GATA3 or HIF-1α regulated gene expression profile  in OEC-M1 cells under hypoxia

overall_design: OEC-M1 cells were transfected with non-targeting or GATA3 or HIF-1α specific siRNAs for 72 hours and total RNA were extracted


title: Identification of genes with altered expression in head and neck cancer

status: Public on Jun 20 2017

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Head and neck cancer arises in the mucosal linings of the upper aerodigestive tract. Many genes display an altered expression, but this had been derived from unpaired tumor-mucosa sample series. In this study paired normal mucosa and tumor samples of the same patients are studied.

overall_design: Transcriptional profiling of 22 tumor samples paired with 22 matched normal mucosa samples

first: Sanne

last: Martens-de Kemp

first: Boudewijn

last: Braakhuis

first: Serge

last: Smeets

first: Quirinus

last: Voorham

first: François

last: Rustenburg

first: Vicky

last: de Boer

first: Arjen

last: Brink

first: Wessel

middle: N

last: van Wieringen

first: Ruud

last: Brakenhoff


title: The enteric nervous system as an immune target in multiple sclerosis

status: Public on Jun 24 2017

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary: Besides symptoms caused by central nervous system (CNS) lesions, the majority of patients with multiple sclerosis (MS) also exhibit gastrointestinal dysfunction that has frequently been noted, but was not directly linked to the autoimmune etiology of the disease.We studied the enteric nervous system (ENS) in a murine model of MS by histology and electron microscopy. Serum IgG against enteric neurons and enteroglia was measured by ELISA and binding to the ENS was confirmed by immunohistochemistry. Target antigens were identified by mass spectrometry. Gastrointestinal dysfunction was determined by measuring dye transit time. RNA expression profiling was conducted with small intestines of MP4-immunized and control-immunized mice.   Data from the mouse model were confirmed in MS patients by immunohistochemistry of the ENS in bowel resectates. In addition, ELISA was performed on plasma samples to detect antibodies against four specific target antigens as identified in the mouse model. ENS degeneration was evident already before the onset of clinical disease in the mouse model. Pathology was predominantly antibody-mediated and caused a significant decrease in gastrointestinal transit, which was associated with severe gliosis of the ENS. Unlike the dense infiltrates that developed in the perivascular compartments of the CNS of MP4-immunized mice, the infiltrates in the ENS consisted of single cells scattered throughout the tissue. RNA expression profiling could support these results, as the expression of inflammatory markers in the small intestine was similar between MP4-immunized and HEL-immunized mice.  We identified four specific target antigens derived from enteric neurons and/or enteroglia. Antibodies against all four target antigens were present in MS patients. MS patients also showed gliosis and signs of ENS degeneration in the small intestine. For the first time, this study establishes a pathomechanistic link between the well-established autoimmune attack on the CNS and the ENS in MS. The presence of ENS pathology prior to CNS degeneration introduces entirely novel ways to explain MS etiology and immunopathogenesis.

overall_design: Global expression profiling.

first: A

last: Wunsch

first: Stefanie

last: Kürten


title: Genome-wide analysis of genes induced in TRAMP mouse prostate tumors after Mobilan injection

status: Public on Jul 29 2017

city: Buffalo

first: Vadim

last: Mett

state: NY

address: 73 High Street

institute: Buffalo BioLabs, LLC

summary: Toll-like receptor 5 is considered an attractive target for anticancer immunotherapy. TLR5 agonists, bacterial flagellin and engineered flagellin derivatives, have been shown to have potent anti-tumor and metastasis-suppressive effects in multiple animal models and to be safe in both animals and humans. Anticancer efficacy of TLR5 agonists stems from TLR5-dependent activation of NF-kB that mediates innate and adaptive anti-tumor immune responses. To extend application of TLR5-targeted anticancer immunotherapy to tumors that do not naturally express TLR5, we created an adenovirus-based vector for intratumor delivery, named Mobilan that drives expression of self-activating TLR5 signaling cassette comprising of human TLR5 and a secreted derivative of Salmonella flagellin structurally analogous to a clinical stage TLR5 agonist, entolimod. Co-expression of TLR5 receptor and agonist in Mobilan-infected cells established an autocrine/paracrine TLR5 signaling loop resulting in constitutive activation of NF-kB both in vitro and in vivo. Injection of Mobilan into primary tumors of the prostate cancer-prone TRAMP mice resulted in a strong induction of multiple genes involved in inflammatory responses and mobilization of innate immune cells into the tumors including neutrophils and NK cells and suppressed tumor progression. Intratumoral injection of Mobilan into subcutaneously-growing syngeneic prostate tumors in immunocompetent hosts improved animal survival after surgical resection of the tumors, by suppression of tumor metastasis. In addition, vaccination of mice with irradiated Mobilan-transduced prostate tumor cells protected mice against subsequent tumor challenge. These results provide proof-of-concept for Mobilan as a tool for antitumor vaccination that directs TLR5-mediated immune response towards cancer cells and does not require identification of tumor antigens.

overall_design: Total RNA obtained from prostate tumors 24 and 48 hours after injection of PBS, Ad-mCherry or Mobilan (two replicates)

first: Andrei

last: Gudkov


title: Transcriptome of tibialis anterior muscle RNA samples from control and OPMD A17.1 mouse treated or not with a gene therapy approach

status: Public on Jun 12 2017

city: Paris

first: Capucine

last: TROLLET

address: GH Pitie Salpetriere Bat Babinski 47 bd de l'hopital

country: France

institute: Myology Research Center UMRS974 INSERM

summary: Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset syndrome characterized by progressive degeneration of specific muscles. OPMD is caused by short GCN repeat expansions within the gene encoding the nuclear poly(A)-binding protein 1 (PABPN1) that extend an N-terminal polyalanine tract in the protein. Mutant PABPN1 aggregates as nuclear inclusions in OMPD patient muscles. We have used the transgenic mouse A17.1 OPMD model that recapitulates the features of the human disorder: progressive muscle weakness, atrophy and formation of PABPN1 nuclear inclusions. Wild-type human PABPN1 contains a stretch of 10 alanines following the initial methionine, which is expanded to 11–18 alanines in OPMD patients. Transgenic A17.1 mouse overexpress an 17 alanine expanded PABPN1 under the control of the HSA promoter. To evaluate a gene therapy approach based on AAV delivery of a ‘suppress and replace’ strategy in OPMD we performed a transcriptomic analysis in treated muscles 18 weeks after injection. Using microarrays, tibialis anterior gene expression was compared between control muscles (FvB), OPMD muscles (A17), AAV-shRNA3x treated muscles (A17 shRNA3X), AAVoptPABPN1 treated muscles (A17 optPABPN1), and AAV-shRNA3x+AAV-optPABPN1 treated muscles (A17 dual).

last: Trollet

first: George

last: Dickson

first: Alberto

last: Malerba

first: Pierre

last: Klein


title: Gene expression profiling of FGFR1 KO mice

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: A novel RCAS-Cre-IRES-PyMT (RCI-PyMT) virus was designed to specifically knockout genes of interest in tumors generated in appropriate mutant mouse hosts. We used this tumor knockout, or TuKO, strategy to concisely ablate fgfr1 in PyMT induced mammary tumors in K19-tva/fgfr1loxP/loxP mice. The similarly injected control K19-tva mice developed mammary tumors exhibiting high metastasis penetration to lung, making this an ideal model for breast cancer metastasis. The fgfr1 TuKO tumors showed significantly decreased primary tumor growth, and most importantly, greatly reduced metastasis to lung. Our study suggests that FGFR1 signaling is a key pathway driving breast cancer lung metastasis and that targeting FGFR1 in breast cancer is an exciting approach to inhibit metastasis.

overall_design: Gene expression microarray analyses were performed on FGFR1 KO K19-tva/fgfr1loxP/loxP mice and control K19-tva  mice.

first: Feng

last: Yang

first: Fengju

last: Chen