title: HIPSTR lncRNA knockdown in H1BP cells

overall_design: H1BP cells were transfected with antisense oligonucleotides (ASOs) targeting HIPSTR (ASO #0, ASO #1 or ASO #2) or control scrambled ASO (ASO CTL); transfections with each targeting ASO were done in duplicate, transfections with control ASO were done in triplicate.


title: Expression data from mouse embryonic fibroblasts wild type and lacking functional Pax7 gene

status: Public on Oct 26 2016

city: Warsaw

first: Areta

middle: Magda

last: Czerwinska

address: Krakowskie Przedmiescie 26/28

department: Faculty of Biology

country: Poland

institute: University of Warsaw

summary:
Myogenic differentiation relies on Pax7 function. We used mouse embryonic fibroblasts lacking functional Pax7 to follow its role in terminally differentiated cells.
Microarray analysis allowed us to compare transcriptomes of mouse embryonic fibroblasts of two genotypes, i.e. Pax7+/+ and Pax7-/-.

overall_design: Mouse embryonic fibroblasts were collected  for RNA extraction and hybridization on Affymetrix microarrays.

middle: M

first: Iwona

last: Grabowska

first: Karolina

last: Archacka

first: Joanna

last: Bem

first: Anna

last: Fogtman

first: Roksana

last: Iwanicka

first: Marta

last: Koblowska

first: Maria

middle: A

last: Ciemerych


title: Gene expression linked to sleep homeostasis in murine cortex

status: Public on Sep 07 2016

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

country: USA

institute: Washington State University, Spokane

summary:
Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence, however, indicates that sleep is necessary for normal brain function and that the need to sleep is a tightly regulated process. Surprisingly molecular mechanisms that determine the need to sleep are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need.
In this study we present an integrated 2 cross-laboratory analysis of the effects of sleep deprivation (SD) in gene expression in the mouse cortex. We also evaluate changes in gene expression genome-wide following various lengths of subsequent recovery sleep. (RS). We demonstrate that changes in gene expression specifically linked to SD or RS, and not to technical factors (e.g. the assay used), requires a novel analysis methodology not previously utilized in the field of sleep research.

overall_design: Cortical samples from mice were analyzed, from groups that were sleep deprived, sleep deprived and allowed to recover for 1, 2, 3, or 6 hours, and circadian control animals that were not sleep deprived. The experimental protocol began at lights on (ZT0) with 13 mice: 1 sacrificed, 4 control mice left undisturbed, and 8 mice kept awake with gentle brushing when attempting to sleep.  After 5 hours of sleep deprivation the mice were randomly assigned to recovery sleep or continued sleep deprivation, and at fixed intervals the mice were sacrificed, dissected and the left cortex retained.  The experimental protocol was repeated 7 times, one animal per timepoint per experimental day, so that 7 independent experiments are represented for each timepoint. All animals were acclimated to the brushing and tapping on cages used during sleep deprivationfor 6 days, and dissections and tissue collection were performed by a single experimenter.

first: Marcos

last: Frank

first: Jason

last: Gerstner

first: John

last: Koberstein


title: Long Noncoding RNA uc.345 promotes tumorigenesis of pancreatic cancer by upregulation of hnRNPL expression

status: Public on Sep 06 2016

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

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

summary: Increasing evidence points to an important functional or regulatory role of long noncoding RNA in cellular processes as well as some cancer diseases result from the aberrant lncRNA expression. LncRNA could participate in the cancer progross and develop a significant role through the interaction with proteins. In the present study, we report a lncRNA termed uc.345 that is up-regulated in tumor tissues, compared to the corresponding noncancerous tissues. We found that a higher uc.345 expression lever was significantly more frequent in tissues with increased depth of invasion and advanced TNM tumor node metastasis T stage. Moreover, uc.345 serves as an independent risk factor for pancreatic cancer patients’ overall survival (OS). Through soft agar assay and tumor xenograft model, our results indicate that uc.345 could stimulate tumor growth in vitro and in vivo. We also found the uc.345 could upregulate the hnRNPL protein level, furthermore, we demonstrate that the inhibition of (hnRNPL) by its association with uc.345 contributes to depress tumorgenesis in vitro. Collectively, these results demonstrate that uc.345 functions as an oncogenic lncRNA that promotes tumor progression and serves as a poor predictor for pancreatic cancer patients' overall survival.

overall_design: We obtained 103 pairs of primary PC and adjacent non-tumor tissues from patients undergoing resection surgery at the Department of General Surgery, Ruijin Hospital in Shanghai from 2011 to 2013. For all cases, two pathologists were in agreement with regard to pathological features and confirmed the PC diagnoses. No local or systemic treatment was conducted in these patients before surgery.

first: Chao

last: Liu

first: Hao

last: Chen


title: MicroRNA-769-3p down-regulated NDRG1 and enhanced apoptosis in MCF-7 during reoxygenation.

status: Public on Oct 23 2016

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

summary: In this study, breast cancer MCF-7 cells were cultured under 0.5% oxygen for 24 h followed by 24 h of reoxygenation. Cells was harvested at 0, 1, 12, and 24 h during reoxygenation, and examined the miRNA profile by Nanostring nCounter. Forty-three miRNAs had dramatic changes as compared with 0 h upon reoxygenation, with 63% (n=27) of the miRNAs up-regulated upon reoxygenation. Among these miRNAs, miR-769-3p, which was down-regulated in MCF-7 upon reoxygenation, was chosen for further investigation.

overall_design: The hypothesis was that the down-regulation of NDRG1 upon reoxygenation was regulated by miRNAs. To examine wether miRNAs regulate NDRG1 under 0.5% O2 concentrations, the miRNA expression profiles of MCF-7 cells under reoxygenation were examined. Cells were harvested at 0 (hypoxia control), 1, 12, and 24 h upon reoxygenation. Each profile was done in triplicate. The genomic profile of miRNAs was measured using NanoString nCounter® miRNA Expression Assays.

first: En-Ching

last: Luo


title: The Role of Serum MicroRNA-6767-5p as a Biomarker for the Diagnosis of Polycystic Ovary Syndrome

status: Public on Aug 31 2016

city: Seoul

first: Do Kyeong

last: Song

address: 911-1 Mokdong, Yangchoen-Ku

country: South Korea

institute: Ewha Womans University School of Medicine

summary: To examine the role of the serum miRNA as a biomarker for the diagnosis of PCOS and its relationship with metabolic and reproductive traits

overall_design: The initial study population consisted of 8 PCOS cases and 9 controls.

first: Hyejin

last: Lee

first: Do-Kyeong

first: Yeon-Ah

last: Sung


title: Coding and Non-coding mRNA expression after exposure of Breast Primary Epithelial Cells to different doses of X-ray

city: Cerdanyola del Valles

first: Mariona

last: Terradas

state: BARCELONA

address: U. Cell Biology, Fac. Biosciences

department: Cell Biology, Animal Physiology and Immunology

country: Spain

institute: Universitat Autonoma de Barcelona

summary: Low and high doses of X-rays are used in medicine as diagnostic and therapeutic tools, respectively. While response to high doses of radiation is well known, contradictions exist about effects of low-dose irradiation. Therefore, improving the knowledge on the consequences of low-dose irradiation could help to address this controversy. Moreover, describing new insights into high-dose irradiation would improve new cancer therapies combining radiation and gene therapy. As long non-coding RNAs (lncRNAs) seems to be engaged to almost all biological functions, including response to DNA damage, we aimed to describe the participation of lncRNAs in the response to different doses of X-ray exposure. We observed that, in human breast epithelial cells, different sets of coding and non-coding transcripts are differentially regulated at moderate and high doses compared to low doses. The validation of expression of five lncRNAs only regulated at high and moderate X-ray doses supports our results. Altogether, we could conclude that response to moderate and high dose irradiation versus response to low-doses also differs in terms of lncRNA expression. Therefore, further studies on the participation of lncRNAs in this response to radiation would help to address controversies regarding low-dose irradiation response and to improve therapies using high-dose irradiation.

overall_design: Breast primary epithelial cells were exposed to 0.02Gy, 0.1Gy and 2Gy of X-rays using medical devices and sham-irradiated samples were used as a control. To irradiate cells at low doses of X-ray, cells growing in 25cm2 flasks were irradiated with two (0.02 Gy) and ten automatic shots (0.1 Gy) under a mammography X-ray diagnostic device (SENO DMR plur, General electric). A Therapax STX 150 machine (Pantak) was used to irradiate BPECs at high doses (2Gy). RNA collection of the samples was done at three different days in order to have biological triplicates per each condition. Afterwards, total RNA was hybridized to Sureprint G3 Human Gene Expression v2 Microarray (Agilent) that includes probes to Broad Institute Human lincRNA catalog (Khalil et al. 2009; Guttman et al. 2009) among other ncRNAs. Differential expression analysis was carried out on non-control probes with an empirical Bayes approach on linear models (limma) (Smyth 2004). Results were corrected for multiple testing according to the False Discovery Rate (FDR) method (Benjamini & Hochberg 1995). Genes were selected as significant using a B-statistic cut-off B>0 and Fold Change (FC) > 1.2 or >-1.2.

last: Martín

first: Maite

last: Huarte

first: Anna

last: Genescà


title: In vitro effect of liver carcinogens aflatoxin B1 and  methapyrilene on transcriptomic profiles in human liver HepaRG cells

status: Public on Sep 17 2016

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Rapidly increasing number of man-made chemicals urges the development of reliable time- and cost-effective approaches for the carcinogen detection and identification. Considering this, the utility of high throughput microarray gene expression profiling for the identification of genotoxic and non-genotoxic carcinogens in vitro was investigated.  Human terminally differentiated hepatic HepaRG cells were treated with model liver carcinogens, genotoxic carcinogen aflatoxin B1 (AFB1) and non-genotoxic carcinogen methapyrilene, at IC10 and IC25 concentrations for 72 hours, and transcriptomic profiles were determined. Treatment of HepaRG cells with IC10 and IC25 concentrations of AFB1 resulted in altered expression of 538 and 3033 genes (p-value ≤0.01 and fold change ≥2.0), respectively, and treatment of HepaRG cells with methapyrilene at the IC10 and IC25 concentrations altered the expression of 1255 and 1861 genes, respectively. Pathway analysis of transcriptomic signatures in HepaRG cells treated with minimally cytotoxic IC10 concentrations of AFB1 and methapyrilene demonstrated a strong enrichment in genes involved in key carcinogen-associated pathways, including receptor-mediated effects, detoxification response, cell death and apoptosis, cell proliferation and survival, oxidative stress and inflammation. Importantly, DNA damage and repair, cell cycle progression, and cell cycle checkpoint control pathways were uniquely activated in AFB1-treated HepaRG cells, whereas receptor-mediated signaling detoxification response pathway was predominantly altered in methapyrilene-treated HepaRG cells. In summary, high throughput microarray gene expression approach identifies specific carcinogen-exposure-associated transcriptomic responses and identifies affected molecular pathways, and categorize pathways associated with carcinogen exposure in a short-term in vitro test.

overall_design: Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with AFB1 at doses 5 µM (IC10) and 25 µM (IC25) and methapyrilene at doses 650 µM (IC10) and 850 µM (IC25). Gene expression profiles in the HepaRG cells treated with AFB1 and methapyrilene for 72 hours were investigated.

first: Kostiantyn

last: Dreval

first: Orish

middle: E

last: Orisakwe

first: Frederick

last: Beland

first: Igor

middle: P

last: Pogribny


title: Transcriptome-based profiling reveals a macrophage pedigree and identifies Irf8 as pivotal for macrophage homeostasis and function

status: Public on Jul 28 2016

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: Recent studies have shown that tissue macrophages (MF) arise from embryonic progenitors of the yolk sac (YS) and fetal liver and colonize the tissues before birth. Further studies have proposed that developmentally distinct tissue MF can be identified based on the differential expression of F4/80 and CD11b, but whether a characteristic transcriptional profile exists is largely unknown. Here, we established an inducible fate mapping system that facilitated the identification of A2 progenitors of the YS as source of F4/80hi but not CD11bhi MF. Large-scale transcriptional profiling of MF precursors from the YS until adulthood allowed the description of a complex MF pedigree. We further identified a distinct molecular signature of F4/80hi and CD11bhi MF and found that Irf8 was vital for MF maturation and the innate immune response. Our data provide new cellular and molecular insights into the origin and developmental pathways of tissue MF.

overall_design: All samples are from mouse tissue at early developmental stages (E8, E9.5, E14) and from adulthood (6 weeks old). For the early developmental time points timed matings were performed. Macrophage populations were isolated from each tissue. RNA was isolated using Arcturus PicoPure isolation kit from yolk sac, brain, liver, kidney and skin samples after FACS sorting. Three replicates per cell population were included. Wildtype  and Irf8 knockout samples were analyzed.

first: Nora

last: Hagemeyer

first: Katrin

last: Kierdorf

first: Kathrin

last: Frenzel

first: Jia

last: Xue

first: Marc

last: Ringelhan

first: Zeinab

last: Abdullah

first: Isabell

last: Godin

first: Peter

last: Wieghofer

first: Marta

middle: J

last: Jordao

first: Frank

last: Rosenbauer

first: Percy

last: Knolle

first: Mathias

last: Heikenwälder

first: Joachim

middle: L

last: Schultze

first: Marco

last: Prinz


title: HIPSTR lncRNA knockdown in HEK293 and H1BP cells

status: Public on Sep 08 2016

city: São Paulo

first: Sergio

last: Verjovski-Almeida

state: São Paulo

address: Av. Vital Brasil 1500

country: Brazil

institute: Instituto Butantan

summary:
Compared to mRNAs, lncRNAs display higher developmental stage-, tissue-, and cell-subtype-specificity of expression, and are generally less abundant in a population of cells.

Here, we identify HIPSTR (Heterogeneously expressed from the Intronic Plus Strand of the TFAP2A-locus RNA), a novel lncRNA gene in the developmentally regulated TFAP2A locus. HIPSTR has evolutionarily conserved expression patterns, its promoter is most active in undifferentiated cells, and depletion of HIPSTR in HEK293 and in pluripotent H1BP cells predominantly affects the genes involved in early organismal development and cell differentiation. HIPSTR is specifically induced and heterogeneously expressed in the 8-cell-stage human embryos during the major wave of embryonic genome activation. We systematically explore the phenomenon of cell-to-cell variation of gene expression and link it to low population-level expression of lncRNAs, showing that, similar to HIPSTR, the expression of thousands of lncRNAs is more highly heterogeneous than the expression of mRNAs in the individual, otherwise indistinguishable cells of totipotent human embryos, primordial germ cells, and stable cell lines.

In these series of microarray experiments we evaluate genome-wide gene expression changes after knockdown of HIPSTR lncRNA in HEK293 and H1BP cells.

overall_design: Refer to individual Series


title: lncRNA expression profiles in OSCC cells cultured under normoxic and hypoxic conditions

status: Public on Jul 26 2016

city: Chengdu

first: Guiquan

last: Zhu

address: No.55 Section 4, Renmin South Road

department: Department of Head Neck Surgery

institute: Sichuan Cancer Hospital

summary: Hypoxic microenvironment plays important roles in the progression of solid tumors including oral squamous cell carcinoma (OSCC). Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. However, it is not clear whether lncRNAs could regulate hypoxia-adaptation of OSCC, and which lncRNAs participate in this process. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa as well as in hypoxic OSCC cells compared with normoxic OSCC cells. Our microarray also identified 942 lncRNAs that were up-regulated and 507 lncRNAs that were down-regulated in cells cultured under hypoxia compared with those cultured under normoxia (Fold Change >= 2.0, P-value <= 0.05).

overall_design: An OSCC cell line Cal-27 was cultured under either 20% O2 (normoxic) or 1% O2 (hypoxic) conditions. Three samples from each group were obtained for microarray study.

first: Ling

last: Li


title: Long noncoding RNA HAS2-AS1 mediates hypoxia-induced invasiveness of oral squamous cell carcinoma

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


title: Diesel exhaust particle (DEP)-treated HBE cells

status: Public on Jun 30 2016

city: Nanjing

first: Xiaobo

address: Dingjiaqiao 87

institute: Southeast University

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

summary: We evaluated the profile of lncRNA and mRNA expression in control and 50μg/ml DEP treated HBE cells using the  Arraystar Human LncRNA Array v3.0 array,7th generation.  Our findings implicates that dysregulation of mitochondria invovled mRNAs may play important role in cytotoxicity of DEP.

overall_design: Examination of lncRNA and mRNA expression in control or DEP-treated HBE cells

first: Rui

last: Chen


title: Gene expression in murine colon mucosa following activation of stromal Hedgehog signalling

status: Public on Aug 02 2016

city: Huddinge

first: Rune

last: Toftgård

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary:
In the intestine, Hedgehog (Hh) signalling orchestrates epithelial homeostasis in a bidirectional loop.  Differentiated enterocytes secrete the ligand leading to active downstream signaling exclusively in the stroma.  In turn, Hh-driven stromal factors contribute to the control of intestinal stem cell numbers and induce epithelial differentiation.
To investigate the consequences of stromal Hh activation on the gene expression level, we performed microarray analysis on full-thickness colonic tissue from Col1a2CreER;Ptch1fl/fl mice (C57BL/6 background). Upon Cre-driven recombination, these mice lack the inhibiting Hh receptor Ptch1 specifically in Col1a2 expressing stroma cells, leading to stroma-specific activation of downstream Hh signaling.

overall_design: RNA was isolated from 1 cm of fresh-frozen whole colonic tissue from Col1a2CreER;Ptch1fl/fl mice (n = 4) and controls (n = 4) starting 1.5 cm from the anus 7 days after administration of 5mg Tamoxifen i.p. to activate Cre.  RNA quality was assessed using the Agilent 2200 Tape Station system; RNA integrity numbers (RIN) >8 were considered sufficient.  Affymetrix Mouse Gene ST 2.0 arrays were used.  Robust multi-array average (RMA) median polish procedures were applied for normalization.

last: Gerling


title: Oviductal vs. ovarian epithelial transformation yields very different tumor phenotypes in Apc fl/fl;Pten fl/fl mice

status: Public on Aug 25 2016

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: We treated 6-8 week old mice that had floxed alleles of both Apc and Pten (for both alleles in each case) that also carry an Ovgp1-iCre-ERT2 transgene, with one of two treatments; a third group received neither treatment. The Ovgp1-iCre-ERT2 expresses Cre recombinase fused to a tamoxifen-inducible fragment of the estrogen receptor, in tissues where the Ovgp1 gene (oviductal glycoprotein 1) is expressed, which is almost exclusively in mouse oviductal epithelium (equivalent to human fallopian tube epithelium = FTE). Treating the mice with tamoxifen permits the Cre recombinase to enter the cell nucleus and inactivate the Apc and Pten genes. Six of the mice were treated with intraperitoneal injection of tamoxifen (0.1g/kg of body weight) dissolved in corn oil on days 1 and 3 and developed oviductal tumors (OdT) yielding 6 of the samples. Four mice (yielding 5 samples) were instead injected with 50 million plaque-forming units of replication-incompetent AdCre into both ovarian bursal cavities on day 1, which inactivated Apc and Pten in the ovarian surface epithelium (OSE), and lead to ovarian tumors (OT). Ovaries were also harvested from four untreated 6-8 week old mice with the same genotype, with two ovaries from each mouse comprising one control sample. RNA was purified from tumor or normal tissue, and targets for Affymetrix arrays synthesized from the mRNAs.  We used Affymetrix Mouse Gene 2.1 ST arrays, which hold 41345 probe-sets, but we largely analyzed just those 25216 probe-sets that were mapped to Entrez gene IDs.  Raw data was processed with Robust Multi-array Average algorithm (RMA).  Data is log2-transformed transcript abundance estimates. We fit a one-way ANOVA model to the three groups of samples.  We supply a supplementary excel workbook that holds the same data as the data matrix file, but also holds the probe-set annotation at the time we analyzed the data, and some simple statistical calculations, which select subsets of the probe-sets as differentially expressed.  Consumers should consider obtaining more up-to-date probe-set annotation for the array platform. We also provide supplementary excel files that show our simple analysis of GSE6008, which consists of 99 human ovarian tumor samples of 4 types, and 4 normal ovary samples, where we fit an ANOVA model to the 5 groups. In yet another supplementary file we show the correlation between each human tumor and mouse tumor, where we correlate the difference in log2-transformed values of each tumor from the average of the normals for the same species, for just those genes that were 1-to-1 best homologs according to build 68 of NCBI's Homologene, in order to see how much the human tumors resemble the mouse tumors.

overall_design: Six oviductal tumor samples from 6 mice with conditional knockout of Apc and Pten driven by an Ovgp1-iCre-ERT2 transgene , 5 ovarian tumor samples from 4 mice with conditional knockout of Apc and Pten driven by injection of AdCre into both ovarian bursal cavities, and 4 normal ovary samples from 4 mice.

first: Rong

last: Wu

first: Yali

last: Zhai

first: Paloma

last: Garcia

first: Anum

last: Naseem

first: Tom

middle: C

last: Hu

first: Eric

middle: R

last: Fearon

first: Kathleen

last: Cho

first: Anthony

middle: N

last: Karnezis


title: AhR signaling reprograms newly activated CD4+ T cells promoting combinatorial expression of regulatory genes to suppress murine GVHD [72 hr]

status: Public on Sep 01 2016

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

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=4-5) were treated i.p. with 15μg/kg TCDD on day 0, or vehicle or 10mg/kg Cl-BBQ on days 0, 1 and 2. Mice were sacrificed on day 3 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

middle: K

last: Ehrlich

first: Nancy

middle: I

last: Kerkvliet


title: RNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and  trauma patients

status: Public on Jun 10 2016

first: Yu

last: Zhang

state: Jiangsu

address: 305 East Zhongshan Road

department: Clinical Laboratory Science

institute: Jinling Hospital

summary: LncRNA and mRNA microarrays were performed to identify differentially expressed lncRNAs and mRNAs in fibroblast-like synoviocytes from rheumatoid arthritis patients compared with fibroblast-like synoviocytes from trauma patients.

overall_design: Fibroblast-like synoviocytes were isolated from synovial tissues. LncRNA and mRNA microarrays were performed using fibroblast-like synoviocytes at passage 3.

first: Xiaojun


title: Gene Expression profiles of normal and tumor colon tissues from CDX2; Dmt1+/+/ApcF/+, CDX2; Dmt1F/F/ApcF/+

status: Public on Aug 18 2016

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

summary: To investigate the detailed molecular mechanisms for the regulatory role of Dmt1 in colon tumorigenesis, microarray gene expression analysis was performed on normal and tumor colon tissue RNA isolated from 3-month-old CDX2; Dmt1+/+/ApcF/+and CDX2; Dmt1F/F/ApcF/+ mice.

overall_design: Global gene expression profiling in colon tissue RNAs isolated from 3-month-old CDX2; Dmt1+/+/ApcF/+ (n=7; shah038, normal; shah040, tumor) and CDX2; Dmt1F/F/ApcF/+ (n=4; shah039, normal; shah041, tumor).

first: Xiang

last: Xue

first: Yatrik

last: Shah


title: Cyclic tensile strain enhances the expression of Indian hedgehog and progression of ossification of the human cervical posterior longitudinal ligament

status: Public on Jun 22 2016

city: Eiheiji city

first: Daisuke

last: Sugita

state: Fukui prefecture

address: Shimoaizuki 23, Matsuoka

department: Orthopaedics and rehabilitation medicine

country: Japan

institute: Fukui University

summary:
The initiation and/or progression of ossification of the posterior longitudinal ligament (OPLL) is associated with cyclic tensile strain, but the pathomechanism of OPLL remains unclear.  Indian hedgehog (Ihh) and its related signaling are key factors in normal enchondral ossification. However, the relation of OPLL to Ihh is unclear.
The purpose of this study is to investigate the contribution of mechanical strain to OPLL and the relation of Ihh to OPLL.

overall_design: Cultured posterior longitudinal ligament cells were subjected to 24 hours of cyclic tensile strain and then analyzed by microarray.

first: Yasuo

last: Kokubo

first: Naoto

last: Takeura

first: Kazuya

last: Honjoh

first: Atsushi

last: Yamagishi

first: Hisashi

last: Oki

first: Hideaki

last: Nakajima

first: Kenzo

last: Uchida


title: Comparison of transcriptomes between DMSO-5uM and Torin1-5uM treated mouse cumulus-oocyte complexes cultured in vitro for 14h

status: Public on Aug 01 2016

first: You-Qiang

last: Su

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary:
We sought to identify the potential specific roles of the MTOR signalling in cumulus cells by comparing the transcriptomes of the Control (treated with the DMSO vehicle) and MTOR-specific inhibitor Torin 1(5uM)-treated cumulus-oocyte complexes that were cultured for 16 hours.
We compared the transcriptomes between DMSO- and Torin 1- treated cumulus-oocyte complexes.

overall_design: 3 individual cumulus-oocyte complex samples of DMSO- and Torin1-treated were collected. Comparison was done between DMSO- and Torin1-treated groups.


title: The major diversification of Vγ1.1+ and Vγ2+ thymocytes in mice occurs after commitment to the γδ T-cell lineage

city: Copenhagen

first: Terkild

middle: Brink

last: Buus

address: Blegdamsvej 3

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
Adult murine gammadelta thymocytes can be divided into two major subsets based on their expression of TCRVgamma1.1 or TCRVgamma2, respectively. gammadelta thymocytes mature through distinct stages characterized by CD24 and CD73 in the following order: immature uncommitted (CD24+CD73-), immature committed (CD24+CD73+) and mature (CD24-CD73+).
In this dataset we have sorted gammadelta thymocytes into 6 distinct populations based on subset and developmental stage and analyzed their gene expression. These data were used to identify 3400 differentially expressed genes during gammadelta thymocyte development and to show that the two major adult gammadelta T cells follow a similar path through early development and mainly diversify after commitment to the gammadelta T cell lineage.

overall_design: 22 samples (6 populations 3-4 biological replicates) were analyzed for differential expression to identify genes shared between cells of the different subsets at each developmental stage.

middle: B

first: Carsten

last: Geisler

first: Jens

last: Lauritsen


title: Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa

first: Guiquan

last: Zhu

summary: Hypoxic microenvironment plays important roles in the progression of solid tumors including oral squamous cell carcinoma (OSCC). Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. However, it is not clear whether lncRNAs could regulate hypoxia-adaptation of OSCC, and which lncRNAs participate in this process. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa as well as in hypoxic OSCC cells compared with normoxic OSCC cells. Our data revealed 2053 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 934 lncRNAs were significantly up-regulated and 1119 lncRNAs were down-regulated in OSCC compared with paired normal mucosa.

overall_design: Six OSCC tissues and paired normal oral mucosa were obtained from 6 patients with OSCC. LncRNA expression profiles were evaluated by an Agilent Human LncRNA Array v3.0 (8 x 60K, Arraystar).

first: Ling

last: Li


title: Expression analysis of a preinvasive pancreatic cancer mouse model with and without p120 catenin

status: Public on Jul 25 2016

city: Baltimore

first: Audrey

middle: Marie

last: Hendley

state: MD

address: 733 North Broadway

department: Human Genetics

institute: Johns Hopkins University

summary: Pancreatic cancer is one of the most deadly cancers with a 5 year survival rate of about 5%.  Therapeutic options are limited, especially for patients that present with late state disease and metastasis.  Although the metastatic burden of pancreatic cancer is usually high, little is known about the mechanisms that regulate delamination and dissemination of epithelial cells from preinvasive and malignant pancreatic lesions.  Here, we used a preinvasive mouse model of pancreatic cancer to conditionally knockout p120 catenin (Ctnnd1).  Mice with biallelic loss of p120 catenin progressively develop high grade PanIN lesions and neoplasia accompanied by prominent acute and chronic inflammatory processes.  Loss of p120 catenin in the context of oncogenic Kras also promotes remarkable apical and basal epithelial cell extrusion.  Abundant single epithelial cells exit PanIN epithelium basally, survive, and display features of malignancy.  Similar extrusion defects are observed following p120 catenin knockdown in vitro, and these effects are completely abrogated by activation of S1P/S1P2 signaling.  Our results establish p120 catenin and S1P/S1P2 signaling as novel regulators of non-EMT mediated epithelial cell invasion in pancreatic neoplasia.

overall_design: Transcriptomes of KCiMist1G; p120wt/wt and KCiMist1G; p120f/f pancreases were compared, with three replicates each, using microarray.

first: Steven

middle: D

last: Leach

first: Jennifer

last: Bailey


title: Mouse mammary tumor cell line exon arrays

status: Public on May 27 2016

city: Bethesda

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: This study presents exon array expression data for multiple mammary tumor cell lines derived from various genetically-engineered mouse models of mammary cancer as well as from cell lines derived from spontaneously arising mouse mammary tumors.

overall_design: Cell lines were harvested during growth phase in culture, RNA extracted and exon array analyses performed.  One sample per cell line was analyzed.

first: Jeffrey

last: Green


title: Gene expression data of cultured primary microglia from neonatal control and Cstb-/- mice.

status: Public on Jun 29 2016

city: Helsinki

first: Inken

last: Körber

address: Haartmaninkatu 8

department: Neuroscience Center

country: Finland

institute: Folkhälsan Institue of Genetics / University of Helsinki

summary:
Cystain B (Cstb) is a ubiquitously expressed cysteine protease inhibitor and mutations of the CSTB gene lead to the neurodegenerative disease progressive myoclonus epilepsy of Unverricht-Lundorg type (EPM1).
We are interested in the microglia-specific, Cstb-dependent gene-expression changes in mice and in this data set, we include gene-level expression data from cultured primary microglia of control and Cstb-/- mice extracted from neonatal mice at P5 and we identified 156 differentially-expressed genes in Cstb-/- microglia.

overall_design: We analyzed 8 samples in total and we compared 4 control microglia samples to 4 Cstb-/- microglia samples. Genes with a fold change > 1.3 and with p < 0.05 in T-test with BH correction were considered differentially expressed.

first: Tarja

last: Joensuu


title: Gene expression profile of mouse Lewis lung carcinoma cell line treated with single or fractionated ionizing radiation doses

status: Public on Jul 07 2016

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: Radiotherapy is one of the most common therapies for cancer. Approximately half of all cancer patients will receive radiotherapy at some point during treatment. Consequences of IR treatment are dose dependent and different sensitivity to IR of various types of cells is well established. To reduce the damage of IR to most sensitive cells of normal (noncancerous) tissue radiotherapy is administered as fractionated dose treatment applying radiation in ~2 Gy fractions every 24 hours, 5 times per week. However, during the therapy intrinsic and acquired tumor radioresistance may result in treatment failures. Comprehensive mechanisms of the resistance to irradiation as well as mechanisms of cellular response to fractionated dose IR remain unclear. Therefore, in the present study we evaluated global gene expression changes in murine Lewis lung carcinoma LLC1 cells following X-ray irradiation of single 2 Gy or 10 Gy and 2 Gy x 5 fractionated doses.

overall_design: Total RNA was harvested from mouse Lewis lung carcinoma cells 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.

first: V

first: K

last: Suziedelis


title: Embryonic neocortical HuR-immunoprecipitated mRNAs

status: Public on Jul 08 2016

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Forkhead-box domain (Fox) containing family members are known autism spectrum associated genes. Here we show that, within the developing neocortex, the distinct phospho-states of a single RNA-binding protein, Hu antigen R, dictate mRNA translation and are sufficient to define distinct Foxp-characterized subpopulations of neocortical projection neurons. This demonstrates the importance of HuR phospho-states within the framework of the developing brain and further confirms the role of mRNA translation in autism pathogenesis.

overall_design: Fetal mouse neocortices were dissected, homogenized, and immunoprecipitated with either anti-HuR or IgG control antibodies.  RNA was prepared from the immunoprecipitates and assayed on Affymetrix Mouse Exon microarrays.

first: Mladen-Roko

last: Rasin


title: Gene expression profiling of SF1 knockdown in human endometriotic stromal fibroblast

status: Public on May 12 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Epigenetic silencing of Steroidogenic Factor 1 (SF1) is lost in endometrial tissue in endometriosis and this is hypothesized to result in de novo local steroidogenesis favoring growth and inflammation. The goal of this study was to evaluate the endometrial specific transcriptional and functional role of SF1.  Expression of SF1 was robustly increased in cultures established from stromal fibroblasts isolated from endometriomas (OsisHESC) over endometrial stromal cells isolated from eutopic sites in healthy proliferative phase endometrial biopsies (HESC). In order to evaluate the role of SF1 in the regulation of genes in fibroblast isolated from human endometriomas, OsisHESC were transfected with scrambled siRNA (siNT) or siRNA targeting SF1 (siSF1).

overall_design:
SF1 siRNA group and Non-targeting siRNA group. In order to evaluate the role of SF1 in the regulation of genes in fibroblast isolated from human endometriomas, OsisHESC were transfected with scrambled siRNA (siNT) or siRNA targeting SF1 (siSF1) and subjected to gene expression profiling.
Two group comparison

first: Yasmin

last: Vasquez

first: San-Pin

last: Wu

first: Yiqun

last: Zhang

first: Francesco

last: DeMayo


title: Effect of exogenous FABP4 (A-FABP/aP2) and FABP5 (E-FABP/mal1) on gene expression in adipose-derived stem cells (ADSC) and 233A cells

status: Public on Jun 23 2016

city: Sapporo

first: Masato

last: Furuhashi

institute: Sapporo Medical University School of Medicine

summary: Gene expression profile of treatment with FABP4 or FABP5 in ADSC and 233A cells was examined.

overall_design: ADSC or 233A cells were treated with and without 1 µM recombinant FABP4 or FABP5.

first: Tokunori

last: Yamamoto


title: mRNA expression profile of Tie2 monocytes in limb ischemia patients and controls

status: Public on Jul 21 2016

city: London

first: Francesca

last: Ludwinski

address: First Floor, North Wing, St Thomas' Hospital

department: Academic Department of Vascular Surgery

country: United Kingdom

institute: King's College London

summary: Tie2-expressing monocytes do not appear to effect revascularisation in critical limb ischemia (CLI) patients, despite a large body of evidence demonstrating their pro-angiogenic potential when isolated from control patients. In order to understand what might cause this loss of angiogenic function, we carried out a whole genome microarray analysis of mRNA isolated from Tie2-expressing monocytes from CLI patients and compared that with age-matched control samples.

overall_design: 12 samples in total

first: Bijan

last: Modarai


title: Whole genome expression microarray analysis in hepatocellular carcinoma cell line, Huh7 cells, treated with siRNA targeting for nuclear factor 90 (siNF90)

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

summary: To identify genes regulated by complex of NF90 and nuclear factor 45 (NF45) in hepatocellular carcinoma, we performed comprehensive analyses of mRNA expression in Huh7 cells depleted of NF90.

overall_design: mRNA expression profile in Huh7 cells depleted of NF90.


title: Comparison of gene expression profiles of colorectal adenocarcinoma HT-29 cells and oral squamous cell carcinoma Ca9-22 cells to determine SLPI-induced cell migration

status: Public on Jun 09 2016

city: Niigata

first: yoshikazu

last: mikami

address: 1-757 Asahimatidori, Chuo-ku

department: Division of Microscopic Anatomy

institute: Niigata University Graduate School of Medical and Dental Sciences

summary: we performed microarray-based gene expression profiling of HT-29, Ca9-22 and SLPI-deficient Ca9-22 cells for high-throughput analysis and for screening differentially expressed genes (DEGs)

overall_design: Cells were seeded on 100-mm cell culture dishes (1 × 10^4 cells/dish), and cultured for 3 days in the growth medium (Minimal Essential Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin) at 37°C in an atmosphere containing 5% CO2. After culture, total RNA was extracted from the cells.

first: Yoshikazu

last: Mikami


title: Primary human blood-derived macrophages (BDMs): control vs. infected

status: Public on Jun 15 2016

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Transcriptional profiling of primary human blood-derived macrophages (BDMs) comparing control untreated BDMs with BDMs exposed with Streptococcus pneumoniae strain D39 (MOI 0.1 and 0.5) for 16 hours)

overall_design: Two-condition experiment, control BDMs vs. infected BDMs. Biological replicates: 3 control replicates, 3 infected replicates MOI 0.1, 2 infected replicates MOI 0.5).

first: Griß

last: Kathrin


title: Overexpression of microRNA-375 in medullary thyroid carcinoma cells hinders cell proliferation and improves the vandetanib efficacy effect in vitro

status: Public on May 22 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
The global microRNA (miRNA) profiling expression was assessed in a large series of both sporadic and hereditary forms of medullary thyroid carcinomas (MTC), and to evaluate the biological function of major found altered miRNAs. For this purpose we investigated miRNA differential expression in tumoral vs adjacent non tumoral tissues from 62 MTC patients, and showed a specific overexpression of miR-375, -129-3p, -376c, -335, -96, -10a, -7, -429 and an underexpression of miR-451 in tumoral tissues. Since miR-375 was  the most up-regulated miRNA, we thus decided to identify its targets by combining a transcriptomic signature of cells transfected either with premiR- or antagomiR-375 and an in silico analysis joining TT-cells mRNA specific signature from Cancer Cell Line Encyclopedia GEO dataset and miRNA prediction algorithms. Using this restrictive approach, we focused on miR-375 target SEC23A and validated a decreased expression of SEC23A by Western blotting and by immunohistochemistry in tumoral vs non tumoral adjacent thyroid epithelium. Furthermore, we observed that overexpression of miR-375 was associated with decreased proliferation and increased vandetanib response in vitro.
Overall, our results  showed an overexpression of miR-375 in MTC in association with a decrease of miR-375-potential targets including SEC23A. Additionnally, we postulate thatmiR-375 overexpression should be evaluated in MTC patients treated  with the tyrosine kinase inhibitor, vandetanib.

overall_design: 2 cell lines: TT and ORI (Nthy ORI 3.1) transfected with the antagomir-375 and premir-375 respectively. For each condition a control condition was provided. A total of 4 conditions: 2 transfections and their 2 respective controls are analyzed. For each condition 2 replica are provided. A total of 8 samples are submitted in this dataset.

first: P

last: Brest

first: A

last: Popa

last: Barbry

first: K

first: S

last: Lassale


title: Effect of deletion of Carnitine Palmitoyltransferase2 in hepatocytes on liver gene expression upon a 24 hour fast

status: Public on Jun 16 2016

first: Michael

middle: J.

last: Wolfgang

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary:
The liver is critical for maintaining systemic energy balance during starvation.  To understand the role of hepatic fatty acid β-oxidation on this process, we generated mice with a liver-specific knockout of carnitine palmitoyltransferase 2 (Cpt2L-/-), an obligate step in mitochondrial long-chain fatty acid β-oxidation.  Surprisingly, Cpt2L-/- mice survived the perinatal period and a 24hr fast with sufficient blood glucose.  The loss of hepatic fatty acid oxidation resulted in a significant loss in circulating ketones that remained unaltered by fasting.  Fasting induced serum dyslipidemia, hepatic steatosis and adaptations in hepatic and systemic oxidative gene expression in Cpt2L-/- mice to maintain systemic energy homeostasis.  Alternatively, feeding a ketogenic diet resulted in severe hepatomegaly, liver damage and death within one week with a complete absence of adipose triglyceride stores.  These data show that hepatic fatty acid oxidation is not required for survival during acute food deprivation but essential for constraining adipocyte lipolysis and regulating systemic catabolism when glucose is limiting.
In this dataset, we include the expression data obtained from dissected mouse liver from mice fasted for 24 hours with and without the deletion of carnitine palmitoyltransferase 2 (i.e. hepatocytes unable to beta-oxidize long chain fatty acids in mitochondria).

overall_design: WildType and KnockOut mice were fasted for 24 hours. Three biologic replicates were compared per class, thus six mice.

first: Jieun

last: Lee


title: Regulation of normal B cell differentiation and malignant B cell survival by OCT2 (expression)

status: Public on May 25 2016

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

summary: The requirement for the B cell transcription factor OCT2 (encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse but that their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This led us to examine the role of OCT2 in germinal center derived lymphomas. ShRNA knockdown showed that almost all DLBCL cell lines are addicted to the expression of OCT2 and its co-activator OCA-B. Genome-wide chromatin Immunoprecipitation analysis and gene expression profiling revealed the broad transcriptional program regulated by OCT2 that includes the expression of STAT3, IL10, ELL2, XBP1, MYC, TERT and ADA. Importantly, genetic alteration of OCT2 is not a requirement for cellular addiction in DLBCL. However, we detected amplifications of the POU2F2 locus in DLBCL tumor biopsies as well as a recurrent mutation of threonine 223 in the DNA binding domain of OCT2. This neomorphic mutation subtly alters the DNA binding preference of OCT2 leading to the transactivation of novel target genes including HIF1a and FCRL3. Finally, by introducing mutations designed to disrupt the OCT2-OCA-B interface we reveal a requirement for this protein-protein interface that might ultimately be exploited therapeutically. Our findings, combined with the predominantly B cell restricted expression of OCT2 and the absence of systemic phenotype in our knockout mice, suggest that an OCT2-targeted therapeutic strategy would be efficacious in both major subtypes of DLBCL whilst avoiding systemic toxicity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Knockdown of OCT2_1196 was tested in ABC DLBCL cell lines (HBL1 n=2, OCI-Ly10 n=3, TMD8 n=2) and GCB DLBCL cell lines (BJAB n=2, HT n=2). Knockdown of OCT2_3410 was tested in ABC DLBCL cell lines (HBL1 n=2, OCI-Ly10 n=4, TMD8 n=2) and GCB DLBCL cell lines (BJAB n=2, HT n=2). Knockdown of OCA-B was tested in ABC DLBCL cell lines (HBL1 n=2, OCI-Ly10 n=2) and GCB DLBCL cell lines (BJAB n=2, HT n=2). Knockdown of OCT2_1196 was tested with and without WT rescue construct in ABC DLBCL cell line (HBL1 n=4). Knockdown of OCT2_3410 was tested with and without WT rescue construct in ABC DLBCL cell line (HBL1 n=4). Knockdown of OCT2_1196 was tested with OCT2 T223A vs. WT rescue construct in ABC DLBCL cell line (HBL1 n=2, SUDHL4 n=4) and GCB DLBCL cell line (BJAB n=4). Mouse knockout (n=4) and wild type (n=4) Pou2f2 OCT2 B cells were tested.


title: Peroxisome proliferator-activated receptor gamma coactivator-1alpha isoforms selectively regulate multiple splicing events on target genes.

status: Public on Jun 07 2016

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

institute: Karolinska Institutet

summary: Endurance and resistance exercise training induce specific and profound changes in the skeletal muscle transcriptome. PGC-1a; coactivators are not only among the genes differentially induced by distinct training methods, but also participate in the ensuing signaling cascades that allow skeletal muscle to adapt to each type of exercise. While endurance training preferentially induces PGC-1a1 expression, resistance exercise activates the expression of PGC-1a2, a3, and a4. These three alternative PGC-1a isoforms lack the arginine-serine (RS) and RNA Recognition Motifs (RRM) characteristic of PGC-1a1. Discrete functions for PGC-1a1 and a4 have been described, but the biological role of PGC-1a2 and a3 remains elusive. Here we show that different PGC-1a variants can affect target gene splicing through diverse mechanisms, including alternative promoter usage. By analyzing the exon structure of the target transcripts for each PGC-1a isoform, we were able to identify a large number of previously unknown PGC-1a2 and a3 target genes and pathways in skeletal muscle. In particular, PGC-1a2 seems to mediate a decrease in the levels of cholesterol synthesis genes. Our results suggest that the conservation of the N-terminal activation and repression domains (and not the RS/RRM) is what determines the gene programs and splicing options modulated by each PGC-1a isoform. By using skeletal muscle-specific transgenics for PGC-1a1 and a4, we could validate in vivo splicing events observed in in vitro studies. These results show that alternative PGC-1a variants can affect target gene expression both quantitatively and qualitatively, and identify novel biological pathways under the control of this system of coactivators.

overall_design: Gene expression profiling after activation by  PGC-1a1, PGC-1a2, PGC-1a3 or PGC-1a4. GFP expression was used as a control.

first: Vicente

last: Martínez-Redondo

first: Paulo

last: Jannig

first: Jessica

middle: M

last: Lindvall

first: Indranil

last: Sinha

first: Igor

last: Cervenka

first: Jorge

last: Correia

first: Manizheh

last: Izadi

first: Amanda

middle: T

last: Pettersson-Klein

first: Leandro

middle: Z

last: Agudelo

first: Alfredo

last: Gimenez-Cassina

first: Patricia

last: Brum

first: Duarte

last: Ferreira

last: Ruas


title: New compounds triggering endoplasmic reticulum stress exert anti-melanoma effects and overcome BRAF inhibitor resistance

status: Public on Jun 01 2016

first: Kevin

last: Lebrigand

summary: We discovered and developed a new series of molecules (thiazole benzenesulfonamides). HA15, the lead compound of this series, displayed anti-cancerous activity on all tested melanoma cells including those isolated from patients and those that developed resistance to BRAF inhibitors. Our molecule displayed activity against other liquid and solid tumors. HA15 also exhibited strong efficacy in xenograft mouse models with melanoma cells either sensitive or resistant to BRAF inhibitors. Transcriptomic, proteomic and biochemical studies identified the chaperone BiP/GRP78/HSPA5 as the specific target of HA15 and demonstrated that the interaction increases endoplasmic reticulum (ER) stress, leading to melanoma cell death by concomitant induction of autophagic and apoptotic mechanisms.

overall_design: Profiling of 3 human melanoma cell lines (SKMel28, Mel501, A375) treated with HA15 at 10 uM or with DMSO was performed using whole genome human microarrays. Cells were incubated with DMSO or HA15 for 6h and then lysed prior to RNA isolation, labelling and hybridization on microarrays. One color experiment, total of 6 samples.

first: S

last: Rocchi

first: B

last: Mari

first: K

first: P

last: Barbry


title: Cancer-associated fibroblasts-secreted CXCL14-regulated LINC00092 mediates ovarian cancer progression by altering glycolysis

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

summary: Epithelial ovarian cancer (EOC) constitutes a major gynecological malignancy, with a reported incidence rate of 3-12/100 000 woman annually. As early symptoms of ovarian cancer are often clinically atypical or absent, the majority of ovarian cancer patients are diagnosed at a late stage, when the five-year survival rate is extremely low. This condition underscores the urgency of early detection of these patients and establishment of new therapeutic targets for successful intervention. Considering that the predominant biological characteristic that differentiates malignant from benign tumors is the ability to metastasize, it is necessary to identify novel metastasis-related molecules for ovarian cancer. In this study, we found that CAFs could significantly increase the metastatic potential of ovarian cancer cells compared with non-cancer associated fibroblasts(NAFs), which is associated with over-expression of CXCL14 in CAFs. We examined the impact of CAF-secreted CXCL14 on the lncRNA expression profiles in ovarian cancer during metastasis.

overall_design: We treated A2780s ovarian cancer cell line with recombinant CXCL14 protein and control respectively and subjected them to Arraystar Human LncRNA microarray v3.0 to profile differential lncRNAs in ovarian cancer upon treatment of CXCL14

first: Linjie

last: Zhao

first: Yanfei

last: Yang

first: Lingzi

last: Lei

first: Lian

last: Xu

first: Min

last: Feng

first: Huiliang

first: Wayne

last: Lau

first: Bonnie

first: Chenlu

last: Wang

first: Xia

first: Yuquan

last: Wei

first: Jan-Ake

last: Gustafsson


title: IFN type I-induced gene expression from brain endothelia

status: Public on Apr 20 2016

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary:
Brain endothelial cells are an essential part of the blood-brain-barrier (BBB) and, as such, are exposed to proinflammatory mediators as well as danger signals during infections. They might function as decisive cells mediating RNA virus- and IFN-mediated sickness behavior.
To better understand how brain endothelial cells modulate sickness behavior associated with virus-induced IFN release, we challenged endothelia with IFNbeta and investigated the transcription profile after IFNAR1 engagement

overall_design: Cultured brain endothelia isolated from adult mice were incubated with IFNbeta; 24h later cells were removed for RNA extraction and hybridization on Affymetrix arrays.

first: Alena

last: Spiess


title: Effect of DNMT3A R882H mutation or WT on gene expression in hematopoietic stem/progenitor cells with NRAS G12D co-transduction (Microarray)

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

summary:
DNA Methyltransferase 3A (DNMT3A) is frequently mutated in various hematopoietic malignancies; however, the underlying oncogenic mechanisms remain elusive. Here, we report that DNMT3A mutational ‘hotspot’ at Arg882 (i.e., DNMT3A-R882H) cooperates with constitutively activated RAS in transforming murine hematopoietic stem/progenitor cells (HSPCs) ex vivo and inducing acute leukemias in vivo. DNMT3A-R882H potentiates aberrant transactivation of ‘stemness’ gene expression programs, notably transcription factors Meis1, Hox-A, Mn1 and Mycn. Mechanistically, R882-mutated DNMT3A directly binds to cis-regulatory elements of these genes and induces focal CpG hypomethylation reminiscent of what was seen in human leukemias bearing DNMT3A R882 mutation. Furthermore, DNMT3A-R882H induced DNA hypomethylation facilitates gene enhancer/promoter activation and recruitment of Dot1l-associated transcription elongation machineries. Inactivation of Dot1l represses DNMT3AR882H-mediated stem cell gene dysregulation and acute leukemogenicity.

In this dataset, we provided microarray data showing effect of R882H-mutated or WT DNMT3A on gene expression among HSPCs with NRAS G12D co-transduction.

overall_design: Microarray analysis of Lin- enriched hematopoietic stem/progenitor cells with retroviral infection of NRAS G12D alone (EV-RAS), DNMT3A R882H with NRAS G12D (RH-RAS) or DNMT3A WT with NRAS G12D (WT-RAS) at day 12 or day 16 post-transduction.

first: Gang

middle: G


title: Multiple levels of transcriptional regulation by PLZF in NKT cell development [MoEx-1_0-st]

status: Public on May 24 2016

city: Chicago

first: Aiping

last: Mao

state: IL

address: 929 East 57th street

department: Pathology

institute: University of Chicago

summary:
To identify genes that PLZF is sufficient to modulate in T cells, we compared CD4+ CD8- (CD4SP) thymocytes that overexpressed PLZF to their wildtype counterparts
The transcription factor PLZF is induced during the development of innate and innate-like lymphocytes to direct their acquisition of a T helper effector program, but the molecular mechanisms involved are poorly understood. Using biotinylation-based ChIP-seq and microarray analysis of both NKT and PLZF-transgenic thymocytes, we identified several layers of regulation of the innate-like NKT effector program: first, PLZF bound and regulated genes encoding cytokine receptors as well as homing and adhesion receptors; second, PLZF bound and activated T helper-specific transcription factor genes that in turn control T helper specific programs; finally, PLZF bound and suppressed the transcription of Bach2, a potent general repressor of effector differentiation in naive T cells. These findings reveal the architecture of the transcriptional program recruited by PLZF and elucidate how a single transcription factor can drive the developmental acquisition of a broad effector program.

overall_design: FACS-sorted CD4+ CD8- (CD4SP) lymphocytes from the thymi of wildtype (2 biological replicates) and PLZF transgenic mice (3 biological replicates) were compared using Mouse Exon 1.0 ST microarrays

first: Albert

last: Bendelac

first: Michael

last: Constantinides


title: Long-noncoding RNAs in basal cell carcinoma

status: Public on Mar 29 2016

city: Bochum

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

summary: A total of 3 patients with basal cell carcinoma (BCC) and 3 healthy individuals (control; non-lesional skin) were enrolled in the study. Punch biopsies (4 mm) were obtained under local anaesthesia and immediately put in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C until RNA extraction.

overall_design: The lncRNA and mRNA expression in BCC was compared to lncRNA and mRNA expression in non-lesional skin (control).


title: Long non-coding RNAs in cutaneous squamous cell carcinoma

status: Public on Apr 13 2016

summary: The expression of lncRNAs in cutaneous squamous cell carcinoma (cSCC) were determined with a commercially available microarray (Arraystar Inc.,Rockville, Maryland USA). The Arraystar human lncRNA Microarray V3.0 containing 30,586 LncRNAs and 26,109 coding transcripts (mRNAs)

overall_design: A total of three patients with cSCC were biopsied. A total of three control (non-lesional skin) were biopsied.


title: Brain Endothelial Specific IFNAR Is Key For Virus-Induced Sickness Behavior And Cognitive Impairment

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

overall_design: Refer to individual Series


title: CaSR modulator in neuroblastoma model [mouse]

status: Public on Mar 30 2016

city: Esplugues

first: Carmen

last: de Torres

state: Barcelona

address: Santa Rosa 39

department: Oncology

institute: Hospital Sant Joan de Deu

summary: CaSR modulation inhibits neuroblastoma growth

overall_design: 8 control and 8 samples treated with CaSR allosteric activator


title: Global genome expression analysis of lamina propria derived WT and Nlrp6-/- Ly6C-hi inflammatory monocytes

status: Public on Mar 27 2016

city: Ann Arbor

first: Sergey

last: Seregin

address: 1150 E Medical Center Drive

institute: University of Michigan

summary:
Nlrp6-/- lamina propria Ly6C-hi monocytes in response to AOM/DSS have deficient TNFα production, but increased production of other pro-inflammatory cytokines as compared to WT
NLRP6 is a member of the Nod-like receptor family, whose members are involved in the recognition of microbes and/or tissue injury.  NLRP6 was previously demonstrated to regulate the production of IL-18 and is important for protecting mice against chemically-induced intestinal injury and colitis-associated colon cancer.  However, the cellular mechanisms by which NLRP6 reduces susceptibility to colonic inflammation remain unclear. Here, we determined that NLRP6 expression is specifically upregulated in Ly6Chi inflammatory monocytes that infiltrate into the colon during dextran sulfate sodium (DSS)-induced inflammation.  Adoptive transfer of WT Ly6Chi inflammatory monocytes into Nlrp6-/- mice was sufficient to protect them from mortality, significantly reducing intestinal permeability and damage.   NLRP6-deficient inflammatory monocytes were specifically defective in TNFα production, which was important for reducing DSS-induced mortality and dependent on autocrine IL-18 signaling by inflammatory monocytes.  Our data reveal a previously unappreciated role for NLRP6 in inflammatory monocytes, which are recruited during intestinal injury to promote barrier function and limit bacteria-driven inflammation.  This study also highlights the importance of early cytokine responses, particularly NLRP6-dependent and IL-18-dependent TNFα production in preventing chronic dysregulated inflammation.

overall_design: Ly6Chi monocytes were sorted from lamina propria of WT or Nlrp6-/- mice at day 10 of AOM/2%DSS. RNA was extracted and hybridized to the mouse 2.1 ST array.

first: Grace

middle: Y

last: Chen

middle: S


title: Transcriptome expression profile of primary mouse embryonic fibroblasts (MEFs) from BAHD1+/+ (WT)  and BAHD1-/- (KO) mice

status: Public on Mar 15 2016

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

institute: INRAE - University PARIS SACLAY

summary: Comparisons of gene expression profiles of BAHD1-KO MEFs to those of wild-type MEFs (sampled at embryonic day E13.5).

overall_design: We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in mouse embryonic fibroblasts.

first: Guillaume

last: Soubigou

first: Marie

last: Wattenhofer-Donze

first: Tania

last: Sorg

first: Jean-Yves

last: Coppee


title: TCR signal strength controls thymic differentiation of discrete proinflammatory γδT cell subsetsistinct TCR signal strength requirements in the thymus

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: The murine thymus produces discrete γδ T cell subsets making either IFN-γ or IL-17, but the role of the TCR in this developmental process remains controversial. Here we generated a non-transgenic and polyclonal model of reduced TCR expression and signal strength selectively on γδ T cells. Mice haploinsufficient for both CD3γ and CD3δ (CD3DH) showed normal αβ thymocyte subsets but specific defects in γδ T cell development, namely impaired differentiation of IL-17-producing embryonic Vγ6+ (but not adult Vγ4+) γδ T cells and a marked depletion of IFN-γ-producing CD122+ NK1.1+ (Vγ1-biased) γδ T cells throughout life. As result, adult CD3DH mice showed defective peripheral IFN-γ responses and were resistant to experimental cerebral malaria. Thus, strong TCR signaling is required within specific developmental windows with distinct Vγ usage and differential cytokine production by effector γδ T cell subsets.

overall_design: We investigated the transcriptional changes associated with reduced TCRγδ signaling in the CD3DH model. Transcriptome-wide analysis of FACS-purified CD3DH or WT γδ thymocytes from E18 or 6-week was carried looking for patterns of gene expression during ontogeny

first: Miguel

last: Muñoz-Ruiz

first: Julie

middle: C

last: Ribot

middle: R

first: Natacha

last: Gonçalves-Sousa

last: Pamplona

first: Dann

middle: J

last: Pennington

first: José

last: Regueiro

first: Edgar

last: Fernandez-Malavé

first: Bruno

last: Silva-Santos


title: Altered gene expressions of mature dendritic cells in inducing T cell immune responses by the presence of bone marrow mesenchymal stem cell (BMSC) or periodontal ligament stem cell (PDLSC)

status: Public on Apr 28 2016

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: To examine the effect of BMSC or PDLSC on mature dendritic cells (mDCs) in inducing T cell immune responses, we utilized the microarray to discover altered gene expressions in mDCs by the presence of each stme cell.

overall_design: We prepared RNA samples from 2 sets of mDC only, 3 sets of both mDC-BM and mDC-PD, and analyized gene expressions via the microarray

first: Jeong-Ho

last: Yun

first: Changsik

last: Shin

first: Daehee

last: Hwang


title: Effect of deletion of carnitine palmitoyltransferase2 on interscapular BAT gene expression upon adrenergic stimulation in thermoneutral acclimatized mice

status: Public on Feb 04 2016

city: Baltimore

first: Michael

last: Wolfgang

summary:
Ambient temperature affects energy intake and expenditure to maintain homeostasis in a continuously fluctuating environment. Here, mice with an adipose-specific defect in fatty acid oxidation (Cpt2A-/-) were subjected to varying temperature to determine the role of adipose bioenergetics to environmental adaptation. Cpt2A-/- brown adipose tissue (BAT) failed to induce thermogenic genes such as Ucp1 and Pgc1α in response to adrenergic stimulation, which is exacerbated by increasing temperature. Thermoneutrality induced a mitochondrial DNA stress in Cpt2A-/- BAT that resulted in a loss of classical interscapular BAT, but did not affect body weight gain or glucose tolerance in response to a high-fat diet.
In this dataset, we include the expression data obtained from dissected mouse interscapular brown adipose tissue from mice acclimatized to thermoneutrality (30C) with and without beta3adrenergic stimulation with and without the deletion of carnitine palmitoyltransferase 2 (i.e., adipose unable to beta-oxidize long chain fatty acids in mitochondria).

overall_design: WildType and Cpt2A KnockOut mice were treated either with or without beta3adrenergic stimulation, thus four classes. Three biologic replicates were compared per class, thus twelve mice.

first: Jieun

last: Lee


title: Expression data from differentiating mouse embryonic stem cells wild type and lacking functional Pax7 gene

status: Public on Feb 26 2016

city: Warsaw

first: Areta

middle: Magda

last: Czerwinska

address: Krakowskie Przedmiescie 26/28

department: Faculty of Biology

institute: University of Warsaw

summary:
Myogenic differentiation relies on Pax7 function. We used embryonic stem cells lacking functional Pax7 to follow its role in derivation of skeletal myoblasts.
Microarray analysis allowed us to compare transcriptomes of undifferentiated and differentiating embryonic stem cells of two genotypes, i.e. Pax7+/+ and Pax7-/- at day 7 and 21 of culture.

overall_design: Undifferentiated mouse embryonic stem cells, embryiod bodies at day 7, and embryoid body outgrowths at day 21 of differentiation  were collected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Anna

last: Fogtman

first: Iwona

last: Grabowska

first: Karolina

last: Archacka

first: Joanna

last: Bem

first: Roksana

last: Iwanicka

first: Marta

last: Koblowska

first: Maria

middle: A

last: Ciemerych


title: Gene expression from splenic cells in response to VSV-M2 and ligands to RIG-I and MDA5

first: Ori

last: Staszewski

summary:
VSV-M2 is recognized by cytosolic RIG-I. Notably, 5'-triphosphate RNA molecules derived from either viral RNA or from the synthetically produced 3pRNA can also induce RIG-I activation. MDA5 stimulation is achieved using complexed poly(I:C), a synthetic analog of viral dsRNA.
To test whether the RIG-I and MDA5 ligands 3pRNA and poly(I:C) can be used in their complexed structures to decipher RNA virus-induced sickness behavior in vivo, we first compared the tissue-specific signaling pathways after systemic challenge with VSV-M2 and the RIG-I and MDA5 ligands, respectively. A whole-genome expression analysis using splenic cells was carried out using an Affymetrix Mouse Gene 2.1 ST Array.

overall_design: Adult wt mice were injected with either VSV-M2, 3pRNA or complexed poly(I:C); 18h (VSV) or 24h later spleens were removed for RNA extraction and hybridization on Affymetrix arrays.

first: Alena

last: Spiess

first: Nora

last: Hagemeyer

first: Thomas

last: Blank

first: Claudia

last: Detje


title: CaSR modulator in neuroblastoma model

first: Carmen

last: de Torres


title: Gene expression patterns associated with histopathology in toxic liver injury

status: Public on Feb 03 2016

city: Ft. Detrick

first: Christine

last: Baer

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

summary: Predicting liver injury after exposure to toxic industrial chemicals is complicated by the large number of potential environmental contaminants, mixtures, and exposure dose and route scenarios. Identifying indicators of end organ injury can complement exposure-based assays and improve predictive power. A multiplexed approach was used to experimentally evaluate a panel of 67 genes predicted to be fibrogenic by computationally mining DrugMatrix, a publicly available repository of gene microarray data. Five-day oral gavage studies in male Sprague-Dawley rats dosed with varying concentrations of three fibrogenic compounds (allyl alcohol, carbon tetrachloride, and 4,4’-methylenedianiline) and two non-fibrogenic compounds (bromobenzene and dexamethasone) were conducted. Fibrosis was definitively diagnosed by histopathology. Transcriptomics data matched the predictions made using the DrugMatrix data with greater than 90% accuracy. Microarray data were verified using a 67-plex panel Bioplex® assay, confirming that the 67-plex panel constituted a biomolecular signature of hepatic fibrosis (Figure). Necrosis and inflammatory infiltration were comorbid with fibrosis. Interaction analysis identified 24 genes specific for the fibrosis phenotype. The protein product of the gene most strongly correlated with the fibrosis phenotype (Pcolce) was dose-dependently elevated in plasma from animals administered fibrogenic chemicals (p<0.05). PCOLCE is a novel biomarker candidate of fibrotic injury. These results support the development of gene panels for liver injury and may suggest bridging biomarkers for molecular mediators linked to histopathology.

overall_design: To induce the pathophysiological effects of exposure to 5 toxicants, rats were dosed by oral gavage for 5 consecutive days (+ 10 minutes from the previous day's dose administration time) with either one of 5 toxicants or the vehicle control. Volumes were based on daily body weight of the animal. Twenty-four hours after the final dose administration, animals were euthanized and livers collected. Exposures for allyl alcohol, bromobenzene, and carbon tetrachloride each had 4 doses (low, mid, mid-high, high) and a vehicle control with an n=5 for a total of 25 animals per toxicant. For dexamethasone, only a high dose was performed with an n=5 for an additional 5 animals. A vehicle control was shared with 4,4’-methylenedianiline (MDA) since the exposure was concurrent with the dexamethasone exposure. For MDA, 3 doses (low, mid, high) were performed along with the shared vehicle control with an n=5 for an additional 20 animals. Liver tissue was analyzed from each animal for a total of 100 arrays. Four arrays did not meet QC criteria and were excluded from analysis. Therefore, only 96 were included and reported here: 22 allyl alcohol, 24 bromobenzene, 25 carbon tetrachloride, 5 dexamethasone, and 20 MDA.

first: Danielle

middle: L

last: Ippolito

middle: E

first: Matthew

last: Permenter

first: B

last: McDyre

first: William

last: Dennis

first: John

last: Lewis

first: Jonathan

last: Stallings


title: Transcriptomic signature of the CD24hiCD38hi transitional B cells associated with an immunoregulatory phenotype in renal transplant recipient.

status: Public on Feb 25 2016

city: Creteil

first: Caroline

last: Pilon

address: 51 avenue du Mal de Lattre de Tassigny

institute: INSERM U955 Eq21, Hopital Henri Mondor

summary: The role of B cells after transplant regarding allograft rejection or tolerance has become a topic of major interest. Recently, in renal transplant recipients, a B cell signature characterized by the overexpression of CD19+CD38hiCD24hi transitional B cells has been observed in operationally tolerant patients and in Belatacept treated patients with significant lower incidence of donor specific antibodies. The phenotypic and functional characterization of these transitional B cells is far to be exhaustive. We present the first transcriptomic and phenotypic analysis associated with this phenotype. Three populations were studied and compared: (i) transitional CD24hiCD38hi (ii) CD24+CD38- and (iii) CD24intCD38int populations.

overall_design: Peripheral blood mononuclear cells were isolated from 5 healthy donors and CD20+ B cells were isolated by magnetic beads. Three B cells populations were then sorted by flow cytometry: CD19+CD24hiCD38hi (test), CD19+CD24+CD38- (control 1) and CD19+CD24intCD38int (control 2)

first: Philippe

last: Grimbert


title: Genome-wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis

status: Public on May 18 2016

city: Hangzhou

first: Dong

last: Chen

address: 79# Qingchun Rd

institute: First Affiliated Hospital, Zhejiang University

summary: We performed a genome-wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8×60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs; The results were confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The differentially expressed lncRNAs and mRNAs were identified through fold-change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods.

overall_design: Twelve primary CRC samples were obtained from six patients with CRC and liver metastasis (Exp G) and six patients with CRC without metastasis (Ctrl G).

first: Weilin

last: Wang


title: Gene expression in a 3-dimensional human epidermal tissue culture model after water-filtered near-infrared irradiation

status: Public on Mar 19 2016

city: Matsumoto

first: Yohei

last: Tanaka

state: Nagano

department: Plastic Surgery

institute: Clinica Tanaka

summary: To clarify the effects of near-infrared radiation, we assessed DNA microarray after water-filtered  near-infrared (1100-1800 nm together with a water-filter that excludes wavelengths 1400-1500 nm) irradiation.

overall_design: We performed 5 and 10 rounds of near-infrared irradiation at 10 J ⁄cm2.

first: Jun

last: Nakayama


title: Pulmonary Carcinoids and Low-Grade Gastrointestinal Neuroendocrine Tumors Show Common MicroRNA Expression Profiles, Different from Adenocarcinomas and Small Cell Carcinomas

status: Public on Feb 01 2016

city: Tokyo

first: Toyoki

last: Yoshimoto

address: Minato-ku, Toranomon 2-2-2

institute: Toranomon Hospital

summary: Background: It is still uncertain whether carcinoids of the lung and gastrointestinal (GI) tract have a common origin or whether they are closer in origin to carcinomas of the same organs. MicroRNA (miRNA) expression may clarify their nature and origin.  Methods: First, to verify whether formalin-fixed paraffin-embedded (FFPE) samples retain the expression signature of the tissue, miRNA expression was compared between FFPE and frozen samples. Second, we selected surgically resected FFPE samples of pulmonary and GI carcinoids, as well as other types of tumors and normal tissues from each organ, and we compared the comprehensive expression patterns of miRNAs by microarray. These data were analyzed by hierarchical clustering and consensus clustering with non-negative matrix factorization (NMF).  Results: The miRNA expression profiles of FFPE and frozen samples correlated quite well. In the first hierarchical clustering, most of the carcinoids formed one major cluster with loose subpartitioning into each organ type, while the second major cluster mainly comprised adenocarcinomas and normal tissues. The NMF approach largely supported hierarchical clustering. In the additional cluster analysis comparing carcinoids to small-cell lung carcinomas (SCLCs), carcinoids formed a distinct cluster, while SCLCs grouped together with pulmonary adenocarcinomas and normal lung tissues in another major cluster. Furthermore, we found some miRNAs that exhibited significant expression in carcinoids.   Conclusion: Carcinoids had a characteristic pattern of miRNA expression, suggesting a common origin for pulmonary and GI carcinoids. The expression profiles were different in carcinoids and SCLCs, indicating distinct histogenesis of these neuroendocrine tumors.

overall_design: A total of 50 carcinoids, 9 SCLCs, 9 adenocarcinomas, 7 olfactory neuroblastomas and 2 schwannomas were enrolled in this study. The 50 carcinoids included 22 pulmonary carcinoids, and 28 NETs G1/G2 (7 gastric, 9 duodenal and 12 rectal tumors.) The adenocarcinomas included 3 pulmonary, 3 gastric and 3 rectal adenocarcinomas. Additionally, 15 normal (non-tumorous) tissues were taken for analysis from 6 pulmonary, 3 gastric, 3 duodenal and 3 rectal carcinoid cases.

first: Yuichi

last: Ishikawa


title: Transcriptome expression profile of placental tissue from BAHD1+/+ (WT)  and BAHD1-/- (KO) mice at embryonic day E18.5

first: Helene

last: Bierne

summary: Comparisons of placenta gene expression profiles of BAHD1-KO mice to those of wild-type littermate mice.

overall_design: We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in the placenta at embryonic day E18.5

first: Olivia

last: Wendling

first: Guillaume

last: Soubigou

first: Tania

last: Sorg

first: Jean-Yves

last: Coppee


title: DNA microarray analysis of Huh7 and JMJD5KO Huh7 cells.

status: Public on Jan 23 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To understand the roles of JMJD5 in liver cells, we performed DNA microarray analysis by using JMJD5KO Huh7 cells. We noticed that several transcriptional factors involved in differentiation to hepatocytes were down-regulated in JMJD5KO Huh7 cells compared to parent Huh7 cells..

overall_design: Gene expression analysis was performed by one-color experiments.

first: Takahisa

last: Kouwaki

first: Toru

last: Okamoto

first: Yoshiharu

last: Matsuura


title: Cells release subpopulations of exosomes with distinct molecular and functional properties

status: Public on Apr 30 2016

city: Oxford

first: Pieter

last: Vader

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

summary:
Cells release nano-sized membrane vesicles that are involved in intercellular communication by transferring biological information between cells. It is generally accepted that cells release at least three types of these extracellular vesicles (EVs): apoptotic bodies, microvesicles and exosomes. Whilst exosomes are assumed to be a homogenous population of EVs, they have a wide range of putative functions. Therefore, we hypothesized that cells release subpopulations of exosomes with distinct molecular compositions and functional properties.  Exosomes were isolated from conditioned medium by differential ultracentrifugation. Sucrose density gradient centrifugation of the resulting exosome pellet revealed the presence of two distinct subpopulations, one smaller, slow migrating population (HD-Exo), and one fast migrating, larger population (LD-Exo).
Interestingly, the exosome subpopulations were found to have differential effects on gene expression in recipient endothelial cells.   In conclusion, we demonstrate that cells release distinct subpopulations of exosomes with unique biophysical properties and molecular compositions that elicit differential effects on recipient cells. Our data supports the heterogeneous nature of exosomes. It also highlights the importance of better discrimination between subpopulations to allow more detailed studies on exosome biology and function, and assist in the development of exosome-based diagnostics and therapeutics.

overall_design: H5V cells incubated with PBS and two subpopulations of exosomes (LD-Exo and HD-Exo).

first: Eduard

last: Willms

first: Henrik

last: Johansson

first: Imre

last: Mäger

first: Yi

last: Lee

first: K

last: Blomberg

first: Mariam

last: Sadik

first: Amr

last: Alaarg

first: C

middle: I

last: Smith

first: Janne

last: Lehtiö

first: Samir

last: EL-Andaloussi

first: Matthew

last: Wood


title: Notch Signaling Plays an Instructive Role in Supporting Cell Development and is Critical for Supporting Cell Survival

first: Angelika

last: Doetzlhofer

address: 855 North Wolfe St.

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

summary: The sensory epithelium of the cochlea is a specialized structure responsible for the perception of sound. While much is understood about the development of the mechanosensory hair cells found within this epithelium, little is known about the development of the glial-like supporting cells. Here, we provide evidence that in addition to its well-characterized inhibitory function, canonical Notch signaling plays a positive, instructive role in the differentiation of supporting cells. Using γ-secretase inhibitor DAPT to acutely block canonical Notch signaling, we identified a cohort of Notch-regulated supporting cell-specific genes, with diverse functions in cell signaling, cell differentiation, neuronal innervation and synaptogenesis.

overall_design: RNA from cochlear epithelial cells was isolated from E15.5 cochlear explants after they have been cultured for 22 hours in the presence of gamma secretase inhibitor DAPT or vehicle control. A total of 6 samples was analyzed in three indepdent microarray experiments. For each microarray experiment there was one control sample and one DAPT treated sample.

first: Dean

last: Campbell


title: Comparison of gene expression in human sarcoma cell line SaOS-2 cells between differentiation and maintenance culture

status: Public on Feb 07 2016

first: Daisuke

last: Okuzaki

summary: We cultured human sarcoma cell line SaOS-2 with or without differentiation and compared gene expression patterns between both cultures by microarray.

overall_design: The experiments were either in triplicate or duplicate.

first: Makoto

last: Fujiwara

last: Okuzak

first: Yasuji

last: Kitabatake


title: Density dependent re-tuning of autoreactive T cells alleviates their pathogenicity in a lymphopenic environment

first: Nevil

middle: John

last: Singh

address: 685 W Baltimore Street

department: Microbiology & Immunology

institute: UMB

summary: In experimental or clinical contexts of lymphopenia, mechanisms that normally maintain peripheral tolerance are weakened, resulting in auto-immunity or graft rejection. We now show that the exaggerated density of self-reactive T cells that can be maintained in such environments is a severe impediment to their complete tolerization. Reducing the frequency of T cells allowed the cell-intrinsic tolerance to progress further and eliminate residual immunopathology, even in lymphopenic hosts without the contribution of regulatory T cells. This stems from the effectively stronger stimulation of the autoreactive T cells, after density reduction, allowing them to tune down their TCR proximal signaling to a greater extent. In addition, this deeper state of tolerance was also accompanied by the modulation of transcriptional and epigenetic machinery in the T cell, which prevented the tolerance from being perturbed by pharmacological activators. These data suggest that, similar to the immunogenic activation of T cells, cell intrinsic tolerance is also a progressive process that can be stabilized at multiple intermediate stages by environmental factors. Adapting tolerance protocols to allow this progression to proceed further can therefore be a viable strategy to successfully tolerize T cells, especially in lymphopenic settings.

overall_design: Eight 2R arrays and five 1R arrays were labelled with Cy3. A standard reference RNA derived from pooled mouse T cells was labeled with Cy5.


title: KRAS-induced transcription analysis in immortalized pancreatic cells

status: Public on Jan 19 2016

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We utilized non-transformed, human pancreatic ductal epithelial (HPDE) cells, previously engineered with the E6 and E7 proteins of the HPV16 virus to emulate loss of p53 and inactivation of the Rb pathway, respectively. Given the frequent activation of KRAS (>90% PDAC tumors) and its early role in pancreatic neoplasia, we sought to engineer HPDE cells containing KRASG12D to provide the appropriate context in which to screen for novel drivers that might represent KRAS effectors.

overall_design:
The KRAS-induced transcription analysis was conducted using RNAs extracted from HPDE cells transduced with either control, wild-type KRAS or KRASG12D(pInducer) with or without DOX (100ng/ml) for 72 h, followed by hybridization of labeled cDNA onto Agilent arrays (Agilent G3 Human GE 8x60K) by the Baylor College of Medicine Genome Profiling Core Facility.
multi-group comparison

first: Fengju

last: Chen

first: Ken

last: Scott


title: Expression data from rat tendon fibroblasts treated with PRP and PPP.

status: Public on Jan 12 2016

first: Christopher

last: Mendias

state: MI

address: BSRB 2017, 109 Zina Pitcher Pl

department: Orthopaedic Surgery

summary: Tendon is a hypocellular tissue that contains functional cable-like units of type I collagen responsible for the transmission of force from muscle to bone. In the setting of injury or disease, patients can develop chronic tendinopathies that are characterized by pain, loss of function and persistent inflammatory changes that are often difficult to treat. Platelet-rich plasma (PRP) has shown promise in the treatment of chronic tendinopathy, but little is known about the mechanisms by which PRP can improve tendon healing. PRP contains many different growth factors and cytokines, and since these proteins can both activate and inhibit various signaling pathways it has been challenging to determine precisely which signaling pathways and cellular responses are most important. Using state-of-the-art bioinformatics tools and genome wide-expression profiling, the purpose of this study was to determine the signaling pathways activated within cultured tendon fibroblasts in response to PRP treatment.

overall_design: Tendon fibroblasts were isolated from rat tail tendons and embedded in 3D type I collagen gels. Cells were treated with PRP or PPP for 24 hours, and total RNA was extracted for hybridization on Affymetrix arrays.

first: Kristoffer

middle: B

last: Sugg

first: Jonathan

middle: P

last: Gumucio

first: Joshua

last: Hudgens


title: Effects of Kielin/Chordin-like Protein (KCP) in Mouse Liver

status: Public on Jan 01 2016

first: Greg

last: Dressler

address: 109 Zina Pitcher Drive

summary:
Liver RNA was collected from three genotypes:  WT controls, KCP knockout (KCP-KO) mutants, and KCP-Transgenic (KCP-Tg) overexpressing mice.
Mice were fed either a normal diet (ND) or a high fat diet (HFD) for 4 weeks before liver RNA extraction.

overall_design: The differential gene expression patterns were noted between all genotypes and diets.

first: Abdul

last: Soofi


title: The effects of TGM1 Mutations in HEK293T and HaCaT cells

status: Public on Dec 31 2015

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Autosomal recessive congenital ichthyosis (ARCI) is a group of rare inherited skin disorders characterized by remarkable hyperkeratosis. Transglutaminase 1 (TGM1) mutations have been reported to be involved in four different phenotypes of ARCI, including lamellar ichthyosis (LI), non-bullous congenital ichthyosiform erythroderma (NBCIE), bathing suit ichthyosis (BSI), and self-improving collodion ichthyosis (SICI) according to the clinical presentation and histopathology. TGM1 has been found as a defective gene in a large amount of patients with LI and some patients with NBCIE, BSI and SICI. To further understand the effect of TGM1 mutations in epidermal cells development, we performed the transcriptome analysis of HEK293T and HaCaT cells transfected with TGM1 shRNA, TGM1 wild-type and mutant clones. The transcriptomic analysis revealed the effects of TGM1 on cell-cell interaction by suppressing genes involved in the gap junctions, tight junctions and desmosomes. These findings suggested that the TGM1 deficiency disturbed the balance of keratinocytes proliferation and differentiation processes and impaired the epithelial barrier function. The results provided the basis for further understanding on the etiology of ARCI.

overall_design: To explore the functional impacts on some of the TGM1mutations identified, we cloned and transfected the TGM1 wild type and mutant clones into HEK293T and HaCaT cells. R142C and R348X sequence mutations observed in ARCI (Autosomal recessive congenital ichthyosis) patients were generated. The shRNA targeting TGM1 and a scrambled negative control were obtained from Invitrogen (Carlsbad, CA). The293T and HaCaT cells were transfected with over-expression clones carry either wild-type or mutated TGM1sequence. Cells were harvested 48 hours post-transfection.

first: Yuqing

last: He

first: Kang

last: Zeng

first: Xin

last: Tian

first: Taek-Kyun

last: Kim

first: Xuemei

last: Li

first: Juanjuan

last: Lin

first: Zhihua

last: Wu

first: Xibao

last: Zhang


title: The lncRNA microarray analysis of 16HBE cell treated with PM2.5 samples in Guangzhou

status: Public on Mar 25 2016

city: Guangzhou

first: Jianjun

address: Xinzao Town, Panyu District

department: School of Public Health

institute: Guangzhou Medical University

summary: In order to assess the alteration of lncRNA expression in 16HBE cell treated with PM2.5 samples, we determined the lncRNA expression profiles in 16HBE cell treated with PBS (control group) and PM2.5 samples (low dose 125 μg/mL and high dose 500 μg/mL) using  lncRNA Microarray.

overall_design: 16HBE Cells were treated with PM2.5 suspension at concentration of 125 μg/mL and 500 μg/mL, and PBS was used in the control group for 48 h. Then, total RNAs were extracted  for lncRNA chip preparation and analysis.

first: Yiqin

last: Xu

first: Yiguo

last: Jiang


title: LncRNA in pediatric AML vs normal bone marrow mononuclear cells

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

summary: Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and the second most common form of leukemia in children. Multiple lncRNAs participate in normal and may be implicated in malignant hematopoiesis associated with blood cell cancers, such as leukemia. Currently, the expression profile of lncRNAs in pediatric AML is unclear. In this study, we evaluated the lncRNA expression profile in the tissue of three pediatric AML patients with lncRNA microarray techniques. In order to gain insight into the function of targets of lncRNAs, GO term and KEGG pathway annotation were applied to the target gene pool. qPCR was performed to evaluate the expression patterns of dys-regulated lncRNAs.

overall_design: Bone marrow specimens were obtained at the time of diagnosis during routine clinical assessment of 3 pediatric patients with AML, who presented at the Department of Hematology and Oncology, Children's Hospital of Soochow University between 2000 and 2011. Additionally, bone marrow samples from 3 healthy donors were analyzed as controls. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.  Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.  Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

first: Lan

last: Cao


title: Molecular effects of different TRPV3 Mutations

summary: To understand the impact of dysfunctional TRPV3 on keratinocyte proliferation and differentiation, we conducted transcriptomic analysis on cells that express cloned different TRPV3 mutations identified in focal palmoplantar keratoderma (FPPK) patients and identified a number of perturbed pathways associated with epidermal cells construction and development. We also analyzed the molecular changes of skin biopsy samples from patients. Our data suggests that TRPV3 dysfunction inhibits keratinocyte differentiation, actives apoptosis pathway resulted in cell death, and disturbs the balance between keratinocyte proliferation and differentiation processes in the skin.

overall_design: To explore the functional impact of the different TRPV3 mutations on cells, we cloned the wild type and mutant TRPV3 clones into expression vector. The wild-type human TRPV3 gene was amplified from cDNA made from a mixture of human tissue total RNA and cloned into pcDNA3.1 (Life Technologies, Carlsbad, CA). The accuracy of the cloned sequence was checked with Sanger sequencing. Quick Change II XL site-directed mutagenesis kit (Agilent, Santa Clara, CA) was used to introduce sequence changes corresponding to mutations observed in patients. The HEK293T cells were transfected using Lipofectamine 2000 (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions. Cells were also transfected with the same plasmid without insert as control.

first: Yumei

last: Liu

first: Ting

last: Chen