title: Tolerance associated gene expression following allogeneic hematopoietic cell transplantation

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

country: USA

institute: Moffitt Cancer Center

summary: Biologic markers of immune tolerance may facilitate tailoring of immune suppression duration after allogeneic hematopoietic cell transplantation (HCT). In a cross-sectional study, peripheral blood samples were obtained from tolerant (n=15, median 38.5 months post-HCT) and non-tolerant (n=17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n=10) for analysis of immune cell subsets and differential gene expression. There were no significant differences in immune subsets across groups. We identified 281 probe sets unique to the tolerant (TOL) group and 122 for non-tolerant (non-TOL). These were enriched for process networks including NK cell cytotoxicity, antigen presentation, lymphocyte proliferation, and cell cycle and apoptosis. Differential gene expression was enriched for CD56, CD66, and CD14 human lineage-specific gene expression. Differential expression of 20 probe sets between groups was sufficient to develop a classifier with > 90% accuracy, correctly classifying 14/15 TOL cases and 15/17 non-TOL cases.   These data suggest that differential gene expression can be utilized to accurately classify tolerant patients following HCT. Prospective investigation of immune tolerance biologic markers is warranted.

overall_design: Samples were collected after allogeneic hematopoietic cell transplantation (HCT) or in healthy control subjects. Peripheral blood samples were obtained from tolerant (n=15, median 38.5 months post-HCT) and non-tolerant (n=17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n=10).

first: Joseph

last: Pidala


title: Retinoblastoma protein promotes oxidative phosphorylation through upregulation of glycolytic genes in oncogene-induced senescent cells

status: Public on May 26 2015

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

summary:
Metabolism is tightly coupled with the process of aging, and tumorigenesis. However, the mechanisms regulating metabolic properties in different contexts remain unclear. Cellular senescence is widely recognized as an important tumor suppressor function and accompanies metabolic remodeling characterized by increased mitochondrial oxidative phosphorylation (OXPHOS). Here we showed retinoblastoma (RB) is required for the increased OXPHOS in oncogene-induced senescent (OIS) cells. Combined metabolic and gene expression profiling revealed that RB mediated activation of the glycolytic pathway in OIS cells, causing upregulation of several glycolytic genes and concomitant increases in the levels of associated metabolites in the glycolytic pathway. Knockdown of these genes by small interfering RNAs (siRNAs) resulted in decreased mitochondrial respiration, suggesting that RB-mediated glycolytic gene activation promotes metabolic flux into the OXPHOS pathway. These results suggest that coordinate transcriptional activation of metabolic genes by RB enables OIS cells to maintain metabolically bivalent states that both glycolysis and OXPHOS are highly active. Collectively, our findings demonstrated a previously unrecognized function of RB in OIS cells.
To understand the role of RB, we investigated the effect of RB1-knockdown in the transcription profile of oncogene-induced senescent (OIS) cells.

overall_design: IMR90 ER:Ras cells were treated with 100 nM 4-OHT for 6 days to induce senescence.  RNA was isolated 6 days after OHT treatment and hybridized to Affymetrix microarrays. SiRNA transfection (control siRNA or siRB1) was performed 4 days before RNA isolation.

first: Mitsuyoshi

last: Nakao


title: The Landscape of Antisense Gene Expression in Human Cancers [II]

status: Public on May 28 2015

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

department: Pathology

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. We found consistent antisense expression in at least 38% of annotated transcripts, which in general is positively correlated with sense gene expression. Investigations of sense/antisense pair expression across tissue types revealed lineage-specific, ubiquitous and cancer-specific antisense loci transcription. Comparisons between tumor and normal samples identified both concordant (same direction) and discordant (opposite direction) sense/antisense expression patterns. Finally, we provide oncoNAT, a catalog of cancer related genes with significant antisense transcription, which will enable future investigations of sense/antisense regulation in cancer.  Using oncoNAT we identified several functional NATs, including NKX2-1-AS that regulates the NKX2-1 oncogene and cell proliferation in lung cancer cells. Overall, this study provides a comprehensive account of NATs and supports a role for NATs regulation of tumor suppressors and oncogenes in cancer biology.

overall_design:
Strand-specific RNA sequencing data (ssRNASeq) of cancer and benign samples. SRP050021 (PRJNA267614).
Processed data files linked to SuperSeries record.

RNA-Seq raw data is available through dbGaP (controlled access) due to patient privacy concerns (phs000937.v1.p1).

first: Arul

middle: M

last: Chinnaiyan


title: Induced pluripotent stem cell models of Zellweger spectrum disorder show cell-type-specific lipid abnormalities

status: Public on May 21 2015

city: Los Angeles

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data from young and old healthy humans, as well as HGPS patients

status: Public on May 30 2015

city: Bethesda

first: Nard

last: Kubben

address: 41 Library Drive

institute: NCI, NIH

summary: HGPS is a rare premature ageing disease, caused by a mutation in the LMNA gene, which activates a cryptic splice site, resulting in the production of a mutant lamin A isoform, called progerin. Sporadic usage of the same cryptic splice site has been observed with normal physiological aging. As it is unknown how HGPS causes premature ageing defects, we set out to determine the gene signature of both young healthy individuals, old healthy individuals, as well as HGPS patients.

overall_design: All cell lines were grown in vitro using MEM tissue culture medium supplemented with 15%  foetal bovine serum, L-glutamine, non-essential amino acids, pyruvate as well as pen/strep. RNA from cells was harvested using the Qiagen RNA isolation kit according to the manufacturer's instructions.

first: Paola

last: Scaffidi


title: Gene expression profiles of PTPRZ1-knocking-down human glioblastoma stem cells

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: Gao-tan Yan Street

department: Southwest Hospital

country: China

institute: Institute of Pathology and Southwest Cancer Center


title: PTPRZ1 disruption-mediated gene expression changes in human glioblastoma stem cells [HG-U133_Plus_2]

summary: Glioblastoma is the most aggressive and lethal malignant brain tumor. Gene expression profiling is useful in determining the genome-wide gene expression changes based on the experimental purpose. In order to interrogate the downstream targets of PTPRZ1, we applied gene expression profiles to screen the altered genes that are responsible for the functional phenotype changes. The results will provide a cue for mechanical analysis with potential translational values.

overall_design: PTPRZ1-knocking down glioblastoma stem cells (GSCs) and control GSCs were used in this study. RNA were isolated using  Primescript RT Master Mix (Takara). Profiling was established by applying Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Yi-fang

last: Ping


title: Role of histone demethylase LSD1 in hepatic cancer metabolism

city: Kumamoto

first: Akihisa

last: Sakamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary:
Transcriptome analysis of LSD1-depleted HepG2 cells revealed that LSD1 regulates the expression of glycolytic and mitochondrial metabolism genes.
We found that LSD1 is an important regulator of glycolysis and mitochondrial respiration in hepatoma.

overall_design: We depleted LSD1 in HepG2 human hepatoma cells using two different siRNAs, and then carried out an expression microarray experiment.

first: Shinjiro

last: Hino


title: Gene expression changes during resistance toward vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor (TKI) therapy in renal cell carcinoma (RCC)

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: This study was performed to understand the gene expression changes that accompany treatment of renal cell carcinoma (RCC) with vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor (TKI) therapy.  Human RCC cell lines were implanted into the flanks of nude beige mice, allowed to reach 12mm in long axis, and then treated with TKIs (sunitinib or sorafenib).  Tumors were excised at 2 timepoints (prior to any therapy and at the 20mm endpoint of the study) and gene expression analysis was performed.

overall_design: Sunitinb or sorafenib were administered to mice bearing either 786-O or A498 xenografts.  Mice were sacrificed and tumors excised for RNA extraction at pretreatment size of 12mm, or at 20mm, the mandated maximum tumor size allowed at our institution.

first: Rupal

last: Bhatt

first: David

last: Panka

first: James

last: Mier

first: Michael

middle: B

last: Atkins


title: Gene expression studies of a human monocyte cell line identify dissimilarities between Copaxone and Probioglat

status: Public on May 22 2015

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

summary: Glatiramer Acetate (GA) has provided safe and effective treatment for multiple sclerosis (MS) patients  for two decades. It acts as an antigen, yet the precise mechanism of action remains to be fully  elucidated, and no validated pharmacokinetic or pharmacodynamic biomarkers exist. In order to better  characterize GA’s biological impact, genome-wide expression studies were conducted with a human  monocyte (THP-1) cell line. Consistent with previous literature, branded GA upregulated antiinflammatory  markers (e.g. IL10), and modulated multiple immune-related pathways. Despite some  similarities, significant differences were observed between expression profiles induced by branded GA  and Probioglat, a differently-manufactured glatiramoid purported to be a generic GA.

overall_design: Cells from a human monocyte cell line (THP-1) were stimulated with either branded GA, purported  generics from several manufacturers including Probioglat by ProbioMed, or vehicle control (mannitol)  for 6, 12, or 24h. RNA was extracted and expression profiled genome-wide using the Affymetrix U133  Plus 2.0 chip. Four batches of GA and one batch of Probioglat were comparatively tested in six  biological replicates each.

first: Sarah

last: Kolitz

first: Fadi

last: Towfic

first: Jason

last: Funt

first: Shlomo

last: Bakshi

first: Kevin

middle: D

last: Fowler

first: Daphna

last: Laifenfeld

first: Augusto

last: Grinspan

first: Maxim

middle: N

last: Artyomov

last: Birnberg

first: Rivka

last: Schwartz

first: Arthur

last: Komlosh

first: Liat

last: Hayardeny

last: Ladkani

middle: R

last: Hayden

first: Benjamin

last: Zeskind

first: Iris

last: Grossman


title: GDF11 is a myokine that inhibits muscle differentiation and induces atrophy during regeneration

status: Public on May 20 2015

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

summary: Age-related frailty may in part be due to a decreased competency in skeletal muscle regeneration. The role of the closely related TGFbeta amily molecules myostatin and GDF11 in regeneration is unclear. The commercially available antibody which in a prior report was used to demonstrate an age-related decrease in GDF11 was found to detect both GDF11 and myostatin, and with this reagent it appears that the combination of GDF11 and myostatin increases with age in serum. Mechanistically, GDF11 and myostatin induce SMAD2/3 phosphorylation, and both inhibit myoblast differentiation and regulate identical downstream signaling. GDF11 injected into adult mice in a model of regeneration induces an increase in smaller fibers and a decrease in satellite cell expansion. There are no signs of benefit from GDF11 to regeneration. Thus, GDF11 appears to be an age-associated myokine that inhibits muscle differentiation, and is thus a target for blockade to treat frailty

overall_design: hSKMCs, treated with 3 doses of either GDF11 or Myostatin (10, 30, or 300ng/mL). Samples were collected at 0, 10hrs and 24hrs. 4 replicates

first: David

middle: J

last: Glass

first: Ieuan

last: Clay


title: Array of CCR6+ ILC3 from the mesenteric lymph node of naïve C57BL/6 mice

city: New York

first: Gregory

middle: F

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

summary:
CCR6+ innate lymphoid cells were sorted from the mesenteric lymph node of naïve C57BL/6 mice
Cells were sort purified as lineage negative, CD127+ CD90.2+ CCR6+ ST2-

overall_design: 4 replicates were performed


title: Expression data in mouse primary mammary tumors

status: Public on May 19 2015

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary:
Many preclinical therapy studies have focused on a small number of well-described mouse allograft or human xenograft models that poorly represent the heterogeneity of human disease.  Here we have assembled a panel of mouse mammary cell lines that metastasize in syngeneic mouse hosts and we have assessed gene expression programs in the untreated primary tumors with the goal of generating information that may be useful to the identification of biomarkers that predict response to therapeutic intervention.
We used microarrays to assess global gene expression programs in primary tumors from 12 metastatic mouse mammary tumor models transplanted orthotopically into syngeneic, fully immunocompetent mouse hosts.  The 12 tumor models used here are based on published cell lines that had been established from either spontaneous mammary tumors or from mammary tumors arising in genetically engineered mouse models.  All cell lines were previously described to be metastatic.

overall_design: Cells were surgically implanted in the #4 mammary fat pads of syngeneic mice and primary tumors were harvested when they reached 0.5-1.0 cm diameter and snap-frozen for later RNA extraction.  4 independent tumors were collected for each of the 12 models.

first: Lalage

last: Wakefield

first: Yu-an

last: Yang


title: DKK1 expression is down-regulated in the lymph node pre-metastatic niche in esophageal cancer

status: Public on May 18 2015

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Lymph node metastasis is a poor prognosis indicator in esophageal cancer. Although tumor spreading currently forms the main basis for therapy selection, the molecular mechanisms underlying the metastatic pathway remain insufficiently understood. Several studies aimed to investigate these mechanisms but focused mainly on regulatory patterns in the tumors themselves and/or the invaded lymph nodes. To date no study has yet investigated the potential changes on transcription level, which take place within the yet non-invaded niche. Here we provide a comprehensive description of these regulations in patients.  In this study the transcriptomic profiles of regional lymph nodes were determined for two patient groups: patients classified as pN1 (metastasis) or pN0 (no metastasis) respectively. All investigated lymph nodes, also those from pN1 patients, were still free of metastasis. The gene expression data was obtained via microarray analysis. Top candidates were validated via PCR and immunohistochemistry.   The results show that regional lymph nodes of pN1 patients differ decisively from those of pN0 patients – even before metastasis has taken place. In the pN0 group distinct immune response patterns were observed. In contrast, lymph nodes of the pN1 group exhibited a clear profile of reduced immune response and reduced proliferation, but increased apoptosis, enhanced hypoplasia and morphological conversion processes. DKK1 was the most significant gene associated with the molecular mechanisms taking place in lymph nodes of patients suffering from metastasis (pN1). We assume that the two molecular profiles observed constitute two different stages of a progressive disease. Finally we suggest that DKK1 might play an important role within the mechanisms leading to lymph node metastasis.

overall_design:
First, samples were classified according to the principal status of the patients exhibiting (pN1 group) or non-exhibiting (pN0 group) metastasis in regional lymph nodes. The comparison of pN1 and pN0 patients should highlight the general differences in regulations that might lead to or prevent from metastasis.
Second, two lymph node samples were collected from each patient, one node located close to the tumor (regional) and the second node distant to the tumor. While the distant nodes served as reference sample the regional nodes were investigated for transcriptional regulations.
Key to the work presented here is that all nodes investigated were made sure to be still metastasis free, independent of the patients’ pN1/pN0 classification and of the location relative to the tumor. This should allow the identification of early changes occurring prior to metastasis homing.

last: Otto

first: Alexandra

last: Koenig


title: The transcriptomic responses of THP1 human monocyte-like cells expressing SP110b to interferon gamma stimulation

city: Taipei

first: Bo-Shiun

last: Yan

address: No. 1, Sec. 1, Ren-Ai Road

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University

summary:
SP110b is an interferon (IFN)-induced nuclear protein and may function as a transcriptional co-activator/repressor. IFNγ activates monocytes/macrophages thereby mediating inflammation. However, uncontrolled activation induces monocyte/macrophage cell death, which may cause immunopathology. We have demonstrated that SP110b expression prevented IFNγ-mediated monocyte/macrophage cell death.
To explore the molecular mechanisms by which SP110b suppresses IFNγ-induced cell death, we performed a genome-wide microarray analysis to identify genetic determinants associated with IFNγ-induced cell death and regulated by SP110b.

overall_design: We sought to identify genetic determinants associated with IFNγ-induced cell death and regulated by SP110b. To that end, THP1 human monocyte-like cells that could be induced by doxycycline (Dox) to over-express SP110b (THP1-SP110b) were generated and 5 experimental groups of THP1-SP110b cells were harvested for RNA extraction and hybridization on Affymetrix microarrays. The 5 groups are as follows: untreated THP1-SP110b cells as control (CON), cells treated with IFNγ for 2 days (IFN_2D), cells treated with Dox plus IFNγ for 2 days (DoxIFN_2D), cells treated with IFNγ for 4 days (IFN_4D), and cells treated with Dox plus IFNγ for 4 days (DoxIFN_4D).

first: Jia-Shiun

last: Leu


title: Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

summary:
Triple-negative (TN) breast cancers need to be refined in order to identify therapeutic subgroups of patients.
We conducted an unsupervised analysis of microarray gene-expression profiles of 107 TN breast cancer patients and undertook robust functional annotation of the molecular entities found by means of numerous approaches including immunohistochemistry and gene-expression signatures. An 87 TN external cohort was used for validation.
Fuzzy clustering separated TN tumours into three clusters: C1 (22.4%), C2 (44.9%) and C3 (32.7%). C1 patients were older (mean = 64.6 years) than C2 (mean = 56.8 years; P = 0.03) and C3 patients (mean = 51.9 years; P = 0.0004). Histological grade and Nottingham prognostic index were higher in C2 and C3 than in C1 (P < 0.0001 for both comparisons). Significant event-free survival (EFS) (P = 0.03) was found according to cluster membership: patients belonging to C3 had a better outcome than patients in C1 (P = 0.01) and C2 (P = 0.02). EFS analysis results were confirmed when our cohort was pooled with external cohort (n = 194; P = 0.01). Functional annotation showed that 22% of TN patients were not basal-like (C1). C1 was enriched in luminal subtypes and positive androgen receptor (luminal androgen receptor [LAR]). C2 could be considered as an almost pure basal-like cluster. C3, enriched in basal-like subtypes, but to a lesser extent, included 26% of claudin-low subtypes. Dissection of immune response showed that high immune response (HIR) and low M2-like macrophages were a hallmark of C3, and that these patients had a better EFS than C2 patients, characterized by low immune response (LIR) and high M2-like macrophages: P = 0.02 for our cohort, and P = 0.03 for pooled cohorts.
We identified 3 subtypes of TN patients: LAR (22%), basal-like with LIR and high M2-like macrophages (45%) and basal-enriched with HIR and low M2-like macrophages (33%). We pointed out that macrophages and other immune effectors offer a variety of therapeutic targets in breast cancer, and particularly in TN basal-like tumours. Furthermore, we showed that CK5 antibody was better suited than CK5/6 antibody to subtype TN patients.

overall_design: Subtyping molecular characterization within a cohort of 107 TN-IHC by means of gene expression profiling

first: Pascal

last: Jézéquel

first: Delphine

last: Loussouarn

first: Catherine

last: Guérin-Charbonnel

first: Loïc

last: Campion

first: Antoine

last: Vanier

first: Hamza

last: Lasla

last: Guette

first: Isabelle

last: Valo

first: Véronique

last: Verrièle

first: Mario

last: Campone


title: caArray_EXP-598: TCGA (LUSC): Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform (jhu-usc)

status: Public on May 14 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: TCGA Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform

overall_design:
EXP-598
Assay Type: Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_TCGA_HumanMethylation450
Organism: Homo sapiens (ncbitax)
Tissue Sites: Lung
Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor
Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED

first: Peter

middle: W

last: Laird


title: The Role of Interleukin-11 in the Development of the Autoimmune Response in Multiple Sclerosis

status: Public on May 15 2015

city: Chapel Hill

first: Silva

last: Markovic-Plese

state: NC

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary:
Our results introduce interleukin (IL)-11 as a new cytokine that may play a role in the development of the autoimmune response in patients with relapsing remitting multiple sclerosis (RR MS).  IL-11 was found to be the highest up-regulated cytokine in the serum and cerebrospinal fluid (CSF) from patients with clinically isolated syndrome (CIS) suggestive of MS.  It was also increased in the serum and CSF of patients with clinically definitive RRMS and during the clinical relapses of the disease.  CD4+ cells represent a predominant cell source of IL-11 in the peripheral circulation, and the percentage of IL-11+CD4+ cells is significantly increased in CIS patients in comparison to healthy controls (HCs).  Furthermore, we have identified IL-11 as a new Th17-promoting cytokine.  IL-11 induces a differentiation of naïve CD4+ T cells into Th17 cells, as well as Th17 memory cell expansion, characterized by secretion of IL-17A, IL-17F, IL-21 and IL-22.  Since the Th17 cytokines IL-17F, IL-21 and TNF- induced differentiation of naïve cells in the IL-11-secreting CD4+ cells, we propose that cross-talk between IL-11+CD4+ and Th17-cells may play a role in the initiation and propagation of the autoimmune response in RRMS.
PBMCs were separated from 15 CIS patients and 7 HCs, and the total RNA was extracted and used for gene array hybridization as described previously. To detect differential gene expression profiles between the CIS patients and HCs, a two class paired test of significance analysis was used.

overall_design: In order to capture complex gene expression changes in the PBMCs derived from 15 CIS patients in comparison to 7 HCs, we performed a comprehensive study using Affymetrix Human Gene array U133 (HG-U133) with 45,000 probe sets representing approximately 33,000 human genes.  The arrays were hybridized for 16 h at 45oC in a GeneChip® Hybridization Oven 640 (Affymetrix), washed and stained with R-phycoerythrin streptavidin in a GeneChip® Fluidics Station 400 (Affymetrix).  The arrays were scanned with a Hewlett Packard GeneArray Scanner.  Affymetrix GeneChip® Microarray Suite 5.0 software was used for washing, scanning, and basic analysis.  To detect differential gene expression profiles between the CIS patients and HCs, a two class paired test of significance analysis of microarrays was used. Differentially expressed genes were determined using a Welch two sample t-test.  A p<0.05 was considered significant.

first: Xin

last: Zhang

first: Yazhong

last: Tao

first: Jianping

last: Jin

first: Yunan

last: Tang


title: Klf4 expression in conventional dendritic cells is required for T helper 2 cell responses

city: St Louis

first: Gary

middle: E

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

summary:
Subset-specific and progenitor gene expression analysis of Klf4+/+ and Klf4-/- DCs.
The two major lineages of classical dendritic cells (cDCs) express and require either IRF8 or IRF4 transcription factors for their development and function. IRF8-dependent cDCs promote anti-viral and T-helper 1 (Th1) cell responses, whereas IRF4-expressing cDCs have been implicated in controlling both Th2 and Th17 cell responses. Here, we have provided evidence that Kruppel-like factor 4 (Klf4) is required in IRF4-expressing cDCs to promote Th2 but not Th17 cell responses in vivo. Conditional Klf4 deletion within cDCs impaired Th2 cell responses during Schistosoma mansoni infection, Schistosoma egg antigen (SEA) immunization, and house dust mite challenge (HDM), without affecting cytotoxic T lymphocyte (CTL), Th1 and Th17 cell responses to herpes simplex virus, Toxoplasma gondii and Citrobacter rodentium infections. Further, Klf4 deletion reduced IRF4 expression in pre-cDCs and resulted in selective loss of IRF4-expressing cDCs subsets in several tissues. These results indicate that Klf4 guides a transcriptional program promoting IRF4-expressing cDCs heterogeneity.

overall_design: Bone marrow progenitors and skin draining LN subsets were harvested from 4 Klf4fl/fl cre negative or Vav1-icre mice and were sorted to >95% purity on the FACS Aria 3.

first: Roxane

last: Tussiwand

first: Kenneth

last: Murphy


title: caArray_fine-00037: Rembrandt_GeneExpression

summary: This is Rembrandt gene expression data (Affymetrix HG-U133Plus2).

overall_design:
fine-00037
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133_Plus_2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain
Material Types: synthetic_DNA, synthetic_RNA
Disease States: MIXED, GBM, OLIGODENDROGLIOMA, ASTROCYTOMA, UNKNOWN, NON_TUMOR, CELL_LINE, UNCLASSIFIED

first: Howard

last: Fine

first: Yuri

last: Kotliarov


title: Human Staufen1 associates to miRNAs involved in neuronal cell differentiation and is required for correct dendritic formation

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Double-stranded RNA-binding proteins are key elements in the intracellular localization of mRNA and its local translation. Staufen is a double-stranded RNA binding protein involved in the localised translation of specific mRNAs during Drosophila early development and neuronal cell fate. The human homologue Staufen1 forms RNA-containing complexes that include proteins involved in translation and motor proteins to allow their movement within the cell, but the mechanism underlying translation repression in these complexes is poorly understood. Here we show that human Staufen1-containing complexes contain essential elements of the gene silencing apparatus, like Ago1-3 proteins, and we describe a set of miRNAs specifically associated to complexes containing human Staufen1. Among these, miR124 stands out as particularly relevant because it appears enriched in human Staufen1 complexes and is over-expressed upon differentiation of human neuroblastoma cells in vitro. In agreement with these findings, we show that expression of human Staufen1 is essential for proper dendritic arborisation during neuroblastoma cell differentiation, yet it is not necessary for maintenance of the differentiated state, and suggest potential human Staufen1 mRNA targets involved in this process.

overall_design: Three or four biological replicates per condition were independently hybridized to GeneChip Human Genome U133 Plus 2.0

first: Joan

last: Peredo

first: Patricia

last: Villacé

last: Ortín

first: Susana

last: de-Lucas


title: Expression data from MLL-rearranged leukemia model

city: Stanford

first: Corina

last: Buechele

address: 1291 Welch Road

institute: Cleary lab

summary: Chromosomal rearrangements involving the mixed-lineage leukemia (MLL) gene occur in primary and treatment-related leukemias, and confer a poor prognosis. Studies based primarily on mouse models have substantially advanced our understanding of MLL leukemia pathogenesis, but often employ supra-physiologic oncogene expression with uncertain implications for human leukemia. Genome editing using site-specific nucleases provides a powerful new technology for gene modification to potentially model human disease, however this approach has not been used to recreate acute leukemia in human cells of origin comparable to disease observed in patients.  We applied TALEN-mediated genome editing to generate endogenous MLL-AF9 and MLL-ENL oncogenes through insertional mutagenesis in primary human hematopoietic stem and progenitor cells (HSPCs) derived from human umbilical cord blood. Engineered HSPCs displayed altered in vitro growth potentials and induced acute leukemias following transplantation in immuno-compromised mice at a mean latency of 14.5 weeks. The leukemias displayed phenotypic and morphologic similarities with patient leukemia blasts including a subset with mixed phenotype, a distinctive feature seen in clinical disease.  The leukemic blasts expressed an MLL-associated transcriptional program with elevated levels of crucial MLL target genes, displayed heightened sensitivity to DOT1L inhibition, and demonstrated increased oncogenic potential ex vivo and in secondary transplant assays. Thus, genome editing to create endogenous MLL oncogenes in primary human HSPCs faithfully models acute MLL-rearranged leukemia and provides an experimental platform for prospective studies of leukemia initiation and stem cell biology in a genetic subtype of poor prognosis leukemia.

overall_design:
BM cells (sorted for hCD45) of leukemic mice (ALL) were used for global gene expression measurement using Affymetrix Microarray GeneChip platform (HG-U133 Plus 2.0). The data together with those from 70 MLL patients (ALL) and 6 control samples (same GeneChip platform) from the leukemia study group were used for unsupervised hierarchical clustering analysis Haferlach T, Kohlmann A, Wieczorek L, et al. Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol. 2010;28(15):2529-2537). Gene expression matrix from the arrays was normalized in the same way using RMA model from Bioconductor affy package. Gene expression values were then independently filtered to remove low variance probes using Bioconductor package, genefilter 1.50. Finally, 25,000 probes were then subjected to unsupervised hierarchical clustering analysis using R packages, ape and heatmap 2.0.
--------------------------------
Stanford Functional Genomics Facility

first: Stephen

middle: H

last: Wong


title: Dendritic cell-derived IL-2 promotes apoptosis of terminally mature cells via a novel autocrine signaling pathway

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary:
Dendritic cells (DCs) are crucial for sensing pathogens and triggering immune response. GM-CSF myeloid dendritic cells (GM-DCs) secrete several cytokines including IL-2 upon activation by pathogen associated molecular pattern (PAMP) ligands. DC IL-2 has been shown to be important for innate and adaptive immune responses, however its importance in DC physiology has never been demonstrated. This is due to ambiguity in expression of the CD122 subunit of the IL-2 trimeric receptor complex crucial for signaling. We show here that autocrine IL-2 signaling is functional in GM-DCs in early time window of stimulation with PAMPs. IL-2 signaling selectively activates the JAK/STAT5 pathway by assembling holo-receptor complexs at the cell surface. Autocrine IL-2 signaling inhibits survival of PAMP matured GM-DCs which is crucial for maintaining immune tolerance and preventing autoimmunity. Our findings suggest immune regulation by a novel autocrine signaling pathway that can potentially be exploited in DC immunotherapy.
Microarray technology was used to understand the role of IL-2 signaling in DC.

overall_design: Microarray was performed to investigate the role of IL-2 signaling in DC physiology. Hence Wt or IL-2-/- BMDCs were either treated or not with curdlan for 6h and taken for microarray.

first: Akhila

last: Balachander

first: Sabrina

last: Nabti

first: Radoslaw

last: Sobota

first: Shihui

last: Foo

first: Francesca

last: Zolezzi

first: Lee

last: Bernett

first: Michael

last: Poidinger

first: Paola

last: Ricciardi-Castagnoli


title: DNA methylation in melanoma is connected to gene expression phenotypes and MITF pathway expression.

status: Public on May 17 2015

city: Lund

first: Martin

last: Lauss

address: Barngatan 2B

department: Dept of Oncology

country: Sweden

institute: Lund University

summary: We subjected 50 stage III/IV tumors and 9 melanoma cell lines to genome-wide methylation analysis using the Illumina Infinium Human Methylation450 BeadChip. Furthermore, we used two technical replicates of light, medium, dark melanocyte, dermal epidermis and fibroblasts (Science Cell Research, USA), and one sample of peripheral blood leukocytes (Promega).

overall_design: Bisulphite converted DNA from the 50 stage III/IV tumors, 9 melanoma cell lines as well as normal cells were hybridised to the Illumina Infinium Human Methylation450 Beadchip.

first: Katja

last: Harbst

first: Göran

last: Jönsson


title: caArray_EXP-520: Gene Expression Profiles Predictive of Outcome and Age in Infant Acute Lymphoblastic Leukemia: a Children's Oncology Group Study

status: Public on May 12 2015

first: Mervi

last: Heiskanen

summary: Gene expression profiling was performed on 97 cases of infant ALL from Children's Oncology Group Trial P9407. Statistical modeling of an outcome predictor revealed 3 genes highly predictive of event-free survival (EFS), beyond age and MLL status: FLT3, IRX2, and TACC2. Low FLT3 expression was found in a group of infants with excellent outcome (n = 11; 5-year EFS of 100%), whereas differential expression of IRX2 and TACC2 partitioned the remaining infants into 2 groups with significantly different survivals (5-year EFS of 16% vs 64%; P < .001). When infants with MLL-AFF1 were analyzed separately, a 7-gene classifier was developed that split them into 2 distinct groups with significantly different outcomes (5-year EFS of 20% vs 65%; P < .001). In this classifier, elevated expression of NEGR1 was associated with better EFS, whereas IRX2, EPS8, and TPD52 expression were correlated with worse outcome. This classifier also predicted EFS in an independent infant ALL cohort from the Interfant-99 trial. When evaluating expression profiles as a continuous variable relative to patient age, we further identified striking differences in profiles in infants less than or equal to 90 days of age and those more than 90 days of age. These age-related patterns suggest different mechanisms of leukemogenesis and may underlie the differential outcomes historically seen in these age groups.

overall_design:
EXP-520
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133_Plus_2
Organism: Homo sapiens (ncbitax)


title: caArray_EXP-578: Gene Expression Profiles of Pediatric B-Precursor High-Risk Acute Lymphoblastic Leukemia (COG Study AALL0232 - Cohort 1).

status: Public on May 13 2015

summary: This experiment comprises 283 CEL files generated on the Affymetrix U133 Plus 2.0 gene expression microarray platform, using patient peripheral blood and bone marrow samples from the first cohort of patients accrued to Children's Oncology Group Study AALL0232. No clinical covariate data is provided at this time as the clinical study is not yet published. Researchers who would like to request outcome or other covariate data are asked to contact Dr. Cheryl Willman,   cwillman@unm.edu,  505.272.5622 (University of New Mexico) and Dr. Steven Hunger,  Stephen.Hunger@childrenscolorado.org (Children's Oncology Group and Children's Hospital Colorado) to arrange a collaboration.

overall_design:
EXP-578
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133_Plus_2
Organism: Home sapien (ncbitax)


title: DNA methylation profiles of fibroblasts and induced pluripotent stem cells (iPSCs) from individuals with Zellweger spectrum disorder (ZSD), a class of peroxisome biogenesis disorder, and healthy controls

city: Los Angeles

first: Joseph

last: Hacia

address: 2250 Alcazar Street, IGM 261

institute: University of Southern California

summary: Zellweger spectrum disorder (PBD-ZSD) is a disease continuum caused by mutations in a subset of PEX genes required for normal peroxisome assembly and function. Their clinical manifestations highlight the importance of peroxisomes in the development and functions of the central nervous system, liver, and other organs. Although much is known about peroxisome assembly and activities, the underlying bases for the cell-type specificity of disease are not fully elucidated. We reprogrammed skin fibroblasts from PBD-ZSD patients into induced pluripotent stem cells (iPSCs) and report their DNA methylation profiles as well as those of matching healthy controls.

overall_design: Dermal fibroblast cultures from 6 PBD-ZSD patient and 3 healthy control donors were reprogrammed into iPSCs by transfection with retroviruses designed to express the human OCT4, SOX2, KLF4 and c-MYC genes. Fibroblasts and iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C with 5% CO2 until confluence for RNA extraction. The overall goal was to confirm the epigenetic reprogramming of iPSCs and identify loci that are differentially methylated between PBD-ZSD patient and healthy control cells in order to gain insights into the pathomechanisms of disease.

middle: G

first: Xiao-Ming

last: Wang


title: Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina]

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development.

overall_design: shRNA knock down of lncRNAs followed by DNA methylation profiling

first: Leo

last: Kurian

first: Aitor

last: Aguirre

first: Juan

middle: C

last: Izpisua-Belmonte


title: Expression data from 128 Desmoids

city: Bordeaux

first: céline

last: brulard

address: 229 cours de l'argonne

institute: Institut Bergonié

summary: One of the main problems in managing desmoids tumors is their locoregional aggressiveness and their high ability to recur after initial treatment. In our work, with the goal to identify molecular markers that can predict Progression-Free Survival, gene-expression screening was conducted on 128 available independent untreated primary desmoid tumors using cDNA microarray. By analyzing expression profiles, we have identified, for the first time, a gene expression signature that is able to predict Progression-Free Survival. This molecular signature identified two groups with clearly distinct Progression-Free Survival in the two sets of subjects. Patients in good prognostic group had achieved a progression-free 2-year survival rate of 86% while patients in poor prognostic group had a progression-free 2-year survival rate of 44%.

first: Sébastien

last: Salas

first: Frédéric

last: Chibon

first: Céline

last: Brulard


title: Analysis of Gene Expression of Human Renal Cell Carcinoma by DNA Microaray in Patients treated with Sunitinib. An Exploratory Study

status: Public on May 11 2015

city: Sao Paulo

first: Glauber

middle: Costa

last: Brito

state: Sao Paulo

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Gene Evaluation of DNA expression from snap-frozen renal cell cancer tissue from 5 patients with locally advanced non-metastatic tumors, submitted to nephrectomy after being treated with 2 cycles of neoadjuvant Sunitinib were compared to match controls comprising of 6 patients with no neoadjuvant intervension using microarray platform Affymetrix Human Genome U133 Plus 2.0 containing 54675 probes. Validation followed using qRT-PCR

overall_design: Exploratory, prospective evaluation of gene expression in renal cell tumor snap frozen tissue after neoadjuvant Sunitinib compared to a control group with no neoadjuvant treatment

first: Carlos

last: Dzik

first: Sabrina

middle: T

last: Reis

first: Nayara

last: Viana

first: Isis

last: Paloppi

first: Miguel

last: Srougi

first: Katia

last: Leite


title: Distinct gene expression patterns of ‘multipotent' versus ‘unipotent' single colony-derived strains (SCDSs) of human bone marrow stromal cells (BMSCs)

city: Bethesda

first: Prasun

middle: J.

last: Mishra

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

summary: Dyskeratosis congenita (DC) is an inherited multi-system disorder, characterized by oral leukoplakia, nail dystrophy, and abnormal skin pigmentation, as well as high rates of bone marrow failure, solid tumors, and other medical problems such as osteopenia.  DC and telomere biology disorders (collectively referred to as TBD here) are caused by germline mutations in telomere biology genes leading to very short telomeres and limited proliferative potential of hematopoietic stem cells.  We found that skeletal stem cells (SSCs) within the bone marrow stromal cell population (BMSCs, also known as bone marrow-derived mesenchymal stem cells), may contribute to the hematological phenotype.

overall_design: At least 5x105 cells from each SCDS were homogenized in Trizol (Invitrogen) for RNA extraction. RNA was purified by using a combination of chloroform phase separation and RNeasy Mini Kits (Qiagen) according to the manufacturer's protocol. RNA was quantified and 5ug was processed for microarray analysis (LMT, NCI, Frederick, MD). RNA was reverse transcribed to form cDNA, and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Three independent replicates for each of the experimental conditions were carried out and analyzed to control for intra-sample variation.


title: Gene expression profiling and secretome analysis differentiate Adult-Derived Human Liver Stem/progenitor Cells and human hepatic stellate cells

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Adult-derived human liver stem/progenitor cells (ADHLSC) are obtained after primary culture of the liver parenchymal fraction. The cells are of fibroblastic morphology and exhibit a hepato-mesenchymal phenotype. Hepatic stellate cells (HSC) derived from the liver non-parenchymal fraction present a comparable morphology as ADHLSC. Because both ADHLSC and HSC are described as liver stem/progenitor cells, we strived to extensively compare both cell populations at different levels and to propose tools demonstrating their singularity.

overall_design: The database include full expression (HGU-219)  measurements samples from 7 Adult-Derived Human Liver Stem/progenitor (n=7) and  human hepatic stellate samples (n=7)

first: S

last: Berardis

first: C

last: Lombard

first: J

last: Evraerts

first: E

last: El

first: P

last: Sancho-Bru

first: L

last: Van

last: Sokal

first: M

last: Najimi


title: caArray_willm-00140: TARGET-ALL Expression: Children's Oncology Group Study 9906 for High-Risk Pediatric ALL

first: Mervi

last: Heiskanen

summary: Gene Expression Classifiers for Minimal Residual Disease and Relapse Free Survival Improve Outcome Prediction and Risk Classification in Children with High Risk Acute Lymphoblastic Leukemia: A Children's Oncology Group Study

overall_design:
willm-00140
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133_Plus_2
Organism: Homo sapiens (ncbitax)
Tissue Sites: Blood, Bone marrow
Material Types: Peripheral Blood, Bone Marrow
Disease States: Childhood Precursor B-Lymphoblastic Leukemia


title: DNA methylation dynamics in human carotid plaques after cerebrovascular events

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

summary: One pending issue in cardiovascular epigenetics is whether cerebrovascular events, a major complication of atherosclerosis, are associated with any specific DNA methylation changes in the carotid plaque. To clarify that topic, we profiled the DNA methylomes of human symptomatic carotid plaques (SCPs) obtained from patients who suffered cerebrovascular events (n=19) and asymptomatic counterparts (ACP; n=19) with a high-density microarray (~485,000 CpG sites, Illumina), and crossed DNA methylation data with RNAseq-based expression data from an independent SCP set (n=8). Few (30) CpGs showed a significant (p<0.05; absolute Delta-Beta>0.20) differential methylation between the two groups. Within SCPs, methylation correlated significantly with post-cerebrovascular event time (PCET; range: 3-45 days; r-value range -0.926 to 0.857; p<0.05) for ~45,000 CpGs, the vast majority of which became hypomethylated with increasing PCET. Hypomethylation was not due to erasure of the gene-body and CG-poor region hypermethylation that accompany the progression of stable lesions, but rather targeted promoters and CpG islands. Noticeably, promoter hypomethylation and increased expression were observed for genes involved in the inhibition of the inflammatory response, defence against oxidative stress and active DNA demethylation. Our data show that only weak changes in the DNA methylome distinguish symptomatic from asymptomatic carotid plaques, but a widespread demethylation resulting in permissive transcriptional marks at atheroprotective gene promoters is established in plaques after a cerebrovascular event, thus mirroring previous observations that ruptured plaques tend to revert to a more stable structure. The identified loci are candidate targets to accelerate the pace of carotid plaque stabilization.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Silvio

last: Zaina

first: Manel

last: Esteller


title: To compare gene signature of  CLL cells from patients with high versus low lymphocyte counts

city: Petach Tikva

first: Uri

last: Rozovski

address: Jabotinsky

department: Leukemia

institute: Beilinson

summary: In chronic lymphocytic leukemia (CLL) the increment in peripheral blood lymphocytes is slower than the expected increment calculated from the cells’ proliferation rate, suggesting that cellular proliferation and apoptosis are concurrent. Exploring this phenomenon, we found overexpression of caspase3, higher cleaved poly (ADP-ribose) polymerase (PARP) levels (P <0.007), and a higher apoptosis rate in cells from patients with high counts compared with cells from patients with low counts. Although we previously found that signal transducer and activator of transcription 3 (STAT3) protects CLL cells from apoptosis, STAT3 levels were significantly higher in cells from patients with high counts than in cells from patients with low counts. Furthermore, overexpression of STAT3 in MM-1 cells did not protect the cells. Rather, it upregulated caspase3 and induced apoptosis. Remarkably, putative STAT3 binding sites were identified in the caspase3 promoter and a luciferase assay, chromatin immunoprecipitation (ChIP), and an electromobility shift assay (EMSA) revealed that STAT3 activated caspase3. However, caspase3 levels increased only when STAT3 levels were sufficiently high. Using ChIP and EMSA, we found that STAT3 binds with low affinity to the caspase3 promoter, suggesting that at high levels, STAT3 activates a negative proapoptotic feedback mechanism.

overall_design: 4 samples from patients with high-count CLL were compared to 4 samples from patients with low-count CLL

first: Zeev

last: Estrov


title: A novel epigenetic regulated gene and involved in phenotypic switch classifies primary melanomas depending on the aggressiveness grade

city: L'Hospitalet de Llobregat

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Expression data of proliferating and differentiating ENS progenitor cells

city: Tuebingen

first: Roland

middle: Alexander

last: Mohr

address: Oesterbergstrasse 3

department: Experimental Embryology

institute: Institute of Anatomy

summary: Postnatal neural progenitors of the enteric nervous system are a potential source for future cell replacement therapies of developmental dysplasia like Hirschsprung's disease. However, little is known about the molecular mechanisms driving the homeostasis and differentiation of this cell pool. In this work, we conducted Affymetrix gene chip experiments to identify differences in gene regulation between proliferation and early differentiation of enteric neural progenitors. We detected a total of 1333 regulated genes that were linked to different groups of cellular mechanisms involved in cell cycle, apoptosis, neural proliferation, and differentiation. As expected, we found a strong inhibition of cell cycle progression as well as an enhanced expression of neuronal and glial markers. We further found a marked inactivation of the canonical Wnt pathway during the beginning of cellular differentiation. Taken together, this data illustrated the various mechanisms taking place during the proliferation and early differentiation of enteric neural progenitor cells.

overall_design: We analyzed 2 groups with 3 samples each: 1 group consistent of cells proliferating for 11 days and 1 group of enterospheres proliferating for 9 days and differentiating for 2 days before RNA extraction

first: Peter

last: Neckel

first: Lothar

last: Just


title: Gene expressions of CD4+ T cells in each developmental stages

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

summary:
The development of T cells has been characterized as taking place over three stages: naïve (Tn), central memory (Tcm), and effector memory (Tem) cells.
Recently, stem cell memory T cells (Tscm) were found to be the least-developed memory subset.
We performed detailed analysis of the gene expression of human CD4+ T cells with clear distinction of the Tn, Tscm, Tcm, and Tem stages.

overall_design: We sorted Tn, Tscm, Tcm, and Tem CD4+ T cells from the peripheral blood of six healthy volunteers to see the differences of gene expression between each developmental stage.

first: Tsutomu

last: Takeuchi


title: A novel epigenetic regulated gene and involved in phenotypic switch classifies primary melanomas depending on the aggressiveness grade (gene expression)

summary: Loss of methylation of a GTPase-activating protein in melanoma mediates higher proliferation, lower migration, and agressiveness of primary melanomas.

overall_design: Gene wide expression analysis of melanoma and breast primary and metastatic related tumorigenic cell lines.

first: Miguel

last: Vizoso


title: caArray_EXP-620: TCGA (Coad): Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform (Jhu-usc)

city: Rockville

address: 9609 Medical Center Drive, 1W378

institute: NCI

summary: TCGA Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform

overall_design:
EXP-620
Assay Type: Methylation
Provider: Illumina
Array Designs: jhu-usc.edu_TCGA_HumanMethylation450
Organism: Homo sapiens (ncbitax)
Tissue Sites: Colon
Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor

last: Laird


title: Novel bio-marker discovery for stratification and prognosis of breast cancer patients

status: Public on May 10 2015

city: Singapore

first: Surya Pavan

last: Yenamandra

address: 30, Biopolis street, #07-01 Matrix

institute: Bioinformatics Institute

summary: The study entails novel bio-marker discovery of Tumor Aggressive Grade signature (TAGs) genes and their role in recurrence free survival of breast cancer (BC) patients. Current BC dataset was used for co-expression analysis of TAGs genes and their role in BC progression. Additionally, recent findings have suggested an importance of structural organization of sense-antisense gene pairs (SAGPs) for transcription, post-transcriptional and post-translational events and their associations with cancer and disease. We studied SAGPs in which both gene partners are protein encoding genes (coding-coding SAGPs), their role in human BC development and demonstrated their potential for BC stratification and prognosis. Based on gene expression and correlation analyses we identified the robust set of breast cancer-relevant SAGPs (BCR-SAGPs). We isolated and characterized the sense-antisense gene signature (SAGS) and evaluated its prognostic potential in various gene expression datasets comprising 1161 BC patients. The methods used included the Cox proportional survival analysis, statistical analysis of clinicopathologic parameters and differential gene expression. The SAGS was effective in identification of BC patients with the most aggressive disease. Independently, we validated the SAGS using 58 RNA samples of breast cancer tumors purchased from OriGene Technologies (Rockville, MD).

overall_design: Sixty two total RNA samples from breast tumors and normal breast epithelium have been purchased from OriGene Technologies in March, 2011. Four RNA samples were obtained from normal individuals. Among 58 breast tumors (58 patients) 56 were diagnosed as ductal breast adenocarcinoma, 1 - as lobular breast adenocarcinoma and 1 - as squamous cell carcinoma. Gene expression data for all the samples were quantified by using whole-genome RNA microarrays (HG-U133 plus 2.0, Affymetrix).

first: Surya

middle: P

first: Oleg

middle: V

last: Grinchuk

first: Luay

last: Aswad

first: Vladimir

last: Kuznetsov


title: Integration of transcriptome and methylome analyses to dissect molecular pathogenesis of primary aldosteronism: comparision between aldosterone-producing adenomas and adjacent adrenal glands [methylome]

status: Public on May 09 2015

city: Setagaya

first: Kazuhiko

last: Nakabayashi

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Primary aldosteronism (PA) is the most common endocrine hypertension comprising 10% of hypertensive patients. A recent series of transcriptome analyses using DNA microarray has shown that neumerous genes are differentially expressed between aldosterone-producing adenoma (APA) and its adjacent adrenal gland (AAG) tissue from the same patient. However, the molecular mechanism(s) of pathogenesis of APA has not yet been fully clarified. Although growing body of evidence has shown that epigenetic abnormalities including DNA methylation play a key role in tumorigenesis, there are few studies with regard to DNA methylation in APA. In the present study, to elucidate the pathogenic relationship between gene expression and DNA methylation in PA, we conducted an integrated analysis of transcriptome and methylome data for paired APA-AAG samples from the same patient. Adrenal specimens were obtained from 7 Japanese patients with APA, who underwent adrenalectomy at Tokyo Medical and Dental University. RNA and DNA samples were extracted from those 7 paired APA and AAG tissues. Gene expression and genome-wide DNA methylation profiles were obtained using SurePrint G3 Human GE 8x60K Microarray (Agilent) and Infinium HumanMethylation450 Beadchip (Illumina), respectively. Transcriptome anlaysis identified 244 significantly (2 fold<) upregulated genes in APA compared to AAG. The upregulated genes include the previously studied genes such as PCP4, ALDH1A2, and CYP11B2, and other genes that have not been previously studied, such as HOXA9, HOXA11, and HOXB9. Gene ontology (GO) analysis for these upregulated genes identified the calcium signaling pathway to be most significantly enriched with the upregulated genes (8 genes). Methylome analysis revealed that APA was globally hypomethylated compared to AAG regardless of gene feature groups, namely, TSS1500, TSS200, 5’UTR, 1stExon, gene body, and 3’UTR. GO analysis for the genes showing hypomethylation at TSS1500/TSS200 regions in APA identified the term “cytokine-cytokine receptor interaction” to be most significantly enriched with hypomethylated genes (37 genes). Integrated analysis of gene expression and genome-wide DNA methylation profiles identified 18 genes that are upregulated and whose TSS1500/TSS200 regions are hypomethylated in APA compared to AAG. These genes include CYP11B2 and MC2R (ACTH receptor). In conclusion, this is the first genome-wide study for PA that integrated transcriptome and methylome data. Global DNA hypomethylation in APA and concordant transcriptional up-regulation of some key genes, such as CYP11B2 and MC2R, may play crucial roles in the pathophysiological significance in PA.

first: Masanori

last: Murakami

first: Takanobu

last: Yoshimoto

first: Ogawa

last: Yoshihiro


title: Integration of transcriptome and methylome analyses to dissect molecular pathogenesis of primary aldosteronism: comparision between aldosterone-producing adenomas and adjacent adrenal glands


title: C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis [HG-U133_Plus_2]

status: Public on May 08 2015

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary:
Objective: An intronic GGGGCC-repeat expansion of C9ORF72 is the most common genetic variant of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The mechanism of neurodegeneration is unknown, but a direct effect on RNA processing mediated by RNA foci transcribed from the repeat sequence has been proposed.
Results: Gene level analysis revealed a number of differentially expressed networks and both cell types exhibited dysregulation of a network functionally enriched for genes encoding ‘RNA splicing’ proteins.  There was a significant overlap of these genes with an independently generated list of GGGGCC-repeat protein binding partners.  At the exon level, in lymphoblastoid cells derived from C9ORF72-ALS patients splicing consistency was lower than in lines derived from non-C9ORF72 ALS patients or controls; furthermore splicing consistency was lower in samples derived from patients with faster disease progression.  Frequency of sense RNA foci showed a trend towards being higher in lymphoblastoid cells derived from patients with shorter survival, but there was no detectable correlation between disease severity and DNA expansion length.
Significance: Up-regulation of genes encoding predicted binding partners of the C9ORF72 expansion is consistent with an attempted compensation for sequestration of these proteins.  A number of studies have analysed changes in the transcriptome caused by C9ORF72 expansion, but to date findings have been inconsistent.  As a potential explanation we suggest that dynamic sequestration of RNA processing proteins by RNA foci might lead to a loss of splicing consistency; indeed in our samples measurement of splicing consistency correlates with disease severity.

overall_design: Gene expression profiling utilised total RNA extracted from motor neurons derived from human ALS patients with an expansion of C9ORF72 (n=8),  and controls (n=3).

first: Johnathan

last: Cooper-Knock

first: Joanna

last: Bury

first: Matthew

last: Wyles

first: Adrian

last: Higginbottom

first: Catherine

last: Gelsthorpe

first: J

last: Highley

first: Guillaume

last: Hautbergue

first: Magnus

last: Rattray

first: Janine

last: Kirby

first: Pamela

last: Shaw


title: Evidence for immune response, axonal dysfunction and reduced endocytosis preceding Lewy body pathology in the substantia nigra in Parkinson’s disease

city: Amsterdam

first: Anke

middle: Akke

last: Dijkstra

address: Van der Boechorststraat 7

department: Anatomy and neurosciences

country: Netherlands

institute: Vu Medical center

summary: Subjects with incidental Lewy body disease (iLBD) may represent the premotor stage of Parkinson’s disease (PD). To identify molecular mechanisms underlying neuronal dysfunction and alpha--synuclein pathology in the premotor phase of PD, we investigated the transcriptome of post-mortem substantia nigra (SN) of iLBD, PD donors and age-matched controls with Braak alpha--synuclein stage ranging from 0-6. In Braak alpha--synuclein stages 1 and 2, we observed deregulation of pathways linked to axonal degeneration, unfolded protein response (UPR), immune response and endocytosis, including axonal guidance signaling, protein kinase A signaling, mTOR signaling, EIF2 signaling and clathrin-mediated endocytosis. In Braak stages 3 and 4, we observed a deregulation in pathways involved in protein translation and cell survival, including mTOR and EIF2 signaling. In Braak stages 5 and 6, we observed deregulation of pathways such as dopaminergic signaling, axonal guidance signaling and thrombin signaling. Throughout the progression of PD pathology, we observed a deregulation of mTOR, EIF2 and regulation of eIF4 and p70S6K signaling in the SN. This implicates that molecular mechanisms related to UPR, axonal dysfunction, endocytosis and immune response are an early event in PD pathology, and may hold the key to altering the disease progression in PD.

overall_design: Control Braak α- synuclein Stage 0: 8 samples;α Braak α-synuclein stage 1-2: 5 samples; Braak α-synuclein 3-4 7 samples; Braak α-synuclein stages 5-6 :8 samples

middle: A

first: Angela

middle: I

last: Ingrassia

first: Rene

middle: X

last: de Menezes

first: Ronald

last: van Kesteren

first: Annemieke

middle: M

last: Rozemuller

first: Peter

last: Heutink

first: Wilma

last: vandeBerg


title: Over-expression of truncated FMRP with 295 amino acid residues: HEK293T cells

city: Fuzhou

first: Xianguo

last: Fu

address: Xihuanbei Road

department: Department of Clinical Genetics and Experimental Medicine

institute: Fuzhou General Hospital

summary: We used microarrays to detail the global gene expression in stably transfected HEK 293T cells of the over-expression of truncated FMRP containing 295 amino acid residues, which were compared with control (stably transfected HEK 293T cells of empty lentiviral vector (pLEX-MCS).

overall_design: Stably transfected HEK 293T cells of empty lentiviral vector (pLEX-MCS) and the over-expression of truncated FMRP were for RNA extraction and hybridization on Affymetrix microarrays.

first: Fenghua

last: Lan


title: Influence of neutrophils in tumor-supportive stromal cells gene expression  in non-Hodgkin B-cell lymphoma

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

summary:
Tumor infiltrating neutrophils (TAN) have been shown to exert both pro- and anti-tumoral activities and their  recruitment and polarization are triggered by tumor-derived signals. Resident mesenchymal stromal cells (MSC)  could contribute to tumor-supportive cell niche and have been shown to display tumor-specific transcriptomic, phenotypic, and functional features compared to normal tissue. In our study, we investigate whether these two cell subsets establish a bidirectional crosstalk in the context of B-cell lymphoma.
We used microarrays to explore how neutrophils could trigger the polarization of tumor-supportive stromal cells.

overall_design: Gene expression analysis were performed on stromal cells (MSC) derived from bone marrow (BM) or tonsil (Resto) of healthy donors. These BM-MSC (n=3) or Resto (n=3) were  primed or not with neutrophils for 1 day to induce stromal modification.

first: Murielle

last: Gregoire

first: Karin

last: Tarte


title: Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus [mRNA]

status: Public on May 07 2015

city: Heidelberg

first: Tobias

last: Bauer

address: Im Neuenheimer Feld 280

department: Theoretical Bioinformatics

institute: German Cancer Research Center

summary: Short hairpin RNA (shRNA) expression strategies that allow safe and persistent target mRNA knockdown are key to the success of many in vitro or in vivo RNAi applications. Here, we propose a novel solution which is expression of a promoterless miRNA-adapted shRNA (shmiRNA) from an engineered genomic miRNA locus. For proof-of-concept, we genetically “vaccinated” liver cells against a human pathogen, by using TALEns or CRISPR to integrate an anti-hepatitis C virus (HCV) shmiRNA into the liver-specific miR-122/hcr gene. Reporter assays and qRT-PCR confirmed anti-HCV shmiRNA expression as well as miR-122 integrity and functionality. Specificity and safety of shmiRNA integration were validated via PCR, cDNA and miRNA profiling, and whole genome sequencing. A subgenomic HCV replicon and a full-length reporter virus, but not a Dengue virus control, were significantly impaired in the modified cells. Our original combination of DNA engineering and RNA expression technologies should benefit numerous applications, from basic miRNA research, to human cell and gene therapy

overall_design: Four Huh7 cells lines at 3 different passages were analyzed. The reference cell line was Huh7 wild type cells (WT). The other three cell lines had an integration of an anti-HCV shmiRNA in the hcr locus and miR-122 intact (T2 31.3) or mutated (TS 30.20 and U6 20.16). RNA was extracted from three different passages.

first: Elena

last: Senis

first: Dirk

last: Grimm


title: Expression data from bone marrow cells of type 2 diabetic mice and wild type mice

city: Suzhou

first: Junjie

last: Yang

address: 708 Renmin Road

institute: Institute for cardiovascular science of Soochow University

summary:
More and more studies pointed out that BM was the primary target of diabetes mellitus-induced damage. The aim of this study was to determine whether distinct gene expression profiles are associated with altered functions of bone marrow cells in diabetes mellitus type 2 mice.
We performed global gene expression analysis in the bone marrow cells of 3 diabetic mice and 3 non-diabetic mice using Affymetrix Gene Chip Mouse Gene 1.0 ST Arrays. The gene expression patterns of diabetic mice were compared with those of nondiabetic ones using fold change. Validity of microarray results was examined by quantitative RT-PCR.

overall_design: The femurs and tibiae of type 2 diabetic mice and wild type mice were excised and the diaphyses flushed using a 25g needle and PBS. RNA was isolated for the collected cells and used for microarray analysis.

first: Takayuki

last: Asahara


title: The fat cell epigenetic signature in post-obese women is characterized by global hypomethylation and differential DNA methylation of adipogenesis genes

status: Public on May 06 2015

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

institute: Karolinska Institute

summary:
Background/Objectives: Obese subjects have increased number of enlarged fat cells which are reduced in size but not number in post-obesity. We performed DNA methylation profiling in fat cells with the aim of identifying differentially methylated DNA sites (DMS) linked to adipose hyperplasia (many small fat cells) in post-obesity.
Subjects/Methods: Genome-wide DNA methylation was analyzed in abdominal subcutaneous fat cells from 16 women examined two years after gastric bypass surgery at a post-obese state (BMI 26±2 kg/m2, mean±s.d.) and 14 never-obese women (BMI 25±2 kg/m2). Gene expression was analyzed in subcutaneous adipose tissue from 9 women in each group. In a secondary analysis, we examined DNA methylation and expression of adipogenesis genes in 15 and 11 obese women, respectively.
Results: The average degree of DNA methylation of all analyzed CpG-sites was lower in fat cells from post-obese as compared to never-obese women (P=0.014). 8,504 CpG sites were differentially methylated in fat cells from post-obese versus never-obese women (false discovery rate 1%). DMS were under-represented in CpG-islands and surrounding shores. The 8,504 DMS mapped to 3,717 unique genes; these genes were over-represented in cell differentiation pathways. Notably, 27% of genes linked to adipogenesis (i.e. 35 of 130) displayed DMS (adjusted P=10−8) in post-obese versus never-obese women. Next, we explored DNA methylation and expression of genes linked to adipogenesis in more detail in adipose tissue samples. DMS annotated to adipogenesis genes were not accompanied by differential gene expression in post-obese compared to never-obese women. In contrast, adipogenesis genes displayed differential DNA methylation accompanied by altered expression in obese women,
Conclusions: Global CpG hypomethylation and overrepresentation of DMS in adipogenesis genes in fat cells may contribute to adipose hyperplasia in post-obese women.

overall_design: Post obese=16, Control group=14.

first: Indranil

last: Sinha

first: Hui

last: Gao

first: David

last: Brodin

first: A

last: Thorell

first: M

last: Rydén

first: Daniel

last: Andersson

first: J

last: Henriksson

first: Alexander

last: Perfilyev

first: Charlotte

last: Ling

last: Dahlman-Wright

last: Arner


title: Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus

last: Bauer

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


title: Expression data from human melanoma specific CD8+ T cell clones

status: Public on May 05 2015

city: Bethesda

first: Udai

last: Kammula

address: 10 Center Drive

department: Surgery Branch

summary:
The optimal T cell attributes for the adoptive immunotherapy of cancer and viral diseases are currently unclear. Recent adoptive transfer clinical trials using ex vivo expanded tumor infiltrating lymphocytes has provided evidence that differentiated effector T cells can mediate durable responses in selected cancer patients. The capacity of these transferred cells to persist in the host was found to strongly correlate with their clinical activity. Thus, there is significant interest in identifying intrinsic markers that define antigen specific effector T cells that can develop into long-lived memory cells rather than undergoing apoptosis after infusion in humans. We recently reported the long term persistence of ex vivo expanded tumor specific CD8+ T effector clones in refractory metastatic melanoma patients after adoptive T cell transfer. By utilizing these highly homogeneous clone populations, we sought to define the pre-infusion cellular and molecular attributes associated with their effector to memory transition. Comparative transcriptional profiling found the pre-infusion clone mRNA expression levels of the IL-7 receptor (IL-7Ra) and the proto-oncogene, c-myc, directly correlated with the level of clonal persistence after adoptive transfer in humans.  The predictive value of these markers was further established by utilizing IL-7R protein, induced pSTAT5, and c-myc mRNA expression to prospectively identify human tumor specific effector clones that could engraft after controlled adoptive transfer into highly immunodeficient mice. These findings support that IL-7R and c-myc expression are valuable cell intrinsic markers that can predict the fate of effector CD8+ T cells after adoptive transfer.
We used microarrays to compare the pre-infusion gene expression profile of melanoma-specific CD8+ T cell clones that would eventually either persist or not after adoptive transfer in humans.

overall_design: We derived ten melanoma-specific CD8+ T cell clones and determined their degree of persistence after adoptive therapy into patients. We performed microarray on the pre-infusion samples of six persisting and four non-persisting clones to obtain a comparative gene signature profile.


title: Prospective derivation of a 'Living Organoid Biobank' of colorectal cancer patients

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: In Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. We report the establishment of tumor organoid cultures from 20 consecutive colorectal (CRC) patients. For most, organoids were also generated from adjacent normal tissue. The organoids closely resemble the original tumor. The spectrum of genetic changes observed within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. Gene expression analysis indicates that the major CRC molecular subtypes are represented. Tumor organoids are amenable to robotized, high-throughput drug screens allowing detection of gene-drug associations. As an example, a single organoid culture was exquisitely sensitive to Wnt secretion (porcupine) inhibitors and carried a mutation in the negative Wnt feedback regulator RNF43 (rather than in APC). Organoid technology may fill the gap between cancer genetics and patient trials, complement cell line- and xenograft-based drug studies and allow personalized therapy design.

overall_design: We generated organoids from healthy tissue and coloncarcinoma tissue. The organoids were trypsinized, plated in matrigel and overlaid with medium.  After three days, RNA was isolated using Qiagen RNAeasy. Medium conditions are the same for all organoids, irrespective of their origin.

last: van de Wetering

first: H

last: Clevers


title: C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis

first: Paul

last: Heath


title: Natalizumab exerts direct signaling capacity and supports a pro-inflammatory phenotype in some patients with multiple sclerosis

status: Public on May 02 2015

city: Wuerzburg

first: Ellen

last: Leich

department: Institute of Pathology

institute: University of Wuerzburg

summary: Natalizumab is a recombinant monoclonal antibody raised against integrin alpha-4 (CD49d). It is approved for the treatment of patients with multiple sclerosis (MS), a chronic inflammatory autoimmune disease of the CNS. Natalizumab blocks leukocyte extravasation across the blood-brain barrier by inhibiting the molecular interaction between integrin alpha-4/beta-1 heterodimers expressed on leukocytes and VCAM-1 on inflammatory-activated CNS endothelium. Here we investigated whether binding of this adhesion-blocking antibody to T lymphocytes modulated their phenotype by direct induction of intracellular signaling events. Natalizumab induced a mild upregulation of IL-2, IFN-gamma and IL-17 expression in activated primary human CD4+ T cells propagated ex vivo from healthy donors, consistent with a pro-inflammatory costimulatory effect on lymphokine expression. Overall, the relative effect of natalizumab was more pronounced in less than in fully activated T cells. Along with this, natalizumab binding triggered rapid MAPK/ERK phosphorylation. Furthermore, it decreased CD49d surface expression on effector cells within a few hours. Sustained CD49d downregulation could be attributed to integrin internalization and degradation. Importantly, also CD4+ T cells from some MS patients receiving their very first dose of natalizumab produced more IL-2, IFN-gamma and IL-17 already 24 h after infusion. Together these data indicate that in addition to its adhesion-blocking mode of action, natalizumab possesses mild direct signaling capacities, which may support a pro-inflammatory phenotype of peripheral blood T lymphocytes. This might explain why a rebound of disease activity is observed in some MS patients after natalizumab cessation.

overall_design: Human CD4+ T cells from healthy donors were stimulated in the absence or presence of natalizumab for 10 days. To recall the developed program and induce cytokine expression, half of the cells were restimulated for a further 8 h.

first: Thomas

middle: F

last: Benkert

first: Lena

last: Dietz

first: Elena

last: Hartmann

first: Andreas

last: Rosenwald

first: Edgar

last: Serfling

first: Mathias

last: Buttmann

first: Friederike

last: Berberich-Siebelt


title: Expression data from human skeletal muscle

status: Public on May 01 2015

city: bunkyo-ku

first: saori

last: kakehi

address: 2-1-1 hongo

department: Graduated shool of medicine

institute: Juntendo University

summary:
The accumulation of intramyocellular lipid (IMCL) is recognized as an important determinant of insulin resistance, and is increased by a high-fat diet (HFD). However, the effects of HFD on IMCL and insulin sensitivity are highly variable.
We used microarrays to detail to identify the genes in skeletal muscle that are related to inter-individual variation of the effects with HFD on the accumulation of intramyocellular lipid and insulin sensitivity.

overall_design: In order to identify the gene expression profile related with inter-individual variation of the effects with high fat diet on the accumulation of intramyocellular lipid and insulin sensitivity, we classified subjects who showed a large increase in intramyocellular lipid and a large decrease in glucose infusion rate by high fat diet as the high-responder (HR), and the subjects who showed a small increase in intramyocellular lipid and a small decrease in glucose infusion rate were classified as the low-responder (LR). In 5 subjects in each group, skeletal muscle sample selected at before (pre) and after (post) 3days high fat diet for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from knockdown and Sendai virus induction experiments in Human cells

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: We have carried out transcriptional profile analysis in macroH2A knockdown cells (Namalwa B cells and HeLa cells) and demonstrated that this histone variant plays positive and negative roles in transcription. We also demonstrated the  role of macroH2A in regulating the response to Sendai Virus infection.

overall_design: three biological replicates on Affymetrix HG133plus2.0 chips.

first: Matthieu

middle: D

last: Lavigne

first: Giannis

last: Vatsellas

first: Dimitris

last: Thanos


title: Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions

city: Aurora

first: Eric

last: Pietras

state: CO

address: 12700 E. 19th Avenue, Research Complex 2 Room 10014

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: To identify the molecular characterisitics of parallel lineage-biased MPP populations arising from hematopoietic stem cells (HSC) we conducted genome-wide analyses of hematopoietic stem, progenitor and mature myeloid cell populations using Affymetrix Gene ST1.0 arrays.

overall_design:
Microarray analysis of 3-5 biological replicates of the indicated hematopoietic populations, isolated by FACS sorting from C57BL/6 mouse BM. Immunophenotypic definitions: Long-term HSC (HSCLT) (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150+); Short-term HSC (HSCST)  (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150-); MPP2  (Lin-/cKit+/Sca1+/Flk2-/CD48+/CD150+); MPP3  (Lin-/cKit+/Sca1+/Flk2-/CD48+/CD150-); MPP4 (Lin-/cKit+/Sca1+/Flk2+); CMP (Lin-/cKit+/FcγR-/CD34+); GMP (Lin-/cKit+/FcγR+/CD34+); Pre-granulocyte (PreGr) (Mac1+/Gr1int); Granulocyte (Gr) (Mac1+/Gr1hi).

HSC and GMP samples listed here were also used as controls for our related microarray study GSE48893.

first: Emmanuelle

last: Passegué


title: Gene expression data: Plasmacytoid dendritic cells (pDCs) of healthy donors and MS patientes before and after IFN beta treatment

city: Piscataway

first: Konstantin

last: Balashov

state: NJ

address: 683 Hoes Lane

department: Neurology

institute: Rutgers-RWJMS

summary:
Multiple Sclerosis (MS) is an immune-mediated chronic inflammatory disease affecting the central nervous system. The cause of MS is not known and the mechanism of IFN-beta, a disease-modifying treatment (DMT) approved for MS, is not well-understood. Oligonucleotide microarrays were used to study gene expression in plasmacytoid denditic cells (pDCs) which are antigen-presenting cells implicated in MS pathogenesis.
We analyzed gene expression in pDCs of healthy controls, untreated and IFN-beta treated MS patients. We were able to identify 60 genes which were abnormally expressed in untreated MS patients and were corrected after treatment with IFN-beta.

overall_design: PDCs were separated from healthy donors and MS patients at two time points: before and 3 months after initiation of treatment with IFN-beta for RNA extraction and hybridization on Affymetrix microarrays. Gene expression data analysis of was done by GeneSpring software (Agilent Technologies). An unpaired t-test was applied to select genes with significant difference in expression between healthy donors and untreated MS patients. A paired t-test was applied to select genes with significant difference in expression in MS patients before and after IFN-beta treatment. To select differentially expressed/regulated genes, the cut-off criteria consisted of a P value < 0.05 and fold change >1.5.

first: Latt

middle: L

last: Aung


title: Comparative genomic, microRNA, and tissue analyses reveal subtle differences between non-diabetic and diabetic foot skin [gene expression]

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

summary: Diabetes Mellitus (DM) is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU) that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS) and healthy non-diabetic foot skin (NFS). MicroRNA (miR) profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05). Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy, vascular complications, or duration of DM, may further compromise tissue’s healing ability leading to development of DFUs.

overall_design: Total RNA including the miRNA fraction was extracted from the samples using the QIAGEN miRNeasy mini kit and following the manufacturer’s instructions. The RNA quality was assessed using the AGILENT bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) to estimate the RNA integrity number (RIN). Samples with a RIN higher than 5 were used for mRNA profiling as described below. We previously described methods for tissue specimen preparation and hybridization. All processing and analysis of microarrays utilized standard protocols at the University of Miami Microarray Core Facility. Briefly, between 100 to 300 ng of total RNA was reverse transcribed, amplified, then the sense strand cDNA synthesized, labeled, and hybridized on arrays. The amplified, fragmented and biotin-labeled cDNAs were hybridized to the Affymetrix GeneChip Human Gene 2.0 ST microarray according to the manufacturer’s recommendations. Arrays were washed and stained using Affymetrix Fluidic stations 450 and scanned using Affymetrix GeneChip scanner 3000 7G. Image analysis was performed using the Affymetrix Command Console Software (AGCC). Resulting CEL files was imported into Expression Console™ Software (Affymetrix, Santa Clara, CA, USA) and underwent gene level normalization and signal summarization. The output files from this step were imported in Transcriptome Analysis Console (TAC) 2.0 Software (Affymetrix, Santa Clara, CA, USA) to identify differentially expressed genes and carry out clustering analysis. Only genes with a p-value lower than 0.05 and a fold-change greater than 2 were confirmed by qPCR in a prospective set of 10 NFS and 10 DFS.

first: Lisa

last: Liang

first: Irena

last: Pastar

first: Ashley

last: Rosa

first: Olivera

last: Stojadinovic

middle: W

last: Zwick

first: Robert

middle: S

last: Kirsner

first: Anna

middle: G

last: Maione

first: Jonathan

last: Garlick

first: Marjana

last: Tomic-Canic


title: Abnormal Mammary Development in STAT1-null Mice is Stroma-Dependent

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Stat1-null mice (129S6/SvEvTac-Stat1tm1Rds homozygous) uniquely develop estrogen-receptor-positive mammary tumors with incomplete penetrance and long latency. We studied the growth and development of the mammary glands in Stat1-null mice. Stat1-null MGs have faulty branching morphogenesis with abnormal terminal end buds. The Stat1-null MG also fails to sustain growth of 129S6/SvEv wild-type and null epithelium. These abnormalities are partially reversed by added progesterone and prolactin. Transplantation of wild-type bone-marrow into Stat1-null mice does not reverse the mammary gland developmental defects. Media conditioned by Stat1-null epithelium-cleared mammary fat pads does not stimulate epithelial proliferation whereas it is stimulated by conditioned media derived from either wild-type or progesterone and prolactin-treated Stat1-null epithelium-cleared mammary fat pads. Microarrays and multiplex cytokine protein assays showed that the mammary gland of Stat1-null mice had lower levels of growth factors that have been implicated in normal mammary gland growth and development. Transplanted Stat1-null tumors and their isolated cells also grow slower in Stat1-null mammary gland compared to wild-type recipient mammary gland. Stat1-null hosts responded to tumor transplants with granulocytic infiltrates while wild-type hosts show a mononuclear response. These studies demonstrate that growth of normal and neoplastic Stat1-null epithelium primarily depends on the hormonal milieu and factors, such as cytokines, from the mammary stroma.

overall_design: Stat1-null mammary glands were compared to 129SvEv WT mammary glands with respect to development, gene expression profiles, growth factors and histology.

first: Jane

middle: Q

last: Chen

first: Alexander

last: Borowsky


title: Comparative genomic, microRNA, and tissue analyses reveal subtle differences between non-diabetic and diabetic foot skin

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

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

overall_design: Refer to individual Series


title: Expression data from PKM1 or PKM2 expressing mouse embryonic fibroblasts.

city: East Lansing

first: Sophia

middle: Y

last: Lunt

state: MI

address: Biomed Phys Sci Rm 2120, 567 Wilson Rd

institute: Michigan State University

summary:
We profiled global gene expression for two separate lines of mouse embryonic fibroblasts and find that deletion of PKM2 and expression of PKM1 does not alter global gene expression profiles.
We used microarrays to futher characterize the effects of PKM1 expression compared to PKM2 expression on global gene expression in mouse embryonic fibroblasts.

overall_design: Primary mouse embryonic fibroblast cells were used for RNA extraction and hybridization on Affymetrix microarrays. Intensity files were RMA normalized using Affymetrix expression console.

first: Matthew

last: Vander Heiden


title: Effects of jasplakinolide on gene expression in cultured vascular smooth muscle cells

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

institute: Lund University

summary:
Actin polymerization can regulate smooth muscle gene expression but the full extent of this regulation is unknown.
To understand the full impact of actin polymerization on smooth muscle gene expression cells were cultured with the actin stabilizing drug jasplakinolide for 24h.

overall_design: Mouse aortic smooth muscle cells in passage 3-4 were cultured for 24h in DMEM 10%FCS with or without 100nM jasplakinolide. RNA was isolated using Qiagen mRNeasy according to standard protocol

first: Karolina

last: Turczynska


title: A novel epigenetic regulated gene and involved in phenotypic switch classifies primary melanomas depending on the aggressiveness grade (Illumina)

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Loss of methylation of a GTPase-activating protein in melanoma mediates higher proliferation, lower migration, and aggressiveness of primary melanomas.

overall_design: Sequencing of bisulfite converted DNA and array based analysis of melanoma, breast, and colon primary and metastatic related tumorigenic cell lines.

first: Miguel

last: Vizoso


title: Expression data from cerebral tumors of WHO grade II and III

status: Public on Apr 30 2015

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

summary:
Molecular profiling of cerebral gliomas distinguishes biologically distinct tumor groups and provides prognostically relevant information beyond histological classification and IDH1/2 mutation status.
We performed microarray-based genome- and transcriptome-wide molecular profiling of primary tumor samples from 137 patients with cerebral gliomas, 61 WHO grade II and 76 WHO grade III tumors.

overall_design: For this study, we screened prospectively recruited patients with a histopathological reference diagnosis of cerebral tumors of WHO grade II and III, known KPS at diagnosis, information on extent of resection by early postoperative neuroimaging, available frozen tissue specimens from the initial operation, and documented clinical outcome.

first: Michael

last: Weller

first: Ruthild

last: Weber

first: Vera

last: Riehmer

first: Bettina

last: Hentschel

first: Markus

last: Kreuz

first: Jörg

last: Felsberg

first: Ulrike

last: Beyer

first: Henry

last: Wirth

first: Kerstin

last: Kaulich

first: Joachim

last: Steinbach

first: Christian

last: Hartmann

first: Dorothee

last: Gramatzki

first: Johannes

last: Schramm

first: Manfred

last: Westphal

first: Gabriele

last: Schackert

first: Matthias

last: Simon

first: Tobias

last: Martens

first: Jan

last: Bostroem

last: Hagel

last: Sabel

first: Dietmar

last: Krex

middle: C

last: Tonn

first: Wolfgang

last: Wick

first: Susan

last: Noell

first: Uwe

last: Schlegel

first: Bernhard

last: Radlwimmer

first: Torsten

last: Pietsch

last: Löffler

first: Andreas

last: von Deimling

first: Hans

last: Binder

first: Guido

last: Reifenberger