title: Cortical transcriptional changes in a chemically-induced neuronopathic Gaucher disease mouse model

status: Public on Aug 30 2016

city: Rehovot

first: Tony

last: Futerman

address: Herzl 234

country: Israel

institute: Weizmann institute of science

summary: Great interest has been shown in understanding the pathology of Gaucher disease (GD) due to the recently-discovered genetic relationship with Parkinson’s disease. For such studies, suitable animal models of GD are required. Chemical induction of GD by inhibition of acid β-glucosidase (GCase) using the irreversible inhibitor, conduritol-B-epoxide (CBE), is particularly attractive, although few systematic studies examining the effect of CBE on development of symptoms associated with neurological forms of GD have been performed. We now demonstrate a correlation between the amount of CBE injected into mice and levels of accumulation of the GD substrates, glucosylceramide and glucosylsphingosine, and show that disease pathology, indicated by altered levels of pathological markers, depends on the dose of CBE and its time of injection. Gene array analysis shows a remarkable similarly in the gene expression profile of CBE-treated mice and a genetic GD mouse model, the Gbaflox/flox;nestin-Cre mouse, with 120 of the 144 genes up-regulated in CBE-treated mice also up regulated in Gbaflox/flox;nestin-Cre mice. Finally, we demonstrate that some aspects neuropathology and some behavioral abnormalities can be arrested upon cessation of CBE treatment during a specific time window. Together, our data demonstrate that injection of mice with CBE provides a rapid and relatively easy way to induce symptoms typical of neuronal forms of GD, which will prove particularly useful when examining the role of specific biochemical pathways in GD pathology, since CBE can be injected into mice defective in components of putative pathological pathways, alleviating the need for time consuming crossing of mice.

overall_design: C57BL/6JOlaHsd, SV129, C3H, FVB mice were i.p. treated with PBS or CBE 25mg/kg day from postnatal day 8-18. Cortex were removed with a spatula and RNA was extracted using the RNeasy mini kit (Qiagen GmbH, Hilden, Germany)

first: Andres

last: Klein

first: Irit

last: Orr

first: Anthony

middle: H


title: Transcriptome of Ameloblastoma using Laser capture microdissection

status: Public on Sep 01 2016

city: Chapel Hill

first: Shijia

last: Hu

state: NC

address: 228 Brauer Hall Campus Box 7450

department: Pediatric Dentistry

country: USA

institute: University of North Carolina

summary: The goal of the study was to characterize the whole genome transcriptome profiles of pure sample population of human ameloblastoma epithelial cells for examination of molecular pathways.

overall_design: Seventeen human ameloblastoma samples were obtained. Both fresh frozen and FFPE samples were used and placed in solution for 1-4 weeks to allow decalcification by EDTA. The tissue was sectioned at -35C at a thickness of 7 microns. These sections were used for laser capture microdissection (LCM) to isolate the neoplastic epithelial portion of the tumors, using static image settings.  Total RNA was extracted from each sample and examined using the whole genome microarray against the Stratagene universal human reference RNA.

first: J

middle: T

last: Wright


title: N1ICD overexpression effect on white adipose tissue

status: Public on Aug 28 2016

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Analysis of inguinal white adipose tissue (WAT) isolated from wildtype (WT) and Notch1 overexpression mice (Ad/NICD). Results provide insight into molecular mechanisms underlying lipodystrophy of Ad/NICD mice

overall_design: Two-condition experiment, WT WAT vs. Ad/NICD WAT. Biological replicates: 4 WT WAT and 4 Ad/NICD WAT

first: Pengpeng

last: Bi

first: Sara

middle: E

last: Wirbisky

first: Chao

last: Wang

first: Jennifer

middle: L

last: Freeman


title: Gene expression profile in response to SDH2 deletion during filament formation in both Spider medium and Spider medium supplemented with 100mM glucose

status: Public on Aug 23 2016

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

country: China

institute: PLA General Hospital

summary: Transcriptional profiling of Candida albicans comparing SDH2 deletion mutant cells with the wild-type cells in both Spider medium and Spider medium supplemented with 100mM glucose

overall_design: The SDH2 deletion mutant sdh2Δ/Δ and the wild-type strain SC5314 were used to perform the microarray experiments. Two-condition experiments: sdh2Δ/Δ vs SC5314 in Spider midium and sdh2Δ/Δ vs SC5314 in Spider midium supplemented with 100mM glucose. Biological replicates: 3 SDH2 deletion mutant sdh2Δ/Δ samples (test group), 3 wild-type strain SC5314 samples (control group), independently grown and harvested. One replicate per array.

first: Yan


title: Meiosis timecourse Rap1

city: Chicago

first: Sean

middle: Erik

last: Hanlon

state: IL

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

institute: University of Chicago

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a [gene expression]

status: Public on Aug 31 2016

city: New York

first: Alexandros

last: Strikoudis

state: NY

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

summary:
Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex.
We used microarrays to detail the global program of gene expression after shControl, shPhf5a, or shPaf1 knockdown in mouse ESCs following 72h knockdown and identified distinct down-regulated and up-regulated genes during this process.

overall_design: Mouse ESCs were transduced with pLKO.1-based backdone lentiviruses expressing shControl, shPhf5a or shPaf1 hairpins, respectively. Cells were selected with puromycin (2μg/mL) for 72h. RNA was extracted using RNeasy kit (Qiagen) and hybridized on Affymetrix microarrays.


title: Meiosis timecourse open chromatin dynamics as measured by FAIRE

summary:
To investigate chromatin organization dynamics during the transition from vegetative growth to meiosis, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in vegetative cells (YPD) and in cells undergoing synchronous meiosis/sporulation in the budding yeast Saccharomyces cerevisiae.
There is growing recognition that the binding of a transcription factor near a gene does not always indicate regulatory function, and further that a single factor may function to either activate or repress its targets depending on the cellular context. We examined these issues through a series of experiments involving the S. cerevisiae transcription factor Rap1, and its function throughout critical metabolic and developmental transitions between vegetative growth, respiratory growth, meiosis and sporulation. We simultaneously monitored the expression of all genes and the genomic binding locations of Rap1 throughout the timecourse. Genes downstream of Rap1 binding were activated and repressed dynamically, but a change - or lack of change - in Rap1 binding status was not predictive of activation, repression, or no change in regulation. Despite this, we show that Rap1 is required, at a given point in time, for both activation and repression of different gene targets, within the same cell. Specification of the transcriptional consequences of Rap1 binding is thus highly promoter-specific. The presence of other transcription factor binding motifs, the subtype of Rap1 motif, and the underlying chromatin structure of the promoter cannot fully account for the observed transcriptional outcomes. There is a better accounting for the dynamic binding behavior of Rap1 including specification of an expanded meiotic target set through a Tup1- dependent nucleosome-loss mechanism. The variable and dynamic association between binding and transcription in this simple unicellular system portends a similarly volatile relationship in more complex eukaryotes. Biological interpretations of transcription factor occupancy should be made cautiously and in conjunction with supporting data obtained under the precise condition of interest.

overall_design: SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3).  Meiosis timecourse with samples collected during vegetative growth (YPD), and 0 hr, 1.5hr, and 3hr after transfer to sporulation media (SM).  3 separate biological replicates were used for each condition/time-point.  Labeled FAIRE enriched DNA from each sample and a labeled genomic DNA common reference were competitively hybridized to Agilent yeast whole genome 4 x 44k tiling microarrays (resolution ~270bp).  The Rap1 ChIP, RNA abundance/expression analysis, and FAIRE analysis were all carried out on the same biological samples. The three FAIRE timecourse replicates correspond to timecourse replicates 1, 4, and 6.

first: Hanlon

last: Sean Erik

first: Lieb

last: Jason D.


title: Gene expression based profiling of Mycobacterium tuberculosis infected primary murine osteoclasts.

status: Public on Aug 15 2016

city: New Delhi

first: Kuldeep

middle: Singh

last: Attri

state: Delhi

address: Sukhdev Vihar

department: Systems Biology

country: India

institute: CSIR-IGIB

summary:
Mycobacterium tuberculosis(Mtb) is known to reside in cells of innate immune system- macrophages and dendritic cells. A variety of non -conventional cell typeslike adipocytes, mesenchyal stem cells and osteoclasts can also be infected with Mtb. However, cellular transcriptional adapations enabling survival of Mtb in these cells remain known.
We used microarrays to understand global changes in transcriptional profiling during macrophage to osteoclast transition in presence of Mycobacterium tuberculosis.

overall_design: Time-series changes in expression were seen in presence of Mycobacterium tuberculosis on 0, 2, 3 and 4 days post infection during macrophage to osteoclast transition.

last: Singh Attri

first: Rajesh

middle: S

last: Gokhale


title: Gene expression data from mouse regulatory T cells

status: Public on Aug 10 2016

city: Montreal

first: Bruce

middle: David

last: Mazer

state: Quebec

address: 1001 boul. Décarie

department: RESP

country: Canada

institute: RI-MUHC

summary:
Intravenous Immunoglobulin (IVIg) is widely used as an immunomodulatory therapy. We have recently demonstrated that IVIg protects against airway hyper-reactivity (AHR) and inflammation in mouse models of allergic airway disease (AAD), associated with induction of Foxp3+ regulatory T cells (Treg). Using DEREG (DEpletion of REGulatory T cell) mice, in which endogenous Treg can be ablated with Diphtheria toxin (DTx) treatment, we demonstrate that IVIg generates a de novo population of induced Treg (iTreg) in the absence of endogenous Treg. IVIg-generated iTreg were sufficient for inhibition of ovalbumin-induced AHR in an antigen-driven murine model of AAD. In the absence of endogenous Treg, IVIg failed to confer protection against AHR and airway inflammation. Adoptive transfer of purified IVIg-generated iTreg prior to antigen challenge effectively prevented airway inflammation and AHR in an antigen-specific manner.
The goal of this study was to characterize the gene expression profile of a pure population of IVIg-generated induced Treg (iTreg).

overall_design:
Treg were isolated from mice sensitized and challenged with ovalbumin (OVA). Animals were treated with IVIg to generate iTreg with or without DTx endogenous Treg pre-depletion. Human serum albumin (HSA) was used as a control protein treatment.
RNA was isolated from 4 biological replicates for each condition. 12 samples in total were hybridized to Affymetrix gene expression microarrays.
variable: treatment: OVA-HSA-OVA - DTx: BMR133, BMR134, BMR135, BMR136
variable: treatment: OVA-IVIg-OVA - DTx:  BMR137, BMR138, BR139, BMR140
variable: treatment: OVA-IVIg-OVA + DTx: BMR141, BMR142, BMR143, BMR144
repeat: biological replicate: eTreg: BMR133, BMR134, BMR135, BMR136
repeat: biological replicate: e_iTreg: BMR137, BMR138, BR139, BMR140
repeat: biological replicate: IVIg-iTreg: BMR141, BMR142, BMR143, BMR144

first: Gabriel

middle: N

last: Kaufman

middle: D


title: GPR41 modulates insulin secretion and gene expression in pancreatic beta-cells and modifies metabolic homeostasis in fed and fasting

status: Public on Aug 17 2016

first: MIchael

last: Walker

address: POB 26

institute: Weizmann Institute of Science

summary:
Insulin secretion by pancreatic b-cells is primarily regulated by glucose; however, hormones and additional nutrients, such as long-chain fatty acids, also play an important role in adjusting insulin output to physiologic needs.
We examined the role of the short chain fatty acid receptor, GPR41, in funcion of pancreatic beta cells. GPR41 was specifically over-expressed in beta cells by using rat insulin promoter II (41 Tg).

overall_design: To further understand GPR41 dependent metabolic phenotype we obsereved in-vivo, we examined mouse islets from 41 Tg and wt littermates. Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Array.

first: Anna

last: Veprik

first: Dana

last: Laufer

last: Weiss

first: Nir

last: Rubins

first: Michael


title: Gene expression of inflammatory monocytes/macrophages after ablative radiotherapy in pancreatic adenocarcinoma

status: Public on Aug 01 2016

city: Philadelphia

first: Anusha

last: Kalbasi

state: Pennsylvania

address: 3400 Civic Center Blvd.

department: Radiation Oncology

institute: University of Pennsylvania

summary:
Ablative RT results in increased expression of CCL2 within the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) and also increased recruitment of CD45+CD11b+Ly6Chi inflammatory monocytes/macrophages.  This increase in CCL2 expression and  recruitment of inflammatory monocytes/macrophages is a mechanism of resistance to the anti-tumor effects of ablative radiotherapy (RT).
We used microarrays to study changes in gene expression patterns of inflammatory monocytes/macrophages sorted from the tumor microenvironment after ablative RT in a subcutenous model of pancreatic adenocarcinoma. From this, we identified 8 genes with an absolute fold change of expression equal to or greater than 2 with a false discovery rate equal to or less than 25 %.

overall_design: A pancreatic cancer tumor cell line derived from spontaneously arising tumors in KrasLSL-G12D/+, Trp53LSL-R172H/+, Pdx1-Cre (KPC) mice was  subcutaneously implanted into 8 week old female C57BL/6 and allowed to grow for 14 days. After 14 days, 4 mice received 20 Gy of radiation, and 4 mice received a sham treatment. One day post treatment, tumors were harvested, and inflammatory monocytes/macrophages were isolated using flow sorting based on a surface expression phenotype of  CD45+ CD11b+ Ly6Chi. From this cell population, total RNA was extracted for creation of cDNA and hybridization on Affymetrix microarrays. From the microarrays, a set of genes associated with radiation treatment of PDAC was identified.

first: Chad

middle: A

last: Komar

first: Gregory

last: Beatty


title: Cathepsin B modulates lysosomal biogenesis and host defense against Francisella novicida infection

status: Public on Aug 04 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Lysosomal cathepsins regulate an exquisite range of biological functions, and their deregulation is associated with inflammatory, metabolic and degenerative disease in humans. Here, we identified a key cell-intrinsic role for cathepsin B as a negative feedback regulator of lysosomal biogenesis and autophagy. Mice and macrophages lacking cathepsin B activity had increased resistance to the cytosolic bacterial pathogen Francisella novicida. Genetic deletion or pharmacological inhibition of cathepsin B downregulated mTOR activity and prevented cleavage of the lysosomal calcium channel TRPML1. These events drove transcription of lysosomal and autophagy genes via the transcription factor TFEB, which increased lysosomal biogenesis and activation of autophagy-initiation kinase ULK1 for clearance of the bacteria. Our results identified a fundamental biological function of cathepsin B in providing a checkpoint for homeostatic maintenance of lysosome population and basic recycling functions in the cell.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in bone marrow-derived macrophages (BMDM) isolated from cathepsin B-/- and wild-type mice.

first: Si

middle: M

last: Man

first: Xiaopeng

last: Qi

first: R

middle: K

last: Malireddi

first: Rajendra

last: Karki

first: Christopher

last: Lupfer

first: Prajwal

last: Gurung

first: Clifford

last: Guy

first: Mohamed

last: Lamkanfi

first: Thirumala

last: Kanneganti


title: Expression data from Tbet+ and Tbet- Memory B cells

city: San Diego

first: Burton

middle: Earle

last: Barnett

state: California

address: 3210 Merryfield Row

institute: Poseida Therapeutics

summary:
The role of antibody and B cells in preventing infection is established. In contrast, the role of B cell responses in containing chronic infections remains poorly understood. IgG2a (IgG1 in humans) can prevent acute infections and T-bet promotes IgG2a isotype switching. However, whether IgG2a and B cell-expressed T-bet influence the host-pathogen balance during persisting infections is unclear. Here we demonstrate that B cell specific loss of T-bet prevents control of persisting viral infection. T-bet in B cells not only controlled IgG2a production, but also mucosal localization, proliferation, glycosylation, and a broad transcriptional program. T-bet controlled a broad antiviral program in addition to IgG2a since T-bet in B cells was important even in the presence of virus-specific IgG2a. Our data supports a model in which T-bet is a universal controller of antiviral immunity across multiple immune lineages.
Naïve, Tbet+, and Tbet- Memory B cells were assayed for gene expression

overall_design: Tbet GFP reporter mice were infected with LCMV clone 13, and target B cell populations were sorted from splenocytes at day 10 post-infection

first: B

first: E

last: Stelekati

middle: J

last: Wherry


title: DNA damage-induced HSPC failure depends on  ROS accumulation downstream of IFN-1 signaling  and Bid mobilization

status: Public on Aug 02 2016

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

summary: Targeted mouse mutants with inactivated Mixed-Lineage-Leukemia-5 (Mll5, MGI:1924825) alleles exhibit numerical, cell cycle and functional abnormalities in their hematopoietic stem and progenitor cell (HSPC) compartments, including hyper-proliferation of otherwise quiescent hematopoietic stem cells, lack of long-term reconstitution potential and profound radiation sensitivity. Most of the HSPC defects are secondary to increased levels of DNA damage and intracellular accumulation of reactive oxygen species (ROS). To obtain first insights into underlying molecular mechanisms, we performed Affymetrix gene chip analysis using total RNA isolated from FACS-sorted Lin-Sca1+Kit+ (LSK) cells of Mll5+/+ and Mll5-/- mice, both with and without prior long-term treatment with the ROS quencher N-Acetyl-L-Cysteine (NAC). As key finding, microarray data revealed elevated hybridization signals for several transcripts of known or putative IFN-1 target genes in LSK cells from Mll5-/- mice irrespective of NAC-treatment. In fact, comprehensive gene set enrichment analysis identified a number of gene sets closely associated with interferon responses that were significantly affected in Mll5-/- LSK cells.

overall_design: RNA was isolated from FACS-sorted Lin-Sca1+Kit+ (LSK) cells of Mll5+/+ and Mll5-/- mice, both with and without prior long-term treatment with the ROS quencher N-Acetyl-L-Cysteine (NAC)

first: M


title: Alternatively activated mononuclear phagocytes from the skin site of infection and the impact of IL-4Rα signaling on CD4+T cell survival in draining lymph nodes after repeated exposure to Schistosoma mansoni cercariae

status: Public on Jul 26 2016

city: Freiburg im Breisgau

first: David

last: Sanin

address: Stübeweg 51

department: Immunometabolism

institute: Max-Planck-Institute für Immunbiologie und Epigenetik

summary: In areas endemic for schistosomiasis, repeated exposure to infective cercariae is a frequent occurrence, and repeated exposure of murine skin to Schistosoma mansoni resulted in CD4+ T cells becoming hypo-responsive. Here potential contributory mechanisms were investigated. In the skin infection site, three mononuclear phagocyte populations were identified (tissue macrophages, dendritic cells, and macrophages) which exhibited up-regulation of genes associated with alternative activation, in particular the gene encoding RELMα. However, in repeatedly infected mice deficient in RELMα, there was no change in the abundance of mononuclear phagocytes in the skin, and CD4+ cells in the skin draining lymph nodes remained hypo-responsive. In mice deficient for IL-4Rα, required for alternative activation, levels of dermal regulatory IL-10 were reduced and there was an increase in the abundance of antigen presenting MHC-IIhigh cells, which was accompanied by increased numbers of CD4+ T cells. Although the absence of IL-4Rα did not translate into increased CD4+ cell responsiveness, they exhibited lower expression of Fas/FasL, resulting in decreased apoptosis/cell death and increased cell viability. This study highlights a mechanism through which IL-4Rα may regulate the immune system through the induction of IL-10 and regulation of Fas/FasL mediated cell death.

overall_design: Mice were infected 1x or 4x with S. mansoni cercariae via the pinnae. Pinnae were harvested 4 days after the final infection and the DEC obtained after an overnight culture in vitro. Cells were then stained with F4/80 APC and MHC-II PE and four different populations sorted (using the MoFlo or the Astrios) based on their expression profiles. Several mice (12-18) from each group were pooled to generate each replicate.

first: Catriona

last: Prendergast

first: Adrian

middle: P

last: Mountford


title: Gene expression profiling in wild-type, Irf5-KO, Lyn-KO and Lyn/Irf5-DKO BMDCs unstimulated or stimulated with CpG-B ODN

status: Public on Jul 25 2016

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

summary: To characterize the relationship between IRF5 and Lyn in innate immune responses at a genome-wide scale, we performed gene expression microarray analysis for wild-type (WT), Irf5-KO, Lyn-KO and Lyn/Irf5-DKO bone marrow-derived dendritic cells (BMDCs) with or without 6 h-stimulation with 150 nM CpG-B ODN. We extracted the transcripts that were upregulated by CpG-B ODN in WT BMDCs, further upregulated in Lyn-KO BMDCs and then downregulated in Lyn/Irf5-DKO BMDCs (fold change ≥ 2, false discovery rate < 0.05). When these 79 transcripts were sorted by their expression levels in Lyn-KO BMDCs, most of the top 20 genes (13 out of 20) were those encoding type I interferons (IFNs), indicating that Lyn particularly suppresses IRF5 induction of type I IFNs.

overall_design: BMDCs from WT, Irf5-KO, Lyn-KO and Lyn/Irf5-DKO mice in a C57BL/6 background were unstimulated or stimulated with CpG-B ODN. Biological triplicate for each genotype were analyzed (24 samples in total).

first: Tatsuma

last: Ban

first: Akira

last: Nishiyama


title: Transcriptional profile of WT and Mmp10-/- bone marrow-derived macrophages after infection with Pseudomonas aeruginosa

city: Seattle

first: Ryan

last: McMahan

state: WA

address: 850 Republican, S-320

institute: University of Washington

summary: Several members of the matrix metalloproteinase (MMP) family control specific immune processes, such as leukocyte influx and chemokine activity. Stromelysin-2 (MMP10) is expressed in numerous tissues after injury; however, little is known of its function. Here, we report that MMP10 is expressed by macrophages in human lungs from patients with cystic fibrosis and induced in mouse macrophages in response to Pseudomonas aeruginosa infection both in vivo and in cultured bone marrow-derived macrophages (BMDM). Whereas all wildtype mice were alive at 48 h post-infection, all Mmp10–/– mice had greater weight loss and died or reached euthanasia criteria with no defect in bacterial clearance. Rather, macrophage numbers in infected Mmp10–/– lungs were about 3-4-fold greater than in wildtypes. Demonstrating that the protective effect of MMP10 was due its production by macrophages, adoptive transfer of wildtype BMDM normalized infection-induced weight loss in Mmp10–/– recipients to wildtype levels. In vivo, the expression of several M1 macrophage markers were elevated and M2 markers reduced in Mmp10–/– lungs, and we saw similar differences between M1-activated wildtype and Mmp10–/– BMDM. Global gene expression analysis revealed that infection-mediated transcriptional changes persisted in Mmp10–/– BMDM long after they downregulated in wildtype cells. These results indicate that MMP10 serves a beneficial role in response to infection by moderating the pro-inflammatory response of infiltrating macrophages.

overall_design: Total RNA from bone marrow-derived macrophages from 3 WT and 3 Mmp10-/- mice for each treatment: media change only, 6h post PA infection or 24 h post PA infection. Samples were hybidized to 18 Affymetrix GeneChip Mouse Gene 2.0 ST arrays.

first: Sina

last: Gharib


title: Gene profile analysis of sorted Sca1+/cKit- BMCs obtained from young and aged mice bearing tumor or not

status: Public on Jul 21 2016

city: Umeå

first: Andreas

last: Sjödin

address: KBC

department: Chemistry

country: Sweden

institute: Umeå University

summary: Sca1+/cKit– hematopoietic BMCs of hosts bearing primary tumors promote the growth of distant tumors that form with a myofibroblast-rich, desmoplastic stroma. BMCs from old mice bearing primary tumors lack this ability

overall_design: Sca1+/cKit- BMCs were isolated from young and old mice bearing Matrigel control or size-matched primary tumors by FACS directly into RLT Plus Buffer (Qiagen Rneasy Plus Micro Kit)

first: Y

last: Qin

first: A

last: Barakat

first: S

last: McAllister


title: Comparison of gene expression in the intestinal metaplasia in Cdx2/IL-1beta mice vs IL-1beta alone

first: John

middle: P.

last: Lynch

state: PA

address: 421 Curie Blvd

department: Medicine

summary:
Cdx2/IL-1beta mice have less intestinal metaplasia at the squamocolumnar junction thanIL-1beta mice alone.
This study was to identify a mechanism for this effect by examining differences in gene expression patterns when Cdx2 is co-expressed.

overall_design: We dissected out intestinal metaplasia nodules from the squamocolumnar junction in Cdx2/IL-1beta mice and Il-1beta mice and measured gene expression on a Mouse Gene 2.0ST Affymetrix array in Oct 2013.

first: Jianping

last: Kong


title: Proneurogenic ligands defined by modeling developing cortex growth factor communication networks

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

institute: Hospital for Sick Children

summary: The neural stem cell decision to self-renew or differentiate is tightly regulated by its microenvironment. Here, we have asked about this microenvironment, focusing on growth factors in the embryonic cortex at a time when it is largely comprised of neural precursor cells (NPCs) and newborn neurons. We show that cortical NPCs secrete factors that promote their maintenance while cortical neurons secrete factors that promote differentiation.  To define factors important for these activities, we used transcriptome profiling to identify ligands produced by NPCs and neurons, cell surface mass spectrometry to identify receptors on these cells, and computational modeling to integrate these data.  The resultant model predicts a complex growth factor environment with multiple autocrine and paracrine interactions. We tested this communication model, focusing on neurogenesis, and identified IFNγ, Nrtn and glial-derived neurotrophic factor (GDNF) as ligands with unexpected roles in promoting neurogenic differentiation of NPCs in vivo.

overall_design: We prepared E16 cortical neuron, E13 cortical precursor and co-cultured E16 cortical neuron and E13 cortical precursor cultures from three independent biological replicates.

first: Scott

last: Yuzwa

first: Guang

last: Yang

first: Michael

last: Borrett

first: Geoff

last: Clarke

first: Gonzalo

middle: I

last: Cancino

first: Siraj

last: Zahr

first: Peter

middle: W

last: Zandstra

middle: R

last: Kaplan


title: New anti-cancer chemicals Ertredin and its derivatives, regulate oxidative phosphorylation and glycolysis and suppress sphere formation in vitro and tumor growth in EGFRvIII-transformed cells.

city: Shinagawa-ku

first: Sonoko

last: Atsumi

state: Tokyo

address: 3-14-23 Kamiosaki

institute: Institute of Microbial Chemistry (BIKAKEN)

summary:
Background: EGFRvIII is a mutant form of the epidermal growth factor receptor gene (EGFR) that lacks exons 2-7. The resulting protein does not bind to ligands and is constitutively activated. The expression of EGFRvIII is likely confined to various types of cancer, particularly glioblastomas. Although an anti-EGFRvIII vaccine is of great interest, low-molecular-weight substances are needed to obtain better therapeutic efficacy. Thus, the purpose of this study is to identify low molecular weight substances that can suppress EGFRvIII-dependent transformation.
Methods: We constructed a new throughput screening system and searched for substances that decreased cell survival of NIH3T3/EGFRvIII spheres under 3-dimensional (3D)-culture conditions, but retained normal NIH3T3 cell growth under 2D-culture conditions. In vivo activity was examined using a mouse transplantation model, and derivatives were chemically synthesized. Functional characterization of the candidate molecules was investigated using an EGFR kinase assay, immunoprecipitation, western blotting, microarray analysis,quantitative polymerase chain reaction analysis, and measurement of lactate and ATP synthesis.
Results: In the course of screening 30,000 substances, a reagent, “Ertredin,” was found to inhibit anchorage-independent 3D growth of sphere-forming cells transfected with
EGFRvIII cDNA. Ertredin also inhibited sphere formation in cells expressing wild-type EGFR in the presence of EGF. However, it did not affect anchorage-dependent 2D growth of parental NIH3T3 cells. The 3D-growth-inhibitory activity of some derivatives, including those with new structures, was similar to Ertredin. Furthermore, we demonstrated that Ertredin suppressed tumor growth in an allograft transplantation mouse model injected with EGFRvIII- or wild-type EGFR-expressing cells; a clear toxicity to host animals was not observed. Functional characterization of Ertredin in cells expressing EGFRvIII indicated that it stimulated EGFRvIII ubiquitination, suppressed both oxidative phosphorylation and glycolysis under 3D conditions, and promoted cell apoptosis.
Conclusion: We developed a high throughput screening method based on anchorage-independent sphere formation induced by EGFRvIII-dependent transformation. In the course of screening, we identified Ertredin, which inhibited anchorage-independent 3D growth and tumor formation in nude mice. Functional analysis suggests that Ertredin suppresses both mitochondrial oxidative phosphorylation and cytosolic glycolysis in addition to promoting EGFRvIII degradation, and stimulates apoptosis in sphere-forming, EGFRvIII-overexpressing cells.

overall_design: Patterns of gene expression in cells treated with Ertredin (sample 2), rotenone (sample 3), and AG1478 (sample 4) were compared with vehicle-control cells (sample 1).

first: Chisato

last: Nosaka

first: Hayamitsu

last: Adachi

first: Tomoyuki

last: Kimura

first: Yoshihiko

last: Kobayashi

first: Hisashi

last: Takada

first: Takumi

last: Watanabe

first: Shun-ichi

last: Ohba

first: Hiroyuki

last: Inoue

first: Manabu

last: Kawada

first: Masakatsu

last: Shibasaki

first: Masabumi

last: Shibuya


title: Microarray analysis of CD14+ CD163high CD160high cells in human intestinal lamina propria

status: Public on Jul 17 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Several innate immune cell subsets have recently been identified to maintain gut homeostasis in both human and mice. Among these subsets, CX3CR1high CD11b+ CD11c+ cells contribute to intestinal tolerance through various mechanisms in mice. However, whether tolerogenic innate myeloid cells are present in the human intestine is not clearly defined. In this manuscript, we identified an intestinal myeloid cell subset possessing tolerogenic ability. HLA-DRhigh CD14+ CD163high cells in the human colon were divided into two subsets based on CD160 expression: CD163high CD160high and CD163high CD160low cells. Both cell subsets exhibited high levels of IL-10 production and high phagocytic activities. CD163high CD160high cells suppressed effector CD4+ T cell proliferation by a Foxp3+ Treg cell induction-independent mechanism. We further observed that the number and suppressive activity of these cells were profoundly decreased in patients with ulcerative colitis (UC). In addition, CD163high CD160high cells in the UC patients showed inflammatory phenotype, such as increased expression of IL6, CD80, and CD86, accompanied with decreased IL10RB expression. Our results highlight that a tolerogenic CD163high CD160high cell subset might be implicated in the prevention of UC development.

overall_design: Gene expression analysis of pooled lamina propria cells (LPCs) (n=12) and human blood CD14+ monocytes (n=7) were performed using Whole Human Genome Microarray Kit, 4x44K (G4112F) as one-color experiments.

first: Soumik

last: Barman

first: Hisako

last: Kayama

first: Kiyoshi

last: Takeda


title: BALF macrophage transcript analysis in response to butylated hydroyxtoluene treatment in mice deficient in TLR4

status: Public on Jul 14 2016

city: Aurora

first: Alison

middle: Kendall

last: Bauer

state: CO

address: 12850 E. Montview Blvd.; Rm 3125

department: Environmental and Occupational Health

institute: University of Colorado Denver

summary: Background: Human lung adenocarcinoma (ADC), the predominant subtype of lung cancer, are at a disadvantage as the disease lacks available biomarkers and is not usually diagnosed until its later stages. We previously demonstrated that Tlr4-mutantmice were more susceptible to BHT-induced pulmonary inflammation (bronchoalveolar lavage macrophages and lymphocytes) and tumorigenesis in comparison to Tlr4-sufficient control mice. Differential transcriptional profiles were also noted in the whole lung tissue of the mice. The study objective was to elucidate the mechanisms underlying the protective effect of Tlr4 including differences in specific innate immune cell populations, their functional responses, and the influence of these cellular differences on the growth of ACD progenitor cell types.  Methods: Following butylated hydroxytoluene (BHT) treatment (tumor promoter;4 weekly ip.injections), BALB (Tlr4-sufficient) and C.C3-Tlr4Lps-d/J (BALBLpsd; Tlr4 mutant) lungs were lavaged, processed for flow cytometry, and frozen for molecular analysis (ELISAs for IGF1, KC, Raybiotech Mouse Cytokine Array). BALF-derived macrophages were collected for phagocytosis and efferocytosis assays. BALF macrophage RNA was also isolated and utilized for Affymetrix gene arrays and real-time quantitative PCR. Enrichment of bronchiolar Clara cells, an ADC progenitor cell, was performed and cells enumerated. Femur bone marrow cells were differentiated into macrophages, and co-cultured with C10 cells, a type II cell line, for a wound healing assay.  Results: Tlr4-deficiency resulted in significantly increased numbers of innate immune cells in whole lung tissue in response to BHT, including macrophages, PMNs, myeloid-derived suppressor cells (MDSC)s and dendritic cells (DCs), in comparison to Tlr4-sufficient mice (p<05). Macrophage functionality was also affected. BHT treated Tlr4-mutant mice demonstrated enhanced phagocytic and efferocytic abilities and wound healing in comparison to macrophages from Tlr4-sufficient and control treated mice (P<0.05). Additionally, Clara cell proliferation was significantly increased in Tlr4-mutant compared to Tlr4-sufficient mice in response to BHT.   Pulmonary cytokine, chemokine and growth factor protein expression also significantly differed among the strains and within macrophages, gene expression and cell surface markers combined demonstrated a more plastic macrophage  phenotype in the Tlr4-mutant mice.  The transcriptome study identified immune pathways important in inflammation, such as phagosome. Conclusion: There are distinct pulmonary innate immune cell populations, with particular emphasis on macrophages, that are likely influencing the enhanced tumor promotion observed in Tlr4-mutant mice. Though not as striking, the pulmonary lymphoid populations may also be affecting the promotion environment, if only via their influence upon the innate immune cells. Future studies will investigate the origins of the macrophages and continued delineation of the lymphoid cell populations.

overall_design: Two strains of mice were used for these studies.  The C.C3-Tlr4Lps-d/J (BALBLpsd) with a dominant negative Tlr4 on a BALB/c background and the BALB/cJ mice with a sufficient Tlr4.  Total RNA was extracted from bronchoalveolar lavage fluid macrophages 3 days following a chronic BHT protocol. (oil controls vs BHT treated for both strains.  BALB oil and BHT treatment n=3 mice per treatment group; BALBLpsd oil controls n=2 per treatment group; BALBLpsd BHT treated n = 3 per treatment group).   Therefore a total of 13 arrays with one BHT exposure times and oil (vehicle) controls.

first: Carla-Maria

last: Alexander

first: Ka-Na

last: Xiong

first: Kalpana

last: Velmurugan

first: Julie

first: Ross

last: Osgood


title: An epithelial integrin regulates the amplitude of protective lung interferon responses

status: Public on Jul 18 2016

first: Geoffrey

last: Neale

summary: Integrins facilitate intercellular movement and communication. Unlike the promiscuous activities of many integrins, β6 integrin is restricted to epithelia and partners exclusively with integrin αV to modulate acute lung injury (ALI). Given that ALI is a complication of respiratory infection, we used mice lacking β6 integrin (β6 KO) to probe the role of the epithelial layer in controlling the lung microenvironment during infection. We found β6 KO mice were protected from disease caused by influenza and Sendai virus infections. They were also protected from disease caused by Streptococcus pneumoniae infection alone and after prior influenza virus infection, the co-infection representing an often-lethal condition in humans. Resistance in the absence of epithelial β6 integrin was caused by intrinsic priming of the lung microenvironment by type I interferons through a mechanism involving transforming growth factor-β regulation. Expression of β6 on epithelia suppresses the production of interferons, providing an advantage to the pathogen. Acute inhibition of β6 function may therefore provide a means to improve outcomes in lung microbial infections.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in resident alveolar macrophage cells from wild-type and β6 integrin knockout mice. Cells were purified by sorting from lung digests. The comparison made was CD11c+, autofluorescent+ cells from wild-type controls to the dominant CD11c+, CD11b+, autofluorescent+ cells in the knockout. Note that conventional CD11c+ alveolar macrophages do not exist in the knockout mice.

first: Victoria

last: Meliopoulos

first: Lee

last: Van de Velde

first: Peter

last: Murray

first: Stacey

last: Schultz-Cherry


title: Dry age-related macular degeneration like pathology in aged 5XFAD mice: Ultrastructure and microarray analysis

city: Seoul

first: Sung Wook

last: Park

address: 101, Daehak-ro

department: Biomedical sciences

country: South Korea

institute: Seoul National University

summary: Age-related macular degeneration (AMD) is a leading cause of blindness in the elderly. There are two types of AMD: dry AMD and wet AMD. While laser-induced choroidal neovascularization has been used extensively in the studies of wet AMD by presenting the main features of human wet AMD, there was no established mouse model which fully recapitulates the cardinal features of human dry AMD. In this regard, lack of appropriate mouse model for dry AMD hampered the translational research on the pathogenesis and development of therapeutic agents. We recently suggested that 5XFAD mice could be a mouse model of dry AMD with regard to the amyloid beta (Aβ) related pathology. In this study, using transmission electron microscope, we analyzed ultrastructure of retinal pigment epithelium (RPE) of 5XFAD mice. Of importance, aged 5XFAD mice had ultrastructural changes of RPE and Bruch’s membrane compatible with cardinal features of dry AMD, including loss of apical microvilli and basal infolding of RPE, increased thickness of Bruch’s membrane, basal laminar and linear deposits, and accumulation of lipofuscin granules and undigested photoreceptor outer segment-laiden phagosomes. Using a threshold of 1.2 fold difference, we found “564” differentially expressed genes of which “190” were up-regulated and “374” were down-regulated in the RPE complex of aged 5XFAD mice. These altered genes were implicated in the pathogenesis of AMD including inflammation and immune response-related genes and retinol metabolism-related genes. Taken together, we suggest that aged 5XFAD mice can be used for dry AMD mouse model.

overall_design: All 5XFAD mice used were heterozygotes with respect to the transgene, and non-transgenic wild-type littermate (WT) mice served as controls.

first: Sung-Wook

first: Jeong-Hun

last: Kim


title: Microarray analysis of CD14+ CD163high CD160high cells in human intestinal lamina propria and CX3CR1high CD11b+ CD11c+ cells in murine intestinal lamina propria

first: Daisuke

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CLAMP Protein Binding Microarray (PBM) experiment

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: To investigate the DNA binding specificity of the CLAMP protein, we have designed a custom PBM to interrogate the binding of CLAMP to DNA sequences extracted from the Drosophila melanogaster genome. Specific regions were extracted based on ChIP-seq data, motif occurence and proximity to gene transcription start sites.

overall_design: N-terminal GST-tagged protein samples were made for the C-terminal four and six zinc finger portions of the protein CLAMP; samples were made by in vitro transcription translation (IVT). IVT reaction mixtures for the two CLAMP constructs were applied directly to the PBM microarray and incubated for 1hour. Microarray-bound protein was fluorescently labeled using Alexa488-conjugated antibodies targeting GST, and the microarray was scanned in using a standard microarray scanner. Median fluorescence intensity over eight replicate probes was reported for each unique DNA sequence on the microarray.

first: Trevor

last: Siggers


title: qPCR array study for cell cycle related genes in Caco-2 cells treated with human lectin ZG16p

status: Public on Jul 13 2016

city: Bunkyo-ku

first: Kyoko

last: Kojima-Aikawa

address: 2-1-1 Otsuka

department: Faculty of Core Research, Natural Science Division

institute: Ochanomizu University

summary: ZG16p (zymogen granule protein 16) is a mannose- and heparin/heparan sulfate-binding lectin highly expressed in the human gut. In this study, the cell cycle related genes regulated by ZG16p were identified by qPCR array. Caco-2, a human adenocarcinoma cell line, was cultured in medium containing ZG16p for 72 h. qPCR array profiling revealed that, with an arbitrary fold change cut-off of 2, ZG16p  significantly (p<0.05) up-regulated the expression of 6 genes, while down-regulated that of 3 genes.

overall_design: qPCR gene expression profiling. Caco-2 cells were cultured with or without ZG16p. Total RNA was extracted from individual cell samples.

first: Akiko

last: Mito

first: Sabine

last: Gouraud


title: Identification of MMP12 as a potential new target for prevention and treatment of cardiometabolic disease

status: Public on Jul 12 2016

city: Vienna

first: Thomas

last: Stulnig

address: Waehringer Guertel 18-20

department: Christian Doppler Laboratory for Cardio-Metabolic Immunotherapy and Clinical Division of Endocrinology and Metabolism, Department of Medicine III

country: Austria

institute: Medical University of Vienna

summary: Obesity is strongly associated with the metabolic syndrome, a compilation of risk factors that predispose individuals to the development of cardiometabolic disease (CMD), i.e. cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM). Controlling or preventing the worldwide epidemic of metabolic syndrome requires novel interventions to address this substantial health challenge. The objective of this study was the identification of potential new targets for the simultaneous prevention and treatment of insulin resistance and atherosclerosis, conditions that underlie T2DM and CVD, respectively. Therefore, we used an unbiased bioinformatics approach to identify molecules that are upregulated in both conditions by combining data from two microarray experiments and two meta-analyses. In the microarray experiments we compared gene expression in white adipose tissue (WAT) of obese mice as well as aortae of obese and atherosclerotic mice to respective lean controls. Furthermore, we performed a meta-analysis of published microarrays investigating atherosclerotic vessels and included a published meta-analysis on T2DM into our analyses. We obtained a pool of thirty-four genes that were upregulated in 3 out of the 4 underlying databases. These included well-known as well as novel crucial molecules for treatment of T2DM and CVD. Macrophage metalloelastase 12 (MMP12) was found highly ranked in all analyses and, therefore, chosen for further validation. Analyses of visceral and subcutaneous white adipose tissue from obese compared to lean mice and humans convincingly confirmed the up-regulation of MMP12 in obesity at mRNA, protein and, of note, activity levels. In conclusion, by this unbiased approach an interesting pool of potential molecular targets or biomarkers for treatment and prevention of CMD was identified with MMP12 being confirmed on multiple levels.

overall_design: WT animals and LDLR-/- on a C57BL/6J background, purchased from Charles River Laboratories (Sulzfeld, Germany) were used. At 9 weeks of age the WT were placed for up to 20 weeks on high fat diet (HFD) (D12492; Research Diets Inc., New Brunswick, NJ, USA) and the LDLR-/- were placed for up to 20 weeks on sucrose-enriched high-fat diet (HFSC) (with 17.5 kcal% from sucrose; (D09071704, Research Diets Inc.). Their respective controls were kept on normal chow diet (NC) for up to 20 weeks. After sacrificing the gonadal white adipose tissue (GWAT) from WT animals on NC (Samples 1-6) or HFD (Samples 7-12)  was collected as well as the whole aortae from LDLR-/- animals on  NC (Samples 13-15) or HFSC (Samples16-18). The collected tissues were immediately snap frozen in liquid nitrogen. RNA was isolated for gene expression microarray analyses at the exon level (GeneChip Mouse Exon 2.0 ST Array, Affymetrix, Santa Clara, CA, USA). To isolate RNA, the frozen tissue samples were homogenized in TRIzol® reagent (Invitrogen/Life Technologies, Carlsbad, CA, USA) and processed based on manufacturer’s instructions. Total RNA (1μg) was then used for GeneChip analysis, individual samples were used in GWAT preparation and three samples were pooled and used for aorta preparations. Terminal-labeled cDNA, hybridization to genome-wide Mouse Gene 2.0 ST Gene Chips and scanning of the arrays were carried out according to the manufacture’s indications (Affymetrix). Output primary row data was analyzed with Expression Console software (Affymetrix).

first: M

last: Amor

first: V

last: Moreno-Viedma

first: A

last: Sarabi

first: N

middle: G

last: Grün

first: B

last: Itariu

first: L

last: Leitner

first: I

last: Steiner

last: Jeitler

last: Bilban

first: K

last: Kodama

last: Butte

first: G

last: Staffler

last: Zeyda

first: T


title: Gene expression profiling reveals cytoplasmic U1 snRNA accumulation may cause cancers

city: Tianjin

first: Shan

last: Gao

address: No 94, weijin road

institute: Nankai University

summary: In this study, we built a model of cytoplasmic aggregation of U1 snRNA in a rat cell line. By comparing the gene expression profiling of U1 snRNA accumulated cells with their controls, 916 (about 4% of 20,000) genes were identified significantly differentially expressed. These 595 over-expressed genes and 321 repressed genes were further analyzed by GO and KEGG pathway enrichment. As a result, three of 12 enriched pathways are well-known cancer pathways, while nine of them were associated to cancers in previous studies. These findings suggest that cytoplasmic U1 snRNA accumulation may cause cancers.

overall_design: These PC-12 cells were sampled for three times (treatment group) and transfected by 4 ug pRIREN-RetroQ vector. The other three samples (control group) were transfected by 4 ug empty pRIREN-RetroQ vectors.

first: Tao

last: Zhang


title: Expression data from induced astrocytes , primary astrocyte and MEFs

status: Public on Jul 07 2016

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: MEFs treated by compounds for 25 days can be induced into astrocytes.  In induced astrocytes, specific astrocytes-related sets of genes are up-regulated, but fibroblasts-related genes are down-regulated.

overall_design: The induced cells sorted for GFP-positive cells by flow cytometry and primary astrocytes and MEFs were parepared  for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the induced astrocytes with primary astrocytes and MEFs.

first: E

last: Tian

first: Charles

last: Warden


title: Propionibacterium acnes inhibits FOXM1 (Forkhead box M1) and induces cell cycle alterations in human primary prostate cells

status: Public on Jul 11 2016

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The composition of the prostate microbiome may influence the fate of the cells that may be relevant to prostate morbidity. Several independent studies have reported the presence of the bacterium Propionibacterium acnes in diseased human prostate tissue. It is unclear if the bacterium is an infectious agent, part of a normal prostate microbiota or if it is derived from the skin and accidentally introduced, for instance during a prostate biopsy. Previous research with prostate cell culture and animal models has revealed the capability of P. acnes to establish a low-grade chronic inflammation. However, the fate of primary prostate cells exposed to P. acnes has not been investigated in molecular detail. Here, we investigated the impact of P. acnes on human primary prostate epithelial cells (PrEC). An initial analysis of the host cell response by microarray technology confirmed the inflammation-inducing capability of P. acnes but also showed the deregulation of genes involved in cell cycle, and more specifically in kinetochore and centromere functionality. In particular, we could show and confirm by qPCR that only viable P. acnes downregulated a master regulator of cell cycle progression, FOXM1, as well as its target genes. It was further shown by flow cytometry that P. acnes was indeed able to alter the cell cycle by increasing the number of PrEC cells in S-phase. In search for a molecular explanation we tested the hypothesis that a P.acnes produced berninamycin A-like thiopeptide, that is a structurally closely related to the known FOXM1 inhibitor siomycin A, is responsible for the effect on FOXM1 and the cell cycle. A knock-out mutant in P. acnes was created that lacked the gene encoding the berninamycin A peptide precursor; this mutant was unable to downregulate FOXM1, suggesting that a berninamycin A-like thiopeptide induces cell cycle alterations in PrEC cells. Interestingly, the gene cluster encoding this thiopeptide is restricted to a subtype of P. acnes that is relatively rare on human skin, but more often found in prostate tissue.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Behnam

last: Sayanjali

first: Gitte

last: Christensen

first: Munir

last: Al-Zeer

last: Meyer

first: Holger

last: Brüggemann


title: Gene expression profiling of Sox2+ Patched1+/- medulloblastoma cells

status: Public on Jul 08 2016

first: John

middle: E

last: Dick

state: Ontario

address: University Health Network, Princess Margaret Cancer Research Tower, E Tower, 8th floor, 8-301

department: Molecular Genetics

institute: University of Toronto

summary:
Only a minority of medulloblastoma cells can self-renew and sustain tumor growth. In the Patched1+/- mouse model, these cells are quiescent and express the stem cell marker Sox2. We sought to define the gene expression profiling of these cells to gain insight into the molecular pathways that govern this population.
Sox2-expressing and Sox2-negative cells were isolated from primary Sox2-eGFP;Patched1+/- tumors as GFP+ or GFP- tumors, respectively.

overall_design: Sox2-eGFP; Patched1+/- mice were sacrificed at the first sign of a brain tumor and their tumors freshly dissected in PBS. Using flow-cytometry, tumors were depleted of CD45+ and Ter119+ cells to remove microglia and hematopoeitic-derived cells, then highly purified Sox2-eGFP+ and Sox2-eGFP- cells were isolated for gene expression profiling

first: Peter

middle: B

last: Dirks

first: Robert

last: Vanner


title: Development of gene expression profiles for murine breast tumours treated with Sunitinib

status: Public on Jul 06 2016

city: Birmingham

first: Joseph

middle: William

last: Wragg

state: West Midlands

address: Edgbaston

department: Institute of Biomedical Research

country: United Kingdom

institute: University of Birmingham

summary: In order to establish a profile of gene expression of tumours treated with sunitinib, 4T1 breast tumours were allowed to establish in Balb/C mice for 1 week. The mice were then treated with 40 mg/kg Sunitinib in PBS and 3.72% DMSO (treatemt group) or PBS-DMSO vehicle alone (no treatment group), daily for the period of the experiment, after which the tumours were resected homogenised and subjected to CD31 microbead separation of endothelial cells and bulk tissue, both of which were subjected to agilent microarray analysis. Treated tumours greater than 250 mm3 (by caliper measurement) after 8 days of treatment were considered resistant to treatment, those smaller than this were considered sensitive to sunitinib treatment.

overall_design: Total RNA was extracted from each tumour sample using the Qiagen miRNAeasy kit, processed into cRNA using the Agilient low input, one colour labelling kit, hybridised onto the 8 x 66k whole mouse genome expression microarrays. Data was normalised in R64 and comparison matrices between treated and untreated endothelum and bulk fractions were constructed. Genes whose expression was significantly altered by sunitinib treatement were taken forward for further analysis.

first: Roy

last: Bicknell


title: Domain-Dependent Effects of Insulin and IGF-1 Receptors on Preadipocyte Gene Expression

status: Public on Jul 01 2016

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary:
Despite a high degree of homology, insulin and IGF-1 receptors (IR/IGF1R) mediate distinct cellular and physiological functions. Here, using chimeric and site-mutated receptors, we demonstrate how domain differences between IR and IGF1R contribute the distinct functions of these receptors.
Receptors with the intracellular domain of IGF1R show increased activation of Shc and Gab-1 and more potent regulation of genes involved in proliferation, corresponding to its higher mitogenic activity. Conversely, receptors with the intracellular domain of IR display higher IRS-1 phosphorylation, stronger regulation of genes in metabolic pathways and more dramatic glycolytic responses to hormonal stimulation.

overall_design: We generated mouse brown preadipocytes in which both insulin and IGF-1 receptors (IR and IGF1R) had been genetically inactivated using Cre-lox recombination. These IR and IGF1R DKO cells were then reconstituted with wild-type mouse IR, IGF1R, or one of two chimeric receptors: IR/IGF1R with the IR extracellular domain (ECD) fused to the IGF1R transmembrane and intracellular domains (ICD) and IGF1R/IR with the ECD of IGF1R fused to the ICD domains of IR. Three independent clones for each line were used for the study. For expression analysis, we serum-starved the preadipocytes clones overnight and stimulated cells with 100 nM insulin, IGF-1 or vehicle for 6 h, and subjected the cellular RNA to analysis using Affymetrix Mouse Gene 2.0 ST arrays.

first: Weikang

last: Cai

first: C

last: Kahn


title: Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

summary: In this study we show that, in embryonic fibroblasts from mice on a high fat diet and treated with Forskolin, ionizing radiation exposure or both, phosphorylation of CREB-binding protein (CREB) by ATM (ataxia-telangiectasia-mutated) and casein kinases 1 and 2 (CK1 and CK2) on a cluster of five phosphorylation sites (the ATM/CK cluster) within the unstructured kinase-inducible domain (KID) provides an additional level of regulation through dynamic modulation of CREB DNA binding activity. Stoichiometric phosphorylation of the ATM/CK cluster in response to DNA damage inhibited cAMP-induced CREB target gene expression, CREB DNA binding activity, and CREB-CRTC2-DNA ternary complex formation proportional to the number of phosphate residues modified. Substoichiometric phosphorylation of the ATM/CK cluster promoted cAMP/Ca2+-regulated transcriptional coactivators (CRTCs) recruitment and CREB activation via an ATM-independent, PKA-dependent pathway. Mice expressing a non-phosphorylatable CREBS111A allele exhibited phenotypes consistent with CREB deregulation, including fasting hyperglycemia, susceptibility to diet-induced obesity, and reduced expression of gluconeogenic genes.

overall_design: Two genotypes: CREB+/+ (wild type) and CREBS111A (non-phosphorylatable CREB KID S111A mutant allele) each control treated, exposed to forskolin, ionizing radiation or both in triplicate and in two batches toataling 48 arrays

first: Randal

middle: S

last: Tibbetts

first: Sang-Hwa

last: Kim


title: Expression data from naive, effector and memory-like ILC2s isolated from mouse lungs and those from effector and memory-like ILC2s isolated from mediastinal lymph node

status: Public on Jun 30 2016

city: Vancouver

first: Laura

last: Mathae

state: British Columbia

address: 675 W.10th Ave

institute: British Columbia Cancer Research Centre

summary: Group 2 innate lymphoid cells (ILC2s) in the lung are stimulated by inhaled allergens. ILC2s do not directly recognize allergens but they are stimulated by cytokines including interleukin (IL)-33 released by damaged epithelium.Lung ILC2s, upon stimulation, produce T helper 2 cell-type cytokines inducing T cell independent allergic lung inflammation. We now report that lung ILC2s, upon activation by an allergen or IL-33, acquire the properties of memory cells. The activated ILC2s initially proliferate and secrete cytokines, followed by a contraction phase as they stop producing cytokines. Nevertheless, some persist long after the resolution of the inflammation and acquire intrinsic capacities to react to unrelated allergens more vigorously than naïve ILC2s, thus mediating a severe allergic lung inflammation. Gene expression profiles of the previously activated ILC2s show a gene signature of memory T cells. These antigen non-specific memory ILC2s may explain why asthma patients are often sensitized to multiple allergens.

overall_design: ILC2s were isolated from mouse lungs from naive and IL-33 injected mice 4 days, 14 days and 4 months after the initial treatment. RNA was extracted from those ILC2 populations and analyzed for gene expression profiles. RNA was also extracted from ILC2s isolated from lung draining mediastinal lymph node (mLN) 4 days and 14 days after IL-33 treatment.

first: Itziar

last: Martinez-Gonzalez

last: Mathä

first: Fumio

last: Takei


title: Nerve-derived Schwann cell precursors, acting in a paracrine fashion, are essential for mammalian digit tip regeneration [MOUSE]

first: Freda

last: Miller

summary: Multi-tissue regenerative capacity is lost in adult mammals with the exception of the distal digit, which regenerates via largely-uncharacterized mechanisms.  Here, we demonstrate that following adult mouse distal digit removal, nerve-associated Schwann cell precursors (N-SCPs) dedifferentiate and secrete growth factors that promote expansion of the blastema and digit regeneration.  Specifically, when N-SCPs were dysregulated or ablated, mesenchymal precursor proliferation in the blastema was decreased, nail and bone regeneration were impaired, and regeneration could be rescued by transplantation of exogenous N-SCPs.  We show that N-SCPs secreted factors that promoted self-renewal of mesenchymal precursors, and we used transcriptomic and proteomic analysis to define candidate factors. Two of these, oncostatin M (OSM) and PDGF-AA, were made by N-SCPs in the regenerating digit, and rescued the deficits in regeneration caused by loss of N-SCPs due to denervation.  Since nerves innervate every peripheral tissue, these results have broad implications for mammalian tissue repair and regeneration.

overall_design: We obtained the blastemas from three independent biological replicates of regenerating mouse digits and four independent biological replicates on uninjured mouse digits.

first: Adam

last: Johnston

first: Scott

middle: A

last: Yuzwa

first: Matthew

last: Carr

first: Neemat

last: Mahmud

first: Mekayla

last: Storer

last: Krause

first: Karen

last: Jones

first: Smitha

last: Paul

first: David

last: Kaplan

middle: D


title: RIP4 inhibits STAT3 Signaling to sustain Lung Adencarcinoma Differentiation

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Evaluation of the role of RIP4 in lung adenocarcinoma revealed that RIP4 inhibits STAT3 signaling in vitro and in vivo. Repression of RIP4 enhanced STAT3 signaling activation in KRAS LSL/G12D/wt; p53flox/flox murine tumors. This promoted cancer dedifferentiation through ECM remodeling

overall_design: Investigation of transcriptional changes in KP tumors expressing shRNA against RIP4 or p53 (control) by microarray (Mouse gene 2.0 ST array from affymetrix)

first: Jawahar

last: Kopparam

first: Johanna

last: Chiffelle

first: Alessandra

last: Piersigilli

first: Mauro

last: Delorenzi

first: Etienne

last: Meylan


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [iPSCs_expression_with_different_culture_conditions]

status: Public on Jun 29 2016

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins.

overall_design: Human induced pluripotent stem cells cultured with different conditions (0ng/ml-100ng/ml basic FGF for 7 days, 0-100ng/ml Activin A for 7 days) (N = 8).

first: Masatoshi

last: Nishizawa

first: Megumi

last: Narita

first: Yoshida

last: Yoshinori


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [iPSC_ESC_lines]

overall_design: Human iPSCs after hematopoietic differentiation (n = 2), human iPSCs after neural differentiation (n = 1), human iPSCs with different culture conditions (n = 8), and human iPSC line forced to express IGF2 gene (n = 1), and its control (n = 1).


title: Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_1]

city: San Francisco

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Chronic inflammation promotes breast tumor growth and invasion by accelerating angiogenesis and tissue remodeling in the tumor microenvironment.  The relationship between inflammation and estrogen, which drives the growth of 70 percent of breast tumors, is complex. Low levels of estrogen exposure stimulate macrophages and other inflammatory cell populations, but very high levels are immune suppressive. Breast tumor incidence is increased by obesity and age, which interact to influence inflammatory cell populations in normal breast tissue. The molecular impact of these factors on tumor initiation and growth is not well-understood. We modeled the difference in gene expression between 195 breast adenocarcinomas and 195 matched adjacent normal breast tissue samples, using age, body mass index (BMI), and tumor subtype as covariates. Age and BMI were independently associated with inflammation in normal tissue but not tumors. Older patients with ER-positive disease had tumors with higher levels of Estrogen Receptor (ER) signaling compared to adjacent normal tissue and had lower relative levels of tumor macrophage expression. We developed a novel statistic to quantify the rewiring of gene co-expression networks and demonstrate that in ER-positive tumors basal gene networks are rewired even though their expression levels of these genes are not significantly different from those in adjacent normal tissue.  Patient age influences the molecular profile of ER-positive breast tumors. Our data support an immunosuppressive effect of estrogen signaling in the breast tumor microenvironment, suggesting this effect contributes to the greater presence of prognostic and therapeutically relevant immune cells in ER-negative tumors.

overall_design: 137 total samples: 43 mammaplastic reduction, 47 breast adenocarcinoma, 47 paired adjacent normal breast tissue

first: Vessela

last: Kristensen


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [Erythroid_lines]

overall_design: iPSC/ESC-derived erythroblasts (n = 6)


title: Identification and successful negotiation of a metabolic checkpoint in direct neuronal reprogramming

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Despite the widespread interest in direct neuronal reprogramming, the mechanisms underpinning fate conversion remain largely unknown. Our study revealed a critical time point after which cells either successfully convert into neurons or succumb to cell death. Co-transduction with Bcl-2 greatly improved negotiation of this critical point by faster neuronal differentiation. Surprisingly, mutants with reduced or no affinity for Bax demonstrated that Bcl-2 exerts this effect by an apoptosis-independent mechanism. Consistent with a caspase-independent role, ferroptosis inhibitors potently increased neuronal reprogramming by inhibiting lipid peroxidation occurring during fate conversion. Genome-wide expression analysis confirmed that treatments promoting neuronal reprogramming elicit an anti-oxidative stress response. Importantly, coexpression of Bcl-2 and anti-oxidative treatments lead to an unprecedented improvement in glial-to-neuron conversion after traumatic brain injury in vivo, underscoring the relevance of these pathways in cellular reprograming irrespective of cell type, in vitro and in vivo.

overall_design: We performed gene expression microarray analysis on mouse embryonic fibroblasts transfected with a viral vector for Ascl1 or empty vector. Cells were then cultured in the absence or presence of forskolin

first: Sergio

last: Gascon

first: Elisa

last: Murenu

first: Giacomo

last: Masserdotti

first: Felipe

last: Ortega de la O

first: Gianluca

middle: L

last: Russo

last: Petrik

first: Aditi

last: Deshpande

first: Christophe

last: Heinrich

first: Marisa

last: Karow

first: Stephen

last: Robertson

first: Timm

middle: T

last: Schroeder

first: Martin

last: Irmler

first: Carsten

last: Bernd

first: José

last: Friedmann Angeli

first: Marcus

last: Conrad

first: Benedikt

last: Berninger

first: Magdalena

last: Götz


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [Undifferentiated human induced pluripotent stem cells]

first: Yoshinori

last: Yoshida

overall_design: Undifferentiated human induced pluripotent stem cells (N = 23)

first: Masatoshi

last: Nishizawa

first: Megumi

last: Narita

first: Yoshida

last: Yoshinori


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [Human pluripotent stem cells-derived hematopoietic precursor cells]

overall_design: human pluripotent stem cell-derived hematopoietic precursor cells (n = 33)


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [iPS_derived_erythroiblasts]

overall_design: iPSC-derived erythroblasts (n = 1)


title: Murine regulatory T cells stimulated by death receptor 3 agonistic antibody

status: Public on Jun 28 2016

city: Tsukuba

first: Yasuhisa

last: Yokoyama

state: Ibaraki

address: 1-1-1, Tennodai

department: Department of Hematology

institute: University of Tsukuba

summary:
CD4+Foxp3+ regulatory T cells (Treg) are a subpopulation of T cells, which regulate the immune system and enhance immune tolerance after transplantation. Donor-derived Treg prevent the development of lethal acute graft and host disease (GVHD) in murine models of allogeneic hematopoietic cell transplantation. It was reported that a single treatment of the agonistic antibody to Death receptor 3 (DR3) in donor mice resulted in the expansion of donor derived Treg and prevented acute GVHD, although the precise role of DR3 signaling in GVHD has not been elucidated.
We analyzed the gene expression profile, immune phenotype, and function of DR3-activated Treg in a murine model of allogeneic hematopoietic cell transplantation.

overall_design: CD4+Foxp3+ Treg were sorted from the mice stimulated with anti-DR3 or control antibody using fluorescence-activated cell sorter for RNA extraction and hybridization on Affymetrix microarrays.

first: Hidekazu

last: Nishikii


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [parental_lines_expression]

overall_design: Expression analysis of parental somatic tissues of human iPSCs used for the present study.

first: Michiyo

last: Koyanagi-Aoi


title: Gene expression profiles of U87 cells after transfection with hsa-miR-145-5p and 31-5p

status: Public on Jun 23 2016

city: Fukuoka

first: Ryota

last: Kurogi

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

department: Department of Neurosurgery

institute: Graduate School of Medical Sciences, Kyushu University

summary: We analyzed the expression profiles of hsa-miR-145-5p or hsa-miR-31-5p-targeting genes relating to invasion or migration after co-overexpression of hsa-miR-145-5p and 31-5p

overall_design: Gene expression profiles of U87 cells after co-transfection with hsa-miR-145-5p and 31-5p mimics, and U87 cells after transfection miR mimic negative control

first: Akira

last: Nakamizo


title: Survivin deficient Hepatocellular carcinoma and non-cancerous tissue of mice

status: Public on Jun 22 2016

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

summary: Hepatocellular carcinoma (HCC) is a deadly cancer lacking efficacious therapies. Latest studies show that cellular senescence and inflammation play key roles in HCC development, likely reflecting its etiological nature of chronic infection. A better understanding of these intertwined processes would facilitate development of therapies for malignant HCCs. Here, we show that malignant HCCs are drastically reduced after deletion of Survivin, an inhibitor of apoptosis protein. Survivin deficiency induces mitosis defect-caused metabolism reprogram and senescence in HCC cells. Survivin additionally protects both senescent and neighboring non-senescent cancer cells from cell death triggered by senescence-associated inflammatory factor TNFα. Importantly, combination of mitosis inhibitor and pro-apoptosis drug, but not alone, synergistically eliminates HCCs, recapitulating the therapeutic effect of genetic deletion of Survivin. By uncovering the role of Survivin in controlling the interaction of senescence and inflammation responses, our findings propose a strategy for HCC therapy by inducing senescence and boosting TNFα-mediated cell death.

overall_design: Three samples are Survivin deleted HCC, three samples are Survivin wild type HCC. Three samples are Survivin deleted non-cancerous tissue, three samples are Survivin wild type non-cancerous tissue.

first: Dan

last: Li


title: Expression data from Lck-Dlx5 lymphoma

status: Public on Jun 24 2016

city: Philadelphia

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

summary:
Lck-Dlx5 induces T-cell lymphoma but the mechanism is unknown.
We used microarrays to detail the global programme of gene expression underlying Dlx5-induced T-cell lymphoma

overall_design: T-cells were isolated from Lck-Dlx5 mice, Lck-MyrAkt2 mice and Wild type littermates for RNA extraction and hybridization on Affymetrix microarrays.

first: Yinfei

last: Tan

first: Eleonora

last: Sementino

first: Joseph

last: Testa


title: Gene expression profile of E18.5 mouse lungs lacking epithelial Hdac3

status: Public on Jun 21 2016

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The molecular mechanism of how lung sacculation occurs is poorly understood. Loss of epithelial Hdac3 results in defects in the proper expansion of distal lung saccules into primitive alveoli. In this microarray, we seek to investigate the gene profile changes caused by loss of Hdac3 to better understand the molecular pathways that are regulated by Hdac3 during lung sacculation.

overall_design: We collected a total of ten E18.5 mouse lung samples in RNA later,  five for the control group or and five for the Hdac3 KO group.

first: Yi

last: Wang

first: Edward

last: Morrisey


title: Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Mouse_15M_SV_Affy)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: Analysis of transcriptome of seminal vesicle from 15-month-old Nkx3.1+/+ mice.

overall_design: Total RNA obtained from seminal vesicle from 15-month-old Nkx3.1+/+ mice. Seminal vesicle was harvested, RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) and purified using an RNeasy kit (Qiagen, Chatsworth, CA). cDNA was labeled using a BioArray High-Yield RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) and hybridized to Affymetrix GeneChips (Mu74AV2).

first: Aditya

last: Dutta

first: Clementine

last: Le Magnen

first: Xuesong

last: Ouyang

first: Cory

last: Abate-Shen


title: Development of gene expression profiles for murine breast tumours overexpression the transcription factor PRH

status: Public on Jun 15 2016

last: Wragg

summary:
In order to establish a profile of gene expression of tumours overexpressing PRH we performed agilient microarray analysis on four 4T1 tumour samples engineered to overexpress PRH, and four control tumours with normal PRH expression. cancer, colorectal metastasis to the liver and matched healthy tissues. The tumours had recieved no treatement prior to resection. The expression profiles were compared by one colour microarray analysis between PRH overexpression and control tumours. Genes consistently differentially expressed between the groups were taken forward for further analysis.
Preparation of the tumours: 4T1 cells were infected with Adenoviral-PRH or empty Adenovirus at MOI 50 for 24 hrs. Adenoviral constructs described in Kershaw, R.M., et al., PRH/HHex inhibits the migration of breast and prostate epithelial cells through direct transcriptional regulation of Endoglin. Oncogene, 2014. 33(49): p. 5592-600. Cells were washed 4x with PBS, trypsinised, washed and resuspended in Opti-mem (Invitrogen) at 1.25x106 cells/ml and kept on ice for 20-30 min before injection. Aliquots 200 μl / 2.5x105 of the cells were injected into the no. 3 fat pad of 6-8 week old female BALB/C mice.

overall_design: Total RNA was extracted from each tumour using the Qiagen miRNAeasy kit, processed into cRNA using the Agilient low input, one colour labelling kit, hybridised onto the 8 x 66k whole human genome expression microarrays. Data was normalised in R64 and comparison matrices between matched Tumour and Healthy endothelum were constructed. Genes upregualated in all the comparisons were taken forward for further analysis.

first: Roy

last: Bicknell


title: Gene expression changes with knock-down of linc-9432

city: Singapore

first: Wanwen

last: Lan

address: 9 Hospital Drive SON Blk C #02-03

country: Singapore

institute: Singapore Eye Research Institute

summary: Comparison of gene expression in pterygium fibroblast cells after 48 h treatment with siRNA to knock down expression of linc-9432 or non-specific oligonucleotide control

overall_design: 21 nM pooled siRNA (Ambion, Life Technologies) or non-specific control oligonucleotides are added to cultured fibroblast cells for 48 hours

first: Louis

last: Tong


title: caArray_nevil-00068: Secretory Activation in Wildetype Mice from Preg12 to Lac9

status: Public on Jun 17 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: The purpose of this experiment was to generate a baseline microarray data set in order to investigate natural changes in gene expression profiles from mid pregnancy throuh mid lactation in the murine mammary gland. Four animals per time point were sacrificed, mammary tissue was collected less the lymph node, and data were gathered using MicroArray Suite v.5.0. The resulting data were used to evaluate the differences in gene expression among the timepoints investigated across secretory activation with emphasis on lipid production and secretion. Further, we hope this data set will serve as a baseline model for pathway perturbation studies.

overall_design:
nevil-00068
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: mg_u74av2
Organism: Mus musculus (ncbitax)
Tissue Sites: murine mammary gland
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Cell Types: Epithelial


title: Analysis of changes in gene expression in skin epidermis upon conditional knockout of PRC2-subunit Eed

status: Public on Jun 14 2016

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

institute: Ben-Gurion University

summary: Analysis of changes in gene expression in skin epidermis upon conditional knockout of the essential Polycomb repressive complex 2 (PRC2) subunit Eed. Loss of Eed in skin epithelium leads to de-repression of key Merkel-differentiation genes, which are known PRC2 targets, and results in ectopic formation of Merkel cells that are associated with all hair types.

overall_design: Gene expression analysis: To determine the  changes in gene expression in skin epidermis upon conditional knockout of Eed, total RNA was isolated from skin epidermis in four biologic replicates from cells in different conditions and hybridized to SurePrint G3 Mouse GE 8X60K microarrays (Agilent).

first: C

middle: N

last: Perdigoto

first: K

last: Dauber

first: I

first: E

last: Ezhkova


title: NUPR1 a new target in liver cancer: implication in controlling cell growth, migration, invasion and sorafenib resistance

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

summary: Sorafenib, an oral multikinase inhibitor, is the only approved agent for the treatment of advanced hepatocellular carcinoma (HCC). However, its benefits is modest, also because its mechanism of action remains elusive, therefore, a better understanding of its molecular action and molecular targets are needed. On the basis of our previous studies, here, we investigated the role of the nuclear protein 1 (NUPR1) in HCC and its role in the context of sorafenib treatment. NUPR1 is a stress-inducible protein over-expressed in different malignancies, however, its role in HCC is not yet fully understood. We found that NUPR1, is over-expressed in 53% of primary human HCC samples. Knockdown of NUPR1 significantly increased cell sensitivity to sorafenib and inhibits cell growth, migration and invasion of HCC cells in vitro and tumorigenicity in vivo. Moreover, NUPR1 silencing influenced expression of target genes RelB and IER3. Unsurprisingly, RelB and IER3 knockdown also inhibited HCC cells viability, growth and migration. By gene expression profiling of HCC cells following stable NUPR1 knockdown, we found that genes functionally involved in cell death and survival, cellular response to therapies, lipid metabolism, cell growth and proliferation, molecular transport and cellular movement were mostly suppressed. Network analysis of dynamic gene expression identified NF-κB and ERK as down-regulated gene nodes, and several genes known to be involved in hepatocarcinogenesis were also suppressed. In addition, we identified Runt-related transcription factor 2 (RUNX2) gene as a NUPR1 down-regulated gene. We also demonstrated that RUNX2 gene silencing inhibited HCC cells viability, growth, migration and increased cell sensitivity to sorafenib. Conclusion: We propose that NUPR1/RELB/IER3/RUNX2 pathway play pivotal role in hepatocarcinogenesis. The identification of NUPR1/RELB/IER3/RUNX2 pathway as a potential therapeutic target may contribute to the development of new treatment strategies for HCC management.

overall_design: To better understand the molecular mechanisms of NUPR1 gene action in ovarian HCC cells, we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon NUPR1 suppression in HCC cells. We compared the gene expression of the previously selected  shRNA-mediated NURP1-knockdown Hep3B clone against the corresponding control (ctrl) clone. The microarray experiments were performed in duplicates, as two hybridizations were carried out for the NUPR1-suppressing cell clone against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.


title: Notch signaling promotes differentiation of mouse mucosal mast cells

city: Tokyo

first: Nobuhiro

last: Nakano

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

department: Graduate School of Medicine

institute: Juntendo University

summary:
Intestinal mucosal mast cells are critically involved in the development of food-induced allergic disorders. However, factors that induce differentiation of mucosal mast cells in the intestinal mucosa are largely unknown.
To identify factors involved in mucosal mast cell differentiation, we compared the gene expression profiles between mucosal mast cells isolated from the small intestine and bone marrow-derived mast cells cultured in the presence of TGF-β or Notch ligand.

overall_design: Mucosal mast cells were isolated from the small intestine of naïve BALB/c mice by flow cytometry. Bone marrow-derived mast cells (BMMCs) were generated by culturing BALB/c bone marrow cells with murine interleukin-3 and stem cell factor for 3-4 weeks, and then cells were cultured for 6 days in the presence or absence of TGF-β or Delta-like 1 (Dll1), which is a Notch ligand. Total RNAs extracted from these cells were processed and hybridized to Affymetrix GeneChips.

first: Asuka

last: Honjo


title: ENOLASE treated PBMC vs Control relative to time

status: Public on Jun 01 2016

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

summary: Time dependant transcriptional profiling of healthy PBMC comparing a-ENOLASE (ENO) treatment to BSA (Control). Kinetic was performed : H0, H5, H20 and H45. Goal was to determine the biological pathways relative to ENO treatment.

overall_design: Two-condition experiment, ENO vs. Control - PBMC. Biological replicates: 3 healthy donors  (P1-P3). Two-color technology : each donor treated by ENO (Cy-5) or control  (Cy-3).


title: T-bet recruits P-TEFb to super-enhancers to regulate T helper cell differentiation (Agilent 2)

status: Public on Jun 08 2016

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

summary:
The transcription factor T-bet induces differentiation of CD4+ T cells into the Th1 lineage and also allows for a degree of functional plasticity. Here, we show that T-bet acts through super-enhancers to recruit the elongation factor P-TEFb. Th1-specific genes are poised for activation in Th2 cells and P-TEFb recruitment activates transcriptional elongation. T-bet also induces extensive P-TEFb binding at super-enhancers, where it acts to stimulate enhancer RNA transcription. P-TEFb inhibition selectively blocks activation of lineage-specific genes and reverses Th1-associated retinitis pathology. T-bet-mediated recruitment of P-TEFb to super-enhancers at otherwise poised genes provides a model for how lineage-specifying factors promote differentiation towards specific cell fates whilst maintaining a degree of functional plasticity.
Transcriptional profiling of mouse Th1 and Th2 cells treated with JQ1, which inhibits P-TEFb recruitment, or the P-TEFb inhibitor Flavopiridol vs DMSO conrol treated cells. Goal was to identify genes which are sensitive to P-TEFb inhibition.

overall_design: Two-condition experiment, unstimulated or reactivated DMSO/drug treated Th1/Th2 cells vs. naïve T cells. Biological replicates: 1

first: Arnulf

last: Hertweck


title: Unlinking a lncRNA from its associated cis element [gene expression]

first: Vikram

last: Paralkar

address: 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension

institute: University of Pennsylvania

summary:
Transcriptome analysis of effect of Lockd knockout on cells
Many long non-coding (lnc) RNAs are reported to regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (Downstream of p27), a 434 bp polyadenylated lncRNA originating 4 kb 3’ to the Cdkn1b gene. Heterozygous and homozygous deletion of the 25 kb Lockd locus reduced Cdkn1b transcription by approximately 35 and 70% respectively in a mouse erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by > 90%, but had no effect on Cdkn1b transcription. The 5’ region of the Lockd gene contains a DNase hypersensitive site, binds numerous transcription factors (TFs), and physically associates with the Cdkn1b promoter in chromosomal conformation capture (NG Capture-C) studies. Thus, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element and not via the lncRNA transcript. These findings demonstrate that the biological functions of a lncRNA cannot be inferred simply from phenotypes that arise after deleting the corresponding genomic locus.

overall_design: We analyzed mouse G1E erythroid cell line clones with Control Lockd (C - 3 replicates) and with Lockd deletion with CRISPR (KO - 4 replicates) using Mouse Gene 2.0 ST Array platform (transcript version). Array data was processed by RMA algorithm.

first: Mitchell

last: Weiss


title: Integrative sequencing reveals alterations in untreated and castration-resistant prostate cancer

status: Public on Jun 05 2016

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

summary: We conducted an integrative sequencing of genomic, transcriptomic and DNA methylation changes in 28 untreated (PC) and 13 castration-resistant prostate cancers (CRPC). We wanted to search for previously unannotated transcripts from the RNA-sequencing data. Transcriptome assembly uncovered 128 previously unannotated prostate cancer-associated transcripts. Trans-acting correlation analysis associated the expression of several TPCATs with prostate cancer-associated transcriptional regulators, such as ERG or AR. The strongest positive correlation was observed between ERG and transcript TPCAT-10-36067 that was expressed in a subset of PCs and CRPCs as well as ETV4-positive PC-3 and ERG-positive VCaP cells. We suppressed the expression of TPCAT-10-36067 with three different siRNAs in PC-3 cells, and studied the changes in the genome-wide expression patterns of the cell line using expression arrays. Gene Ontology enrichment analysis indicated that cell cycle, mitosis and Aurora signaling were the most extensively affected processes. Experimental assay showed that the siRNA suppression of TPCAT-10-36067 had a dramatic effect on the growth, invasiveness, and rate of apoptosis of prostate cancer cells.

overall_design: Two different siRNAs targeting TPCAT-10-36067 were chosen for the expression array experiments. We transfected the siRNAs to the PC-3 prostate cancer cell line which expresses TPCAT-10-36067. Gene expression arrays were made for both experiments in two replicates with dye swap comparing the RNA from transfected cell line with a non-transfected cell line.

first: Kati

middle: K

last: Waltering

first: Matti

middle: J

last: Annala

first: Kimmo

last: Kartasalo

first: Kirsi

last: Tuppurainen

first: Leena

last: Latonen

first: Simo

middle: P

last: Leppänen

first: Serdar

last: Karakurt

first: Outi

last: Saramäki

first: Mauro

last: Scaravilli

first: Janne

last: Seppälä

first: Hanna

last: Rauhala

first: Olli

last: Yli-Harja

first: Robert

last: Vessella

first: Teuvo

last: Tammela

first: Wei

last: Zhang

first: Tapio

last: Visakorpi

last: Nykter


title: Expression data from  mouse breast cancer tissue: Serglycin heterozygous and knock-out conditions

city: Uppsala

first: Ananya

last: Roy

address: Dag Hammarskjöldsväg

institute: Uppsala University

summary:
Serglycin proteoglycans contribute to proper storage and secretion of inflammatory mediators in hematopoietic cells. Serglycin is also expressed in cancer cells where increased expression has been linked to poor prognosis.
In the present study we report that serglycin proteoglycan is absolutely required for metastasis in  the MMTV-PyMT-driven mouse breast cancer model. Serglycin seems to play a role in  promoting epithelial to mesenchymal transition, cancer-related inflammation and  extravasation. Our results suggest that serglycin and serglycin-dependent mediators are  potential drug targets to prevent metastatic disease/dissemination of cancer.

overall_design: 6 total breast tumor samples were analyzed. 3 of SG+/- and 3 of SG-/- tumour tissue. Raw data was normalized using the robust multi-array average (RMA) method. To identify potential serglycin-regulated mediators of metastasis, we performed a microarray expression analysis of RNA isolated from SG+/- and SG-/- breast tumor tissue. The expression analysis identified 672 genes with a significantly altered expression level, at log2 fold >±1,2. Strikingly, only six genes were up-regulated in the SG-/- PyMT+ tumor cells compared to SG+/- PyMT+ tumor cells while 666 were significantly down-regulated.

first: A

first: M

last: Åbrink


title: Expression profiling of dendritic cell (DC) progenitors from Gata2 conditional knockout mice

status: Public on May 31 2016

city: Sendai

first: Tohru

last: Fujiwara

address: 2-1 Seiryo-cho, Aoba-ku

department: Hematology and Rheumatology

institute: Tohoku University Graduate School of Medicine

summary: Transcriptional profiling of mouse comparing in vitro-derived DC progenitors from control and Gata2 conditional knockout mice. Two-condition experiment, Control DCs vs. G2 Knockout DCs. Biological replicates: 4 control, 3 Gata2 knockout, independently grown and harvested. One replicate per array.

overall_design: Dendritic cells (DCs) are critical immune response regulators; however, the mechanism of DC differentiation is not fully understood. Heterozygous germline GATA2 mutations induce GATA2 deficiency syndrome, characterized by monocytopenia, a predisposition to myelodysplasia/acute myeloid leukemia, and a profoundly reduced DC population, which is associated with increased susceptibility to viral infections, impaired phagocytosis, and decreased cytokine production. To define the role of GATA2 in DC differentiation and function, we studied Gata2 conditional knockout and haploinsufficient mice. Gata2 conditional deficiency significantly reduced the DC count, whereas Gata2 haploinsufficiency did not affect this population. GATA2 was required for the in vitro generation of DCs from Lin−Sca-1+Kit+ cells, common myeloid-restricted progenitors, and common dendritic cell precursors, but not common lymphoid-restricted progenitors or granulocyte-macrophage progenitors, suggesting that GATA2 functions in the myeloid pathway of DC differentiation. Moreover, expression profiling demonstrated reduced expression of myeloid-related genes, including mafb, and increased expression of T-lymphocyte-related genes, including Gata3 and Tcf7, in Gata2-deficient DC progenitors. In addition, GATA2 was found to bind an enhancer element 190-kb downstream region of Gata3, and a reporter assay exhibited significantly reduced luciferase activity after adding this enhancer region to the Gata3 promoter, which was recovered by GATA sequence deletion within Gata3 +190. These results suggest that GATA2 plays an important role in cell fate specification toward the myeloid versus T lymphocyte lineage by regulating lineage-specific transcription factors in DC progenitors, thereby contributing to DC differentiation.

first: Koichi

last: Onodera

first: Hideo

last: Harigae


title: Transcriptome of Keratocystic odontogenic tumor (KCOT) using Laser capture microdissection

status: Public on May 22 2016

city: Chapel Hill

first: Shijia

last: Hu

address: 228 Brauer Hall Campus Box 7450

department: Pediatric Dentistry

institute: University of North Carolina

summary: The goal of the study was to characterize the whole genome transcriptome profiles of pure sample population of KCOT epithelial cells for examination of molecular pathways.

overall_design: Twenty human KCOT samples were obtained. Both fresh frozen and FFPE samples were used and placed in solution for 1-4 weeks to allow decalcification by EDTA. The tissue was sectioned at -35C at a thickness of 7 microns. These sections were used for laser capture microdissection (LCM) to isolate the neoplastic epithelial portion of the tumors, using static image settings.  Total RNA was extracted from each sample and examined using the whole genome microarray against the Stratagene universal human reference RNA.

first: J

last: Wright