title: Immunopathogenesis of renal inflammation during the progression, remission and relapse of renal disease in the NZB/W murine lupus model

status: Public on Aug 20 2013

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan


title: Identification of novel copy number alterations by high-resolution aCGH from FFPE cutaneous melanoma samples

status: Public on Jul 01 2013

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array.  We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates.
Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE

overall_design: We examined 34 primary melanoma formalin-fixed and paraffin-embedded (FFPE) samples by using array comparative genomic hybridization (aCGH) for DNA copy number alterations (CNAs). Genomic DNA was extracted, referred to a sex-matched diploid commercial control DNA (Promega Corporation, Madison, WI, cat. G1417 and G1521), and hybridized on the Agilent SurePrint G3 Human CGH Microarray 8x60k, cat. G4827A.

first: Luigi

last: Pasini

first: Alessandro

last: Quattrone

first: Valentina

last: Adami

first: Sebastiana

last: Boi

first: Chiara

last: Cantaloni


title: Rocaglamide selectively inhibits the G1-S-phase transition in cancer cells by activation of the ATM/ATR-mediated Chk1/2 cell cycle checkpoints

status: Public on Oct 12 2013

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

summary: The cell division cycle is tightly controlled in normal cells. Cancer cells are characterized by deregulation in cell division cycle, which is associated with increased DNA replication and elevated cellular proliferation. Recently, genetic studies indicate that cyclin dependent kinases CDK2, CDK4 and CDK6 are not essential for the mammalian cell cycle, instead, they are only required for the proliferation of specific cell types.Thus, targeting the activities of CDK2, CDK4 and CDK6 may be a promising approach for cancer treatment. Rocaglamides (Roc) (= Flavaglines), derived from the traditional Chinese medicinal plant Aglaia, are a group of naturally occurring herbal chemicals characterized by a cyclopenta[b]benzofurans skeleton. A number of Roc derivatives have been found to have potent inhibitory effects on tumor growth with IC50 concentrations at the nM rages. Roc-mediated inhibition of proliferation was first found to be associated with inhibition of protein synthesis in 1998. In this study, using the representative Roc-A compound we revealed a novel mechanistic function of Roc. We show that Roc-A induces rapid activation of ATM (ataxiatelangiectasia mutated) and ATR (ataxia-telangiectasia and Rad3-related) kinases. Activated ATM and ATR in turn activate the downstream checkpoint kinases CHK1 and CHK2. The latter then phosphorylate Cdc25A that leads to a phosphorylation-mediated degradation of Cdc25A. Usually, ATR and ATM are activated in response to DNA damage. However, in this study we show that Roc-A does not directly induce DNA breaks. To elucidate the molecular mechanism by which Roc-A activates ATM and ATR we performed a time-resolved microarray analysis to compare Roc-A-inducible genes in malignant vs. normal T lymphocytes. Based on the dynamic gene responses we found that Roc-A stimulates in Jurkat, but not in normal T lymphocytes, a set of genes responsive to DNA damage and nucleotide excision repair. This finding provides a hint of the molecular bases for Roc-induced activation of ATM and ATR. This finding also revealed a new scope for cancer treatment using Roc-A.

overall_design: The isolation time points for Roc A treated D6 T-cells were recorded at t=[1,2,3,4,6,8,10,14,20,28,36] hours after stimulation. Post-stimulation time points for Jurkat cells are t=[0.5,1,2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,36]. Unstimulated control time points were taken at t=[0,4,10,16,24,36] hours for Jurkat cells at t=[0,6,14,24,36] hours.

first: Min

last: Li-Weber

first: Jennifer

last: Neumann

first: Melanie

last: Boerries


title: Cisplatin treated melanoma and melanocyte cell lines

city: Callaghan

first: Nikola

last: Bowden

state: NSW

address: University Dr

department: School of Medicine and Public Health

country: Australia

institute: University of Newcastle

summary: Nucleotide excision repair (NER) orchestrates the repair of helix distorting DNA damage, induced by both ultraviolet radiation (UVR) and cisplatin. There is evidence that the global genome repair (GGR) arm of NER is dysfunctional in melanoma and it is known to have limited induction in melanoma cell lines after cisplatin treatment. The aims of this study were to examine mRNA transcript levels of regulators of GGR and to investigate the downstream effect on global transcript expression in melanoma cell lines after cisplatin treatment and in melanoma tumours.

overall_design: One melanocyte, three primary melanoma (MM200, IgR3, Me4405) and two metastatic melanoma (Mel-RM and Sk-mel-28) cell lines were treated with cispltain and gene expression profile data collected at 0, 6 and 24 hours. Biological duplicates were treated and RNA was collected for each cell line at each timepoint. The duplicated were run sperately on the WGGEX beadarrays and the results of the duplicates averaged for publication.     The transcript expression results were cubic spline normalised using BeadStudio 2.0 software (Illumina, USA), and the remaining analyses was performed using GeneSpring GX 11.0. To account for bias or skewing of expression results all the gene expression profiles and each individual gene were normalized to the median resulting in two way normalisation. For visualisation of the results the data was log transformed.

middle: A

first: Kelly

last: Avery-Kiejda

first: Xu

middle: D

last: Zhang

first: Peter

last: Hersey

first: Rodney

middle: J

last: Scott


title: Microarray Study Reveals Hormone-Modulated Gene Transcription During Human Podocyte Differentiation

status: Public on May 30 2013

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 2123 Adelbert Road, RT400-L

department: Biochemistry

country: USA

institute: Case Western Reserve University

summary: Glomerular podocytes are highly differentiated kidney cells that constitute one of the key components responsible for removing toxins and metabolic waste while preserving nutrients in the bloodstream in the renal glomerulus. In addition, podocytes contribute significantly to the formation of the glomerular basement membrane and the integrity of the vascular endothelium. Thus, podocyte injury and/or loss of podocytes results in impaired blood filtration and causes many common renal diseases characterized by severe proteinuria (protein in the urine) and hypoalbuminemia (low levels of blood albumin). Small lipopholic molecules such as steroids, fatty acids, prostaglandins and vitamin metabolites control many aspects of animal development, cell proliferation and differentiation, and homeostasis through binding to their intracellular receptors. Upon binding to their cognate ligands, these nuclear receptors (NRs) are capable of turning on or off of an array of gene networks. By doing so, they regulate a whole spectrum of cellular activities. The ability of small molecule hormones to regulate NR activity makes them excellent pharmaceutical targets. Clinical evidence and animal studies have implicated several NRs in contributing to podocyte development and disease. Recent studies from animals and cultured human or mouse podocytes indicate that synthetic hormones including estradiol, glucocorticoid, retinoid, pioglitazone, vitamin D3 and WY-14643 protect or rescue podocytes from experimental injury. Post treatment of injured podocytes with ligands for the above-mentioned NRs restores cytoskeletal architecture of the podocytes. Nonetheless, the mechanisms underlying the ability of these hormones in protecting podocytes remain largely unexplored. This is partly due to our limited knowledge of the target genes controlled by these hormones. In order to elucidate the mechanisms by which Dex, VD3 and ATRA elicit their renoprotective activity, we initiate a gene expression profiling study to identify the target genes of these hormones in cultured human podocytes.

overall_design: The temperature-sensitive cultured human podocytes (HPCs) were maintained in culture media of RPMI supplemented with 10% FBS, 1% antibiotics and the Insulin-Transferrin-Selenium at the permissive (undifferentiated) temperature of 33 Celsius degree. The 70%~80% confluent HPCs were induced to in vitro differentiate by culturing at 37 Celsius degree for 2 days then with incubation of vehicle (equal volume of DMSO), 100 nM all-trans retinoic acid (ATRA), 100 nM dexamethasone (Dex), or 100 nM vitamin D3 (VD3) treatment for 3 more days. The undifferentiated HPCs with vehicle (equal volume of DMSO) treatment was included as a control. The total RNAs of these cells were isolated using USB prepEase RNA spin kit following the manufacturer's instructions. Total 1 microgram RNA at 100 nanogram per microliter for each sample were sent for a single-channel gene expression microarray studies using HumanRef-8 chip (V3_0_R3_11282963) on Illumina BeadStation platform. The RNA were converted to aRNA and appropriately labelled using MessageAmp Biotin aRNA Amplification Kit (Ambion) following the manufacturer's instructions. The raw data were collected by scanning the chip on Illumina BeadStation. Background subtracted raw data were exported and the following analysis was done in R/Bioconductor environment. Thus, we were able to compare the gene expression profiles between differentiated and undifferentiated HPCs with or without hormone treatment.

first: Xiwen

last: Cheng

first: Simran

last: Khurana

first: Leslie

last: Bruggeman


title: Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling

status: Public on Jul 30 2013

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression profiles of primary cortical neurons after knocking down Cugbp1

status: Public on Apr 18 2013

city: Nagoya

first: Shinsuke

last: Ishigaki

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

country: Japan

institute: Nagoya University School of Medicine

summary: To clarify the functional properties of Cugbp1, we established the differentially expressed alternative exons in Cugbp1-silenced primary cortical neurons by using exon-sensitive microarray technology.

overall_design: We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Cugbp1 or control. RNA was harvested 11 days after transfection.

first: S

first: D

last: Honda

first: Y

last: Fujioka

first: A

last: Masuda

first: K

last: Ohno

first: G

last: Sobue


title: Expression profiles of primary cortical neurons after knocking down Tdp-43 and Cugbp1


title: Increased metallothionein expression reflects steroid resistance in renal allograft recipients.

status: Public on May 21 2013

city: Bodegraven

first: Niels

last: Rekers

state: Nederland

address: Achter Nieuwstraat

department: Immunohematology and Blood Transfusion

country: Netherlands

institute: Leiden University Medical Center

summary:
Steroid-refractory acute rejection is a risk factor for inferior renal allograft outcome. We aimed to gain insight into the mechanisms underlying steroid resistance by identifying novel molecular markers of steroid-refractory acute rejection.
Eighty-three kidney transplant recipients (1995-2005), who were treated with methylprednisolone during a first acute rejection episode, were included in this study. Gene expression patterns were investigated in a discovery cohort of 36 acute rejection biopsies, and verified in a validation cohort of 47 acute rejection biopsies.
In the discovery set, expression of metallothioneins (MT) was significantly (P<0.000001) associated with decreased response to steroid treatment. Multivariate analysis resulted in a predictive model containing MT-1 as an independent covariate (AUC=0.88, P<0.0000001). In the validation set, MT-1 expression was also significantly associated with steroid resistance (P=0.029). Metallothionein expression was detected in macrophages and tubular epithelial cells. Parallel to the findings in patients, in vitro experiments of peripheral blood mononuclear cells from 11 donors showed that non-response to methylprednisolone treatment is related to highly elevated MT levels.
High expression of metallothioneins in renal allografts is associated with resistance to steroid treatment. Metallothioneins regulate intracellular concentrations of zinc, through which they may diminish the zinc-requiring anti-inflammatory effect of the glucocorticoid receptor.

overall_design: Transcriptional profiles of 40 renal allograft biopsy samples were analyzed using Illumina HumanRef-8 v3.0 BeadChips (Illumina, San Diego, CA). Expression profiles were investigated in total RNA isolated from biopsy samples of 18 patients with steroid responsive acute rejection and 18 patients with steroid resistant acute rejection. Four biopsies, taken during acute decrease of graft function but with no histomorphologic indication of rejection, were included as controls.

middle: V

first: Ingeborg

middle: M

last: Bajema

first: Marko

last: Mallat

first: Jaqueline

last: Anholts

first: Yvonne

last: de Vaal

first: Malu

last: Zandbergen

first: Geert

middle: W

last: Haasnoot

first: Erik

last: van Zwet

first: Johan

last: de Fijter

first: Frans

middle: H

last: Claas

first: Michael

last: Eikmans


title: Gene expression profiles of human breast cancer cell lines

status: Public on May 11 2013

city: New York

first: Yongzhong

last: Zhao

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

summary: Numerous epithelial-to-mesenchymal transition (EMT)-promoting transcription factors have been implicated in tumorigenesis or metastasis, as well as chemoresistance of cancer. However, the underlying mechanism mediating these processes is unclear. Here we report that Foxq1, a forkhead box-containing transcription factor and EMT-inducing gene, promotes stemness traits and chemoresistance in mammary epithelial cells. We identify Twist1, Zeb2, and PDGFRα and β as Foxq1 downstream targets using an expression profiling assay. Further studies reveal that PDGFRα and β can be directly regulated by Foxq1, or indirectly through Twist1. Knockdown of both PDGFRα and β shows more significant effects on reversing Foxq1-promoted oncogenesis in vitro and in vivo than knockdown by either PDGFRα or β alone. PDGFRβ, but not PDGFRα, shows potent effects in reversing Foxq1-promoted stemness traits. Moreover, pharmacological inhibition or gene silencing of PDGFRs sensitize mammary epithelial cells to chemotherapeutic agents in vitro and in vivo. These findings collectively indicate PDGFRs as critical mediators underlying breast cancer tumorigenesis and chemoresistance driven by EMT promoting genes, which have potential clinical implications for cancer therapy.

overall_design: The purpose of these experiments is to investigate the downstream targets of several transcriptional factors including Foxq1 and IRX5. Another purpose is to compare the expression pattern between basal-like breast cancer cells including MDA-MB231, SUM159 and SUM1315.

first: Guojun

last: Wu


title: DNA unmethylome profiling by covalent capture of CpG sites (microarray)

status: Public on Aug 27 2013

city: Toronto

first: Viviane

last: Labrie

state: Ontario

address: 250 College st.

country: Canada

institute: Centre for Addiction and Mental Health

type: Methylation profiling by genome tiling array

summary: Here we present an approach for the mapping of unmethylated DNA. Our technique is based on DNA methyltransferase-directed transfer of activated groups (mTAG) and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interogation on tiling microarrays or next generation sequencing.

overall_design: mapping of unmethylated DNA

first: Edita

last: Kriukienė

first: Tarang

last: Khare

first: Giedrė

last: Urbanavičiūtė

first: Audronė

last: Lapinaitė

first: Karolis

last: Koncevičius

first: Daofeng

last: Li

first: Ting

last: Wang

first: Shraddha

last: Pai

first: Carolyn

last: Ptak

first: Juozas

last: Gordevičius

first: Sun-Chong

first: Artūras

last: Petronis

first: Saulius

last: Klimašauskas


title: Expression profiles of primary cortical neurons after knocking down Tdp-43

first: Shinsuke

last: Ishigaki

summary: To clarify the functional properties of Tdp-43, we established the differentially expressed alternative exons in Tdp-43-silenced primary cortical neurons by using exon-sensitive microarray technology.

overall_design: We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Tdp-43 or control. RNA was harvested 11 days after transfection.

first: S

first: D

last: Honda

first: Y

last: Fujioka

first: A

last: Masuda

first: K

last: Ohno

first: G

last: Sobue


title: Wild type vs. Ptbp2 KO mouse E18.5 cortex RNA

status: Public on May 31 2013

first: Donny

last: Licatalosi

address: 10900 Euclid Ave

summary: To assess the requirement of Ptbp2 for alternative mRNA expression in mouse brain

overall_design: RNA from the cortex of 4 wild type and 4 Ptbp2 KO E18.5 mice.  One array per sample (biological replicate), 8 arrays total.

first: Robert

middle: B

last: Darnell


title: FoxO1 target Gpr17 activates AgRP neurons to regulate food intake.

status: Public on Apr 09 2013

first: Hongxia

last: Ren

state: NY

address: 1150 St Nicholas Ave, Rm237

department: Medicine

institute: Columbia University

summary:
Hypothalamic neurons expressing Agouti-related peptide (AgRP) are critical for initiating food intake, but druggable biochemical pathways that control this response remain elusive. Thus, genetic ablation of insulin or leptin signaling in AgRP neurons is predicted to reduce satiety but fails to do so. FoxO1 is a shared mediator of both pathways, and its inhibition is required to induce satiety. Accordingly, FoxO1 ablation in AgRP neurons of mice results in reduced food intake, leanness, improved glucose homeostasis, and increased sensitivity to insulin and leptin. Expression profiling of flow-sorted FoxO1-deficient AgRP neurons identifies G-protein-coupled receptor Gpr17 as a FoxO1 target whose expression is regulated by nutritional status. Intracerebroventricular injection of Gpr17 agonists induces food intake, whereas Gpr17 antagonist cangrelor curtails it. These effects are absent in Agrp-Foxo1 knockouts, suggesting that pharmacological modulation of this pathway has therapeutic potential to treat obesity.
We used microarrays to detail the change of gene expression in AgRP neurons after knocking out FoxO1.

overall_design: AgRP neurons from control and KO mice were collected by FACS. Gene expression was analyzed by microarray.

first: Domenico

last: Accili

first: Erica

last: Seigneur

first: Leelamma

last: Panicker

first: Ching-Kang

last: Chen

first: William

middle: F

last: Simonds


title: A stem cell model of diabetes due to glucokinase deficiency

status: Public on Apr 05 2013

first: Haiqing

last: Hua

address: 3960 Broadway

summary: Diabetes is a disorder characterized by loss of beta cell mass and/or beta cell function, leading to deficiency of insulin relative to metabolic need. To determine whether stem cell derived-beta cells faithfully reflect the phenotypes of a diabetic subject, we generated induced pluripotent stem cells from diabetic subjects (MODY2) with heterozygous loss-of-function of the gene encoding glucokinase (GCK). These stem cells differentiated into beta cells with an efficiency comparable to controls, and expressed markers of mature beta cells, urocotin-3 and zinc transporter 8 upon transplantation into mice. While insulin secretion in response to arginine or other secretagogues was identical to cells from healthy controls, GCK mutant beta cells required higher glucose levels to stimulate insulin secretion. Importantly this glucose-specific phenotype was fully reverted upon gene sequence correction by homologous recombination. Our results demonstrate that stem cell-derived beta cells reflect beta cell-autonomous phenotypes of MODY2 subjects, providing a platform for mechanistic analysis of specific genotypes on beta cell function.

overall_design: Induced pluripotent stem cells with munations in the glucokinase gene were differentiationed into pancreas cells using published protocol (D'Amour et al, 2006) with certain modifications. 1 million cells(fibroblast or stem cells or differentiated pancreatic cells) was used for RNA extraction and labeling using the Illumina total prep RNA amplification kit.

first: Dieter

last: Egli


title: Disruption of Ttll5/Stamp gene (Tubulin tyrosine ligase-like protein 5/SRC-1 and TIF2 associated modulatory protein gene) in male mice causes sperm malformation and infertility

status: Public on Mar 28 2013

city: Bethesda

first: WeiPing

state: MD

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

department: GCL

institute: NIDDK/NIH

summary: Tubulin tyrosine ligase-like family member 5 (TTLL5/STAMP) has multiple activities in cells. TTLL5 is one of 13 TTLLs, has polyglutamylation activity, augments the activity of p160 coactivators (SRC-1 and TIF2) in glucocorticoid receptor-regulated gene induction and repression, and displays steroid-independent growth activity with several cell types. To examine TTLL5/STAMP functions in whole animals, mice were prepared with an internal deletion that eliminated several activities of the Stamp gene. This mutation causes both reduced levels of STAMP mRNA and C-terminal truncation of STAMP protein. Homozygous targeted mutant (Stamptm/tm) mice appear normal except for marked decreases in male fertility associated with defects in progressive sperm motility. Abnormal axonemal structures with loss of tubulin doublets occur in most Stamptm/tm sperm tails in conjunction with substantial reduction in tubulin polyglutamylation, which closely correlates with the reduction in mutant STAMP mRNA. The axonemes in other structures appear unaffected. There is no obvious change in the organs for sperm development of wt vs. Stamptm/tm males despite the levels of wt STAMP mRNA in testes being 20-fold higher than in any other organ examined. This defect in male fertility is unrelated to other Ttll genes or 24 genes previously identified as important for sperm function. Thus, STAMP appears to participate in a unique, tissue-selective TTLL-mediated pathway for tubulin polyglutamylation that is required for sperm maturation and motility and may be relevant for male fertility.

overall_design: Testes RNA samples for EXON arrays from WT and KO with three biological replications

first: Geun-Shik

last: Lee

first: Yuanzheng

last: He

first: Edward

last: Dougherty

first: Maria

last: Jimenez-Movilla

first: Matteo

last: Avella

first: Sean

last: Grullon

first: David

middle: S

last: Sharlin

first: Chunhua

last: Guo

first: John

last: Blackford

first: Smita

last: Awasthi

first: Zhenhuan

last: Zhang

first: Stephen

middle: P

last: Armstrong

first: Edra

last: London

first: Weiping

first: Jurrien

last: Dean

last: Simons


title: Intestinal label-retaining cells are secretory precursors expressing Lgr5

status: Public on Feb 27 2013

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

summary: The epithelial lining of the small intestine is continuously renewed from a small number of stem cells including Lgr5 expressing crypt base cells that have been shown to be a rapidly cycling stem cell population in homeostasis. Alternative markers of intestinal stem cells have variously identified populations as rapidly cycling or quiescent with proposed roles for the latter as a parallel or reserve stem cell population. However, the exact nature of quiescent crypt cells remains unknown. Here by applying novel mouse models that permit their isolation and characterisation as label-retaining cells (LRCs), and for the first time performing lineage tracing from them, we show quiescent cells to be committed secretory precursors that are capable of recall to the stem cell state. We reveal LRCs to be a small subset of the rapidly cycling Lgr5 expressing population committed along the Paneth-enteroendocrine lineage. Significantly, after injury and subsequent regeneration they are clonogenic, as shown by both lineage tracing and organoid growth demonstrating that they can be recalled to the stem cell pool. These findings in establishing quiescent cells as an effective clonogenic reserve during injury provides a motivation for investigating their role in the maintenance of cancer growth following adjuvant treatment.

overall_design: Six age and sex (female) matched Cyp1a1-H2B-YFP mice ten days post βNF induction were used comparing three cell populations from each.  Following epithelial isolation, single cell preparation and staining with anti-CD24 anitbody and UEA-1 lectin, 30,000 cells were flow sorted for each population: Paneth cells (Paneth) were defined as CD24+/UEA+, YFP-LRCs (YFPpos) as CD24+/UEA-/YFP+ and LCCs (YFPneg) as CD24+/UEA-/YFP-.  Microarray expression comparison was then performed to identify unique markers of each population.  RNA amplification and hybridisation was performed at the Paterson Institute, Manchester, UK, Microarray Facility using Nugen Ovation Pico WTA System for amplification and then hybridisation to a Mouse Exon 1.0 ST Array.  Arrays were scanned using an Affymetrix GeneChip scanner 3000 running GCOS software.

first: Simon

last: Buczacki

first: Heather

middle: I

last: Zecchini

first: Anna

last: Nicholson

middle: R

first: L

last: Vermeulen

first: Richard

last: Kemp

first: Doug

last: Winton


title: Effect of simultaneous activation of TGFbeta and TLR4 pathway in human monocytes

status: Public on Dec 15 2012

city: Utrecht

first: Karlijn

last: van Keulen

address: Heidelberglaan 100, G02.523

department: division heart and lungs

institute: University Medical Center Utrecht

summary: To better understand the interaction of TGFbeta and Toll-like-receptor 4 (TLR4) signaling in monocytes, we performed microarray analysis. We identified a unique set of genes whose expressions in monocytes were regulated by simultaneous stimulation of TLR4 and TGFβ signaling.

overall_design: THP-1 cells, a human monocytic cell line, were stimulated for 24 hours with PBS as control, LPS (100ng/ml), TGFbeta1 (1ng/ml) or LPS (100ng/ml) + TGFbeta1 (1ng/ml). After 24 hours of stimulation, total RNA was isolated and prepared for genome wide analyses using Illumina HumanRef8 V3.0 Beadchips. In total 32 arrays were analyzed including 8 samples of PBS-stimulated monocytes, 8 samples of LPS-stimulated monocytes, 8 samples of TGFbeta1 stimulated monocytes and 8 samples of monocytes stimulated with LPS + TGFbeta1.

first: J

middle: K

first: Dominique

last: de Kleijn

first: S

last: Lim

first: Peter

last: van der Spek

first: Sigrid

last: Swagemakers

first: Gerard

last: Pasterkamp


title: Gene expression profile changes in PKC-inhibitor-pretreated HT1080 cells cells after TLR3 stimulation

status: Public on Apr 03 2013

first: Ganes

middle: C.

last: Sen

address: 9500 Euclid Avenue NE-20

institute: Cleveland Clinic

summary: TLR3 stimulation by extracellular dsRNA (e.g. polyIC) induces expression of numerous genes. The inhibition of PKC by Go6976 prior to TLR3 stimulation leads to an ablation of expression of IRF-3-dependent genes.

overall_design: Total RNA extracted from HT1080 cells with or without 1 h pretreatment with 5 uM Go6976, after 6 h of treatment with dsRNA (polyIC), compared to untreated controls


title: Leukocyte gene expression in depressed and non-depressed renal cell carcinoma patients

status: Public on Apr 01 2013

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary: Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from renal cell carcinoma patients.  The primary research question is whether gene expression differs as a function of patient's level of depression as measured by CESD score > 16.


title: Transcriptional profiles of MET transformed osteoblast clones (MET-HOB) and mesenchymal stem cells (MSC) where osteoblast differentiation was induced

status: Public on Feb 28 2013

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: The osteogenic differentiation process consists in a well-coordinated multi-step sequence of events, in which each stage is characterized by the expression of distinct protein markers, as well as by individual morphological features. In order to precisely identify the step at which cells are permissive to MET-driven transformation, we used expression profiling. We compared the transcriptional profiles of MET-HOB and MSC cells where osteoblast differentiation was induced.

overall_design: Using microarrays, we evaluated the expression profiles of MET-HOB and MSC cells where osteoblast differentiation was induced, by culturing cells in the presence of ascorbic acid, α-glycerophosphate and dexamethasone for 7, 14 and 21 days

first: Nadia

last: Dani

first: Martina

last: Olivero

first: Katia

last: Mareschi

first: MarjanMarja

last: vanDuist

first: Silvia

last: Miretti

first: Sara

last: Cuvertino

first: Salvatore

last: Patané

first: Riccardo

last: Ferracini

last: Scotlandi

first: Franca

last: Fagioli

first: MariaFlavia

last: DiRenzo


title: Genome-wide gene expression analysis of  primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines MUM2B and OCM1A

status: Public on Feb 14 2013

first: Li

last: Zhang

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

summary: Gene expression in primary uveal melanoma cells and normal cell controls

overall_design: The HumanHT-12 v3 gene expression microarray (Illumina) was used to analyze RNA isolated from snap-frozen primary uveal melanoma tissue isolated from enucleated eyes and from normal cell controls.

first: Saunthararajah

last: Yogen


title: Genome wide array analysis of endosseous implant adherent cellular phenotypes

status: Public on Sep 27 2012

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

summary: Objective: to identify the early molecular processes involved in osseointegration associated with a micro roughened and nanosurface featured implants.

overall_design: Thirty-two titanium implants with surface topographies exhibiting nanoscale features (AT-I) and microrough surface without nanoscale features (AT-II) were placed in the tibiae of 8 rats and subsequently harvested at 2 and 4 days after placement. Total RNA was isolated from cells adherent to retrieved implants. A whole genome microarray using the Affymetrix Rat gene 1.1 ST Array  was used to describe the gene expression profiles that were differentially regulated by the implant surfaces.

first: Ghadeer

middle: N

last: Thalji


title: Differential induction of TLR3-dependent innate immune signaling by closely related parasite species_II

status: Public on Mar 29 2013

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: The closely related protozoan parasites Toxoplasma gondii and Neospora caninum display similar life cycles, subcellular ultrastructure, invasion mechanisms, metabolic pathways, and genome organization, but differ in their host range and disease pathogenesis.   Type II (γ) interferon has long been known to be the major mediator of innate and adaptive immunity to Toxoplasma infection, but genome-wide expression profiling of infected host cells indicates that Neospora is a potent activator of the type I (α/β) interferon pathways typically associated with antiviral responses.  Infection of macrophages from mice with targeted deletions in various innate sensing genes demonstrates that host responses to Neospora are dependent on the toll-like receptor Tlr3 and the adapter protein Trif.  Consistent with this observation, RNA from Neospora elicits TLR3-dependent type I interferon responses when targeted to the host endo-lysosomal system.  Although live Toxoplasma fail to induce type I interferon, heat-killed parasites do trigger this response, albeit much weaker than Neospora, and co-infection studies reveal that T. gondii actively suppresses the production of type I interferon.  These findings reveal that eukaryotic pathogens can be potent inducers of type I interferon and that related parasite species interact with this pathway in distinct ways.

overall_design: Human foreskin fibroblasts (HFF; line BJ-5ta) were cultured to confluency in T25 flasks, infected with one representative of each of the three architypial strains of Toxoplasma gondii: GT1 (type I), Prugniaud (type II) and VEG (type III), or the closely related parasite species, Neospora caninum (strain Nc-Liv).   RNA was collected from biological replicates for expression profiling by microarray.  Uninfected HFF cells were used as a reference.

first: Daniel

last: Beiting

first: Lucia

last: Peixoto

first: Paul

last: Davis

first: David

last: Roos


title: Genes regulated by GRK3 in PC3 prostate cancer cells

status: Public on Jan 31 2013

city: Houston

first: Wenliang

last: Li

state: TX

address: 1825 Pressler Street

department: Brown Foundation Institute of Molecular Medicine

institute: University of Texas at Houston

summary: To identify genes regulated by GRK3 in human cancer cells.

overall_design: Extracted total RNAs from cultured cells, processed samples and hybridized on Illumina Ref8-v3 BeadChips


title: Flow dependent gene expression in the rat aorta under physiological conditions

status: Public on Dec 24 2012

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

summary: Objective: Shear forces play a key role in the maintenance of vessel wall integrity. Current understanding regarding shear-dependent gene expression is mainly based on in vitro or in vivo observations with experimentally deranged shear, hence reflecting acute molecular events in relation to flow. Our objective was to combine computational fluid dynamic (CFD) simulations with global microarray analysis to study flow-dependent vessel wall biology in portions of the entire aorta under physiological conditions.   Methods and Results: Animal-specific WSS magnitude and vector direction were estimated using CFD based on aortic geometry and flow information acquired by MRI. Two distinct flow pattern regions were identified in the normal rat aorta; the distal part of the inner curvature being exposed to low WSS and a non-uniform vector direction, and a region along the outer curvature being subjected to markedly higher levels of WSS and a uniform vector direction. Microarray analysis identified numerous novel mechanosensitive genes, including Hand2, trpc4 and slain2, and confirmed well-known ones, such as klf2 and BMP4. Three genes were further validated for protein , including Hand2, which showed higher expression in the endothelium in regions exposed to disturbed flow. Gene ontology analysis revealed an over-representation of genes involved in transcriptional regulation.

overall_design: Microarray analysis of two distinct flow pattern regions were identified in the normal rat aorta. Tissue pieces from groups of five animals were pooled for each region giving total of 28 pools; 14 paired sample pools of high and low wall shear stress.

first: Hanna

last: Björck

first: Johan

last: Renner

first: Shohreh

last: Maleki

first: Siv

middle: E

last: Nilsson

last: Kihlberg

first: Matts

last: Karlsson

first: Tino

last: Ebbers

first: Per

last: Eriksson

first: Toste

last: Länne


title: Deep Clonal Profiling of Formalin-Fixed Paraffin-Embedded Clinical Samples

status: Public on Dec 31 2012

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.

overall_design: A total of 23 test samples were each hybridized with a pooled 46,XX commercial reference (Promega catalog# G1521, Madison, WI). Twenty-two of the test samples included flow-sorted fresh frozen and formalin-fixed paraffin-embedded tumor samples. The tissues included pancreatic adenocarcinomas, breast carcinomas, small cell carcinoma of the ovary, glioblastoma, and bladder carcinoma. The last test sample was a pancreatic adenocarcinoma cell line (A10-74).

first: Tara

last: Holley

first: Elizabeth

last: Lenkiewicz

first: Lisa

last: Evers

first: Waibhav

last: Tembe

first: Christian

last: Ruiz

first: Joel

last: Gsponder

first: Lukas

last: Bubendorf

first: Mark

last: Stapleton

first: Doug

last: Amorese

first: Christophe

last: Legendre

first: Heather

last: Cunliffe

first: Ann

last: McCullough

first: Barbara

last: Pockaj

last: Craig

first: John

last: Carpten

last: Von Hoff

first: Christine

last: Iacobuzio-Donahue

middle: T


title: Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1

status: Public on Dec 19 2012

first: Angela

last: Ting

state: Ohio

address: 9500 Euclid Ave/NE50

department: Genomic Medicine

summary: We conducted gene expression profilling of common prostate cell lines for comparison with genome-wide DNA methylation profiles for the same cell lines to study the impact of differential DNA methylation in prostate cancer.

overall_design:
Total RNA was extracted from 3 biological replicate sets of PrEC, RWPE-1, DU 145, and LNCaP cells.
This Series represents the gene expression profiling data only. The methyl-Seq data were submitted directly to SRA and are represented by accession SRA049689.1.


title: ChIP-chip of 6 chromatin marks (FAIRE, H3K4me1, H3K4me3, H3K27me3, H3R17me2, H3AZAce) in breast cancer cell line MCF7

status: Public on Jan 01 2013

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

institute: University of Chicago IGSB

type: Genome binding/occupancy profiling by genome tiling array

summary: Altered gene expression patterns in human diseases reflect perturbations in the transcriptional networks that regulate cellular state. In breast cancer, Nuclear Receptors (NRs) play a prominent role in governing gene expression. NRs have prognostic utility and are therapeutically important targets. Here we describe a complete regulatory map for twenty-four NR proteins that are expressed in the breast cancer cell line MCF-7, as well as fourteen additional breast cancer associated transcription factors (TFs) and six key chromatin state markers.

overall_design: Input DNA was used as control against all 6 Chromatin ChIPchip samples grown in complete medium. All samples are done in triplicates.

first: Ralf

last: Kittler

first: Sujun

last: Hua

first: Lijia

last: Ma

first: Yuwen

last: Liu

first: Chao

last: Cheng

last: Gerstein

first: Kevin

last: White


title: Transcriptional response to dengue infection in peripheral blood mononuclear cells of Nicaraguan children

status: Public on Mar 01 2013

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

summary:
We measured fever-day-specific genome-wide transcript abundance patterns in 105 peripheral blood mononuclear cell (PBMC) samples collected from 41 children hospitalized with dengue virus (DENV) infection in Nicaragua, and from 8 healthy controls.  DF1 = primary DF; DF2 = secondary DF; DHF = Dengue Hemorrhagic Fever; DSS = Dengue Shock Syndrome.
Samples were collected from pediatric patients with DENV infection at the Hospital Infantil Manuel de Jesus Rivera (HIMJR) in Managua, Nicaragua.  Enrollment criteria consisted of hospitalized patients younger than 15 years of age whose parents or guardians completed the informed consent process, and for children 6 years and older who provided assent, and who presented with acute febrile illness of less than 7 days duration with one or more of the following symptoms or signs at the time of evaluation: headache, arthralgia, myalgia, retro-orbital pain, positive tourniquet test, petechiae, and signs of bleeding. Children were considered to have dengue if DENV was detected by RT-PCR or by isolation in cell culture, if an IgM ELISA indicated seroconversion between the acute and convalescent sample, and/or if there was a > 4-fold increase in DENV-specific antibodies between the acute and convalescent phase. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood within four hours of collection and stored in Trizol at -80 oC


title: Effect of prenatal exposure to nicotine on kidney structure and gene expression in rats

status: Public on Dec 25 2012

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

summary: Here, we investigated whether prenatal exposure to nicotine alters kidney glomerular mass and genome-wide gene expression profiles in two genetically distant strains of rats, namely spontaneously hypertensive rats (SHR) and Brown Norway (BN) rats. Nicotine or saline were administered to BN and SHR dams via osmotic pumps throughout gestation. Kidneys from 9-week-old male offspring were studied.

overall_design: Equal amounts of RNA from individual animals were pooled within each of the four experimental groups SHR (nicotine: n=13; saline: n=12) and BN (nicotine: n=12; saline: n=12) and hybridized with the Rat RAE-230a GeneChip (Affymetrix).

first: Zdenka

last: Pausova


title: The small molecule compound P2 in HCT116p53-/- and HCT116p53+/+ cells

status: Public on Nov 23 2012

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

summary: Global gene expression in HCT116p53-/- and HCT116p53+/+ cells

overall_design: HCT116p53-/- and p53+/+ were untreated and treated with P2 small molecule compound at 25 microM, total RNA was isolated and gene expression was analyzed using Illumina chips

first: Vita

last: Golubovskaya

first: Baotran

last: Ho

first: Song

first: David

last: Ostrov

first: William

last: Cance


title: Expression profiles of primary motor neurons after knocking down Fus

status: Public on Nov 21 2012

city: Nagoya

first: Shinsuke

last: Ishigaki

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University School of Medicine

summary:
To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary motor neurons by using exon-sensitive microarray technology.
To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary glial cells by using exon-sensitive microarray technology.
To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary cerebellar neurons by using exon-sensitive microarray technology.

overall_design:
We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Fus or control. RNA was harvested 11 days after transfection.
We analyzed total RNA of primary glial cells infected with lentivirus expressing shRNA against mouse Fus or control. RNA was harvested 11 days after transfection.
We analyzed total RNA of primary cerebellar neurons infected with lentivirus expressing shRNA against mouse Fus or control. RNA was harvested 9 days after transfection.

first: Y

last: Fujioka

first: S

first: A

last: Masuda

first: K

last: Ohno

first: G

last: Sobue


title: Specific kinesin expression profiles associated with taxane resistance in breast cancer

status: Public on Dec 01 2012

city: Grand Rapids

first: Min-Han

last: Tan

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

summary: Purpose: Breast cancer is a genetically heterogenous disease with subtypes differing in prognosis and chemosensitivity. The basal-like breast cancer (BLBC) molecular subtype is associated with poorer outcomes, but is more responsive to taxane-based chemotherapy. We evaluated the role of kinesins, motor proteins interacting with microtubules, in influencing taxane resistance. Experimental Design: Kinesin (KIF) expression was studied in one local dataset comprising all taxane resistant breast cancers in relation to taxane resistance. Data in the NCI-60 cell line dataset (GSE5846) nd the MDACC dataset (GSE20194) is separately detailed. Results: In the local dataset, the kinesin KIF26B is overexpressed in taxane-resistant residual breast cancers post-chemotherapy. Conclusions: We show that kinesin overexpression correlates with taxane resistance in BLBC cell lines and tissue. Our results suggest a potential approach to overcoming taxane resistance through concurrent or sequential use of kinesin inhibitors, highlighting the ATP-binding domain as a drug development target.

overall_design: Kinesin (KIF) expression was studied in one local dataset comprising all taxane resistant breast cancers in relation to taxane resistance. Data in the NCI-60 cell line dataset (GSE5846) and the MDACC dataset (GSE20194) is separately detailed.

first: Charis

last: Eng


title: Promoter context-specific positive and negative transcriptional regulation of Glucocorticoid Receptor target genes by coregulator G9a

status: Public on Nov 02 2012

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

summary:
A549 lung cancer cells were not infected (NI), transfected by plasmids containing shG9a (sequence targeting G9a gene) or shNS (non-specific sequence).
These cells were treated with dex to identify subsets of genes regulated by dex (hormone) and G9a (EHMT2)

overall_design: Cells (NI/shNS/shG9a) were treated with 100nM dex for 24h and total RNA was extracted to identify differentially expressed genes

first: Michael

last: Stallcup

first: Kimberly

middle: D

last: Siegmund

first: Danielle

last: Bittencourt

first: Kwang

last: Jeong

first: Irina

last: Ianculescu

first: Daniel

last: Gerke


title: ChIP-chip of 38 nuclear receptors and NR co-factors in breast cancer cell line MCF7

first: Jie

last: Zhou

summary:
Altered gene expression patterns in human diseases reflect perturbations in the transcriptional networks that regulate cellular state. In breast cancer, Nuclear Receptors (NRs) play a prominent role in governing gene expression. NRs have prognostic utility and are therapeutically important targets. Here we describe a complete regulatory map for twenty-four NR proteins that are expressed in the breast cancer cell line MCF-7, as well as fourteen additional breast cancer associated transcription factors (TFs) and six key chromatin state markers.
The CEL files for the 38 NRs ChIP-chip presented in the paper are included, together with the results bar files, except 5 previsouly published ones: ER [GSE10800], RARA, RARG, FOXA1, GATA3 [GSE15244]. The supplementary bed file contains all 200,140 binding sites of all 38 TFs reported in the paper.

overall_design:
Input DNA was used as control against all 38 ChIPchip samples. All samples are done in triplicates.  We mapped the binding sites in the bacterial artificial chromosome (BAC) transgenic MCF7 cells in which we tagged the transcription factors with a modified LAP (localization and affinity purification) tag containing green fluorescent protein (GFP). Goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP) was used to perform ChIP experiments in those transgenic lines.

*Bed files for binding sites of each of 38 factors (TR2L and TR2S are two isoforms of TR2) were provided as additional results files.

Please note that the folllowing data files are re-processed from Dr. Sujun Hua's GSE10800 and GSE15244 uploads.
ESR1.bed
FOXA1.bed
GATA3.bed
RARA.bed
RARG.bed
Since the authors have updated the analysis pipeline and presented the changed results in the associated publication, these updated results are included in the records (Dr. Sujun is one of the contributors in this work).

first: Ralf

last: Kittler

first: Sujun

last: Hua

first: Lijia

last: Ma

first: Yuwen

last: Liu

first: Chao

last: Cheng

first: Mark

last: Gerstein

first: Kevin

last: White


title: The data of differentially regulated exons from mouse testes - wild-type and Dazap1 mutant

status: Public on Jun 01 2013

city: Taipei

first: Hsiang-Ying

last: Chen

address: 128 Sec. 2, Academia Rd.

country: Taiwan

institute: IBMS

summary: The binding of Deleted in Azoospermia Associated Protein 1 (DAZAP1) to splicing mutations in the BRCA1 and NF1 genes that caused exon exclusion suggest a role for DAZAP1 in RNA splicing. To elucidate the biological functions of DAZAP1 and to search for its natural RNA substrates, we compared the exon usages of wild-type and Dazap1 mutant testes by exon microarrays.

overall_design: We used wild-type and Dazap1 mutant mouse testes. Each genotype has three replicates. 6 total samples were analyzed.

first: Hsiang

middle: Y

first: Pauline

last: Yen


title: Interferon alpha induced gene expression in SOCS1 and SOCS3 overexpressing melanoma and hepatoma cell lines.

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

summary: Interferon-alpha (pegylated interferon and ribavirin) is used as standard-of-care therapeutic for chronic hepatitis C virus infection. Besides good cure in some patients other patients do not benefit from the treatment dependent on the virus type and host factors. One class of putative effector proteins is the family of Suppressors of cytokine signalling (SOCS). They act in a classical negative feedback-loop against the action of interferons and many other cytokines. It has been proven that some of them, in particular SOCS1 and SOCS3, inhibit the expression of interferon induced antiviral proteins. Their mode of action depends on the signal they are interfering with. In relation to the interferon-gamma pathway, they are thought to act on the interferon-alpha receptors by masking its recognition site for the Janus kinases (JAK), by blocking the kinase activity of the JAKs and coincidentally hindering STAT molecules from binding to the kinases. They are also thought to ubiquitinate the JAKs resulting in their proteosomal degradation. The function of SOCS proteins in suppressing the interferon-alpha pathway has not yet been characterized exhaustively. This study should unveil links to understand the resistance in interferon-alpha therapy. As results we got almost complete silencing of JAK-STAT signaling in SOCS1 over-expressing cells and tissue-dependent partially suppressed gene induction in SOCS3 over-expressing cell lines.

overall_design: Two human cancer cell lines (ME-15, HuH-7) were stably transfected with pcDNA3.1-SOCS plasmids in presence of geneticin and daughter cell lines were generated after singularization of cells. Next, original cell lines as well as SOCS1 and SOCS3 over-expressing cell lines were treated with 1000 U/ml interferon-alpha for 4 or 24 hours or in normal culture medium. Cells lines obtained from SOCS4 plasmid transfections were screened as additional control. Gene expression levels of cell cultured in control (0 for 4 hours, 2 for 24 hours) or interferon-alpha supplemented medium for 4 hours (1) or 24 hours (4) were analyzed. mRNA abundance was measured in triplicates using 12x8-sample commercial Illumina microarrays (HumanRef 8, version 3) and scanner system (iScan) as well as reagents recommend by Illumina (Illumina® TotalPrep Kit).

first: Ulrich

last: Certa


title: Analysis of liver RNA from SRSF3 hepatocyte knockout mice versus wild-type littermates

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

institute: UCSD

summary: Livers from three SRSF3HKO mice and 3 wild-tyope littermates were used to analyze changes in exon utilization and gene expression.

overall_design: two genotypes, three replicates each

first: Nicholas

middle: J

first: Supriya

last: Sen


title: Corelation between RISC complex, LINE-1 RNA and Global hypomethylation in head and Neck cancer cell line.

status: Public on Nov 05 2012

city: Bangkok

first: Chureerat

last: Phokaew

address: 1873 Phayathai Road

department: Department of Medicine

country: Thailand

institute: Chulalongkorn Univerisity

summary: One of most common events in carcinogenesis is loss of DNA methylation (hypomethylation) from sequence of transposable element (TEs) including long interspersed nuclear element-1 (LINE-1). Naturally, LINE-1 and other TEs within gene body region (intragenic) will suppress by fully methylated CpG sequences in order to keep prevent incorrect transcriptional start site (TSSs) that cause genome instability. To study character of intragenic LINE-1 promoter hypomethylation or gene body methylation status, within Head and Neck squamous cell carcinoma (HNSCC) cell, LINE-1 promoter methylation status was detected with CU-L1 (unique intragenic LINE-1) and COBRALINE-1 (whole genome LINE- 1) PCRs. Each intragenic LINE-1 promoter hypomethylation have unique pattern depending on cell types and impact of LINE-1’s host gene within cell. From CU-L1 PCR 16 genes, EPHA3 and PPP2R2B are only two genes that normally induce expression by hypermethylated in gene body region, intragenic LINE-1 promoter. LINE-1 promoter hypomethylation level induce global and specific LINE-1 expression and also repress LINE-1’s host genes expression, which confirm by 5’- aza-2-deoxycytidine induced DNA hypomethylationin HNSCC cell that cause EPHA3 become greater down- regulated. Since LINE-1 RNA can express via promoter hypomethylation, knockdown LINE-1 RNA can lead increasing of EPHA3 in HNSCC cell. LINE-1 RNA was concern as key factor on LINE-1 host’s gene regulation by consequence of gene body hypomethylation. RNA molecule can regulate gene by RNAi pathway and Epigenetics mechanism, within both machinery require RISC proteins. Next, knockdown RISC protein, DICER1 gene can investigate possibility role that LINE-1 RNA regulate LINE-1 host gene. Within yeast cell, overexpress retrotransposon transcript was control by endo-siRNA pathway, which require DICER1 like protein for produce endo-siRNA from precursor molecule that include retrotransposon transcript. With CU-DREAM analyse microarray results by intersection datas for check the connection between factors on gene regulation including DICER1, LINE-1 RNA, DNA hypomethylation and HNSCC carcinogenesis model. According to CU-DREAM analysis for HNSCC cell panel, DICER1 involved pathway may induce hypermethylation on gene body region which relate to TSS and intragenic LINE-1 promoter region. While LINE-1 RNA involved pathway select to induce hypermethylation on gene without LINE-1 promoter, LINE-1 RNA have in tran function. In conclusion, intragenic LINE-1 promoter hypomethylation cause releases of LINE-1 RNA for regulate genes during HNSCC carcinogenesis via RISC protein.

overall_design: Oligonucleotides specific target on LINE-1 was inserted into Psilencer 3.1 vector hygro H1 promoter. (Ambion, Austin, Texas, USA) and transfection was mediated by FuGENE ® HD (Roche), sequence shown in appendix. Oligosynthesis siRNA specific to DICER1 purchased from santa cruz biotechnology for transient tranfection, inc was dilute with RNASE free dH2O to reach 10μM. In a 12 well plate, seed 6 x 105 cells per well in 1 ml antibiotic-free normal growth medium supplemented with 10% FBS. In next day, perform transfection those siRNA at 100 nM with Lipofectamine 2000 reagent (Invitrogen Cat: 11668-027) according to the manufacturer's instructions. Cell was collect at 48h after transfection step by Trizol reagent (Life technologies, Inc.) in order to collect total RNA from each sample for hybridize on beadchip according to the protocol.

first: Apiwat

last: Mutirangura


title: FOXC1 in human trabecular meshwork cells is involved in regulatory pathway that includes miR-204, MEIS2, and ITGβ1

status: Public on Nov 01 2012

city: Tehran

first: hassan

last: paylakhi

address: Jalale aleahmad

country: Iran

institute: Tarbiat Modares University

summary: To identify genes whose expressions in primary human trabecular meshwork (TM) cell cultures are affected by the transcription factorfoxc1 and to identify genes that may have roles in glaucoma. Expression profiles derived using microarrays were compared between TM control cells and cells treated with foxc1 siRNAs.

overall_design: TM1 and TM2 cells were cultured in 6 well plates were transfected with either of two FOXC1 specific siRNAs or scrambled siRNA (as control). The scrambled siRNA treatment was performed in duplicate for each TM. Forty eight hours after exposure to siRNAs, cells were harvested and RNA was extracted. Considering the two siRNAs for FOXC1 transcription factor, the two scrambled siRNA treatments, and the two TM primary cultures, we performed 8 array hybridizations.

first: Elahe

last: Elahi

first: Seyed

last: Paylakhi


title: The disparate twins: A comparative study of CXCR4 and CXCR7 in SDF-1α-induced gene expression, invasion and chemosensitivity of colon cancer

status: Public on Aug 10 2012

city: Heidelberg

first: Doreen

last: Heckmann

institute: DKFZ

summary:
In colorectal cancer, increased expression of the CXC chemokine receptor 4 (CXCR4) has been shown to provoke metastatic disease due to the interaction with its ligand stromal cell-derived factor 1 (SDF-1). Recently, a second SDF-1 receptor, CXCR7, was found to enhance tumor growth in solid tumors. Albeit signaling cascades via SDF-1/CXCR4 have been intensively studied, the significance of the SDF-1/CXCR7-induced intracellular communication triggering malignancy is still only marginally understood. In tumor tissue of 52 colorectal cancer (CRC) patients, we observed that expression of CXCR7 and CXCR4 increased with tumor stage, tumor size, and lymph node infiltration. Asking whether activation of CXCR4 or CXCR7 might result in a similar expression pattern, we performed microarray expression analyses using lentivirally CXCR4- and/or CXCR7-overexpressing SW480 colon cancer cell lines with and without stimulation by SDF-1α. Gene regulation via SDF-1α/CXCR4 and SDF-1α/CXCR7 was completely different and partly antidromic. Expressions of the differentially expressed genes AKR1C3, AXL, EGFR, IGFBP7, IL24, TNNC1, TRIP6 were confirmed by qPCR. Differentially regulated genes were assigned by GO to migration and lipid metabolic processes.
Furthermore, using the in silico gene set enrichment analysis we showed for the first time that expressions of miR-217 and miR-218 were increased in CXCR4 and reduced in CXCR7 cells after stimulation with SDF-1α. As expected, their putative target mRNAs were inversely expressed. Functional assays exerted that exposure to SDF-1α resulted in strongly amplified invasiveness and chemosensitivity of CXCR4-expressing cells. CXCR7 overexpression led to reduced invasiveness which could only be marginally increased by SDF-1α. The CXCR4 antagonist plerixafor significantly reduced invasiveness of CXCR4-overexpressing cells only. Similarly, compared to control cells, CXCR4 cells showed increased sensitivity against 5-FU, while CXCR7 cells were more chemoresistant. These opposing results for CXCR4- or CXCR7-overexpressing colon carcinoma cells demand an unexpected attention in the clinical application of chemokine receptor antagonists like Plerixafor.

overall_design: 24 samples

first: Patrick

last: Maier

first: Stephanie

last: Laufs

first: Li

last: Li

first: Frederik

last: Wenz

first: Jens

middle: W

last: Zeller

first: Stefan

last: Fruehauf

first: Heike

last: Allgayer


title: FGF inhibition directs BMP4-mediated differentiation of Human Embryonic Stem Cells to syncytiotrophoblast

status: Public on Oct 17 2012

city: Berlin

first: smita

last: sudheer

address: Ihnestraße 63-73

institute: Max Planck Institute for Molecular Genetics

summary: Bone morphogenetic protein (BMP) signaling is known to support differentiation of human embryonic stem cells (hESCs) into mesoderm and extraembryonic lineages, whereas other signaling pathways can largely influence this lineage specification. Here, we set out to reinvestigate the influence of ACTIVIN/NODAL and fibroblast growth factor (FGF) pathways on the lineage choices made by hESCs during BMP4-driven differentiation. We show that BMP activation, coupled with inhibition of both ACTIVIN/NODAL and FGF signaling, induces differentiation of hESCs, specifically to βhCG hormone-secreting multinucleated syncytiotrophoblast and does not support induction of embryonic and extraembryonic lineages, extravillous trophoblast, and primitive endoderm. It has been previously reported that FGF2 can switch BMP4-induced hESC differentiation outcome to mesendoderm. Here, we show that FGF inhibition alone, or in combination with either ACTIVIN/NODAL inhibition or BMP activation, supports hESC differentiation to hCG-secreting syncytiotrophoblast. We show that the inhibition of the FGF pathway acts as a key in directing BMP4-mediated hESC differentiation to syncytiotrophoblast.

overall_design: Human embryonic Stem Cells (hESCs) were treated under defined conditions (N2B27) with BMP4 (B), SB431542 (SB) (ACTIVIN/NODAL inhibitor), SU5402 (SU) (FGFR1 inhibitor), FGF2 (F) either alone or in various combinations as mentioned, followed by isolation of total RNA.

first: Smita

last: Sudheer

first: Raghu

last: Bhushan

first: Beatrix

last: Fauler

first: Hans

last: Lehrach

first: James

last: Adjaye


title: The protein kinase KIS impacts gene expression in the neonate brain

status: Public on Sep 05 2012

city: Worcester

first: Alexandre

last: Maucuer

state: MA

address: 364 Plantation Street

institute: INSERM

summary: The protein kinase KIS (product of the gene UHMK1) is expressed during mouse brain development and is proposed to control gene expression through the phosphorylation of splicing factor SF1. We compared the expression of transcripts in wild type and KIS-ko newborn mouse brain (females) using affymetrix exon 1st arrays.

overall_design: Six pairs of wildtype and KIS-ko brains from littermate female newborn mice were processed for Affymetrix exon 1st array hybridization. Analysis was performed at the exon level using PLIER normalisation and the Affymetrix Expression Console.


title: The anti-inflammatory IL-1 receptor antagonist (IL-1ra) protects against the development of islet autoimmunity.

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary:
Through gene expression profiling in cultured lymphocytes and PBMCs from a large set of T1D patients and controls, we demonstrate that IL-1ra may protect against the development of islet autoimmunity and T1D through down-regulating a large number of inflammatory genes and pathways.

Keywords: autoimmunity; IL-1Ra;Type 1 diabetes (T1D)

overall_design: To elucidate the molecular mechanism underlying the action of IL-1ra, we profiled gene expression in peripheral blood mononuclear cells (PBMC) cultured with sera from low or high IL-1ra subjects.  To avoid potential heterogeneity in responder cells from different subjects, PBMCs from one healthy donor were cultured for six hours with 20% of sera from six subjects with low IL-1ra and six subjects with high IL-1ra.  Gene expression in the cultured cells was analyzed with the Illumina HumanRef-8 v3.0 beadchips

first: S

last: Purohit

first: R

last: Podolsky

first: Y

last: Jin

first: A

last: Sharma

first: P

last: Yang

first: H

last: Wang

first: D

last: Hopkins

first: L

last: Steed

first: M

first: W

last: Zhi

first: B

last: Bode

last: Anderson

first: J

last: Reed

last: Huang

last: Nechtman

first: E

last: Miller

last: Pederson

last: Schatz

last: Muir

middle: A

last: McIndoe

first: K

last: Barriga

first: G

last: Eisenbarth

last: Rewers


title: Expression data from Hh signaling-deficient OP9 stromal cells

status: Public on Jul 12 2012

city: Baltimore

first: Stephen

last: Desiderio

address: 733 N. Broadway

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary:
In the bone marrow B cell development occurs in initimate and essential association with stromal cells.  Known effects of stromal cells on B cell development have been shown to be mediated through direct contact and by soluble factors produced by stromal cells.
Our findings suggest that cell-nonautonomous Hh signaling may play an important role in B cell lymphopoiesis.  We therefore interrogated OP9 stromal cells for Hh-dependent transcripts that may confer B lymphopoietic identity.

overall_design: We generated OP9 stromal cells deficient in Hh signaling through targeting the non-redundant, pathway-obligate GPCR Smoothened.  OP9 cells were transduced with RNAi pLKO.1-Puro lentiviral particles expressing a scrambled control shRNA (NT) or shRNA targeting Smoothened (Smo-kd).  RNA from stable NT and Smo-kd OP9 cells were isolated in triplicate and global changes in transcripts were analyzed using the Affymetrix Mouse Exon 1.0 ST gene chip.

first: Christopher

middle: L

last: Cooper


title: Expression profiles of primary cortical neurons after knocking down Fus

status: Public on Jul 24 2012

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

institute: Nagoya University Graduate School of Medicine

summary: To clarify the functional properties of FUS, we established the differentially expressed alternative exons in FUS-silenced primary cortical neurons by using exon-sensitive microarray technology.

overall_design: We analyzed total RNA of primary cortical neuron infected with lentivirus expressing shRNA against mouse Fus or control. RNA was harvested 11 days after transfection.

first: Shinsuke

last: Ishigaki

first: Kinji

last: Ohno


title: Genome-wide analysis of CD8 cells laser captured from skin biopsies during the mucocutaneous HSV-2 reactivation

status: Public on Jul 26 2012

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

summary: Analysis of CD8 cells at the gene expression level during the genital HSV-2 reactivation. We would like to get a comprehensive overview on gene expression of CD8 T-cells during the post healing phases of HSV-2 reactivation. The hypothesis is that CD8 T-cells play a immune surveillance function during the post healing phases.

overall_design: CD8 cells were immunofluorescently stained and laser captured from post healing biopsies and contralateral control biopsies, total RNA were purified from captured cells and cDNA were amplified from the total RNA using NuGEN pico kits


title: Gene expression profiling of CD4+myelin basic protein specific T cells

status: Public on Aug 23 2012

city: Göttingen

first: alexander

last: flügel

address: waldweg 33

department: Department of Neuroimmunology

institute: Institute for Multiple Sclerosis Research

summary:
CNS autoimmunity is induced by autoreactive  T cells reactive against CNS antigen. However how these T cells become able to transgress the blood brain barrier is not CNS autoimmunity is induced by autoreactive  T cells reactive against CNS antigen. Here a gene expression profile of the pathogenic T cells in different functional states was performed.
These studies were performed in a classical model of multiple sclerosis, experimental autoimmune encephalomyelitis in Lewis rats induced by transfer of CD4+myelin basic protein specific T cells.
We found that on their way to the CNS T cells fundamentally reprogram their gene expression profile, by down-regulating their activation program and up-regulating cell locomotion molecules.

overall_design: Total RNA extracted from ex vitro myelin specific T cells (blasts and resting state, day 2 and 7 after antigen challenge respectively) or isolated from the spleen (3 days p.t.) was used to perform a genome-wide transcriptional profiling assay (Rat Genome 230, Affymetrix)-

first: Francesca

last: Odoardi

first: Vijay

last: Ulaganathan

first: Claudio

last: Lottaz

first: Wilfried

last: Nietfeld

first: Alexander

last: Flügel


title: Array-based Comparative Genomic Hybridization of Melanoma Cell Lines

status: Public on Aug 27 2012

city: Philadelphia

first: Katherine

last: Nathanson

address: 421 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
This study explored the role of targeting protein for Xklp2 (TPX2), located with 20q11.2, in melanoma pathogenesis, based on initial findings that it was commonly gained and overexpressed.
TPX2 copy number was evaluated in melanoma cell lines compared to control DNA.

overall_design: Thrity-three cell lines were analyzed by Agilent SurePrint G3 Human CGH Microarray 2x400K. Samples were compared to Human Female DNA from Promega.

first: Bin

last: Li

first: Maurizia

last: DPalma

first: Xiaowei

last: Xu

first: Clemens

last: Krepler

first: Bradley

last: Wubbenhorst

first: Kurt

last: D'Andrea

first: Richard

last: Letrero

first: Rosalie

last: Elenitsas

first: Hong

last: Wu

first: Lynn

middle: M

last: Schuchter

first: Keiran

last: Smalley

first: Meenhard

last: Herlyn


title: Transcriptional profiles of unfractionated lymph nodes cells obtained from completely protected, non protected and unvaccinated control rhesus macaques seven days prior to, and four and fourteen days after wt SIVmac239 challenge by microarray analysis.

status: Public on Aug 09 2012

city: Cleveland

first: Peter

last: Wilkinson

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Live-attenuated SIV vaccines (LAVs) remain the most efficacious of all vaccines in nonhuman primate models of HIV/AIDS, yet the basis of their robust protection remains poorly understood. Here, we demonstrate that the degree of LAV-mediated protection against intravenous (IV) wildtype (wt) SIVmac239 challenge strongly correlates with the magnitude and function of SIV-specific, effector-differentiated T cells in lymph node (LN), but not with such T cell responses in blood or with other cellular, humoral and innate immune parameters. Maintenance of protective T cell responses was associated with persistent LAV replication in LN, which occurred almost exclusively in follicular helper T cells. Thus, effective LAVs maintain lymphoid tissue-based, effector-differentiated, SIV-specific T cells that intercept and suppress early wt SIV amplification and, if present in sufficient frequencies, can completely control and perhaps clear infection -- an observation that provides rationale for development of safe, persistent vectors that can elicit and maintain such responses.

overall_design: There are four protection outcome groups: unvaccinated control (C), complete protect (CP), non-protect (NP) and partial protect (PP). Respectively for these groups, there are 7, 9, 6 and 4 animals sampled seven days pre-challenge (minus7PCD); 9, 13, 5 and 5 animals sampled four days post-challenge (4PCD) and 8, 11, 5 and 3 fourteen days post-challenge (14PCD).

first: Yoshinori

last: Fukazawa

first: Haesun

last: Park

first: Mark

last: Cameron

first: Francois

last: Lefebvre

last: Lum

first: Noel

last: Coombes

first: Eisa

last: Mahyari

first: Shoko

last: Hagen

first: Jin

last: Bae

first: Marcelo

last: Delos Reyes

first: Tonya

last: Swanson

first: Alfred

last: Legasse

first: Andrew

last: Sylwester

first: Scott

middle: G

last: Hansen

last: Smith

first: Petra

last: Stafova

first: Rebecca

last: Shoemaker

first: Yuan

first: Kelli

last: Oswald

first: Michael

last: Axthelm

first: Adrian

last: McDermott

first: Guido

last: Ferrari

first: David

middle: C

last: Montefiori

first: Paul

last: Edlefsen

last: Piatak

first: Jeffrey

last: Lifson

first: Rafick

last: Sékaly

first: Louis

last: Picker


title: Genome-wide analysis of cellular NMD substrates that regulated by Upf1, PNRC2 or CTIF in HeLa cell

status: Public on Jul 23 2012

city: Seoul

first: Kyoung Mi

last: Kim

address: Anam-Dong

department: School of Life sciences and biotechnology

country: South Korea

institute: Korea University

type:
Expression profiling by array
Third-party reanalysis

summary: The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein (CBP) 80 and 20. During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNAs increases in the cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is one of NMD-inducing features. Using chimeric reporter constructs and confocal microscopy, we find that the uORF of CDKN1A mRNA is actively translated and modulates a translational efficiency of the main downstream ORF. Our findings provide the biological insights into the possible role of NMD in diverse pathways mediated by CDKN1A. The microarray analysis performed to analize the cellular NMD substrates that regulated by Upf1, PNRC2 and/or CTIF in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, PNRC2 and CTIF. Results provide important information that vast range of cellular NMD substrates are reqired CTIF.

overall_design: Total RNA obtained from HeLa cells with downregulation of Upf1, PNRC2 or CTIF by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication.

first: Kyoung

first: Hana

last: Cho


title: Expression and function of PML-RARA in the multipotent hematopoietic progenitor cells of Ctsg-PML-RARA mice

status: Public on Aug 14 2012

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

summary: Because PML-RARA-positive acute promyelocytic leukemia (APL) is a morphologically differentiated leukemia, much speculation has been made about whether its leukemic cell of origin might be committed myeloid precursor (e.g., a promyelocyte) vs. a hematopoietic stem/progenitor cell (HSPC). We originally targeted PML-RARA expression with CTSG regulatory elements, based on the early observation that this gene was maximally expressed in cells with promyelocyte morphology. Here, we show that both Ctsg and PML-RARA targeted to the Ctsg locus (in Ctsg-PML-RARA mice) are detected in the purified KLS cells of these mice (Kit+Lin-Sca+ cells, which are highly enriched for HSPCs), and this expression results in biological effects in multi-lineage competitive repopulation assays. Although PML-RARA is indeed expressed at high levels in the promyelocytes of Ctsg-PML-RARA mice, it does not significantly alter the transcriptional signature of these cells, or induce their self-renewal. In sum, these results suggest that in murine models, PML-RARA acts primarily to affect the function of multi-potent progenitor cells, rather than promyelocytes. Since PML/Pml is normally expressed in the HSPCs of both humans and mice, and since some human APL samples contain TCR rearrangements and express T lineage genes, we suggest that the very early hematopoietic expression of PML-RARA in our mouse model may closely mimic the physiologic expression pattern of PML-RARA in human APL patients.

overall_design: Bone marrow from individual mice expressing PML-RARA from the murine Ctg locus (mCG-PR) and littermate controls was harvested from both femurs and tibia. Standard cell lysis was performed, and total RNA was extracted from the cells and analyzed using the Affymetrix Mouse Exon 1.0 ST platform.

first: John

middle: S

last: Welch

first: Lukas

last: Wartman

first: Geoffrey

last: Uy

first: Jeffery

last: Klco

first: Rakesh

last: Nagarajan

first: Timothy

last: Ley


title: 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary (tiling array)

status: Public on Aug 24 2012

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

institute: University of Toronto

summary:
5-hydroxymethylcytosine (5-hmC), a derivative of 5-methylcytosine (5-mC), is abundant in the brain for unknown reasons. We mapped the genomic distribution of 5-hmC and 5-mC in human and mouse tissues using glucosylation of 5-hmC coupled with restriction enzyme digestion, and interrogation on microarrays. We detected 5-hmC enrichment in genes with synapse-related functions in the brain.
We also identified significant, tissue-specific differential distributions of these DNA modifications at the exon-intron boundary, in both human and mouse.  This boundary change was mainly due to 5-hmC in the brain, but due to 5-mC in non-neural contexts. This pattern was replicated in multiple independent datasets, and the brain-specific change in 5-hmC was validated using single-molecule sequencing. Moreover, in the brain, constitutive exons contained higher levels of 5-hmC, relative to alternatively-spliced exons. Our study suggests a novel role for 5-hmC in RNA splicing and synaptic function in the brain

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The β-glucosyltransferase (BGT) enzyme transfers a glucose molecule specifically to the hydroxymethyl group of 5-hmC, thus rendering it resistant to digestion by the methylation insensitive MspI enzyme at the ChmCGG target site;  5-hmC is thus detected by differential resistance to MspI-digestion with and without glucosylation of genomic DNA (gDNA).  HpaII (targets the same site, CCGG) cannot cut CmCGG or ChmCGG, and conceptually its difference with MspI digestion is a measure of both 5-mC and 5-hmC. Subtraction of 5-hmC from the HpaII-based estimate therefore measures 5-mC. These estimates were measured on respective Affymetrix whole-genome tiling arrays  (2.0 R )

first: Tarang

last: Khare

first: Saulius

last: Klimasauskas

first: Arturas

last: Petronis


title: Spontaneous Latency in a Rabbit Model of Pulmonary Tuberculosis

status: Public on Jul 11 2012

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

institute: Public Health Research Institute at UMDNJ

summary:
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is an exquisitely adapted human pathogen capable of surviving for decades in the lungs of immune competent individuals in absence of disease. The World Health Organization estimates that 2 billion people have latent TB infection (LTBI), defined by positive immunologic response to Mtb antigens with no clinical signs of disease. A better understanding of host and pathogen determinants of LTBI and subsequent reactivation would benefit TB control efforts.  Animal models of LTBI have been hampered mainly by an inability to achieve complete bacillary clearance.  We have characterized a rabbit model of LTBI in which, similar to most humans, complete clearance of pulmonary Mtb infection and pathology occurs spontaneously. The evidence that Mtb-CDC1551-infected rabbits achieve LTBI, rather than sterilization, is based on the ability of the bacilli to be reactivated following immune suppression.
The microarray experiments involves comparison of: 1) Changes in rabbit gene expression between Mtb-CDC1551 infected and uninfected animals at 2,4,8 and 12 weeks post infection.

overall_design: New Zealand White rabbits were infected with Mtb CDC1551 at 3.5log10 (on day 0).   Lung tissue from Mtb-infected rabbits were isolated from uninfected (control) and at 2, 4, 8 and 16 weeks post infection and used for total RNA extraction. Total rabbit lung RNA was used for microarray analysis to determine infection induced changes in host gene expression.

first: Gilla

last: Kaplan


title: Effect of prolonged stretch on transcript profile of human pregnant myometrium

status: Public on Jun 15 2012

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

summary: Context: Increased uterine stretch appears to increase the risk of preterm labour, but the mechanism is unknown.  Objectives: To identify a targetable mechanism mediating the effect of stretch on human myometrium.  Design: Myometrial explants, prepared from biopsies obtained at elective caesarean delivery, were either studied acutely, or were maintained in prolonged culture (up to 65 h) under tension with either a 0.6 g or 2.4 g mass, and compared using in vitro contractility, whole genome array, and qRT-PCR.  Results: Increased stretch for 24 or 65 h increased potassium-induced and oxytocin-induced contractility. Gene array identified 62 differentially expressed transcripts after 65 h exposure to increased stretch. Two probes for gastrin-releasing peptide (GRP), a known stimulatory agonist of smooth muscle, were among the top five up-regulated by stretch (3.4-fold and 2.0-fold). Up-regulation of GRP by stretch was confirmed in a separate series of 10 samples using qRT-PCR (2.8-fold, P = 0.01). GRP stimulated contractions acutely when added to freshly obtained myometrial strips in 3 out of 9 cases, but Western blot demonstrated expression of the GRP receptor in 9 out of 9 cases. Prolonged incubation of stretched explants in the GRP antagonists PD-176252 or RC-3095 (65 and 24 h respectively) significantly reduced potassium chloride and oxytocin-induced contractility.  Conclusion: Stretch of human myometrium increases contractility and stimulates the expression of a known smooth muscle stimulatory agonist, GRP. Incubation of myometrium in GRP receptor antagonists ameliorates the effect of stretch. GRP may be a target for novel therapies to reduce the risk of preterm birth in multiple pregnancy.

overall_design: 9 paired samples of human myometrium cultured under low (0.6g) or high (2.4g) tension

first: Mark

last: Tattersall

first: Yolande

last: Cordeaux

first: D

first: Gordon

last: Smith


title: Transcriptome analysis of immediate early events in mRNA-mediated cellular reprogramming of human foreskin fibroblasts

status: Public on Jul 04 2012

first: Katharina

last: Drews

address: Ihnestr. 63-73

department: Vertebrate Genomics

summary: In this study human neonatal foreskin fibroblasts (HFF1 and BJ) were lipofected with an equal mixture of human reprogramming factor-encoding mRNAs. The cells were lysed and total RNA was harvested 24 hours post-transfection. Gene regulation was evaluated with respect to corresponding mock-transfected, Lipofectamine-treated control fibroblasts. For comparison, wildtype (un-treated) HFF1 and BJ fibroblasts as well as undifferentiated HFF1- and BJ-derived induced pluripotent stem cells and human embryonic stem cells (generated and maintained in our laboratory (refer to GSE26575) were included in the analysis.

overall_design: Total RNA obtained from untreated human neonatal foreskin fibroblasts, reprogramming factor- and mock(Lipofectamine-treated)-transfected human neonatal fibroblasts, undifferentiated hESCs and iPSCs (derived from human neonatal foreskin fibroblasts).

first: James

last: Adjaye


title: Mechanisms and pathways of bone metastasis: challenges and pitfalls of performing molecular research on patient samples

status: Public on Jul 06 2012

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

summary: The molecular mechanisms underlying the development of bone metastases in breast cancer remain unclear. Disseminated tumour cells (DTCs) in the bone marrow of breast cancer patients are commonly identified, even in early stage disease, but their potential to initiate metastases is not known. The mechanism whereby DTCs become overt metastatic tumour cells (MTCs) is therefore, an area of considerable interest. This study explored the analysable yield of genetic material from human biopsy samples in order to describe differences in gene expression between DTCs and bone MTCs. Thirteen breast cancer patients with bone metastases underwent a CT-guided bone metastasis biopsy and a bone marrow biopsy. Tumour cells were enriched and gene expression profiling was conducted to identify differentially expressed genes. The analysable yield of sufficient RNA for microarray analysis was 60% from bone metastasis biopsies and 80% from bone marrow biopsies. A signature of 133 candidate genes differentially expressed between DTCs and MTCs was identified. Several genes relevant to breast cancer metastasis to bone (osteopontin, CTGF, parathyroid hormone receptor, EGFR) were significantly overexpressed in MTCs as compared to DTCs. Biopsies of bone metastases and bone marrow rarely yield enough tissue for robust molecular biology studies using clinical samples. The findings obtained however are interesting and seem to overlap with the bone metastasis gene expression signature described in murine xenograft models. Larger biopsy specimens or improved RNA extraction techniques may improve analysable yield and feasibility of these techniques.

overall_design: Gene expression profiling was utilized to compare DTCs obtained from bone marrow aspirates (A) to MTCs isolated from Computed Tomography (C) guided biopsies of bone metastases.

first: Dong

first: Thomas

middle: R

last: Cawthorn

first: Susan

last: Done

last: Clemons


title: Differential Response Following Spinal Cord Injury in EphA4 Knockout

status: Public on May 24 2012

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

institute: University of Melbourne

summary: Mice lacking the developmental axon guidance molecule EphA4 have previously been shown to exhibit extensive axonal regeneration and functional recovery following spinal cord injury.  To assess mechanisms by which EphA4 may modify the response to neural injury, a microarray was performed on spinal cord tissue from mice with spinal cord injury and sham injured controls. RNA was purified from spinal cords of adult EphA4 knockout and wild-type mice four days following lumbar spinal cord hemisection or laminectomy only and was hybridised to Affymetrix All-Exon Array 1.0 GeneChips.  While subsequent analyses indicated that several pathways were altered in EphA4 knockout mice, of particular interest was the attenuated or otherwise altered expression of a number of inflammatory genes, including Arginase 1, expression of which was lower in injured EphA4 knockout compared to wild-type mice. Immunohistological analyses of different cellular components of the immune response were then performed in injured EphA4 knockout and wild-type spinal cords. While numbers of infiltrating CD3+ T cells were low in the hemisection model, a robust CD11b+ macrophage / microglial response was observed post-injury. There was no difference in the overall number or spread of macrophages / activated microglia in injured EphA4 knockout compared to wild-type spinal cords at two, four or fourteen days post-injury, however a lower proportion of Arginase-1 immunoreactive macrophages / activated microglia was observed in EphA4 knockout spinal cords at four days post-injury. Subtle alterations in the neuroinflammatory response in injured EphA4 knockout spinal cords may contribute to the regeneration and recovery observed in these mice following injury.

overall_design: Comparison was made between gene expression in wild-type and knockout samples both before and after injury. 3 replicates per group.

first: Kathryn

last: Munro

first: Ann

last: Turnley


title: A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes [HumanRef-8 v3.0]

status: Public on Jul 09 2012

city: Los Angeles

first: Simone

last: de Jong

state: California

address: 695 Charles E. Young Drive south

institute: UCLA

summary: Gene expression analyses in whole blood reveal a network of genes related to schizophrenia

overall_design: Weighted gene co-expression analyses applied to human whole blood gene expression data of schizophrenia cases and healthy controls

first: Marco

middle: P

last: Boks

first: Tova

middle: F

last: Fuller

first: Eric

last: Strengman

first: Esther

last: Janson

first: Carolien

last: de Kovel

first: Anil

last: Ori

first: Nancy

last: Vi

first: Flip

last: Mulder

first: Jan

last: Blom

first: Birte

last: Glenthoj

first: Chris

last: Schubart

first: Wiepke

last: Cahn

first: Rene

last: Kahn

first: Steve

last: Horvath

first: Roel

last: Ophoff


title: Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKβ

status: Public on Jun 30 2012

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Notch signaling is frequently hyperactivated in breast cancer, but how the enhanced signaling contributes to the tumor process is less well understood. In this report, we identify the proinflammatory cytokine interleukin-6 (IL-6) as a novel Notch target in breast tumor cells. Enhanced Notch signaling upregulated IL-6 expression at the transcriptional level, leading to activation of autocrine and paracrine JAK/STAT signaling. IL-6 upregulation was mediated by non-canonical Notch signaling, as it could be effectuated by a cytoplasmically localized Notch intracellular domain and was independent on the DNA-binding protein CSL. Instead, Notch-mediated IL-6 upregulation was controlled by two other factors: IKKβ, a protein in the NF-kB signaling cascade, and p53. Activation of IL-6 by Notch required IKKβ function, but interestingly, did not engage canonical NF-κB signaling, in contrast to IL-6 activation by inflammatory agents such as tumor necrosis factor, which requires canonical NF-κB signaling. With regard to p53 status, IL-6 expression was upregulated by Notch when p53 was mutated or lost, but restoring wildtype 53 into p53-mutated or -deficient cells abrogated the IL-6 upregulation. Furthermore, Notch-induced genome-wide transcriptomes from p53 wildtype and -mutated breast tumor cell lines differed extensively, and in a subset of genes upregulated by Notch in a p53-mutant cell line, upregulation was reduced by wildtype p53. In conclusion, we identify IL-6 as a novel non-canonical Notch target gene, and reveal roles for p53 and IKKβ in non-canonical Notch signaling in breast cancer and in the generation of cell context-dependent diversity in the Notch signaling output.

overall_design: 30 microarray samples consisting of MCF7 (ER+, wild-type p53, luminal type B breast cancer) and MDA-MB-231 (ER-, mutated p53, basal breast cancer) cells cultured on immobilized 1 μg/ml JAGGED1-Fc or 1 μg/ml DLL4-Fc or 1 μg/ml Fc control with or without 5 μM DAPT for 6 hours in 3 biological replicates.

first: Shaobo

last: Jin

first: Anders

last: Mutvei

first: Indira

last: Chivukula

first: Emma

last: Andersson

first: Daniel

last: Ramsköld

first: Rickard

last: Sandberg

first: Kian

last: Lee

first: Isabella

last: Screpanti

first: Lorenz

last: Poellinger

first: Cecilia

last: Sahlgren

first: Urban

last: Lendahl


title: 26 mouse ES EB samples affymetrix exon array (affymetrix exon array)

status: Public on Jun 01 2012

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

summary: Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied.

overall_design: In this study, we analyzed 26 mouse samples using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

first: Chunjiang

last: He

first: Zejuan

last: Li

first: Ping

last: Chen

first: Hao

last: Huang

first: Laurence

last: Hurst

first: Jianjun


title: DC populations incubated with rAd5, rAd28, rAd35, TLR7/8-ligand, or unexposed

first: Peter

last: Wilkinson

summary: Recombinant adenovirus vectors (rAds) are being investigated as vaccine delivery vehicles in pre-clinical and clinical studies. rAds constructed from different serotypes differ in receptor usage, tropism, and ability to activate cells, aspects of which likely contribute to their different immunogenicity profiles. Here, we compared the infectivity and cell stimulatory capacity of rAds of serotype 5 (rAd5), 28 (rAd28) and 35 (rAd35) in association with their immunogenicity. We found that rAd28 and rAd35 infected, and led to the in vitro maturation and activation of both human and mouse dendritic cells (DCs) more efficiently than did rAd5. In stark contrast to rAd5, rAd28 and rAd35 induced production of interferon-alpha (IFNα) and stimulated interferon-related intracellular pathways. However, the in vivo immunogenicity of rAd28 and rAd35 was significantly lower than that of rAd5. Deletion of IFNα signaling during vaccination with rAd28 and rAd35 vectors increased the magnitude of the insert-specific T-cell response to levels induced by vaccination with rAd5 vector. The negative impact of IFNα signaling on the magnitude of the T cell response could be overcome by increasing the vaccine dose, which was also associated with greater polyfunctionality and a more favorable long-term memory phenotype of the CD8 T cell response in the presence of IFNα signaling. Taken together, our results demonstrate that rAd-induced IFNα production has multiple effects on T cell immunogenicity, the understanding of which should be considered in the design of rAd vaccine vectors.

overall_design: FACSAria-purified DC populations were incubated with rAd5, rAd28, rAd35, TLR7/8-ligand, or unexposed, for 24 hours. RNA samples from incubated myeloid DCs (mDCs; n=5 for Ad5, Ad35 and mock; n=4 for Ad28 and TLR7/8-ligand) and plasmacytoid DCs (pDCs; n=5 for Ad28; n=4 for mock; n=3 for Ad35 and TLR7/8-ligand; n=2 for Ad5) were prepared using the Illumina BeadStation assay and hybridized to Illumina RefSeq-8 V3 BeadChips.

first: Matthew

last: Johnson

first: Constantinos

last: Petrovas

first: Takuya

last: Yamamoto

first: Ross

last: Lindsay

first: Karin

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