title: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors

status: Public on Sep 15 2016

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

summary: Malignant  (type II) testicular germ cell tumors (TGCT) are considered tumors of embryonic germ cell  ancestry that diverge morphologically as seminoma (SE), and nonseminomas (NS), the latter including embryonal carcinoma (EC), teratoma (TE), yolk sac tumor (YS) and choriocarcinoma. We have analyzed the genomes and epigenomes of pure histological forms of TGCT (n=130) and 128 matched adjacent normal testicular tissues for TGCT core and subtype-specific DNA methylome profiles and somatic copy number aberrations (SCNA). Original data were compared with published data sets focused on differentiated and pluripotent states. First, we identified pan-TGCT recurrent erasure of maternal and paternal germline imprints and DPPA3 (STELLA), consistent with an embryonic  germ cell ancestry. Beyond these conserved properties, we identified TGCT subtype-dependent epigenomic congruency with pluripotent versus somatic reference lineages, thereby establishing competency for lineage-conforming methylation reprogramming in the multi-potent common ancestor of TGCT. Notable subtype programming distinctions are as follows: the SE methylome reflects a ground-state of germ cell erasure; EC is found to harbor pervasive embryonic stem cell (ESC)-like CpH (non-CpG) methylation, absent in other TGCT and non-germ cell tumors and differentiated tissues. EC was further distinguished by ESC-like hypomethylation of NANOG, contrasting with NANOG methylation in TE, YS, and somatic tissues. Thus, EC methylomes present a novel mixed ESC/embryonic germ cell epigenomic state.  TE global methylation was most convergent with somatic tissue; however, and unique among TGCT subtypes, TE manifested hypermethylation of the H19 paternal germline DMR. The YS methylome most closely resembled extra-embryonic trophoblast. The total set of findings provides evidence for a multi-potent TGCT stem cell whose progeny may harbor pluripotent, primordial germ/gonocyte, and somatic lineage-defining methylation marks. Despite such competency, no TGCT subtype restored erased parental germline imprints. TE is the exception, with H19 hypermethylation. Benign testis adjacent to TGCT exhibited a bimodal epigenotype distribution determined by spermatogenesis and significantly associated with high versus low Johnsen score. Overall, TGCT methylomes are trapped in a core embryonic germ cell-like state of DPPA3/STELLA and imprint erasure, while differential somatic and pluripotent reprogramming profiles are otherwise established.

middle: K

last: Killian

first: Lambert

middle: C

last: Dorssers

first: Britton

last: Trabert

first: Ad

last: Gillis

middle: B

last: Cook

first: Yonghong

last: Wang

first: Joshua

last: Waterfall

first: Holly

last: Stevenson

first: William

middle: I

last: Smith Jr

first: Natalia

last: Noyes

first: Parvathy

last: Retnakumar

first: Hans

last: Stoop

last: Oosterhuis

first: Katherine

last: McGlynn

first: Leendert

last: Looijenga


title: Gene expression profiling of the astrocyte transcriptome in multiple sclerosis normal appearing white matter reveals a neuroprotective role

status: Public on Sep 19 2016

city: Sheffield

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary: Gene expression profiling has been performed on astrocytes isolated using laser capture microdissection (LCM) from multiple sclerosis normal appearing white matter (NAWM) and control WM to identify whether specific glial changes exist in NAWM which contribute to lesion development or prevent disease progression

overall_design: Expression profiling of astrocytes from Multiple sclerosis NAWM and from Neurologically normal control WM.

first: Rachel

last: Waller

first: M

middle: N

last: Woodroofe

first: Stephen

last: Wharton

middle: G

last: Ince

first: Simona

last: Francese

middle: R

first: Alex

last: Cudzich-Madry

first: Ruth

middle: H

last: Thomas

first: Natalie

last: Rounding

first: Basil

last: Sharrack

first: Julie

middle: E

last: Simpson


title: Expression data from fractionated prostate epithelial cells (fetal and adult)

city: Los Angeles

first: Isla

middle: P

last: Garraway

state: CA

address: 10833 LeConte Avenue

department: Urology

country: USA

institute: UCLA

summary:
Subset of adult prostate basal cells and fetal prostate epithelial cells have enhanced tubule-initiating capability in vivo.  Features associated with this process may be co-opted in cancer cells
We used microarrays to contrast gene expression profiles of fetal and adult tubule-initiating cells compared to basal and luminal epithelial cells that can be isolated from bening prostate tissue specimens.

overall_design: FACS sorting of dissociated fetal and adult tissue specimens was performed with Epcam, CD44, and CD49f antibodies. The following populations were isolated for Gene expression analysis:  Epcam+CD44- (fetal prostate epithelial cells/tubule-initiating cells), Epcam+CD44-CD49fHi (adult tubule-initiating cells), Epcam+CD44+CD49fHi (adult basal cells), Epcam+CD44-CD49fLo (adult luminal cells)


title: Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells - Implications for myeloma bone disease

status: Public on Sep 20 2016

city: Wuerzburg

first: Julia

last: Dotterweich

address: Friedrich-Bergius-Ring 15

department: Orthopedic Center for Musculoskeletal Research

country: Germany

institute: University of Wuerzburg

summary: In this study we analyzed the myeloma cell contact-mediated changes on the transcriptome of skeletal precursor cells. Therefore, human mesenchymal stem cells (MSC) and osteogenic precursor cells (OPC) were co-cultured with the representative myeloma cell line INA-6 for 24 h. Afterwards, MSC and OPC were separated from INA-6 cells by fluorescence activated cell sorting. Total RNA of MSC and OPC fractions was used for whole genome array analysis.

overall_design: Primary MSC from the cancellous bone from the acetabulum received from donors after total hip arthroplasty were isolated as described by Noth et al., 2002 (PMID:12382974) and expanded in DMEM/Ham´s F12 medium including 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin and 50 µg/ml L-Ascorbic acid 2-phosphate. MSC were passaged at least once before they were used for experiments. Osteogenic precursor cells (OPC) were generated by incubating MSC with DMEM High Glucose medium for two weeks supplemented with 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin, 10 mmol/l beta-glycerophosphate, 100 nmol/l dexamethasone, and 50 µg/ml L-Ascorbic acid-2-phosphate. The myeloma cell medium consisted of RPMI 1640 medium, 20% FCS, 100 µg/ml gentamicin, 2 mmol/l L-glutamine, and 1 mmol/l sodium pyruvate. One day before co-culturing, confluent MSC and OPC monolayers were adapted to cell culturing conditions by incubating them with a 1:1 (v/v) mixture of MSC/myeloma cell medium and OPC/myeloma cell medium and INA-6 cells were stained with 5 µmol/l Cell Tracker® Green 5-chloromethylfluorescein diactetate. Afterwards, INA-6 cells were washed with PBS and used for co-culture. After 24 h, cells were trypsinized and separated by fluorescence activated cell sorting (BD FACS AriaTM III cell sorter). The control cells were treated accordingly. Cell pellets of MSC and OPC fractions were lysed in RA1 buffer containing 1% 2-mercaptoethanol and stored at -80°C until total RNA extraction. Total RNA was isolated with the NucleoSpin® RNA II kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer´s instructions. The whole genome array analysis was performed using the Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix, High Wycombe, United Kingdom). Each 5 control specimens and 5 co-cultured samples of both MSC and OPC were used for hybridization.

first: Katrin

last: Schlegelmilch

first: Alexander

last: Keller

first: Beate

last: Geyer

first: Doris

last: Schneider

first: Sabine

last: Zeck

first: Robert

middle: J

last: Tower

first: Regina

last: Ebert

first: Franz

last: Jakob

first: Norbert

last: Schütze


title: Neuroprotection by a novel immunomodulatory peptide [P9 mice]

status: Public on Sep 17 2016

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

summary:
Perinatal brain injury is a major clinical problem associated with high neonatal mortality and morbidity and an increased risk of life-long chronic disabilities. Despite improved survival rates, the absolute numbers of neurological handicaps of perinatal origin have not decreased. There is currently no pharmacological treatment providing neuroprotction in neonates. As activation of the innate immune response is a key contributing factor to brain injury in both term and preterm infants we investigated the therapeutic potential of novel immunomodulatory innate defence regulator peptides (IDRs) in perinatal brain injury. IDR-1018 significantly reduced the production of inflammatory mediators by LPS-stimulated microglia cells in vitro.
IDR-1018 was also neuroprotective in a clinically-relevant animal model of neonatal brain injury, exerting effects on regulatory molecules of TLR-, Ca2+- and p53-signaling. Of utmost importance, IDR-1018 markedly protected both white and grey brain matter when administered after the injury, thus has tremendous applicability to the clinical setting. Here we demonstrate for the first time that peripheral administration of an immunomodulatory peptide is neuroprotective in vivo in a clinically relevant model of perinatal brain damage.

overall_design: 5 samples each for 8 groups were used for a total of 40 samples. Groups were: LPS-sensitized hypoxic-ischemic with injured and uninjured hemispheres (LPS/HI) (2 groups), LPS/HI + IDR-1018 (2 groups), IDR-1018, LPS, LPS+IDR-1018, and Vehicle.

first: Hayde

last: Bolouri

first: Karin

last: Sävman

first: Wei

last: Wang

first: Joakim

last: Ek

first: Anitha

last: Maurer

first: Edie

last: Dullaghan

middle: D

first: Henrik

last: Hagberg

last: Hancock

first: Kelly

middle: L

last: Brown

first: Carina

last: Mallard


title: Tumor-Associated Macrophages Promote Colorectal Tumor Development Through Remodeling of Its Extracellular Matrix

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
Ly6Chi monocytes massively infiltrate the CRC-tumors by virtue of their CCR2 expression and further mature into Ly6CloF4/80hi CD64hiMHCII+ TAM upon tumor progression. We demonstrated that TAM-deficient tumors display impaired tumor-growth via alternation of the ECM morphology, structure and composition. Using advanced high-resolution optical imaging to visualize the tumoral-ECM macromolecule network together with transcriptomic and proteomic approaches we unraveled that TAM play critical role in the deposition, linearization and cross-linking of collagenous ECM. Remarkably, we show that cues embedded in ECM by TAM-mediated remodeling activity promote tumor cell proliferation in vitro and orthotopic tumor development in vivo.
Abnormal remodeling of the extracellular matrix (ECM) structural and compositional is a hallmark of many cancers. While tumor associated macrophages (TAM) are considered pivotal players in mounting pro-tumoral functions, their role in tumor-ECM remodeling remains largely ambiguous. We found that TAM-deficient CRC tumors established in Ccr2-/- mice exhibited attenuated growth. Advanced molecular imaging revealed that the enhanced deposition, linearization and cross-linking of collagen fibers typical to tumor growth were absent in the Ccr2-/- tumors. Integrating transcriptomic and proteomic approaches we defined a TAM signature of ECM remodeling enzymes, structural and affiliated proteins involved with the synthesis and assembly of collagen. The Ccr2-/- tumors displayed altered ECM composition with 348 proteins that were differentially expressed in comparison with WT tumors, among them 46 were ECM related. Decellularized 3D ECM fragments extracted from WT tumors, but not from Ccr2-/- tumors or upstream healthy colon, enhanced tumor cell proliferation in vitro and tumor development in the native colonic environment indicating that TAM have a critical role in priming pathological ECM cues.

overall_design: 8 Samples (arrays) were performed. We generated pairwise comparison between all the different macrophages stages, using Partek Genomics Suite. Genes with p≤5%[FDR] and a fold-change difference of  ≥2 or <-2 were selected.

first: Ran

last: Afik

first: Ehud

last: Zigmond

first: Milena

last: Vugman

first: Anjana

last: Shenoy

first: Elad

last: Bassat

first: Zamir

last: Halpern

first: Tamar

last: Geiger

first: Irit

last: Sagi

first: Chen

last: Varol


title: DNA Methylation profiles of benzene hematotoxicity

status: Public on Sep 12 2016

city: beijing

first: ai

middle: aa

last: gao

address: NO10, Xi tou tiao, Youanmen,Fengtai District

country: China

institute: School of Public Health, Capital Medical University

summary: To identify potential methylation biomarkers in occupationally benzene-exposed individuals and to elucidate mechanisms of benzene hematotoxicity.

overall_design: Bisulfite converted DNA from peripheral blood mononuclear cells of four patients of chronic benzene poisoning, four workers exposed to benzene levels ranging from < 1 ppm and four health controls matched age and gender without benzene exposure samples was hybridized to the Illumina Infinium HumanMethylation450 BeadChip array.

first: Ai

last: Gao


title: Purification of functional human ES/iPSC-derived midbrain dopaminergic progenitors using LRTM1

status: Public on Sep 09 2016

city: Kyoto

first: Bumpei

last: Samata

address: 53 Kawahara-cho, Shogoin

country: Japan

institute: Kyoto university

summary: Human induced pluripotent stem cells (iPSCs) can provide a promising source of midbrain dopaminergic (mDA) neurons for cell replacement therapy for Parkinson's disease (PD). However, iPSC-derived donor cells inevitably contain tumorigenic or inappropriate cells. To eliminate these unwanted cells, cell sorting using antibodies for specific markers such as CORIN or ALCAM have been developed, but neither marker is specific for ventral midbrain. Here, we employed a double-selection strategy for cells expressing both CORIN and LMX1A::GFP and report a novel cell surface marker to enrich mDA progenitors, LRTM1. When transplanted into 6-OHDA-lesioned rats, human iPSC-derived LRTM1+ cells survived and differentiated into mDA neurons in vivo, resulting in significant improvement in motor behavior without tumor formation. In addition, LRTM1+ cells exhibited efficient survival of mDA neurons in the brain of an MPTP-treated monkey. Thus, LRTM1 can provide a powerful tool for efficient and safe cell therapy for PD patients.

overall_design: Differentiated mouse ESC-derived neural progenitors just after sorting (day9 CORIN+LMX1A::GFP+, day9 CORIN-LMX1A::GFP+) and mouse fetal ventral mesencephalon on E11.5 (CORIN+, CORIN-) were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

last: Takahashi


title: Human polar body transfer eliminates the transmission of inherited mitochondrial DNA variants [methylation]

status: Public on Sep 11 2016

city: Shanghai

first: Hongying

last: Sha

state: Shanghai

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

institute: Fudan University

type: Methylation profiling by genome tiling array

summary: Although polar body transfer (PBT) has the potential to prevent the transmission of inherited mitochondrial DNA (mtDNA) diseases, the PBT technique is still at an early stage, as no human data are publicly available for PBT. Here, we investigated the comparative values of first and second PBT (PB1T, PB2T), spindle-chromosome and pronuclear transfer (ST, PNT), modified ST and PNT (mST and mPNT) to explore the efficiency and safety of these approaches. A comparative analysis confirmed that PB1T, mST, PB2T and mPNT could be used to donate mtDNA without resulting in significant heteroplasmy or alterations in the methylation profile and gene expression. Importantly, PB1T produced reconstructed embryos and embryonic stem cells (ESCs) in every generation with undetectable donor mtDNA. However, donor mtDNA seems to have a tendency to be amplified in generations of mPNT-ESCs with up to 3% heteroplasmy. These results suggest that PB1T holds great potential in eliminating mtDNA variants.

overall_design: Nine samples, one negative control and one positive control  were analysised, each sample replicate three times.


title: Affymetrix HG-U133 Plus 2 array data of iPSCs and iPSC-derived-NSPCs

status: Public on Sep 14 2016

city: Shinjuku-ku

first: Keiko

last: Sugai

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: iPSC-derived NSPCs, which were induced by two different protocols (Embryoid body or Neural rosette) followed by expansion in free-floating culture  (neurospheres), had closely resembled profiles.

overall_design: Affymetrix HG-U133 Plus2 Array analyses were performed according to the manufacturer's directions on three iPSCs, and their neural induced derivatives using two different protocols. Two independent inductions were performd to each iPSC (T1 and T2).

first: Masaya

last: Nakamura


title: Expression data from Human Adipose tissue

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Adipose inflammation is a key component of cardiometabolic disease. We used microarray to profile gene expression changes in adipose tissue following administration of LPS (3ng/kg IV) to healthy human volunteers.

overall_design: We obtained subcutaneous adipose biopsies from healthy volunteers at baseline, and at 4-, 12- and 24-hours following evoked endotoxemia (LPS), to examine gene expression changes during inflammation.

first: Muredach

last: Reilly


title: DNA methylation analysis of neuroblastoma cell lines treated with epigenetic drugs

status: Public on Sep 08 2016

city: Heidelberg

first: Manuel

last: Wiesenfarth

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on the neuroblastoma methylome was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in histone modification and RNA expression.

overall_design: The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC and EPZ-6438. Controls were treated with solvent (DMSO). DNA was isolated, bisulphite converted and hybridised to the llumina HumanMethylation450 BeadChip

first: Kai

middle: O

last: Henrich

first: Sebastian

last: Bender

first: Maral

last: Saadati

first: Moritz

last: Gartlgruber

first: Chunxuan

last: Shao

first: Carl

last: Herrmann

first: Martha

last: Parzonka

first: Daniel

last: Dreidax

first: Matthias

last: Fischer

first: David

last: Duffy

first: Peter

last: Schmezer

first: Christoph

last: Plass

first: Thomas

last: Höfer

first: Axel

last: Benner

first: Stefan

middle: M

last: Pfister

first: Frank

last: Westermann


title: Human polar body transfer eliminates the transmission of inherited mitochondrial DNA variants

first: Hongying

last: Sha

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

overall_design: Refer to individual Series


title: Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis.

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: Transcriptome analyses of normal gingival fibroblasts after knockdown of DLX5 and RUNX2 long forms.

overall_design: Knockdown of DLX5 and RUNX2 long forms by lenti virus vector

first: Akira

last: Saito

first: Yoko

last: Yamaguchi

first: Mitsuhiro

last: Ohshima


title: Treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL


title: Expression data from human cornea epithelial and stromal cells and tissue-engineered anterior lamelar corneas

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

institute: UNIVERSITY OF GRANADA

summary:
The objective of this study was to analyze gene expression associated to the process of cell and tissue differentiation of bioengineered human anterior lamelar corneas
We used microarrays to detail the global programme of gene expression associated to bioengineered corneas differentiation

overall_design: Total RNA was isolated from 1) primary cell cultures of human cornea epithelial cells (established from cornea donors); 2) primary cell cultures of human cornea stromal keratocytes (established from cornea donors); 3) bioengineered anterior lamelar corneas consisting of corneal keratocytes immersed within fibrin-agarose biomaterials and epithelial cells on top

first: Miguel

last: Alaminos

first: Ingrid

last: Garzón

first: Miguel-Ángel

last: Martín-Piedra

first: Víctor

last: Carriel


title: Patterns of changes in DNA global methylation following the treatment with GC/RA and with GC/RA plus AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

summary: Comprehensive characterization of the DNA methylome regulated by the treatment with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and the relationship of these features with the status of BRG1 and MYC in lung cancer cell lines.

overall_design: MYC amplified cell lines and BRG1 mutant cell lines were treated  with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and their methylation was then measured

first: Octavio

middle: A

last: Romero Ferraro

first: Manuel

last: Torres Diz

first: Montse

last: Sánchez-Céspedes


title: DNA methylation data from primary neuroblastoma tumors

first: Maral

last: Saadati

department: Biostatistics

summary: Genome wide DNA methylation profiling of primary neuroblastomas. The Illumina  450k methylation array was used to obtain DNA methylation profiles across approximately 485,000 CpGs in 105 neuroblastomas. Tumors were derived from 40 low-risk, 9 intermediate-risk and 56 high-risk patients.

overall_design: Bisulphite converted DNA from the 105 samples were hybridised to the llumina HumanMethylation450 BeadChip

first: Kai

last: Henrich

first: Sebastian

last: Bender

first: Moritz

last: Gartlgruber

first: Chunxuan

last: Shao

first: Carl

last: Herrmann

first: Martha

last: Parzonka

first: Daniel

last: Dreidax

first: Matthias

last: Fischer

first: David

last: Duffy

first: Peter

last: Schmezer

first: Christoph

last: Plass

first: Thomas

last: Höfer

first: Axel

last: Benner


title: Differential expression of genes in human CD8+ T cell clones expanded with eAPC vs eAPC:4-1BBL

status: Public on Sep 01 2016

first: Abhishek

middle: K

last: Srivastava

state: MD

address: 10 Center Drive. Room 3-5888

institute: NIH

summary:
To understand the molecular mechanism of 4-1BB co-stimulation on T cells, CD8+ T cell clones were expanded with either eAPC or eAPC:4-1BBL.
The global programme of gene expression identified distinct classes of up-regulated genes in T cell clones expanded with eAPC:4-1BBL (4-1BB costimulation) compared to eAPC (without co-stimulation).

overall_design: Microarray analysis was performed (day 3 and day 7) on CD8+ T cell clones expanded with either eAPC or eAPC:4-1BBL in media containing IL-2 (50cu/ml), and anti-CD3 antibody (25ng/ml).

first: Biman

middle: C

last: Paria

first: Udai

middle: S

last: Kammula


title: Effect of MCMV infection on gene expression in ovaries of pregnant and non-pregnant mice

status: Public on Sep 03 2016

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

institute: University of Cambridge

summary:
Affymetrix Gene ST 1.0 arrays were performed on total RNA obtained from ovaries of 5 female mice (pregnant or non-pregnant; mock or MCMV infection).
Mice were infected 9.5 days post conception with 2x10e05 PFU MCMV i.v.. RNA was prepared at 5 days post infection (14.5 days post conception).

overall_design: Total RNA prepared from ovaries of 5 mice per condition was pooled and subjected to microarray analysis. Data were normalised using RMA.

first: Jonjic

last: Stipan

first: Dölken

last: Lars


title: Microarray skeletal muscle miR-499 overexpressing mice

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

summary:
This experiment was conducted to identify target genes of the microRNA-499 in skeletal muscle of transgenic mice that overexpressed miR-499.
The following abstract from the submitted manuscript describes the major findings of this work.

Coupling of mitochondrial function and skeletal muscle fiber type by a miR-499/Fnip1/AMPK circuit. Jing Liu, Xijun Liang, Danxia Zhou, Ling Lai, Tingting Fu, Yan Kong, Qian Zhou, Rick B. Vega, Min-Sheng Zhu, Daniel P. Kelly, Xiang Gao, and Zhenji Gan.

Upon adaption of skeletal muscle to physiological and pathophysiological stimuli, muscle fiber type and mitochondrial function are coordinately regulated. Recent studies have identified pathways involved in control of contractile proteins of oxidative type fibers. However, the mechanism for coupling of mitochondrial function to muscle contractile machinery during fiber type transition remains unknown. Here, we show that the expression of the genes encoding type I myosins, Myh7/Myh7b and their intronic miR-208b/miR-499 parallels mitochondrial function during fiber type transitions. Using in vivo approaches in mice, we found that miR-499 drives a PGC-1a-dependent mitochondrial oxidative metabolism program to match shifts in slow-twitch muscle fiber composition. Mechanistically, miR-499 directly targets Fnip1, a known AMP-activated protein kinase (AMPK)-interacting protein that negatively regulates AMPK, a known activator of PGC-1a. Inhibition of Fnip1 reactivated AMPK/PGC-1a signaling and mitochondrial function in myocytes. Restoration of the expression of miR-499 in the mdx mouse model of Duchenne muscular dystrophy (DMD) reduced the severity of DMD. Thus, we have identified a miR-499/Fnip1/AMPK circuit that can serve as a mechanism to couple muscle fiber type and mitochondrial function.

Keywords: muscle, contractile fiber type, mitochondrial function, microRNA, gene regulation

overall_design: RNA from three wild-type (non-transgenic (NTG)) and three miR-499 overexpressing (MCK-miR-499) mice was analyzed. three replicates of each are provided.

last: Kelly


title: Treatment of Venous Leg Ulcers with a Bioengineered Living Cell Construct Reactivates the Acute Wound Healing Response

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

summary: Chronic non-healing venous leg ulcers (VLUs) are a widespread debilitating disease with high morbidity and associated costs, as approximately $15 billion annually are spent on the care of VLUs. Despite their socioeconomic burden, there is a paucity of novel treatments targeted towards healing VLUs, which can be attributed to both lack of pathophysiologic insight into VLU development as well as lack of knowledge regarding biologic actions of VLU-targeted therapies. Currently, the bioengineered bilayered living cellular construct (BLCC) skin substitute is the only FDA-approved biologic treatment for healing VLUs. To elucidate the mechanisms through which the BLCC promotes healing of chronic VLUs, we conducted a clinical trial (NCT01327937) in which patients with non-healing VLUs were treated with either standard care (compression therapy) or with BLCC together with standard care. Tissue was collected from the VLU edge before and 1 week after treatment, and samples underwent comprehensive microarray, mRNA and protein analyses. Ulcers treated with BLCC skin substitute displayed three distinct patterns suggesting the mechanisms by which BLCC shifted a non-healing into a healing tissue response: it modulated inflammatory and growth factor signaling; it activated keratinocytes; and it attenuated Wnt/β-catenin signaling. In these ways, BLCC application orchestrated a shift of the chronic non-healing ulcer microenvironment into a distinctive healing milieu resembling that of an acute, healing wound. Our findings also provide first patient-derived in vivo evidence of specific biologic processes that can be targeted in the design of therapies to promote healing of chronic VLUs.

overall_design: Study participants (ClinicalTrial.gov No. NCT01327937 (9)) were recruited from patients presenting to the wound clinic at the University of Miami with VLUs. All subjects, from Screening (Day -28) through Day 0 visit, received the standard-of-care including a dressing regimen of a foam dressing and a 4 layered compression bandage system. Participants with non-infected target ulcers of >5cm2 that had not reduced in area by >40% during the 4-week screening period were randomized to either the control group receiving standard-of-care compression therapy (foam dressing plus four layered compression bandage system, changed weekly by the Investigator), or to the treatment group receiving weekly BLCC applications (Apligraf®, Organogenesis, Inc.) along with standard-of-care compression therapy. Prior to all applications, the BLCC was fenestrated in a standardized manner using a #11 blade with 6 fenestrations per 44 cm2. Skin biopsy specimens were obtained from the non-healing edges of VLU’s at the time of randomization (week 0) as well as one week later (week 1). Specimens were clinically designated by a physician as the most proximal skin edge to the ulcer bed. All patients were debrided and local lidocaine injection was used for anesthesia. After Week 5, all patients were monitored in the wound clinic for 12 weeks or until wound closure was achieved.

first: Rivka

last: Stone

first: Olivera

last: Stojadinovic

first: Ashley

last: Rosa

first: Evangelos

last: Badiavas

first: Miroslav

last: Blumenberg

first: Marjana

last: Tomic-Canic


title: Primary neuroblastoma tumors

first: Maral

last: Saadati

type:
Expression profiling by array
Methylation profiling by array


title: Expression data from hMSC-TERT4 cells after siZNF25 knockdown

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

country: Australia

institute: University of New South Wales

summary:
Differentiation of human skeletal stem cells (hMSC) into osteoblasts is regulated by a few well described transcription factors. Our study used clustering and gene expression data to identify a novel transcription factor. ZNF25, which we showed is involved in osteoblast differentiation.
We used microarrays to study gene expression of hMSC-TERT4 cells after siZNF25 knockdown. hMSC-TERT4 cells were sampled as undifferentiated hMSC and as differentiated osteoblasts.

overall_design: hMSC-TERT4 cells were transfected with siZNF25. Gene expression was analysed using Affymetrix microarrays at days 0 post osteoblast induction and days 14 post osteoblast induction.

first: Marc

last: Wilkins

first: Linda

last: Harkness

first: Moustapha

last: Kassem


title: Gene Expression analysis of the HIVAN1 Susceptibility Locus in the FVB-HIVAN1CAST  congenic strain

first: Ali

last: Gharavi

state: New York

address: 1150 Saint Nicholas Ave., Room 413

department: Medicine/Nephrology

summary:
Expression profiling comparing healthy kidneys of wild-type FVB mice and wild-type full congenic FVB-HIVAN1CAST mice
HIV-1 transgenic mice on the FVB/NJ background (TgFVB) represent a validated model of HIV-associated nephropathy (HIVAN).  A major susceptibility locus, HIVAN1, was previously mapped to chromosome 3A1-A3 in a cross between TgFVB and CAST/EiJ (CAST) strains, and introgression of a 51.9 Mb segment encompassing HIVAN1 from CAST into TgFVB results in accelerated development of nephropathy. We performed genome-wide expression profiling of whole kidneys from wild-type (without the HIV-1 transgene) full congenic FVB-HIVAN1CAST and FVB mouse strains, with the goal of identifying genes with differential renal expression in the HIVAN1 locus that may be associated with the development of nephropathy upon exposure to HIV-1.  We only profiled healthy wild-type kidneys because the profound histopathological lesions of HIV-1 transgenic mice introduce many secondary gene expression changes that can confound interpretation of transcriptomic data.

overall_design: We performed microarray analysis with the Affymetrix ST 1.0 gene arrays on kidney RNA from 20 FVB-HIVAN1CAST congenic mice (11 females / 9 males) and 19 FVBN/J littermates (10 females / 9 males). Sample preparation, labeling and hybridization were performed as per Affymetrix recommended protocol.  Signal intensities were normalized using the RMA method.

first: Natalia

last: Papeta

first: Ami

last: Patel

first: Vivette

last: D’Agati


title: Global transcriptome dysregulation in second trimester fetuses with FMR1 expansions

city: Boston

first: Lillian

last: Zwemer

state: MA

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

summary: Using cell-free fetal RNA from amniotic fluid supernatant samples, the gene expression profiles of fetuses with varying FMR1  5’ UTR CGG repeat lengths were compared to gestational age- and sex-matched controls. Broad patterns of genome-wide expression changes were identified when comparing fetuses with expanded FMR1 alleles to those with normal length FMR1 alleles. Genes with altered expression include those related to ubiquitination, mitochondrial function and neuronal/synaptic architecture as well as genes previously linked to other intellectual disabilities and abnormalities of motor function.

overall_design: Whole-transcriptome expression microarray study using cell-free fetal RNA from the amniotic fluid supernatant to compare gene expression in fetuses with expanded FMR1 alleles (12 males with a premutation, six females with a premutation, and two males and two females with a full-mutation) to gestational age- and sex-matched control samples from fetuses with normal length FMR1 alleles.

first: Sally

last: Nolin

first: Patricia

last: Okamoto

first: Marcia

last: Eisenberg

first: Heather

last: Wick

first: Diana

middle: W

last: Bianchi


title: Expression data from pulmonary arterial endothelial cells treated with siRNA control or siGLS in stiff or soft matrix

city: Nice

first: Thomas

last: BERTERO

address: 28 Av de Valombrose

department: Medical School

country: France

institute: IRCAN, Nice CNRS UMR 7284 - INSERM U1081 - UNS

summary:
Dysregulation of vascular stiffness and cellular metabolism occur early in pulmonary hypertension (PH). Yet, the mechanisms by which biophysical properties of extracellular matrix relate to metabolic processes and downstream PH phenotypes remain undefined. In cultured endothelial and smooth muscle cells and confirmed in PH-diseased human samples, we found that ECM stiffening activates the mechanosensitive factors YAP/TAZ to increase glycolysis and induce glutaminase (GLS) expression and glutaminolysis. Glutaminolysis replenishes aspartate for anabolic biosynthesis, thus sustaining proliferation and migration within stiff ECM. In vitro GLS inhibition blocks aspartate production, consequently reprogramming entire cellular proliferative pathways, while aspartate restores proliferation. In a rat model in vivo, GLS inhibition prevents hemodynamic and histologic manifestations of PH. Thus, mechanical ECM stiffening sustains vascular cell growth and migration through YAP/TAZ-dependent glutaminolysis – a paradigm that advances our understanding of the connections of mechanical stimuli with dysregulated vascular metabolism and identifies new metabolic drug targets in PH.
We used microarrays to decipher the global program of gene expression  involved in response to matrix stiffening and determined the implication of glutaminolysis (GLS) in these process

overall_design: PAECs were transfected with an siRNA control (siNC) or a siRNA against GLS (siGLS) and cultivated on soft hydrogel (1kPa) or stiff hydrogel (50kPa). After 48h of transfection cells were lysate and RNA extract for hybridization on Affymetrix microarrays.

last: Bertero

first: Stephen

middle: Y

last: Chan


title: AhR signaling reprograms newly activated CD4+ T cells promoting combinatorial expression of regulatory genes to suppress murine GVHD

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University


title: Differential gene expression profiling of matched primary renal cell carcinoma and metastases reveals upregulation of extracellular matrix genes

city: Jacksonville

first: Daniel

last: Serie

address: 4500 San Pablo Rd

institute: Mayo Clinic

summary: It is unknown if gene expression profiles from primary RCC tumors differ from patient-matched metastatic tumors. Thus, we sought to identify differentially expressed genes between patient-matched primary and metastatic RCC tumors in order to understand the molecular mechanisms underlying the development of RCC metastases.

overall_design: We compared gene expression profiles between patient-matched primary and metastatic RCC tumors. We employed Affymetrix U133 Plus2 microarrays to assess gene expression on 15 pairs of primary RCC (14 clear cell RCC, 1 papillary) tumors and patient-matched pulmonary metastases, across 54,675 probesets.

first: Jeanette

last: Eckel-Passow

first: Thai

middle: H

last: Ho


title: Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan

status: Public on Oct 04 2016

city: Uppsala

first: Åsa

last: Johansson

state: Sweden

address: BMC, Husarg 3

department: IGP

country: Sweden

institute: Uppsala University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays an important role in development of disease and the process of aging. In this study we examine DNA methylation at 476,366 sites throughout the genome of white blood cells from a population cohort (N = 421) ranging in age from 14 to 94 years old. Age affects DNA methylation at almost one third (29%) of the sites (Bonferroni adjusted P-value <0.05), of which 60.5% becomes hypomethylated and 39.5% hypermethylated with increasing age. DNA methylation sites that are located within CpG islands (CGIs) more often become hypermethylated compared to sites outside an island. CpG sites in promoters are more unaffected by age, whereas sites in enhancers more often becomes hypo- or hypermethylated. Hypermethylated sites are overrepresented among genes that are involved in DNA binding, transcription regulation, processes of anatomical structure and developmental process and cortex neuron differentiation (P-value down to P = 9.14*10−67). By contrast, hypomethylated sites are not strongly overrepresented among any biological function or process. Our results indicate that the 23% of the variation in DNA methylation is attributed chronological age, and that hypermethylation is more site-specific than hypomethylation. It appears that the change in DNA methylation partly overlap with regions that change histone modifications with age, indicating an interaction between the two major epigenetic mechanisms. Epigenetic modifications and change in gene expression over time most likely reflects the natural process of aging and variation between individuals might contribute to the development of age-related phenotypes and diseases such as type II diabetes, autoimmune and cardiovascular disease.

overall_design: Bisulphite converted DNA from 732 samples were hybridized to the Illumina Infinium 450K Human Methylation Beadchip


title: Microarray analysis of minor salivary glands from patients with primary Sjögren’s syndrome (SS) or non-SS

status: Public on Aug 31 2016

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary: Objective. A variety of chemokines contribute the pathogenesis of Sjögren’s syndrome (SS). However, the comprehensive analysis as for clinically potent ckemokines in SS has not been performed. In this study, focusing on CXC chemokines, we investigated the precise molecular mechanism and the clinical significance through chemokine and its receptor in the autoimmune lesions of primary SS.   Methods. Gene expression profiles in the lip salivary glands (LSGs) from pSS patients and controls were analyzed using DNA microarray. Expression of chemokines and their receptor of biopsy samples of pSS pathients and controls were detected by immunofluorescence analysis. In addition, in vitro experiments using human salivary gland ductal and acinar cell lines were performed to analyze the expression of chemokines and signaling pathwaycytokines by qRT-PCR, ELISA, and Western blot analysis.   Results. Gene expression profiles and immunohistochemical analysis revealed that IFN-γ-induced CXCL9 and CXCL10 were significantly increased in LSGs of pSS patients. In vitro experiments revealed that the protein expression of CXCL10 in ductal and acinar cells was differentially regulated by IFN-γ or TNF-α via NF-κB or JAK/STAT pathway. Moreover, CXCR3 expression was detected mainly in CD68+ macrophages, CD123+ plasmacytoid dendritic cells (pDCs), and in a few CD3+ T cells. Finally, Spearman's rank analysis revealed a negative correlation between the existence of CXCR3+ cells and pathological grading in LSG tissues of pSS patients (r: -0.019, p<0.01).  Conclusion. These results suggest that CXCL10/CXCR3 axis plays in a key role in autoimmune response by interaction between immune cells and target cells in the pathogenesis of pSS.

overall_design: Using Affymetrix GeneAtlas System, we determined the gene expression profiles of minor salivary glands from 2 primary SS and 2 non-SS patients.

first: Keiko

last: Aota


title: Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1

first: Raymond

last: Pagliarini

address: 250 Massachusetts Ave, Room 3C-292

institute: Novartis

summary: High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl) amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1R132H. Synthesis of the 4 separate diastereomers identified the (S,S)-diastereomer (IDH125) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1wt. Initial SAR exploration identified the key tolerances and potential for optimization. X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors which can penetrate the blood-brain barrier, and aided rational optimization. Potency improvement and modulation of the physico-chemical  properties identified (S)-3-(2-(((S)-1-(5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl)ethyl)amino)pyrimidin-4-yl)-4-isopropyloxazolidin-2-one (IDH889) with good in-vivo exposure and in-vivo activity in a mutant IDH1 xenograft mouse model.   identified the (S,S)-diastereomer (IDH125) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1wt. Initial SAR exploration identified the key tolerances and potential for optimization.   X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors which can penetrate the blood-brain barrier, and aided rational optimization. Potency improvement and modulation of the physico-chemical  properties identified (S)-3-(2-(((S)-1-(5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl)ethyl)amino)pyrimidin-4-yl)-4-isopropyloxazolidin-2-one (IDH889) with good in-vivo exposure and in-vivo activity in a mutant IDH1 xenograft mouse model

overall_design: 30 samples from cell culture with one or two replicates. Possible controls are treated with DMSO, other comparsions can be made between WT and mutant cell lines.

first: Julian

middle: R

last: Levell

first: Young

last: Cho

last: Caferro

first: Gregg

last: Chenail

first: Ina

last: Dix

first: Julia

last: Dooley

first: Brant

last: Firestone

first: Pascal

last: Fortin

first: John

last: Giraldes

first: Ty

last: Gould

first: Kara

last: Herlihy

first: Tami

last: Hood

first: Raviraj

last: Kulathila

first: Fallon

last: Lin

first: Gang

last: Liu

first: Simon

last: van der Plas

first: Kelly

last: Slocum

first: Troy

last: Smith

first: Barry

last: Toure

first: Trixie

last: Wagner

first: Xiaoling

last: Xie

first: Liping

middle: X

last: Xu

first: Ming

first: Fan

last: Yang

first: Remi

last: Terranova

first: Arne

last: Mueller


title: Gene expression data before and after interferon-gamma stimulatinon

city: Houston

first: Hao

last: Zhao

state: TX

address: 7455 Fannin St

institute: The University of Texas MD Anderson Cancer Center

summary: Three of the melanoma cell lines show higher expression fold change after stimulation than the other 3.

overall_design: We applied interferon-gamma stimulation to 6 melanoma cell lines and defined 3 responders and 3 responders according to the interfereon-gamma pathway gene expression fold change after stimulation.

first: Padmanee

last: Sharma

first: Jianjun

last: Gao

first: Lewis

last: Shi

first: Jianfeng

last: Chen

first: Liangwen

last: Xiong


title: AhR signaling reprograms newly activated CD4+ T cells promoting combinatorial expression of regulatory genes to suppress murine GVHD [48 hr]

first: Susan

last: Tilton

summary:
AhR activation during the first 3 days of an immune response is sufficient to reprogram CD4+ T cells, resulting in prevention of GVHD.   To identify the early transciptional signature of AhR activation in CD4+ T cells, we performed analyses on mice treated with 2 different AhR ligands, TCDD and Cl-BBQ, in comparison with vehicle treated mice.
Transcriptional responses were measured by global microarray analysis of donor alloresponding CD4+ T cells from spleen and lymph nodes.

overall_design: CFSE labeled splenocytes from C57Bl/6 mice were i.v. injected into B6D2F1 host mice (day 0). F1 mice (n=4) were treated i.p. with 15μg/kg TCDD on day 0, or vehicle or 2mg/kg Cl-BBQ on days 0 and 1. Mice were sacrificed on day 2 and alloresponding CD4+ T cells (at least 2 cell divisions based on CFSE dilution) were isolated by pan-CD4 microbeads followed by FACS sorting.

first: Allison

last: Ehrlich

first: Nancy

middle: I

last: Kerkvliet


title: β-glucans are Masked but Contribute to Pulmonary Inflammation During Pneumocystis Pneumonia

city: Bethesda

first: Joseph

middle: A.

last: Kovacs

address: 10 Center Dr

department: CCMD

summary: β-glucans, which can activate innate immune responses, are a major component in the cell wall of the cyst form of Pneumocystis. In the current study we examined whether β-1,3 glucans are masked by surface proteins in Pneumocystis, and what role β-glucans play in Pneumocystis-associated inflammation. For 3 species, including P. jirovecii, which causes Pneumocystis pneumonia (PCP) in humans, P.  carinii, and P. murina, β-1,3 glucans were masked in most organisms, as demonstrated by increased exposure following trypsin treatment. Using Q-PCR and microarray techniques, we demonstrated in a mouse model of PCP that treatment with caspofungin, an inhibitor of β-1,3 glucan synthesis, for 21 days, decreased expression of a broad panel of inflammatory markers, including IFN-γ, TNF-α, IL-1β, IL-6, and multiple chemokines/chemokine ligands. Thus, β-glucans in Pneumocystis cysts are largely masked, which likely decreases innate immune activation; this mechanism presumably was developed for interactions with immunocompetent hosts, in whom organism loads are substantially lower. In immunosuppressed hosts with a high organism burden, organism death and release of glucans appears to be an important contributor to deleterious host inflammatory responses.

overall_design: Gene expression microarrays from 4 samples of mouse lung tissues infected with Pneumocystis and treated with caspofungin compared with 3 samples of untreated and 4 samples uninfected.

first: Geetha

last: Kutty

first: A

last: Davis

first: Gabriela

last: Ferreyra

first: Monica

last: Sassi

first: Lisa

last: Bishop

first: Grace

last: Handley

first: Brad

last: Sherman

first: Ju

last: Qiu

first: Richard

last: Lempicki


title: Integration of cell type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy

status: Public on Aug 30 2016

city: Los Angeles

first: Rosane

last: Teles

state: California

address: 10833 Le Conte Ave, CHS 52-121

institute: UCLA

summary: Transcriptome profiles derived from the site of human disease has led to the identification of genes that contribute to pathogenesis, yet the complex mixture of cell types in these lesions has been an obstacle for defining specific mechanisms.  Leprosy provides an outstanding model to study host defense and pathogenesis in a human infectious disease, given its clinical spectrum which interrelates with the host immunologic and pathologic responses. Here, we investigated gene expression profiles derived from skin lesions for each clinical subtype of leprosy, analyzing gene co-expression modules by cell type deconvolution.  In lesions from tuberculoid leprosy patients, those with the self-limited form of the disease, dendritic cells were linked with MMP12 as part of a tissue remodeling network that contributes to granuloma formation.  In lesions from lepromatous leprosy patients, those with disseminated disease, macrophages were linked with a gene network that programs phagocytosis.  In erythema nodosum leprosum, neutrophil and endothelial cell gene networks were identified as part of the vasculitis that results in tissue injury.  The present integrated computational approach provides a systems approach towards identifying cell-defined functional networks that contribute to host defense and immunopathology at the site of human infectious disease.

overall_design: 6 ENL lesions

first: Megan

last: Inkeles

first: Delila

last: Pouldar

first: Priscila

last: Andrade

first: Cressida

last: Madigan

first: David

last: Lopez

first: Mike

last: Ambrose

first: Mahdad

last: Noursadeghi

first: Euzenir

last: Sarno

first: Thomas

last: Rea

first: Maria

last: Ochoa

first: M

middle: L

last: Iruela-Arispe

first: William

last: Swindell

first: Tom

last: Ottenhoff

first: Annemieke

last: Geluk

first: Barry

last: Bloom

first: Matteo

last: Pellegrini

first: Robert

last: Modlin


title: ZNF750 is a lineage-specific tumor suppressor in squamous cell carcinoma [CaSki]

status: Public on Aug 25 2016

city: Singapore

first: Phillip

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary:
ZNF750 controls epithelial homeostasis by regulating epidermal-differentiation genes, a role underscored by its pathogenic mutations in esophageal squamous cell cancers (SCCs). However, the precise role of ZNF750 in SCC cell biology remains unclear. In this study, we report that ZNF750 is exclusively deleted, mutated and underexpressed in human SCCs, and low ZNF750 expression is associated with poor survival. Restoration of wildtype, but not mutant ZNF750 protein uniquely inhibited the malignant phenotype of SCC cells both in vitro and in vivo. Notably, ZNF750 promoted the expression of a LncRNA (TINCR) which mediated both cancer-inhibition and differentiation-induction effects of ZNF750. In addition, ZNF750 potently suppressed cell migration by directly inhibiting the transactivation of LAMC2. Together, our findings characterize ZNF750 as a crucial SCC-specific suppressor and uncover its novel anticancer-associated functions.
Gene expression profile in CaSki following ZNF750 overexpression was examined by microarray gene expression analysis.

overall_design: To explore genes regulated by ZNF750 in squamous cell carcinoma, total RNA was isolated in biologic duplicate from CaSki either with ectopic expression of GFP (as control) or ZNF750, and hybridized to Affymetrix HG-U133 2.0 Plus arrays.

first: Masaharu

last: Hazawa

first: De-Chen

last: Lin

first: Harish

last: Handral

first: Liang

last: Xu

first: Ye

last: Chen

first: Yan-Yi

last: Jiang

first: Anand

last: Mayakonda

first: Ling-Wen

last: Ding

first: Xuan

last: Meng

first: Arjun

last: Sharma

first: Sharon

last: Samuel

first: Mohammad

last: Movahednia

first: Richard

last: Wong

first: Henry

last: Yang

first: Cao

last: Tong

first: H

middle: P


title: Genome wide Affymetric Microarray analysis for RIPK1 dependent inflammatory changes in Bone Marrow Derived Macrophages (BMDMs)

status: Public on Sep 07 2016

first: Alexei

last: Degterev

address: 37 tyler street

department: Biochemistry

institute: Tufts University

summary:
Gene level expression estimate using the Whole Transcript (WT) Assay approach of the Gene 1.0 ST Array System for Mouse. This assay was done to identify the RIPK1-dependent gene expression changes in mouse BMDMs.
Cost-effective gene-level analysis based on whole-transcript coverage.

overall_design: We analyzed Bone Marrow Derived Macrophages (BMDMs) under 4 different conditions (Control, LPS, LPS/zVAD, LPS/zVAD/Nec-1) to assess inflammatory changes in RIPK1 kinase dependent manner compared to LPS, LPS/zVAD plus RIPK1 inhibitor Nec-1 and control.

first: Malek

last: Najjar


title: miR-30-5p functions as a tumor suppressor by targeting BCL9

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary: Deregulated Wnt/b-catenin signaling underlies the pathogenesis of a broad range of human cancers including multiple myeloma (MM). Thus, the b-catenin transcriptional complex has emerged as a high-priority pharmacologic target. The BCL9 oncogene is a critical transcriptional co-activator of b-catenin, and studies from our laboratory have implicated this transcriptional complex in MM disease initiation and progression. Micro RNAs regulate the expression of oncogenes and tumor suppressor genes, and because they play important roles as biologic inhibitors of cancer growth, they have great potential as novel therapeutic agents. Here we provide evidence for a role of miR-30s family in regulating expression of BCL9 and as a novel therapeutic agent in MM.

overall_design: Ectopic expression of miR-30s and shBCL9 were associated with decreased expression of BCL9, Wnt reporter activity, and expression of Wnt downstream target genes, as well as inhibition of proliferation and migration and promotion of apoptosis of MM cells.

first: Ruben

middle: D

last: Carrasco

first: Jianjun

last: Zhao

middle: E


title: Expression data from human osteosarcoma cells after transfected miR-1

status: Public on Aug 27 2016

first: Zhenfeng

last: Duan

state: Massachusetts

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

summary: Evaluate the effect of miR-1 regulated gene expression in osteosarcoma cells.

overall_design: The U-2OS and KHOS osteosarcoma cell lines were seeded into the 100mm cell culture plate, then transfected miRSelect pEP-miR-1 or miRSelect pEP-miR-Null into the two cell lines with Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours. After that, total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer's instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Gene Chip U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 is first and most comprehensive whole human genome expression array. This array completes coverage of the whole human genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 25-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-1 treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 fold change or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

first: Chao

last: Han


title: Regulation of Energy Metabolism and Mitochondrial Biogenesis Independently from the SIRT1-PGC1a Pathway in Human Skeletal Muscle during Lipid Overfeeding

status: Public on Aug 29 2016

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: The adaptive mechanisms in response to excess energy supply are still poorly known in humans. Our aims were to define metabolic responses and changes in gene expression in skeletal muscle of healthy volunteers during fat overfeeding.

overall_design: Healthy lean and overweight subjects were submitted to a high fat diet during 56 days. Skeletal muscle biopsies were taken at Day 0 and Day 56.

first: Kevin

last: Seyssel

first: Maud

last: Alligier

first: Emmanuelle

last: Meugnier

first: Martine

last: Laville

first: Hubert

last: Vidal


title: DNA methylation analysis of HCT116 cells after PBS, 5-Aza-CdR, vitamin C and combination treatment

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Genomide DNA methylation profiling of HCT116 cells after PBS, 5-Aza-CdR, vitamin C and combination treatment.  The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in HCT116 cells.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Minmin

last: Liu

first: Gangning

last: Liang


title: Expression data of CLL cells with and without NFAT2 expression

city: Tübingen

first: Melanie

last: Märklin

department: Medical Hospital

institute: University of Tübingen

summary: Chronic lymphocytic leukemia (CLL) is a disorder of mature B cells. Most patients are characterized by indolent disease and an anergic phenotype of their leukemia cells which refers to a state of unresponsiveness to B cell receptor stimulation. Using the Eµ-TCL1 mouse model, we show that B cell-specific ablation of NFAT2 leads to the loss of the anergic phenotype culminating in a significantly compromised life expectancy and histological transformation to aggressive disease. We further define a gene expression signature of anergic CLL cells consisting of several NFAT2-dependant genes employing microarray technology.

overall_design: Splenic CLL cells from Eµ-TCL1 mice with and without NFAT2 expression (n=3 per gorup) were isolated and ex vivo analyzed for gene expression. We sought after differentially expressed NFAT2 target genes, which were responsible for the aggressive phenotype in TCL1 mice without NFAT2 expression.

first: Martin

last: Müller


title: HOXA5 inhibits metastasis and associates with prolonged survival in lung cancer

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Homeobox genes comprise a family of regulatory genes that contain a common homeobox domain and act as transcription factors. Changes in the expression of homeobox genes are observed in many cancers, including leukaemia, colon, skin, prostate, breast, and ovarian cancers. Recent studies indicate that homeobox A5 (HOXA5) may serve as a tumour suppressor gene in breast cells. However, the precise role of HOXA5 in lung cancer remains unclear. Using microarrays and an invasion/metastasis lung adenocarcinoma cell line model, we showed that the expression of HOXA5 is negatively correlated with cancer cell invasion ability. The ectopic expression of HOXA5 in highly invasive cancer cells suppressed cell migration, invasion, and filopodia formation in vitro and inhibited metastatic potential in vivo. The knockdown of HOXA5 expression via a HOXA5-specific siRNA was able to promote the invasiveness of lung cancer cells. Furthermore, HOXA5 expression was associated with improved overall survival and disease-free survival in non-small cell lung cancer patients with wild-type EGFR (P = 0.0199 and 0.0345, respectively). Genome-wide transcriptome and pathway analyses indicated that these effects of HOXA5 may be associated with the regulation of cytoskeletal remodelling. In summary, our studies provide new insights into how HOXA5 may contribute to the suppression of metastasis in lung cancer.
We used microarrays to profile the global gene expression of HOXA5-overexpressing cells compared with mock control cells and identified the pathways involved in HOXA5-induced biofunctional alterations.

overall_design: The stably pooled HOXA5-overexpressing cells and mock control cells were selected with 2 mg/ml G418 in CL1-5 cells, human lung adenocarcinoma cells. We compare the  HOXA5-expressing profiles with the mock controls to identify the possible mechanisms of HOXA5-induced pathways in lung cancer cells.

first: Chi-Chung

last: Wang

first: Jeremy

middle: J

last: Chen


title: Two faces of polarized macrophages: differential effects of M1 and M2 macrophage subtypes on lung cancer progression

summary:
Macrophages in tumor microenvironment have been characterized as M1- and M2-polarized subtypes. This study sought to investigate the effects of different macrophage subtypes on the biological behavior and global gene expression profiles of lung cancer cells.  Expression microarray and bioinformatics analyses indicated that the different macrophage subtypes mainly regulated genes involved in cell cycle, cytoskeletal remodeling, coagulation, cell adhesion and apoptosis pathways in A549 cells, a pattern that correlated with the altered behavior of A549 cells observed after coculture with macrophage subtypes.
We used microarrays to identify the global gene alterations in lung cancer cells A549 after culture in conditioned media from different subtype macrophages.

overall_design: Lung cancer cells, A549, were cultured in M0, M1, M2a and M2c macrophages conditioned media for two weeks. The different subtype macrophages were differentiated by IFN-gamma, LPS, IL-4 and IL-10.

first: Ang

last: Yuan

first: Yi-Jing

last: Hsiao

first: Hsuan-Yu

first: Huei-Wen

first: Chao-Chi

last: Ho

first: Yi-Chia

first: Pan-Chyr

last: Yang


title: PARVA promotes invasion through inducing phosphorylation of ILK signaling in lung cancer

summary:
Alpha-parvin (PARVA) is known to involve in the linkage of integrins, regulation of actin cytoskeleton dynamics, and cell survival. However, the role of PARVA in cancer progress is still unclear. Here, we identify PARVA as a potential oncogene from a lung cancer invasion cell line model by expression microarrays. Overexpression of PARVA enhances cell invasion, colony formation ability, and endothelial cell tube formation but knockdown of PARVA inhibits invasion and tube formation in vitro. PARVA also promotes tumorigenicity, angiogenesis, metastasis and mortality by in vivo tumorigenesis and metastasis mouse models. To explore the underlying mechanism, the PARVA-regulated signaling pathways were analyzed in PARVA-overexpressing cells compare with mock controls by expression microarrays.
We used microarrays to profile the global gene expression of PARVA-overexpressing cells compared with mock control cells and identified the pathways involved in PARVA-induced biofunctional alterations.

overall_design: The stably pooled PARVA-overexpressing cells and mock control cells were selected with 1mg/ml G418 in CL1-0 cells, human lung adenocarcinoma cells. We compare the  PARVA-expressing profiles with the mock controls to identify the possible mechanisms of PARVA-induced pathways in lung cancer cells.

first: Ay-Huey

last: Huang


title: Gene expression profiling of genes differentially expressed by oral carcinoma Ca9-22 and SLPI-deficient Ca9-22 (ΔSLPI) cells

status: Public on Aug 22 2016

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

institute: RIKEN

summary: We used the myoma model in conjunction with gene expression profiling with microarray data as an efficient tool for high throughput analysis and to screen for differentially expressed genes. Our aim was to identify candidates playing an important role in SLPI and/or MMP-promoted tumor invasion by comparing oral carcinoma Ca9-22 cells, which highly express secretory leukocyte protease inhibitor (SLPI) gene, with SLPI-deficient Ca9-22 cells.

overall_design: In oral carcinoma Ca9-22 and SLPI-deficient Ca9-22 (ΔSLPI) samples, gene expression profiling was performed with the Affymetrix Human Genome U133 Plus 2.0 Array. Two arrays for 2 cell lines were analyzed.

first: Yoshikazu

last: Mikami


title: Methyl-CpG-Binding Protein MBD2 plays a critical role in maintenance and spread of DNA methylation of CpG islands and shores in cancer (methylation)

status: Public on Aug 24 2016

city: Darlinghurst

first: Elena

last: Zotenko

state: NSW

address: 384 Victoria St.

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour suppressor genes The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the meditation of gene silencing by interaction with histone deacetylases and histone methyltransferases.  However the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD may proteins play in modulation of the methylome remain unclear.  Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells.  Here, we use functional genetic approaches to investigate if MBD2 plays an active role in promoting DNA methylation.  First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions.  Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer, highlighting a potential active role of MBD2 in promoting cancer specific hypermethylation.  Importantly, co-immunoprecipiation of MBD2 reveals that MBD2 associates with DNA methyltransferase (DNMT) enzymes 1 and 3A.  Together our results demonstrate that MBD2 plays a critical role in “rewriting” the cancer methylome at specific regulatory regions.

overall_design: LNCaP prostate cancer cell line clones with reduced MBD2 expression were establised by using shRNA to MBD2 and scrambled control clones were established with scrambled control shRNA. To interrogate methylation changes induced by MBD2 knock-down we profiled three stably transfected scrambled control clones and three MBD2 knockdown clones on Illumina HumanMethylation450K arrays. Differential methylation analysis was carried out to identified CpG sites hypo-/hyper-methylated as a result of MBD2 knockdown.


title: Blockage of hemichannels alters gene expression in osteocytes in a high magneto-gravitational environment

city: Xi’an

first: Huiyun

last: Xu

state: Shanxi

address: 127 West Youyi Road,Xi’an Shaanxi,710072,P.R.China

department: School of Life Sciences

institute: Northwestern Polytechnical University

summary:
We tested how Cx43 hemichannels which mediate the exchange of small molecules between cells and extracellular environment impact genome wide gene expression under conditions of abnormal gravity and magnetic field.
we subjected osteocytic MLO-Y4 cells to a high magneto-gravitational environment and used microarray to examine global gene expression and a specific blocking antibody was used to assess the role of Cx43 hemichannels.

overall_design: Microarray analysis was conducted to identify the alterations of global gene expression profile of osteocytic MLO-Y4 cells under HMGE. Furthermore, the effects of Cx43 hemichannels on gene expression were investigated by using a potent, Cx43 hemichannel-blocking antibody Cx43(E2)

first: Dandan

last: Ning

first: Dezhi

last: Zhao

first: Yunhe

first: Dongdong

first: Sumin

last: Gu

first: Jean

last: Jiang

first: Peng

last: Shang


title: Expression data in lung tissue from moderate COPD patients, healthy smokers and nonsmokers

city: Barcelona

first: Ricardo

last: Bastos

address: Rosellón  149-153

department: Cell Biology, Neurosciences and Immunology

institute: IDIBAPS/University of Barcelona

summary:
Chronic obstructive pulmonary disease (COPD) is a progressive and irreversible chronic inflammatory lung disease. The abnormal inflammatory response of the lung, mainly to cigarette smoke, causes multiple cellular and structural changes affecting all of its compartments, which leads to disease progression. The molecular mechanisms underlying these pathological changes are still not fully understood
The aim of this study was to identify genes and molecular pathways potentially involved in the pathogenesis of COPD

overall_design: Peripheral lung tissue samples from moderate COPD patients, smokers and nonsmokers were obtained. All patients were undergoing lung resection for localized carcinomas. RNA was extracted and processed for further hybridization on Affymetrix microarrays

first: Susana

middle: G

last: Kalko


title: Thymic XCR1+ dendritic cells undergo a functional maturation irrespective of type I interferon and of the microflora

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

institute: CIML

summary: Dendritic cells (DC) play critical roles in central and peripheral T cell tolerance. DC found in the steady-state periphery undergo an homeostatic, tolerogenic, maturation that promotes interaction with naive T cells and induction of abortive responses. In contrast, thymic DC are thought to exist solely in an immature state. In this study, we show that XCR1+ thymic DC constitutively mature into a stage characterized by high levels of molecules involved in T cell activation. This unanticipated mature stage corresponded to a third of the XCR1+ thymic DC and fully accounted for their ability to cross-present self-antigens to developing T cells. Transcriptomic analysis of the XCR1+ DC found in thymus and steady-state periphery revealed that their maturation involves profound and convergent changes. Unexpectedly, maturation resulted in down-regulation of genes conferring their specific function on XCR1+ DC. Paradoxically, upon maturation, central and peripheral tolerogenic XCR1+ DC up-regulated many genes thought to drive pro-inflammatory T-cell responses. These events occur independtly of type I interferons and of the microlofora, since the same maturation pattern is observed in XCR1+ tDcs from control, Ifnar1-KO and germ-free mice. Thus, our results reveal that thymic XCR1+ DC undergo constitutive maturation and emphasize the common mechanisms operating for both central and peripheral tolerance induction by XCR1+ DC.

overall_design: DC were isolated from thymus organ as previously described (Luche et al., Eur J Immunol. 2011;41:2165-75.PMID: 21630253), from B6 SPF control, B6 germ-free and Ifnar1-KO mice. DC subsets were sorted by flow cytometry according to the marker combinations described in the Sample records' phenotype field.

first: Hervé

last: Luche

first: Sandrine

last: Henri

first: Rabie

last: Chelbi

last: Dalod

first: Bernard

last: Malissen


title: Methyl-CpG-Binding Protein MBD2 plays a critical role in maintenance and spread of DNA methylation of CpG islands and shores in cancer

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

overall_design: Refer to individual Series


title: DNA methylation profiling of polycystic ovarian syndrome (PCOS)

city: Odense C

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

summary: Genome-wide DNA methylation analysis on PCOS using Illumina HumanMethylation 450K BeadChips in 30 PCOS patients and 30 healthy controls

overall_design: Case-control design


title: Genome-wide single base resolution profiling of 5-methyl and 5-hydroxymethylcytosine in glioblastoma

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

summary: Through parallel processing of genomic DNA with bisulfite and oxidative bisulfite treatments on Illumina 450K arrays we resolved both 5mC and 5hmC in glioblastoma tissues. We developed and applied a novel technique for estimating 5mC, 5hmC, and unmethylated proportions from array data to glioblastoma tissues and compare with normal brain tissue. Genomic distribution of 5hmC was associated with features of transcription despite the glioblastoma genome being relatively depleted of 5hmC. When integrating 5mC and 5hmC data using a Gaussian finite mixture model approach, we observed significant associations between 5hmC levels and gene-sets involved in immune and RNA regulatory processes. We also observed an enrichment of 5hmC in introns, enhancer regions, and genes that are actively transcribed in glioblastomas from TCGA. Significant differences in patient survival were observed among classes of 5hmC obtained from a recursively partitioned mixture model.

overall_design: Glioblastoma dervied (n=30) DNA was subjected to tandem bisulfite and oxidative bisulfite conversion with an input of 4ug per sample using the TrueMethyl® kit v.1.1 (Cambridge Epigenetix) protocol optimized for Illumina HumanMethylation450 arrays.

middle: C


title: The tissue is the issue: Improved methylome analysis from paraffin-embedded tissues by application of the HOPE-technique

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: Genome wide DNA methylation profiling of DNA  samples obtained from normal lung tissue and lung carcinoma, either fixed by formalin (FFPE), HOPE (paraffin embedded) or cryo-preserved. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpGs.

overall_design: Bisulphite converted DNA from the 36 samples were hybridized to the Illumina HumanMethylation450 Beadchip.

first: Torsten

last: Goldmann


title: Gene expression profiling of splenic XCR1+ dendritic cells from untreated or day 1.5 MCMV-infected mice

summary: The goal of this experiment was to use global gene expression profiling to assess the global genetic reprogramming of spleen XCR1+ DC early after MCMV infection in vivo, using on Affymetrix Mouse Gene 1.0 ST Array.

overall_design: Comparison of the gene expression programs of XCR1+ dendritic cells isolated from the spleen of untreated versus d1.5 MCMV-infected wild-type C57BL/6 mice.

first: Anissa

last: Fries

first: Elena

last: Tomasello


title: Spatial intratumor heterogeneity of epigenetic alterations in esophageal squamous cell carcinoma

status: Public on Aug 20 2016

first: Huy

middle: Q

last: Dinh

address: 8700 Beverly Blvd

department: Center for Bioinformatics and Functional Genomics

institute: Cedars Sinai Medical Center

summary: Esophageal squamous cell carcinoma (ESCC) is among the most common malignancies, but little is known about the spatial intratumor heterogeneity (ITH) and the temporal clonal evolutionary processes in this cancer. Interestingly, the epigenetic profiling also showed strong evidence of spatial ITH, and the phyloepigenetic trees were extremely similar with the phylogenetic ones, indicating the interplay and co-dependency of genetic and epigenetic alterations in ESCC. We found that several genes were both mutated and hypermethylated at their promoters, such as ASXL1 and EPHA7. Our integrated investigations of the spatial ITH and the temporal clonal evolution might provide insights into developing biomarkers for early diagnosis of ESCC, as well as personalized therapeutic targets for treating this malignancy.

overall_design: DNA methylation profiles of 12 tumor regions and 2 matched normal esophageal epithelial tissues from three M-WES-examined ESCC cases (ESCC01, ESCC03 and ESCC05) were performed using Illumina Infinium HumanMethylation450K platform (Illumina, San Diego, CA) at the Epigenome Center of University of Southern California.

first: De-Chen

last: Lin

first: Benjamin

last: Berman

first: H

last: Koeffler


title: The TCR activation acts as a tumor suppressor mechanism in T-ALL

city: Marseille

first: Mohamed

last: BELHOCINE

address: 163, Avenue de Luminy

institute: INSERM

summary: Developmental checkpoints in stem/progenitor cells are critical to the determination, commitment and differentiation into distinct lineages. Cancer cells often retain expression of lineage-specific checkpoint proteins, but their potential impact in cancer remains elusive. T lymphocytes mature in the thymus following a highly orchestrated developmental process that entails the successive rearrangements and expression of T-cell receptor (TCR) genes. Low affinity recognition of self-peptide/MHC complexes (self-pMHC) presented by thymic epithelial cells by the TCR of CD4+CD8+ (DP) cortical thymocytes transduces positive selection signals that ultimately shape the developing T cell repertoire. DP thymocytes not receiving these signals die by lack of stimulation whereas those that recognize self-pMHC with high affinity undergo TCR-mediated apoptosis and negative selection. In T-cell acute lymphoblastic leukaemia (T-ALL), leukaemic transformation of maturating thymocytes results from the acquisition of multiple genetic and epigenetic alterations in oncogenes and tumour suppressor genes, that disrupt the normal regulatory circuits and drive clonal expansion of differentiation-arrested lymphoblasts. We show here that TCR triggering by negatively-selecting self-pMHC prevented T-ALL development and leukaemia maintenance in mice. Induction of TCR signalling by high affinity self-pMHC or treatment with monoclonal antibodies to the CD3 signalling chain (anti-CD3) caused massive leukaemic cell death and a gene expression program resembling that of thymocyte negative selection. Importantly, anti-CD3 treatment hampered leukaemogenesis in mice transplanted with either mouse or patient-derived T-ALLs. These data provide a rationale for targeted therapy based on anti-CD3 treatment of T-ALL patients and demonstrate that endogenous developmental checkpoint proteins are amenable to therapeutic intervention in cancer cells.

overall_design: Gene expression data from four culture conditions was performed for the following cells: ALL-SIL-TCRα/β-GFP co-cultured on OP9-DL1 for 48 h, ALL-SIL-TCRα/β-GFP without co-culture, ALL-SIL cells transduced with TLX shRNA (sh-TLX), and ALL-SIL transduced with sh-control vectors. All conditions are performed in two replicates.

first: Amélie

last: Trinquand

first: Nuno

last: dos Santos

first: Christine

last: Tran Quang

last: Belhocine

first: Cindy

last: Dacosta de Jesus

first: Ludovic

last: Lhermitte

first: Melania

last: Tesio

first: Michael

last: Dussiot

first: David-Alexandre

last: Gros

first: François-Loïc

last: Cosset

first: Els

last: Verhoeyen

first: Françoise

last: Pflumio

first: Norbert

last: Ifrah

first: Herve

last: Dombret

first: Salvatore

last: Spicuglia

first: Lucienne

last: Chatenoux

first: Olivier

last: Hermine

first: Elizabeth

last: Macintyre

first: Jacques

last: Ghysdael

first: Vahid

last: Asnafi


title: Microarray analysis of the brain response to cutaneous Aldara treatment

status: Public on Aug 19 2016

city: Glasgow

first: Alison

last: McColl

address: B3-34 120 University Place

institute: University of Glasgow

summary:
Analysis of whole mouse brain following peripheral, cutaneous immune stimulation with Aldara cream or aquaeous control cream. Results provide insight into the central response to peripheral inflammation
Microarrays were used to investigate the global gene expression of mouse brains following peripheral, cutaneous application of Aldara cream or control cream

overall_design: C57BL/6 mice were treated with 80mg topical Aldara cream or aquaeous control cream every 24 hours for 5 consecutive days. 24 hours following the final application, brains were removed and RNA was extracted using RNeasy Mini Kit (Qiagen). 5 brains from each group were analysed using full genome Affymetrix GeneChip array

first: Carolyn

last: Thomson

first: Gerard

last: Graham

first: Jonathan

last: Cavanagh


title: Gene expression profiling of mouse spleen XCR1+ DC at steady state, 3 hours after polyI:C or 12 hours after STAg i.v. injection

first: Marc

last: DALOD

summary: The goal of this experiment was to use global gene expression profiling to compare the global genetic reprogramming of spleen XCR1+ DC upon in vivo stimulation with a viral-type ligand, polyI:C which strongly induces type I interferons, versus with a ligand derived from an intracellular parasite which strongly induces IFN-g.

overall_design: DC were isolated as previously described (Robbins SH et al. Genome Biol. 2008. PMID: 18218067; Baranek T et al. Cell Host Microbe. 2012. PMID: 23084923), from the spleens of wild-type C57BL/6 mice 12 hours after i.v. injection of 20µg of STAg. DC subsets were sorted by flow cytometry according to the marker combinations described in the “characteristics: phenotype” field for each sample. The data for spleen XCR1+ DC isolated from untreated control animals or from mice that had been injected i.v. with 100µg polyI:C 3 hours before organ harvest have been previously published and are available in the GEO database GSE39556 series. The complete dataset representing: (1) the Samples corresponding to STAg stimulation and (2) the untreated control Samples and the Samples corresponding to polyI:C stimulation from Series GSE39556 (re-processed using RMA), is linked below as a supplementary file.

first: Yannick

last: Alexandre

first: Rabie

last: Chelbi

first: Sabrina

last: Carpentier

first: Karine

last: Crozat

last: Dalod


title: Defining the mechanisms and consequences of glycolytic metabolism in human pluripotent stem cells

status: Public on Aug 16 2016

city: Los Angeles

first: Heather

last: Christofk

address: 615 Charles E Young Drive South

department: Molecular and Medical Pharmacology/ Biological Chemistry

institute: University of California, Los Angeles

summary: The balance between glycolytic and oxidative metabolism shifts during differentiation of human embryonic stem cells (hESCs) and during reprogramming of somatic cells into pluripotent stem cells.  However the contribution of glycolytic metabolism to various stages of pluripotency is not well understood.  Additionally, few tools have been developed that modulate pluripotent stem cell glycolytic metabolism to influence self-renewal or differentiation.  Here we show that the degree of human pluripotency is associated with glycolytic rate, whereby naive hESCs exhibit higher glycolytic flux, increased MYC transcriptional activity, and elevated nuclear N-MYC levels relative to primed hESCs.  Consistently, the inner cell mass of human blastocysts also exhibits increased MYC transcriptional activity relative to primed hESCs and elevated nuclear N-MYC levels.  Expression of the lactate transporter, monocarboxylate transporter 1 (MCT1), is strongly associated with the pluripotent state, and reduction of glycolysis using a small molecule inhibitor towards MCT1 decreases self-renewal of naïve hESCs and feeder-free cultured primed hESCs, but not that of primed hESCs grown in feeder-supported conditions.  Lastly, reduction of glycolytic metabolism via MCT1 inhibition in feeder-free primed hESCs enhances neural lineage specification.  These findings validate the association between glycolytic metabolism and pluripotency, reveal differences in the glucose metabolism of feeder- versus feeder-free cultured hESCs, and show that pharmacologic regulation of glycolysis can influence self-renewal and initial cell fate specification of human pluripotent stem cells.

overall_design: We hypothesized that human pluripotent stem cells, cultured with or without feeder cells (Mouse Embryonic Fibroblasts, or MEFs), might display different metabolic phenotyes, and secreted factors by MEFs might be responsible for reprogramming the metabolism of human pluripotent stem cells.  To test these hypotheses, we generated whole genome microarray data from human embryonic stem cell lines, with or without feeders, and feeder-free hESCs treated for 24 hours with MEF-conditioned or unconditioned medium. In addition, to understand how glycolysis inhibition changes the gene expression of human pluripotent cells, our study also included human embryonic stem cells treated for five days with DMSO or 250 nM AZD3965, a small molecule inhibitor towards monocarboxylate transport 1, or MCT1.

first: Wen

last: Gu


title: A fraction of steady state splenic XCR1+ dendritic cells undergo an homeostatic maturation as assessed by their upregulation of CCR7 or of IL-12, and by their profound genetic reprogramming

summary: XCR1+ dendritic cells (DC) have been shown to excel in antigen cross-presentation for the activation of naïve CD8 T cells. This property was reported to be associated to the subset of the XCR1+ DC expressing IL-12b upon ex vivo stimulation for 24 h with a mixture of CpG, IFN-γ, and GM-CSF (Lin ML et al. Proc Natl Acad Sci USA. 2008. PMID: 18272486). DC found in the steady-state non-lymphoid tissues undergo an homeostatic, tolerogenic, maturation and migrate to the draining lymph nodes to interact with naive autoreactive T cells and induction their peripheral tolerance. In contrast, spleen DC are thought to exist solely in an immature state. The aim of this study was to re-examine heterogeneity within steady state spleen XCR1+ DC, in particular examining whether this population encompass a fraction of mature DCs as assessed through their expression of CCR7 and/or the Il12b gene. Indeed, we show that a small fraction of XCR1+ spleen DC constitutively mature into two distinct but likely successive activation stages characterized as CCR7+ and CCR7+Il12b+ respectively, and correlated with increasing ability to cross-present antigen to naïve CD8 T cells. Transcriptomic analysis of the subsets of XCR1+ DC found in steady state spleen unexpectedly showed that their homeostatic maturation was unexpectedly associated with up-regulated of many genes thought to drive pro-inflammatory T-cell responses and previously found to be commonly induced upon maturation of distinct DC subsets in response to stimulation by various microbial-type stimuli (Vu Manh TP et al. Eur J Immunol. 2013. PMID: 23553052). Thus, our results reveal that spleen XCR1+ DC undergo constitutive maturation and emphasize the common mechanisms operating upon homeostatic, tolerogenic, DC maturation versus microbial-type stimuli-induced, immunogenic, DC maturation.

overall_design: DC were isolated from the spleen of untreated Il12b-EYFP reporter mice (Reinhardt RL et al. J Immunol. 2006. PMID:16849470) mice as previously described (Robbins SH et al. Genome Biol. 2008. PMID: 18218067; Baranek T et al. Cell Host Microbe. 2012. PMID: 23084923). DC subsets were sorted by flow cytometry according to the marker combinations described in the “characteristics: phenotype” field for each sample.


title: Characterization of gene expression profile in HBV-related liver fibrosis patients

status: Public on Aug 21 2016

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

summary: Hepatitis B virus (HBV) infection is a leading risk factor for liver fibrosis (LF) and hepatocellular carcinoma. Emerging evidence indicates that host genetic, virological and immunological factors will influence the fibrotic progress. Many previous studies have focused on specific pathways or genes included in LF mechanism, however global view of the whole genome expresion profile in HBV related LF patients never been studied, and the mechanisms underlying the promotion of liver fibrosis progression remain obscure. Here we collected liver biopsy samples from 124 chronic hepatitis B (CHB) patients and used Affymetrix HG U133 Plus 2.0 microarray to quantify the transcriptome of these patients. Through integrated data analysis, including geneset enrichment analysis (GSEA), weighted gene co-expression analysis (WGCNA), differential expressed gene (DEG) screening, trend test, principle component analysis (PCA) etc., we identified several key pathways and hub genes participated in the initiation and exacerbation of liver fibrotic progress. The function of these hub genes were also validated by in vitro and in vivo experiments using HepG2, Huh7 and LX-2 cell lines and transgenic mice. This is the first large-scale study investigating the gene expression profile in HBV-related LF patients which will be crucial for unlocking the gene functions and gene-gene correlations in fibrosis progess.

overall_design: Liver biopy samples from 124 CHB patients were collected. The pathological Scheuer Score of each sample were evaluated base on the inflamation and fibrosis severity. Gene expresson of samples in different stage were compared and analyzed.

first: Lungen

last: Lu

first: Jiming

last: Zhang

first: Zhenghong

last: Yuan

first: Xinxin


title: Expression data from HepG2 cell treated with Herb CRATOXYLUM COCHINCHINENSE LOUR

status: Public on Aug 18 2016

city: Kajang

first: Yun-Kwan

last: NG

state: Selangor

address: Lot PT21144, Jalan Sungai Long, Bandar Sungai Long,

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
Microarray data of  HepG2 were derived at various timepoints.
Fold-change of the regulated genes were compared among various timepoints.

overall_design: Treated HepG2 and untreated HepG2 were harvested. Fold change of genes among timepoints were derived.

first: Y

last: Ng

first: Z

last: Thaw

last: Lim

last: Yang


title: Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

status: Public on Aug 17 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: To evaluate the prognostic relevance of molecular subtypes and key transcription factors in pancreatic ductal adenocarcinoma (PDAC), we performed gene expression analysis of whole-tumor tissue obtained from 118 surgically resected PDAC and 13 control samples.

overall_design: Genome wide expression profiling on 118 PDAC samples and 13 control samples.

first: Maria

middle: M

last: Binda

first: Joke

last: Allemeersch

first: Anke

last: Van den broeck

first: Olivier

last: Govaere

first: Johan

last: Swinnen

first: Tania

last: Roskams

first: Stein

last: Aerts

first: Baki

last: Topal


title: Broad and largely overlapping molecular changes arise in thymic and peripheral XCR1+ dendritic cells upon tolerogenic and immunogenic maturation [reanalyzed samples]

first: Marc

last: DALOD

type:
Expression profiling by array
Third-party reanalysis

summary: This series contains re-analyzed samples from GSE39555, GSE39556 and GSE15907.

overall_design: DC were isolated from lymphoid organs as previously described (Vremec et al., 2000). Normalized data are available on the SuperSeries record, GSE71171.

first: Laurence

last: Ardouin

first: Hervé

last: Luche

first: Frédéric

last: Montanana Sanchis

first: Rabie

last: Chelbi

first: Sabrina

last: Carpentier

first: Alaa

last: Shawket

first: Yannick

last: Alexandre

first: Claude

last: Grégoire

first: Anissa

last: Fries

first: Thien

last: Vu Manh

first: Samira

last: Tamoutounour

first: Karine

last: Crozat

first: Elena

last: Tomasello

first: Audrey

last: Jorquera

first: Sandrine

last: Henri

last: Dalod

first: Bernard

last: Malissen


title: Epigenetic clonality confers por prognosis in colorrectal cancer patients (FOLFIRI)

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:
In CRC, 1) to identify epigenetic changes at inter-tumor and intra-tumor level, and 2) to relate intra-tumor clonality to clinical, molecular and histopathologic parameters. From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). Clinical, molecular, and histopathologic parameters were stablished. Epigenetic analysis was performed using Infinium 450K beadchip (Illumina) and R statistics. Intra-tumor regions clustered together by patient. The biggest epigenetic changes were in IF vs DTS/CB. By patient, the most often divergent region was IF (49.4%) comparing with DTS and CB (25.3% in both). It did not correlate with histopathologic, molecular and clinical parameters.Epigenetic clonality is higher at intra-tumor level. The highest changes are observed in IF vs DTS/CB. No association with histopathologic, molecular, and clinical characteristics was found.
Cohort of CRC patients (N=17) who recieved quemotherapy (FOLFIRI)

overall_design: From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). When available, metastasis and normal tissue were also collected.

first: Anna

last: Martinez-Cardus

first: Manel

last: Esteller


title: Pax5 drives the metabolic shift in the development of pB-ALL as a result of BCR/ABLp190 susceptibility

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: We used microarrays to investigate gene expression changes in tumor-bearing  Sca1-BCR/ABLp190 and Sca1-BCR/ABLp190+Pax5+/- mice. We also analyze gene expression changes in preleukemic Sca1-BCR/ABLp190 and Sca1-BCR/ABLp190+Pax5+/- mice

overall_design: Tumor-bearing bone marrows of seven Sca1-BCR/ABLp190+Pax5+/-  and two Sca1-BCR/ABLp190 mice compared with B220+ bone marrow B cells from five WT mice. Preleukemic proB and preB cells of bone marrows of three Sca1-BCR/ABLp190+Pax5+/- and three Sca1-BCR/ABLp190 mice compared with proB and preB cells of bone marrows of three WT mice

first: Alberto

last: Martín-Lorenzo

first: Franziska

last: Auer

first: Lai

middle: N

last: Chan

first: Idoia

last: García-Ramírez

first: Carolina

last: Vicente-Dueñas

first: Inés

last: González-Herrero

first: Guillermo

last: Rodríguez-Hernández

first: Christoph

last: Bartenhagen

first: Martin

last: Dugas

first: Michael

last: Gombert

last: Ginzel

first: Oscar

last: Blanco

last: Orfao

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Maria

last: Begoña García-Cenador

first: Francisco

last: García-Criado

first: Julia

last: Hauer

first: Markus

last: Müschen

last: Sánchez-García

first: Arndt

last: Borkhardt


title: Broad and largely overlapping molecular changes arise in thymic and peripheral XCR1+ dendritic cells upon tolerogenic and immunogenic maturation

first: Marc

last: DALOD

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

overall_design:
DC were isolated from lymphoid organs as previously described (Vremec et al., 2000). DC subsets were sorted by flow cytometry according to the marker combinations described in the 'characteristics: phenotype' field for each sample for each individual series.

GeneChip Mouse Gene 1.0 ST (GPL6246) and GeneChip Mouse Genome 430 2.0 (GPL1261) DAT files were processed using Affymetrix Gene Chip Operating System to generate .CEL files. Normalization of the raw Affymetrix expression data with Robust Multi-chip Analysis were performed through Bioconductor in the R statistical environment (version 3.0.2) using the oligo package (GPL6246) and the affy, affyPLM and yaqcaffy packages (GPL1261). For genes symbol with several probeSets, the most variant probSet has been selected. The two platforms where merged by the unique genes symbols. Quantile Normalization was applied on the merged expression arrays to generate Matrix 1. PCA analysis revealed a strong platform effect. Partial Least Square (PLS) was performed to remove the platform effect and yield Matrix2 which was used for subsequent analyses.  The data matrices contain log2 values.


title: Epigenetic clonality confers por prognosis in colorrectal cancer patients

first: Sebastian

last: Moran

overall_design: Refer to individual Series