title: Cell type-specific expression atlas of the early Arabidopsis thaliana embryo

summary: The establishement of the first plant tissues occurs during embryo development. Indeed, cell types that will form the Arabidopsis root stem cell niche are first specified during 16-cell (16C), early globular (EG) and late globular (LG) stage of embryonic development. While some regulatory factors are known, we do not yet understand the genetic networks underlying the specification of these cell types. One main reason for this is the difficulties in adapting genome-wide approaches to the cellular level. Here, we have adapted such an approach (INTACT) to generate microarray-based cell type-specific transcriptomic profiles at 16C to LG stage for use in determining the role of the transcriptome in cell specification and differentiation during root stem cell niche formation.

overall_design: We manually pollinated flowers and isolated cell type-specific nuclei from embryos using the INTACT method and cell type-specific markers at 16-cell stage (72h after pollination), EG  stage (81h after pollination) and LG (100h after pollination) of development. Following RNA isolation, microarray-based transcriptomic profiling was performed on 3-4 pooled biological replicates each.


title: RF003-V1: The expression of ERAP2 and LST1 distinguishes between Glucocorticoid-Responders and Non-Responders in Rheumatoid Arthritis

status: Public on Nov 11 2017

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary:
Objective: Glucocorticoids (GC) have been a cornerstone of Rheumatoid arthritis (RA)-therapy for the last decades. However, about a third of RA-patients do not respond adequately. As monocytes and T-cells play an important role in RA-pathogenesis, the differential gene expression of these cells before pulse therapy with methylprednisolone was evaluated in order to find predictors for clinical response to GC.

Methods: CD14-positive and CD4-positive cells were isolated by MACS sorting from five GC-Responders meeting the European League against Rheumatism (EULAR) response criteria and five Non-Responders. The clinical response was measured by disease activity score (DAS28) at the end of pulse therapy (3x 1000mg Methylprednisolone) at day 5. Cellular RNA was hybridized to Agilent 4x44K microarray chips and differentially expressed genes were calculated by MAANOVA. False discovery rate (FDR) was used as multiple testing correction. Selected genes were verified by quantitative real-time PCR (qPCR).

Results: Eight genes were differentially regulated in CD14-cells and 4 genes in CD4-T-cells of GC-Responders compared to Non-Responders. Up-regulation of ERAP2 in monocytes and CD4-cells and LST1 and FAM26F in CD4-Tcells of GC-Responders was verified by qPCR and correlated with DAS28 at day 5 and (for LST1 and FAM26F) with smoking.

Conclusion:  As ERAP2 and LST1 are implicated in autoimmune disease, their increased expression in GC-Responders before GC-therapy may constitute not only a new tool for prediction of the clinical response to GC in RA, but also warrants further investigation to elucidate their role in the inflammatory process of RA.

overall_design: PBMC from patients were obtained before therapy by centrifugation of heparinized blood over Ficoll-Hypaque (Amersham Biosciences). CD14+ monocytes and CD4+ T-cells were isolated by positive (CD14-cells) or negative (CD4-cells) selection by AutoMACS (Miltenyi Biotec, Auburn, CA) and the respective isolation kits for CD14- or CD4- isolation (Miltenyi Biotec). Purity of the viable population assessed by flow cytometry was generally >90%.  RNA was isolated using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands).   All patient sample cRNAs were labeled with cy5,  and co-hybridized with reference cRNA, labeled with cy3 on Human Whole Genome Gene Expression Microarrays v1. Differences between responders (RF-iv-r-) and non-responders (RF-iv-nr-) were analyzed.

first: Ruth

middle: D

last: Fritsch-Stork

first: Sandra

last: Cardoso

first: Jasper

last: Broen

middle: G

last: Koerkamp

first: Frank

last: Holstege

first: Arno

last: Concepcion

first: Alexander

last: Ploner

first: Barbara

last: Giovannone

first: Floris

middle: P

last: Lafeber

first: Johannes

middle: W

last: Bijlsma


title: Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo

status: Public on Nov 06 2017

city: Wageningen

first: Joakim

last: Palovaara

state: Gelderland

address: Stippeneng 4

department: Biochemistry

institute: Wageningen Univeristy

summary: Due to its inaccessibility, transgenic methods have been recently developed to isolate tissue- or cell-specific nuclear RNA from the Arabidopsis embryo for transcriptomic profiling. While these approaches have made the it possible to conduct transcriptomic studies at the cellular level, only nuclear and not whole celluar RNA can be isolated. The question thus arrises if nuclear RNA is a reasonable proxy for whole cellular mRNA. To answer this, microarray-based transcriptomic profiling was used to determine genome-wide expression in nuclei and cells isolated from whole 16-cell stage Arabidopsis embryos.

overall_design: We manually pollinated flowers and either isolated whole embryos (manually using an micromanipulator; cEMB) or the nuclei from embryos (using the INTACT method and a whole embryo marker; nEMB) at 16-cell stage (16C) of development (72h after pollination). Following RNA isolation, microarray-based transcriptomic profiling was performed on 3 biological replicates each.


title: Expression data from CTCL patient skin lesion [Agilent]

status: Public on Nov 08 2017

city: Shanghai

first: Jie

last: Zheng

address: 197 Ruijin Er Rd

department: Dermatology

country: China

institute: Ruijin Hospital

summary:
Cutaneous T cell lymphoma (CTCL) can have clinical and histological features resembling benign inflammatory dermatosis (BID) and can be difficult to diagnose especially at the early stage of CTCL.
We used microarrays to detail the global alteration of miRNA transcriptome and generate a diagnosis and prognosis signature.

overall_design: Patient skin biopsy samples were collected for RNA extraction and hybridization on Agilent microarrays. We pooled 3-8 samples per group into one Agilent sample.

first: Xiaoyan

last: Shen


title: Gene expression data in aortic tissue from rats with experimental preeclampsia, healthy pregnancy and non pregnant rats

status: Public on Nov 01 2017

city: Groningen

first: Marijke

last: Faas

address: Hanzeplein 1

institute: University Medical Center Groningen

summary:
Normal pregnancy requires adaptations of the maternal vasculature. During preeclampsia these adjustments are not well established, resulting in maternal hypertension and proteinuria. The effects of preeclampsia on the maternal vasculature are not yet fully understood. We aimed to identify gene expression differences in the aorta between non pregnant, healthy pregnant, and experimental preeclamptic rats using a genome wide approach.
Whole aortic tissue was isolated from rats with low-dose LPS-induced preeclampsia, healthy pregnant and non-pregnant rats. Gene expression was measured by a whole genome microarray.

overall_design: 3 groups were compared. Preeclamptic animals (n=5), healthy pregnant animals (n=5), and non pregnant animals (n=4)

first: Simone

middle: V

last: Lip

first: Anne

middle: M

last: van der Graaf

first: Marjon

last: Wiegman

first: Sicco

middle: A

last: Scherjon

first: Mark

last: Boekschoten

first: Torsten

last: Plösch


title: Optogenetic neural stem cells microarray

status: Public on Nov 04 2017

city: Singapore

first: Daniel

middle: Boon Loong

last: Teh

address: 28 Medical Drive, #05-COR

country: Singapore

institute: National University of Singapore

summary:
We elucidate the transcriptome effects of optogenetics on developing neural stem cells population.
The application of optogenetics in neural stem cell (NSC), allow photo-modulation of NSC in an activity-dependent manner. This provided spatio-temporal tool for studying activity dependent neurogenesis, including the potential of regulating the differentiation and maturation process of transplanted NSC. Currently, this is mainly driven by virally transfected of Channelrhodopsin-2 (ChR2) gene, which also requires high irradiance and complex in vitro stimulation systems. Additionally, despite the extensive application of optogenetics in neuroscience, the question of what transcriptome changes does optogenetic stimulation induced in developing NSCs have not been elucidated yet. To address these questions, we established a NSC line, expressing high light-sensitivity step-function opsin (SFO) variant of the chimeric channelrhodopsin, ChRFR(C167A) (~40x higher than ChR2), via the non-viral piggyBac transposon system. We set up a simple low-irradiance optogenetics stimulation-incubation system, which sufficiently induced depolarization in differentiating NSCs. We significantly enhance neurogenesis with low power optogenetic stimulation by 3 folds. Through microarray analysis, we have identified the genes and signaling pathways in axonal remodeling, synaptic plasticity and microenvironment modulation from optogenetic stimulation. Our results elucidate the transcriptome effects of optogenetics and the ability to drive neurogenesis with low irradiance optogenetics.

overall_design: Two groups were compared between each other, control (non-stimulated) and stimulated group. Each group contains three replicates.

middle: B


title: A distance-related model identified PDCD6IP as a local host protective factor in colorectal cancer

city: Beijing

first: Honglin

last: Guo

address: Panjiayuan Nanli 17#, Chaoyang Distinct

department: Department of Etiology and Carcinogenesis

institute: National Cancer Institute/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College

summary: Tumor-host interactions play an important role in cancer initiation and progression. To investigate changes in local host factors associated with proximity to the tumor, the global gene expression profiles of cancer tissues and histologically normal tissues taken at various distances from the tumor (1 cm, 5 cm and the proximal end of the resected sample) from 32 rectal cancer patients were used to establish a distance-related model. Two distance-related expression patterns were considered, one with a trend toward gradual down-regulation and one with a trend toward gradual up-regulation as the distance from the tumor decreased. Gene Ontology (GO) analysis highlighted 7 genes enriched in the endosomal sorting complex required for transport (ESCRT) machinery in the group with a pattern of gradual down-regulation. Survival analysis of patients in the TCGA colorectal cancer (CRC) dataset revealed that higher expression of two of these genes (PDCD6IP and CHMP2B) was associated with a better prognosis (p = 0.021, p = 0.031). A tissue array confirmed that patients with up-regulated PDCD6IP expression in cancer tissue compared with normal tissue had better prognoses (p = 0.04). In conclusion, we built a distance-related model to study the local tumor-host interactions and identified PDCD6IP as a local host protective factor in CRC.

overall_design: The samples were collected from 32 rectal cancer patients who underwent surgical resection at the Cancer Institute and Hospital, Chinese Academy of Medical Sciences from 2014 to 2015. We collected rectal cancer tissue samples (T) and histologically normal tissue samples located at varying distances from the tumors, including 1 cm away from the tumor (N1), 5 cm away from the tumor (N5) and as far as possible away from the tumor (N15).

first: Weigen

last: Zeng


title: IDENTIFICATION OF ADULT ZEBRAFISH CONE PHOTORECEPTOR-ENRICHED GENES

status: Public on Oct 31 2017

city: Dublin

first: Breandan

last: Kennedy

address: Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute, University College Dublin

summary:
Cone photoreceptors are specialised sensory retinal neurons responsible for photopic vision, colour perception and visual acuity. Retinal degenerative diseases are a heterogeneous group of eye diseases in which the most severe vision loss typically arises from cone photoreceptor dysfunction or degeneration. Establishing a method to purify cone photoreceptors from retinal tissue can accelerate the identification of key molecular determinants that underlie cone photoreceptor development, survival and function. The work herein describes a new method to purify enhanced green fluorescent protein (EGFP)-labelled cone photoreceptors from adult retina of Tg(3.2TαCP:EGFP) zebrafish. Electropherograms confirmed downstream isolation of high-quality RNA with RNA integrity number (RIN) >7.6 and RNA concentration >5.7 ng/µl obtained from both populations. Reverse Transcriptase-PCR (RT-PCR) confirmed that the EGFP-positive cell populations express known genetic markers of cone photoreceptors that were not expressed in the EGFP-negative cell population. This work is an important step towards the identification of cone photoreceptor-enriched genes, protein and signalling networks responsible for their development, survival and function. In addition, this advancement facilitates the identification of novel candidate genes for inherited human blindness.
In order to analyse and sort samples by flow cytometry, values for FSC and SSC were displayed in a logarithmic scale, as this is normally the default starting display. This allowed for the identification of different sub-populations of cells present in the retina, which were mixed with unwanted cell debris and cell fragments.  Since there were multiple cell populations, different levels of auto-fluorescence were thus successfully detected. It was therefore important to change the strategy and display side scatter and fluorescence characteristics of control and EGFP samples, which ultimately allowed the identification of the extremely well-defined population of EGFP-cone photoreceptors. This improved sorting process minimised RNA degradation. The purified EGFP+ cone photoreceptors represent ~5% of the original dissociated population, which is consistent with humans, wherein the total number of cones (6 million) in the retina is approximately 20 times the one of rods (120 million) (Williamson and Cummins 1983). This work allows high-quality RNA to be obtained from sorted-adult cone photoreceptors. RNA integrity is assessed via 28S and 18S rRNA (Imbeaud et al 2005), and our electropherogram results demonstrate production of high-quality RNA with two clearly visible ribosomal peaks (28S and 18S) from EGFP-sorted cones. In addition, the RNA Integrity Number (RIN), an algorithm for assigning integrity values to RNA based on 28S to 18S rRNA ratios (Sambrook et al 1989; Imbeaud et al 2005; Schroeder et al 2006), had a value of 7.6, higher than the minimum-required 7.0. RNA yields of 5.7 ng/µl were relatively high  and sufficient for downstream profiling. RT-PCR confirmed expression of the cone specific gene gnat2, and promoter fragment TαC, but not the retinal pigment epithelium specific gene rpe65 in flow cytometry-sorted GFP-positive photoreceptors (GFP+ cells). rpe65 was neither present in flow cytometry-sorted GFP-negative cones (GFP- cells) as this gene is only expressed in the retinal pigment epithelium (RPE). This study therefore permits the identification of cone photoreceptor-enriched genes, protein and signalling networks responsible for their development, survival and function. In addition, this advancement facilitates the identification of novel candidate genes for inherited human blindness.

overall_design:
Retina Dissection
Adult zebrafish were euthanised in 2 mg/ml of Benzocaine for approximately 10 seconds. Eyes were enucleated with sterilised forceps and kept in ice-cold DEPC-PBS. The optic nerve was used to hold down the eye while the cornea was perforated using a fine Tungsten needle. Diamond jeweller’s needles were used to peel off corneal and scleral tissue. The neural retina was dissected free of retinal pigment epithelium (RPE) and the lens was removed and kept in cold DEPC-PBS.

Cell Dissociation
30 retinae were collected into 2 sterile Eppendorf tubes. Chemical retinal dissociation was initiated by the addition of 0.05% Trypsin diluted in DEPC-PBS. Suspensions were then mechanically triturated with a P-200 followed by a 0.8 x 40 mm surgical needle and a 0.5 x 16 mm needle. Trypsin inhibitor (1 mg/ml) was then added and suspensions were centrifuged at 1200 rpm for 5 minutes. Dissociated retinae were filtered using a 50 μm CellTrics®Sterile Filters to remove aggregates and non-dissociated tissue.  Dissociated retinae were incubated at 4C for 5 minutes before cells were centrifuged at 1400 rpm for 6 minutes. Cell number was counted using the Trypan Blue exclusion assay (Sigma) and haemocytometer.

Flow Cytometry Analysis
Flow cytometry was performed with a Beckman Coulter Cyan ADP with Summit Software or BD Accuri C6 with CFlow Plus Software. Cell sorting utilised a BD FACSAria with a 70. In order to obtain an optimised cell sorter performance the BDAccudrop (a set of QC beads) was used prior to sample sorting to ensure that the maximum amount of target cells  were correctly collected. This set of QC beads is normally used in the cell sorting process in order to calculate the drop formation and thus ensure that cells being sorted are actually “in the sorted drop”. The BDAccudrop therefore performs the important function to check that no other cells contaminates the “target drop”. EGFP excitation used 488 nm lasers and emission was collected with a 530/30 (BD Accuri C6 and BD FACSAria cell sorter) or 530/40 nm (BC Cyan ADP) band pass filters. Cell sorting and analysis was performed in samples with freshly made DEPC-PBS. 250 µl of cold DEPC-PBS was placed in collection Eppendorf tubes to minimise mechanical cell damage during sorting. For better identification of target cells from tissue, logarithmic scales were used for FSC and SSC. To remove non-cellular events (e.g. debris, air bubbles or electrical noise) which could interfere with analytical processes, an electronic threshold was applied on the FSC detector, to limit the acquisition of events by the flow cytometer so that only signals with an intensity greater than or equal to the threshold channel value were appropriately processed. The electrical pulse of aggregated events have a scatter signal with bigger area compared to single events (singlets), as well as a different area/width ratio, which allowed the removal of these aggregated events by generating regions. As shown in Figure 2, two regions  named “Singlet 1” and “Singlet 2” were drawn around the single events permitting the exclusion of aggregated events from the analysis and further sorting. The low-frequency EGFP cells were identified using a bivariate histogram of EGFP fluorescence versus SSC. Non-transgenic wildtype samples helped identify background autofluorescence levels. The gating strategy was based on EGFP fluorescence intensity. Scatter values allowed the identification and sorting of single EGFP events by flow cytometry, which corresponds to cone photoreceptors.

RNA Isolation and Analysis
RNA was isolated with the RNeasy Micro Kit (Qiagen) protocol (Mack et al 2007) in order to increase the final RNA concentration; its main steps are described below. Sorted-cells were pelleted for 2 minutes at 14,000 rpm, then homogenized with 350 μl Buffer RLT + 3.5 μl β-Mercaptoethanol using a 25-gauge needle. Lysate placed into QIAshredder spin columns was centrifuged for 2 minutes at 14,000 rpm and flow-through was stored at -80 C.  Flow-through from 3 replicate experiments was pooled to increase RNA yield. 350 μl of 70% ethanol was added. Samples were transferred to RNeasy MinElute spin columns, centrifuged for 15 seconds at 10,000 rpm and the flow-through discarded. Wash and elution steps were performed according to the manufacturer’s instructions  RNA was quantified with an ND-1000 Spectrophotometer (Nano-Drop Technologies). RNA quality was evaluated with the Agilent 2100 Bioanalyzer (Pico-Assay).

Reverse Transcriptase-PCR
A two-step reverse transcription was performed on 1 μg total RNA with a Reverse Transcriptase cDNA sysnthesis system, SuperScript III® VILOTM cDNA Synthesis Kit (Invitrogen) at 50°C, after priming with random hexamers. cDNA was used in standard PCR reactions with 1 μl cDNA per 25 μl PCR reaction, in standard PCR conditions, with extension times adjusted to 1 minute per kilobase of target amplicon. Primers for β-actin, TαC (3.2-kb promoter fragment of the zebrafish cone transducin alpha subunit), gnat2 (guanine nucleotide-binding protein G protein) and rpe65 (retinal pigment epithelium-specific protein 65 kDa) were designed complementary to Expressed Sequence Tags (ESTs) identified after BLAST analysis of EST databases.

The Affymetrix GeneChip® Zebrafish Genome Array was hybridized and processed using the standard Affymetrix protocol.

first: Antonino

last: Glaviano

first: Alfonso

last: Blanco

first: Sarah

last: McLoughlin

first: Maria

middle: L

last: Cederlund

first: Andrew

last: Smith

first: Theresa

last: Heffernan

first: Beata

last: Sapetto-Rebow

first: Yolanda

last: Alvarez

first: Jun

last: Yin

first: Breandán

middle: N


title: MyoD and FoxO3 mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation (Foxo3 ChIP-seq)

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation.

overall_design: Foxo3 ChIP-seq experiments performed in myoblast and myotube.

first: Huating

last: Wang

first: Hao

last: Sun

first: Ping

last: Hu

first: Xianlu

last: Peng

first: Karl

middle: K

last: So

first: Liangqiang

last: He

first: Yu

last: Zhao


title: Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and a pSCL4- S. clavuligerus mutant

status: Public on Oct 25 2017

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

country: Spain

institute: University of León

summary:
The objective is to analyze the differential expression between the wild strain and a pSCL4- S. clavuligerus mutant
Experiment type  Expression profiling by array

overall_design: Nine experimental conditions were assayed, two strains (S. clavuligerus ATCC 27064 and S. clavuligerus pSCL4-), in three and six culture times, respectively (12h, 36h, 70.5h for S. clavuligerus ATCC 27064; and 12h, 22.5h, 36h, 46.5h, 60h, 70.5h for S. clavuligerus pSCL4-). Two biological replicates for each condition.

first: R

last: Álvarez-Álvarez

first: Y

last: Martínez-Burgo

first: A

last: Rodríguez-Garcia

first: P

last: Liras


title: Massive and reproducible production of liver buds entirely from human pluripotent stem cells

status: Public on Nov 03 2017

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

summary: Organoid technology provides a revolutionary paradigm towards therapy, yet to be applied in humans mainly because of the reproducibility and scalability challenges. Here, we overcome these limitations by evolving scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC). By conducting massive ‘reverse’ screen experiments, we identified effective triple progenitor populations for generating liver buds in a highly reproducible manner: hepatic endoderm, endothelial and septum mesenchyme progenitors. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass-producing homogenous and miniaturized liver buds on a clinically relevant large scale (>108-cell scale). Vascularized and functional liver tissues generated entirely from iPSC significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacture platform for multi-cellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations.

overall_design: Transcriptome profiling of iPSC derived liver buds (iPSC-LB), progenitor populations for generating liver buds (iPSC-tHE/iPSC-EC/iPSC-MC) and human liver tissue of various developmental stages.

first: Takanori

last: Takebe

first: Masaru

last: Koido

first: Hideki

last: Taniguchi


title: Study gene expression specifically regulated by intrinsically active HOG1

status: Public on Nov 30 2017

city: SINGAPORE

first: CHEN

last: BAI

state: SINGPAORE

address: 1 CREATE WAY, INNOVATION WAY, 03-09, NUS-HUJ Cellular & Molecular Mechanisms of Inflammation Programme

department: MICROBIOLOGY

institute: NATIONAL UNIVERSITY OF SINGAPORE

summary: To monitor changes in the transcriptome  following activation of Hog1 per se, we used a previously established inducible expression system of intrinsically active Hog1 proteins

overall_design: the genes encoding HOG1WT, HOG1D170A and HOG1D170A+F318L, cloned downstream of the MET3 promoter, were introduced into hog1∆ cells . JBY13 cells harboring an ‘empty’ plasmid served as a control. The MET3 promoter is shut off when the growth media contains methionine, and is rapidly induced when methionine is removed.

first: B

last: Chen


title: Uncovering the mechanisms of phosphorus recycling and lipid class remodeling under P limitation by integration of transcriptomics and lipidomics data of Nannochloropsis oceanica.

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: In the present study the effect of phosphorus (P) limitation was investigated in the microalgae Nannochloropsis oceanica. Algal cultures were analysed for transcriptomic and lipidomic changes during P-limited growth, with sample time points: 24h, 48h, 53h, 58h and 70h. The transcriptome data identified unique P acquiring genes and the results were also supported by corresponding changes in the lipidome dataset, which showed a lipid class shift from phospholipids to phosphorus-free lipids under P-limitation. During the exponential growth phase a gradual 6-fold reduction of the cellular P level induced RNA transcripts encoding proteins acquiring P from inorganic and organic sources. For this process 6 novel purple acid phosphatases and 5 unique Pi transporters were identified. Additionally, increased gene expression of 2 triose-phosphate transporters (TPTs) indicated the importance of the carbon-to-phosphorus balance for the plastidial anabolic processes. Phospholipid degradation was shown to be an early response to P limitation, by overexpression of sets of 2 novel glycerophosphoryl diester phosphodiesterases (GDPDs), and 3 patatin-like phospholipases of type A. To compensate for phospholipid degradation, the transcriptome and lipidome level showed increased synthesis of sulfoquinovosyl diacylglycerol (SQDG), and diacylglyceroltrimethylhomoserine (DGTS). Phosphorus limitation triggered the lipid class shift in both the exponential growth phase and the triacylglycerol (TAG) accumulation period to release P and increase the organic C:P ratio.

overall_design: Axenic pre-cultures of Nannochloropsis oceanica CCMP1779 were grown in f/2 medium without silica in three 2 L Nalgene optically clear flasks (Thermo Fisher Nalgene®) under constant light (350 µmoL photons m-2 s-1), at 23°C. The Nalgene optically clear flasks were aerated with sterile-filtered air. The pre-cultures were grown to the exponential growth phase (OD750nm= 0.40, ~8*106 cells / mL), mixed, harvested, and washed with sterile seawater by centrifugation (4,700xg, 20 min). The experimental cultures were inoculated to an OD750nm of 0.06 (~2.5*106 cells / mL) in either f/2 medium without silica (36.38 μM PO43-, +P cells) or f/2 medium without silica with a reduced phosphate concentration (2.79 μM PO43-, -P cells). Three biological replicates of the algal cultures were established for each of the mentioned growth conditions. Samples of phosphate depleted cells were harvested at 24h, 48h, 54h, 58h and 72h, while samples from phosphate replete cultures were harvested after 24h.

first: Alice

last: Mühlroth

first: Aimen

middle: E

last: Assimi

first: Juliette

last: Jouhet

first: Olav

last: Vadstein

first: Eric

last: Maréchal

first: Martin

middle: F

last: Hohmann-Marriott

first: Atle

last: Bones

first: Torfinn

last: Sparstad


title: Candida albicans_NSC319726 treated_vs._control transcriptome data

city: Washington

first: Dongmei

last: Li

state: DC

address: 3900 Reservoir Rd Med dent SE318

department: Microbiology

country: USA

summary: We investigated the antifungal mechanism of action (MOA) of compound NSC319726 against C. albicans SC5314. We used transcriptome analysis of wild type C. albicans treated or not with compound. Exponentially growing cells were treated for 60 min with 4 μg/ml of NSC319726.

overall_design: Exponentially growing cells were treated for 60 min with 4 μg/ml of NSC319726. The total RNAs were extracted from treated and control cells, then used to synthesize cDNA for microarray assays with Agilent DesignID 037557 that contains 6101 genes in duplicate.

first: Nuo

last: Sun

first: Richard

last: Calderone


title: Introduction of the TERT and BMI1 Genes into Murine Dermal Papilla Cells Ameliorates Hair Inductive Activity

status: Public on Dec 06 2017

city: Tokyo

first: Masahiro

last: Kiso

address: 1-21-1 Toyama Shinjuku-ku

department: Regenerative Medicine, Research Institute

institute: National Center for Global Health and Medicine

summary: Dermal papilla cells (DPCs) are located at the bottom of hair follicles and play important roles on hair induction by interacting with epidermal cells. DPCs are promising cell sources for hair regeneration therapy for alopecia patients. However, freshly isolated DPCs rapidly lose their hair inductive activity and proliferative potential under culture conditions. We examined the effects of telomere reverse transcriptase (TERT) and B-cell-specific Moloney murine leukemia virus insertion region 1 (BMI1) on extending the life span of murine DPCs as well as on hair inductive activity.TERT and BMI1 genes were introduced into murine DPCs using lentivirus vectors. Hair inductive activity of transfected DPCs (t-DPCs) was determined by in vivo chamber assay in nude mice. Transcripts between intact dermal papillae (DPs) and cultured DPCs were compared by microarray analysis.

overall_design: To investigate the hair follicle-related gene expression, transcripts between intact DPs and DPCs at several culture stages [wild-DPC (wP0 and wP5) and t-DPC transfected  (tP18)] were compared.

first: Hitoshi

last: Okochi


title: Altered microRNA expression in sciatic nerve following injury in rat model (0d-14d)

city: Nantong

first: Lili

last: Zhao

address: 19 Qixiu

institute: Nantong university

summary: We used microarrays to distinguish the miRNA expression differences among different time points in sciatic nerve after injury.

overall_design: We generated proximal sciatic nerve (SN) tissues (0.5cm) at 0d, 1d, 4d, 7d and 14d after sciatic nerve resection.

first: Yu

last: Bin

first: Xiao

middle: S

last: Gu


title: The histone variant H2A.Z promotes initiation of meiotic recombination (expression)

status: Public on Oct 24 2017

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

institute: Kazusa DNA Research Institute

summary: Meiotic homologous recombination is a critical DNA-templated event for sexually-reproducing organisms. It is initiated by a programmed formation of DNA double strand breaks (DSBs), mainly formed at recombination hotspots, and is, like all other DNA-related processes, under great influence of chromatin structure. For example, local chromatin around hotspots directly impacts DSB formation. In addition, DSB is proposed to occur in a higher-order chromatin architecture termed “axis-loop”, in which many loops protrude from proteinaceous axis. Despite many recent insightful studies, still much remains unknown about how meiotic DSBs are generated in chromatin structure. Here, we show that the highly conserved histone H2A variant H2A.Z promotes meiotic DSB formation in fission yeast. Subsequent investigation revealed that H2A.Z is neither enriched around hotspots nor axis sites, and that transcript levels of DSB-promoting factors were maintained in the absence of H2A.Z. Instead, we found that H2A.Z facilitates chromatin binding of various proteins required for DSB formation. Strikingly, artificial tethering of one of such proteins, Rec10, to chromatin partially restored DSB reduction in H2A.Z-lacking cells. Based on these, we conclude that fission yeast H2A.Z promotes initiation of meiotic recombination partly through delivering DSB-related proteins onto chromatin.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Meiosis was induced in h+/h- diploid cells by nitrogen withdrawal and mRNA was purified and analyzed from wild-type and pht1Δ diploid cells 1.5 and 3 hours after the induction.

first: Shintaro

last: Yamada

first: Da-Qiao

last: Ding

first: Yurika

last: Fujita

first: Yasushi

last: Hiraoka

first: Hiroshi

last: Murakami

first: Kunihiro

last: Ohta

first: Takatomi


title: Application of the TGx-28.65 genomic biomarker to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human cells

status: Public on Oct 16 2017

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

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

overall_design: Refer to individual Series


title: Transcriptome analysis of plasmid-induced genes sheds light on the role of type I IFN  as adjuvant in DNA vaccine against infectious salmon anemia virus

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

summary: A previous study showed that a plasmid expressing IFNa (pIFNa) strongly enhanced protection and antibody production of a DNA vaccine against infectious salmon anemia virus (ISAV) in Atlantic salmon. The vaccine consisted of a plasmid (pHE) expressing the virus hemagglutinin-esterase as an antigen.  To increase the understanding of the adjuvant effect of pIFNa, here compared transcriptome responses in salmon muscle at the injection site at week 1 and 2 after injection of pIFNa, pHE, plasmid control (pcDNA3.3) and PBS,respectively. A major was that both the control plasmid pcDNA3.3 and pHE caused responses similar to pIFNa, but at lower magnitude. Plasmid DNA may thus by itself have adjuvant activity as observed in mammalian models. Notably, pHE had a lower effect on many immune genes including ISGs and chemokines than pcDNA3.3, which suggested an inhibitory effect of the viral protein

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Fish was injected with plasmids, uninjected and PBS injected fish was control. The injected sites were edxcised for RNA extraction and gene expression analyses

first: Børre

last: Robertsen

first: Mehrdad

last: Sobhkhez


title: Microarray analysis of exosomal miRNAs from different liver cancer cells

first: Wen

last: Yang

address: 225 Changhai Road

department: Eastern Hepatobiliary Surgery Institute

institute: Second Military Medical University

summary: To explore how tumor-derived exosomes activate fibroblasts and foster lung metastasis of liver cancer. MiRNAs encapsulated in exosomes are abundant and play an important role in cell-cell communication. Therefore, we hypothesized that tumor-derived exosomal miRNAs mediate fibroblasts activation. To identify the specific miRNAs involved, we conducted microarrays to generate miRNAs profiles of exosomes derived from the four liver cancer cell lines with different migration and invasion abilities. CSQT-2 and HCC-LM3 cells were high metastatic cancer cells, versus to HepG2 and MHCC-97L cells. We divided them into the following groups: CSQT-2 versus HepG2 (with different origins), HCC-LM3 versus MHCC-97L (with the same origin) and compared the up-regulated miRNAs in both two high-metastatic cancer cells-derived exosomes. Then, these up-regulated miRNAs were subjected to validation to define the most important exosomal miRNAs in regulating fibroblast activation and contributing to lung metastasis of liver cancer.

overall_design: Equal number of different cells were cultured with fresh DMEM supplemented serum which was depleted of exosomes for 48 hours and conditioned medium(CM) was collected for exosomes isolation.Three independent experiments were performed.

first: Hongyang

last: Wang


title: Comparative expression of whole duodenum from intestinal Arx deficient mice and control littermates

status: Public on Dec 08 2017

city: Philadelphia

first: Natalie

last: Terry

state: PA

address: 3615 Civic  Center Blvd

institute: The Children's Hospital of Philadelphia

summary:
The enteroendocrine lineage secretes hormones which direct the digestion, absorption, and motility of the intestine. Arx is a transcription factor expressed specifically in the enteroendocrine cells. With intestinal-specific loss of Arx, hormonal expression is disrupted.
We used microarrays to determine the differential expression of genes from the whole duodenum after removal of Arx, a gene specifically expressed in the enteroendocrine lineage, in the intestinal epithelium compared to littermate controls at postnatal day 5.

overall_design: Whole duodenum was dissected from postnatal day 5 mice. RNA extraction was performed with Trizol and then RNA was hybridized on Agilent 2-color microarray.

first: Klaus

middle: H

last: Kaestner


title: The genomic landscape of the fungal specific SWI/SNF complex subunit, Snf6, in Candida albicans

status: Public on Oct 28 2017

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

type: Genome binding/occupancy profiling by genome tiling array

summary: We have focused our investigation on the characterization of the role of the fungal specific SWI/SNF subunit, Snf6. Our data show that, although the C. albicans subunit has only limited sequence similarity to other fungal orthologs, Snf6 was copurified with SWI/SNF complex subunits including the catalytic ATPase subunit, Snf2. We show that Snf6 plays a critical role in biological processes that are essential for fungal pathogenesis including carbon metabolic flexibility, stress response and morphogenesis. The Snf6 regulon was determined by combining both genome-wide location (ChIP-chip) and transcriptional profiling (microarrays) to identify targets of the SWI/SNF complex under both yeast- and hyphal-promoting conditions.

overall_design: We performed genome wide occupancy experiments (YPD, 30oC and YPD, 37oC ) with Snf6p  to determine their binding sites. To complement with genome wide occupancy experiments, we performed a transcription profile with an snf6 Grace strain under yeast and hyphae conditions (YPD+/- tet, 30oC and YPD+10%serum +/- tet , 37oC ).

first: Yaolin

last: Chen

first: Adnane

last: Sellam

first: Malcolm

last: Whiteway


title: Application of the TGx-28.65 genomic biomarker to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human cells [BT]

summary: In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for human health risk assessment purposes. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles in human TK6 cells exposed to 28 well-known compounds, and it comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl]benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival (RS) and increases in apoptosis. A strong significant increase in micronucleus induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were less than 2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only induces a small increase in MN, this response is sufficient to induce a cellular DNA damage response that is likely relevant for risk assessment. Benchmark dose modeling revealed that BT is much more potent than DO; the BT benchmark dose for MN induction was similar to that of benzo[a]pyrene, (BaP: a genotoxic carcinogen), which was used as a positive control. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.

overall_design: This experiment examined the whole genome transcriptional response of human TK6 cells exposed to 3 concentrations of 1,2,4-benzenetriol (15, 20 and 30 µg/ml).  TK6 cells were exposed to the test compound for 4 hours followed by a recovery time of 3-4h in fresh media at 3 different concentrations, including a low, a medium, and a high concentration, in addition to a negative vehicle control (water (+S9)) and a positive control (benzo[a]pyrene at 10 µg/ml).  Each concentration and time point had 3 biological replicates. There were a total 13 samples (26 arrays) included in the final analysis using a two-colour dye swap design.

first: Andrew

last: Williams

first: Byron

last: Kuo

first: John

last: Wills

first: Carol

middle: D

last: Swartz

first: Leslie

last: Recio

first: Heng-Hong

last: Li

first: Albert

middle: J

last: Fornace Jr

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: The distinct roles of class I and II RPD3-like histone deacetylases in salinity stress response

status: Public on Oct 15 2017

city: Yokohama

first: Akihiro

last: Matsui

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To understand affected genes by HDA19 and HDA5/14/15/18 under salinity stress conditions, hda19 and hda5/14/15/18 mutants and control (Col-0) plants were analyzed under normal and salinity stress conditions using Arabidopsis custom microarrays (GEO array platform: GPL19830).

overall_design: Microarray analysis was conducted using hda19, hda5/14/15/18, and Col-0 plants subjected to non-stress and 125 mM NaCl salt-stress condition for 2 h.

first: Minoru

last: Ueda

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Identification of differentially expressed circRNAs in OLF

status: Public on Oct 27 2017

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

summary:
Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the circRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis, which revealed a panel of circRNAs that were specifically regulated in ligament tissues of human undergoing ossification.
To identify transcriptional regulators for OLF, we compared the circRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis.

overall_design: The circRNA expression profile of 4 OLFs and 4 normal LF tissues were analyzed by microarray analysis.

first: Wei

last: Hong

first: Yuan

last: Xue

first: Yawei

last: Han

first: Liandong


title: Endothelium-derived extracellular vesicles promote splenic monocyte mobilization in myocardial infarction

city: Oxford

first: Naveed

last: Akbar

state: United Kingdom

address: Radcliffe Department of Medicine, University of Oxford

department: Cardiovascular Medicine

country: United Kingdom

institute: University of Oxford

summary: Endothelium-derived extracellular vesicles modulate monocyte gene expression

overall_design: THP-1 monocytes were exposed to human umbilical cord vein endothelail cell derived extracellular vesicles

first: Janet

last: Digby


title: miRNA expression data from adult mouse Prefrontal Cortex following high fat diet exposure (8 weeks, starting on PND28)

city: Zurich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

department: Institute for Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich - Vetsuisse

summary:
High-fat diet (HFD) feeding during adolescence induces robust impairments in prefrontal-dependent cognition. Moreover, it also provokes multiple changes at the cellular and synaptic scales within the mPFC, suggesting that major transcriptional events are elicited by HFD during this maturational period. While it has been speculated that the nature of this transcriptional reprogramming may involve epigenetic effects, such as microRNA expression, this question to date remains unanswered. Here, we addressed this issue by performing unbiased genome-wide transcriptional profiling of miRNAs in the mouse mPFC following adolescent HFD.
We performed unbiased genome-wide transcriptional profiling of miRNAs in the mouse mPFC following adolescent HFD

overall_design: C57BL/6N male where exposed to HFD or Low fat diet (LFD) for 8 weeks starting from PND28. (HFD:consisting of 60% of calories from fat; LFD 10% of calories from fat ). We then performed genome wide miRNA expression analyses, validations, behavioral analyses.

first: Marie

last: Labouesse

first: Annamaria

last: Cattaneo


title: The histone variant H2A.Z promotes initiation of meiotic recombination (ChIP)

first: Kazuto

last: Kugou

overall_design: S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested four hours after the induction. ChIP was performed using anti-H2A.Z antibodies.

first: Shintaro

last: Yamada

first: Da-Qiao

last: Ding

first: Yurika

last: Fujita

first: Yasushi

last: Hiraoka

first: Hiroshi

last: Murakami

first: Kunihiro

last: Ohta

first: Takatomi


title: In utero cigarette smoke (IUS) exposure, sex differences and disease associations in the developing human fetal lung transcriptome

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Whole human fetal lung microRNA transcriptome profiles from estimated gestational ages 54 to 137 days post conception. Maternal cigarette smoking status is indicated by cotinine levels measured in the corresponding placenta.

overall_design: Whole lung transcriptome profiles, lung development, human fetus, in utero cigarette smoke exposure

middle: T

first: Roger

last: Gaedigk

first: Carrie

last: Vyhlidal

first: J

last: Leeder

first: Scott

last: Weiss

first: Kathleen

last: Haley

first: Kelan

middle: G

last: Tantisira

first: Sunita

last: Sharma


title: Identification of gene expression changes in DLBCL cells by DNMT1 knockdown

status: Public on Oct 10 2017

city: Kubang Kerian

first: Kah Keng

last: Wong

state: Kelantan

address: School of Medical Sciences, Health Campus

department: Department of Immunology

country: Malaysia

institute: Universiti Sains Malaysia

summary: To identify differentially expressed genes in HT GCB-DLBCL cell lines transduced with non-silencing control shRNA or DNMT1 shRNA.

overall_design: HT cells were transduced with lentivirus vectors expressing shRNA non-silencing control or shRNA targeting DNMT1 (shDNMT1) in duplicate for each shRNA.

first: Kah

first: Suet

last: Loo


title: Application of the TGx-28.65 genomic biomarker to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human cells [DO]

first: Julie

last: Buick

overall_design: This experiment examined the whole genome transcriptional response of human TK6 cells exposed to 3 concentrations of disperse orange (50, 500 and 750 µg/ml).  TK6 cells were exposed to the test compound for 4 hours followed by a recovery time of 3-4h in fresh media at 3 different concentrations, including a low, a medium, and a high concentration, in addition to a negative vehicle control (DMSO (+S9)) and a positive control (benzo[a]pyrene at 10 µg/ml).  Each concentration and time point had 3 biological replicates. There were a total 13 samples (26 arrays) included in the final analysis using a two-colour dye swap design.

first: Andrew

last: Williams

first: Byron

last: Kuo

first: John

middle: W

last: Wills

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Heng-Hong

last: Li

first: Albert

last: Fornace Jr

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: The histone variant H2A.Z promotes initiation of meiotic recombination

first: Kazuto

last: Kugou


title: An integrative model of cirrhosis-associated hepatocarcinogenesis in rat: histological, biochemical and molecular approaches

status: Public on Oct 12 2017

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

summary: The present study aimed at proposing a novel chemically-induced cirrhosis-associated rat hepatocarcinogenesis model, involving the characterization of histological, biochemical and molecular features. Male Wistar rats received a single dose of diethylnitrosamine (DEN, 200 mg/Kg body weight [b.wt.]), and were submitted to several cycles of thioacetamide (TAA, 200 mg/Kg b.wt.), during 23 weeks. Blood and liver were collected from untreated and DEN/TAA-treated groups.  Liver samples were processed for global gene expression (cDNA microarray), histopathological (HE) and collagen content (picrosirius red) evaluations, immunohistochemical (Ki-67, GST-P and α-SMA), biochemical (catalase, glutathione peroxidase and glutathione-S-transferase) and gelatin zymography (MMP-2 and 9) analysis. Using a very stringent analysis (FDR<0.01 and fold change>3), gene expression array evidenced 359 differentially expressed genes upon DEN/TAA regimen. Gene Ontology and functional analyses showed several upregulated genes involved in extracellular matrix organization, mainly collagen type I α1 and 2 (Col1α1, Col1α2) and tissue inhibitor of metalloproteinase 1 and 2 (Timp1 and Timp2) genes. In addition, glutathione S-transferase, pi 1 and 2 (Gstp1 and Gstp2) genes were markedly upregulated. In contrast, functional analyses also revealed the downregulation of antioxidant response genes, as catalase, glutathione peroxidase 1 and glutathione S-transferase mu type 3 (Cat, Gpx1 and Gstm3). In agreement with gene expression data, our model presented extensive liver cirrhosis with increased α-SMA expression and collagen deposition, as well as marked development of preneoplastic GST-P positive hyperplastic lesions and some neoplasms. Besides, we observed a decrease in total glutathione peroxidase, total glutatione-S-tranferase and catalase activities. The characterization of a suitable cirrhosis-associated hepatocarcinogenesis model could provide insights into molecular characteristics of the human disease and be applied to evaluate potential preventive and therapeutic approaches.

overall_design: Male Wistar rats received a single dose of diethylnitrosamine (DEN, 200 mg/Kg body weight [b.wt.]), and were submitted to several cycles of thioacetamide (TAA, 200 mg/Kg b.wt.), during 23 weeks. Blood and liver were collected from untreated and DEN/TAA-treated groups. Liver samples were processed for global gene expression (cDNA microarray).

first: Guilherme

middle: R

last: Romualdo

first: Tony

last: Grassi

first: Renata

last: Goto

first: Mariana

last: Tablas

first: Ana

middle: A

last: Fernandes

first: Bruno

last: Cogliati

first: Luís

last: Barbisan


title: Mycobacterium tuberculosis Infection Modulates Adipose Tissue Biology

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Mycobacterium tuberculosis (Mtb) primarily resides in the lung but it can also persist in extrapulmonary sites. Macrophages are considered the prime cellular habitat in all tissues. Here we demonstrate that Mtb resides inside adipocytes of fat tissue where it expresses stress-related genes. In addition, Mtb infection induces changes in adipose tissue biology depending on the route of administration and stage of infection. At day 14 post-systemic Mtb infection, F4/80+ (inducible nitric oxide synthase-positive) iNOS+ cells (M1 macrophages) as well as CD3, CD4 and CD8 T cells were present, and by day 28, B220+ cells had arrived in adipose tissue. In contrast, mice infected via aerosol only showed infiltration of F4/80+ cells that do not express iNOS or arginase 1 (Arg1) and CD3, CD4 and CD8 T cells. Gene expression analysis of adipose tissue of aerosol Mtb-infected mice provided evidence for upregulated expression of genes associated with T cells and NK cells at 28 days post-infection. Moreover, IFN-gamma-producing NK cells and Mtb-specific CD8 T cells were found in perigonadal fat, specifically CD8+CD44-CD69+ and CD8+CD44-CD103+ subpopulations. Gene expression analysis of selected NK cells and Mtb-specific CD8 T cells in perigonadal fat of infected mice revealed that they produced IFN-gamma and transcribed the lectin-like receptor Klrg1 whereas CD27 and CD62L transcript levels were downregulated consistent with an effector phenotype. Sorted NK cells expressed higher levels of Klrg1 upon infection, as well. Our results reveal the ability of Mtb to persist in adipose tissue in a stressed state, and that NK cells and Mtb-specific CD8 T cells infiltrate infected adipose tissue where they produce IFN- and assume an effector phenotype. We conclude that Mtb exploits adipose tissue as niche, to which CD8 T cells and NK cells are attracted.

overall_design: Microarray experiments were performed as single-color hybridizations on SurePrint G3 Mouse GE 8x60K microarray (Agilent-028005) .

first: Macarena

last: Beigier-Bompadre

first: January

last: Weine III

first: Volker

last: Brinkmann

first: Kai

last: Matuchewski

first: Stefan

last: Kaufmann


title: Expansion of SFTPC+ cells from human induced pluripotent stem cell-derived CPMhigh progenitor cells by forming alveolar organoids

status: Public on Oct 02 2017

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

summary: Microarray analysis was performed on CPMhigh progenitor cells, P0 SFTPC+ cells,  P2 SFTPC+ cells, and P5 SFTPC+ cells derived form human induced pluripotent stem cells (B2-3 SFTPC-GFP reporter hiPSCs), and parental 201B7 hiPSC-derived proximal airway epithelial cells (PAECs) and primary isolated human adult alveolar epithelial (adult AT2) cells, respectively.

overall_design: CPMhigh progenitor cells stepwisely induced from hiPSCs were isolated using fluorescence activated cell sorting (FACS) on day 21. Isolated CPMhigh cells were cocultured with human fetal lung fibroblasts forming alveolar organoids (AOs). P0 SFTPC+ cells were isolated from AOs on Day 35. We further expanded SFTPC+ cells by passaging in AOs. Passaged SFTPC+ cells were isolated on Day 63 and Day 105 (P2 and P5, respectively).

first: Yuki

last: Yamamoto

first: Isao

last: Ito


title: Transcriptome profiling of OsFBK1 rice transgenics

status: Public on Oct 05 2017

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Rice transgenic plants of the F-box encoding gene, OsFBK1, in the Pusa Basmati 1 (PB1) variety have been found to display differences in the anther and root phenotypes. In order to elucidate changes at the transcriptome level, microarray of the roots of 14-day-old seedlings of over-expresseion (OE) and knock-down (KD) lines along with vector control (VC) and wild type (WT) were carried out.

overall_design: Seedlings of OsFBK1-OE, OsFBK1-KD, VC and WT grown for fourteen days at 28±1oC . RNA from the roots were extracted from each sample and hybridized on rice Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis. Overall, eight samples were analyzed representing the transgenic lines and wild type.

first: Pratikshya

last: Borah

middle: P


title: miRs  expression profile to predict HNSCC patients at high risk to develop recurrence

city: Aviano

first: Francesca

last: Citron

state: PN

address: Via F.Gallini 2

department: Molecular Oncology

country: Italy

institute: C.R.O. of Aviano - National Cancer Institute

summary: A miRs expression profiling of a total of 746 miRs (664 human + 82 viral) in 72 Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors to classify patients at high risk to develop recurrences

overall_design: In the study presented here, we screened a cohort of 44 HNSCC primary tumors, followed up for two years, for the expression of a total of 746 miRs, to identify a miRs signature that classify patients at high risk to develop recurrences

first: Andrea

last: Vecchione

first: Gustavo

last: Baldassarre

first: Jerry

last: Polesel


title: Transcriptional signature of human pro-inflammatory TH17 cells [ex vivo TH17 cells]

status: Public on Sep 29 2017

first: Dan

last: Hu

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: Human peripheral blood IFN-γ+IL-17+ (TH1/17) and IFN-γ–IL-17+ (TH17) CD4+ T cells display distinct transcriptional profiles in high-throughput transcription analyses. Compared to TH17 cells, TH1/17 cells have similar gene signatures to mouse pathogenic TH17 cells.

overall_design: CD4+ T cells isolated from PBMC of healthy donors (n=5) were stimulated with PMA and ionomycin for 3hr. TH1/17, TH17, TH1 (IFN-γ–IL-17-) and DN (IFN-γ and IL-17 double negative) CD4+ T subsets were sorted utilizing a capture assay that separates live CD4+ T subsets based on differential secretion of IL-17 and/or IFN-γ. sorted CD4 T cell subsets were subjected to gene expression analysis using the nCounter Nanostring Custom Codeset HuTH17.

first: Howard

middle: L

last: Weiner


title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer (miRNA)

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

institute: Hospital La Paz Institute for Health Research

summary: Background. One of the major limitations associated to the platinum use is the resistance that almost invariably will progress in lung and ovarian cancers. In the current study, we sought to identify epigenetically regulated miRNAs as novel biomarkers of platinum-resistance in those tumor types. Methods. We combined transcriptomic data from miRNA and mRNA under the influence of an epigenetic reactivation treatment, followed by qRT-PCR and epigenteic validations for an accurate candidate selection in 23 human cancer cell lines. Functional analysis were performed to study their biological and therapeutic implications, that were further tested in 257 primary samples obtained from lung and ovarian tumors. Results. We identified a group of 9 miRNAs belonging to the CM19 cluster and 7 potential miRNA-targets potentially involved in resistance development, in both tumor types. Deregulation of miR-7, -132, -335 and -148a may be a common event in the development of CDDP-resistance. miR-7 presented specific methylation in the resistant subtypes and its reexpression, decreased cell viability, suggesting a possible cell sensitization to cisplatin. Our translational approach indicated that miR-7 methylation is a frequent event that may play an important role in the early establishment of NSCLC tumorigenesis, and seems to play an additional platinum-predictive role in ovarian cancer.  Conclusions. miR-7 is a novel potential epigenetic biomarker tool for the selection of ovarian cancer patients with higher risk to earlier relapse and worst response to platinum-based chemotherapy. Funding. FIS (ISCIII): PI12/00386, PI13/01450, PI15/00186, and FEDER/FSE (Una manera de hacer Europa).

overall_design: Total RNA from Sensitive (S), Resistant (R) and Resistant under epigenetic reactivation treatment cells (RT) was extracted by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment. Labelled cDNA from the 12 cell lines was hybridized by duplicate into Agilent platforms for microRNA microarrays “Agilent miRNA microarray (8 x 15K)”

first: O

last: Vera

first: J

last: Jimenez

last: Pernía

first: C

last: Rodriguez-Antolin

first: F

last: Sánchez Cabo

last: Soto

first: R

last: Rosas

last: Rodriguez

first: S

last: Lopez-Magallon

first: I

last: Esteban

first: A

last: Dopazo

last: Rojo

last: Belda

last: Alvarez

last: Benitez

last: Perona

last: De Castro

last: Ibanez de Cáceres


title: RORα coordinates thalamic and cortical maturation to instruct barrel cortex development.

status: Public on Sep 30 2017

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

summary: The retinoic acid orphan receptor alpha (RORα) is well known for its role in cerebellar development and maturation as revealed in the stagerrer (Stg) mutant mouse line. However it’s potential involvement for the development of other brain regions has not been assessed.  Here we describe a new role of RORα in the development of the thalamic and cortical circuits that leads to the assembly of columnar barrel structures in the primary somatosensory cortex. Microarray analyses comparing gene expression in the thalamus and cortex of the Stg, showed a down-regulation of genes that have been involved in the control of TCA or cellular maturation of layer IV neurons. Overall, our study outlines a new role of RORα for the coordinated maturation of the thalamus and cortex during early postnatal life, and shows that it is required to initiate the transcription of genes involved in barrel formation.

overall_design: Gene expression analysis of cortex and VB from control and Stagerrer mutant mice at P5-P6. Experiments were done in dye-swap with 4 biological replicates (4 litters)

first: Tania

last: Vitalis

first: Marie-Claude

last: Potier

first: Jean

last: Mariani

first: Patricia

last: Gaspar


title: Dietary medium-chain saturated fatty acids induce gene expression of energy metabolism-related pathways in adipose tissue of abdominally obese subjects

status: Public on Sep 28 2017

city: Wageningen

first: Juri

middle: C

last: Matualatupauw

address: PO Box 17

department: Human Nutrition

country: Netherlands

institute: Wageningen University

summary: High MC-SFA intake resulted in a downregulation of gene expression of pathways related to complement system and inflammation, and an upregulation of gene expression of pathways related to citric acid cycle, electron transport chain and lipid metabolism in adipose tissue. Based on our results, we hypothesize that the beneficial effects of MC-SFAs on prevention of fat accumulation may be mediated by increases in gene expression related to energy metabolism in the adipose tissue. Additionally, decreases in inflammation-related gene expression in the adipose may potentially have beneficial effects in relation to cardiometabolic diseases.

overall_design: In this 12 week, randomized, double-blind, diet intervention study, participants consumed 60 g milk protein (whey or casein) and 63 g milk fat (high MC-SFA or low MC-SFA) daily in a 2 by 2 factorial design. We used microarrays to measure whole genome gene expression in adipose tissue in a subpopulation of 12 participants, 6 in the casein + low MC-SFA group and 6 in the casein + high MC-SFA group, before and after intervention.

first: Mette

last: Bohl

first: Søren

last: Gregersen

first: Kjeld

last: Hermansen

first: Lydia

last: Afman


title: Discovery of Central Nervous System Infiltration in Zebrafish T Cell Acute Lymphoblastic Leukemia

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

institute: University of Padua

summary: Gene expression analysis to identify molecular mechanisms that regulate motility and CNS invasiveness of malignant hMYC-ER and hlkT-lymphoblasts

overall_design: Class comparison between hMYC-ER and hlkT-lymphoblasts

first: Geertruy

last: te Kronnie


title: Induction of SFTPC+ cells from human induced pluripotent stem cell-derived CPMhigh progenitor cells by forming alveolar organoids

first: Shimpei

last: Gotoh

summary: Microarray analysis was performed on P0 SFTPC+ cells, P0 SFTPC- cells and CPMhigh progenitor cells derived form human induced pluripotent stem cells (B2-3 SFTPC-GFP reporter hiPSCs), respectively.

overall_design: CPMhigh progenitor cells stepwisely induced from hiPSCs were isolated using fluorescence activated cell sorting (FACS) on day 21. Isolated CPMhigh cells were cocultured with human fetal lung fibroblasts forming alveolar organoids (AOs). P0 SFTPC+ cells and P0 SFTPC- cells were isolated from AOs on Day 35.

first: Yuki

last: Yamamoto


title: Characterization of rubella-specific humoral immunity following two doses of MMR vaccine using proteome microarray technology

status: Public on Sep 23 2017

city: Rochester

first: Gregory

middle: A.

last: Poland

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: This study uses proteome microarray technology/data to identify predictive biomarkers of neutralizing antibody response and potential new correlates of protective immunity in rubella virus serology.

overall_design: In the study presented here, a well-characterized cohort of 75 high and 75 low rubella virus-specific neutralizing antibody responders after two MMR vaccine doses was used to acquire microarray antibody measurements to all rubella virus proteins. These data were used in multivariate penalized logistic regression modeling of rubella-specific neutralizing antibody response after vaccination.

first: Iana

last: Haralambieva

first: Michael

last: Gibson

first: Richard

middle: B

last: Kennedy

first: Inna

last: Ovsyannikova

first: Nathaniel

last: Warner

first: Diane

middle: E

last: Grill


title: Isolation of human iPSC and ESC-derived mesDA progenitor cells by immunomagnetic cells sorting (MACS)

status: Public on Sep 25 2017

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

summary: Human embryonic and induced pluripotent stem cells are a promising cell source for the future treatment of Parkinson´s disease. It has been shown that mesencephalic dopaminergic (mesDA) neurons arise from the midbrain floor plate in which FOXA2 acts as a key transcription factor. We identified IAP which is specifically co-expressed with FOXA2 positive cells and is suitable to isolate mesDA progenitors utilizing MACS Technolog.The sorted iPSCs were viable, enriched for midbrain specific markers, lacked expression of pluripotency markers, and differentiated into mature dopaminergic neurons in vitro. IAP might be used as a tool to purify mesDA progenitor cells for regenerative therapy  in PD patients

overall_design: human iPSC and ESC-derived mesDA progenitor cells were sorted for IAP positive cells on day 16 of differentiation. In addition, IAP neagtive and unsorted fraction were subjected to RNA extraction and hybridized on Agilent microarray . The dataset comprises 27 samples divided into three samples of each group.

first: Daniela

last: Lehnen

first: Michail

last: Knauel

first: Silvia

last: Rüberg

first: Timon

last: Hick

middle: I


title: Gene expression changes in primary GBM neurosphere cultures after 24 hours of CDK7 inhibition

status: Public on Sep 06 2017

city: Clayton

first: Sam

last: Greenall

state: VIC

address: 27-31 Wright Street

department: Centre for Cancer Research

country: Australia

institute: Hudson Institute of Medical Research

summary: CDK7 controlls both global gene transcription and cell cycle progression. To see what global gene changes were occuring after application of THZ1 to GBM cells, we conducted the following microarray analyses.

overall_design: Two distinct GBM neurosphere cell lines were treated in quadruplicate with DMSO vehicle or 200 nM of the irreversible CDK7 inhibitor THZ1. After 24 hours, total RNA was harvested from the samples and hybridised to the arrays.

first: Terry

last: Johns


title: Difference of gene expression after knockdown CRNDE expression.

city: Guangzhou

first: wang

middle: yi

last: qing

country: China

institute: South Medical University

summary: To identify the genes targeted by CRNDE and explore the mechanism of action of CRNDE on CRC tumorigenesis, gene expression profiling was performed on CRNDE knockdown DLD1 cells s and on control cells.

overall_design: Either of the stable cell lines,DLD1-NC and DLD1-shCRNDE,is collected three times independently.

first: H

last: Jiang

first: Y

last: Wang


title: Transcriptional signature of human pro-inflammatory TH17 cells [TH17 clones]

first: Dan

last: Hu

summary: Human IL-10– and IL-10+ TH17 clones maintained their pro- or anti-inflammatory characteristics after long-term culture. There were similarities between human IL-10– vs. IL-10+ TH17 clones and mouse pathogenic vs. non-pathogenic TH17 cells.

overall_design: From healthy donors (n=5), CD4+ T cells clones were established from CCR6+CCR4+CXCR3– memory CD4+ T cells that were enriched for TH17 cells 14, 18 and screened for clones producing IL-17 with or without co-secretion of IL-10.

first: Howard

last: Weiner


title: Dysregulated Placental Micrornas In Early And Late Onset Preeclampsia

status: Public on Sep 07 2017

city: Athens

first: George

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

summary: Introduction: To determine the miRNA expression profile in placentas complicated by Preeclampsia (PE) and compare it to uncomplicated pregnancies. Methods: Sixteen placentas from women with PE, including 11 with early onset PE (EOPE) and 5 with late onset PE (LOPE), as well as 8 from uncomplicated pregnancies were analyzed using miRNA microarrays. For statistical analyses the MATLAB® simulation environment was applied. The over-expression of miR-518a-5p was verified using Quantitative Real-Time Polymerase Chain Reaction. Results: Overall, 44 miRNAs were found deregulateddysregulated in PE complicated placentas. Statistical analysis revealed that miR-431, miR-518a-5p and miR-124* were over-expressed in EOPE complicated placentas as compared to controls whereas miR-544 and miR-3942 were down-regulated in EOPE. When comparing the miRNA expression profile in cases with PE and PE- growth restricted fetuses (FGR), miR-431 and miR-518a-5p were found over-expressed in pregnancies complicated by FGR. Additionally, up- regulation of miR-124, miR-423-3p and miR-518a-5p was associated with proteinuria. Discussion: Specific miRNAs can differentiate EOPE and LOPE from uncomplicated pregnancies representing putative PE-specific diagnostic biomarkers. Among them, miR-518a-5p emerged as a potential diagnostic indicator for EOPE cases as well as for FGR and proteinuria associated PE complicated placentas designating its potential link to the severity of the disease.

overall_design: Placental samples were collected from 16 women with PE (n=11 with Early Onset Pre-Eclampsia (EOPE) and n=5 diagnosed with Late Onset Pre-Eclampsia (LOPE)) and from 8 with uncomplicated term pregnancies at the time of cesarean section in the 3rd Department of Obstetrics and Gynecology at National and Kapodistrian University of Athens.  A total of 24 samples has been processed and examined.

first: Alexandra

last: Lykoudi

first: Aggeliki

last: Kolialexi

first: Maria

last: Braoudaki

first: Charalampos

last: Siristatidis

middle: K

last: Papaioanou

last: Tzetis

first: Ariadni

last: Mavrou

first: Nikolas

last: Papantoniou


title: Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health

status: Public on Sep 15 2017

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

summary: Circulating ex-RNAs altered in plasma after acute exercise target pathways involved in inflammation, including miR-181b-5p.

overall_design: Plasma circulating miRNAs were measured before and after exercise by the ABCAM FirePlex platform

first: Saumya

first: Ashish

last: Yeri


title: Gene expression profiling of low-dose irradiated human BM-MSCs

status: Public on Sep 01 2017

first: Aya

last: Fujishiro

address: Sakyo-ku

department: Transfusion Medicine and Cell Therapy

institute: Kyoto University Hospital

summary: In bone marrow (BM), there are two different types of stem/progenitor cells. With respect to hematopoiesis, hematopoietic stem/progenitor cells (HPCs) produce mature blood cells and mesenchymal stromal/stem cells (MSCs) support this. The influence of exposure to low-dose radiation on human HPCs has been investigated, and generation of both immature and mature hematopoietic cells from human HPCs is compromised. On the other hand, the influence of exposure to low-dose radiation on MSCs is not known. This gene expression profiling was created for investigation how low-dose irradiation affects BM-MSCs genomically.

overall_design: BM samples from healthy adult volunteers were purchased from AllCells (Emeryville, CA). Human BM-MSCs were isolated according to our previously published methods (Yao H, Stem Cells 2014;32:2245). BM-MSCs were exposed to 0.1 Gy of γ-radiation (Cesium137) at 0.8 Gy/min by a Gammacell Irradiator (Best Theratronics, Ontario, Canada). 24 hours after irradiation, total RNA were collected from the irradiated BM-MSCs.

first: Yasuo

last: Miura

first: Tatsuo

last: Ichinohe


title: Expression data from A549 cells after treatment with bradykinin

status: Public on Sep 18 2017

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

institute: Graduate School of Medicine, University of the Ryukyus

summary:
Analysis of A549 cells treated with bradyikinin.
In this dataset, we include the expression data obtained from A549 cells after treatment with bradykinin. We confirmed that A540 cells expressed bradykinin B2 receptor. Results provide insight into the effect of bradykin on MAP kinase pathway.

overall_design: A549 dells were treated with 100 nM bradykinin for 30min.

first: Shunsuke

last: Izumi

first: Hideyuki

last: Yamamoto


title: CNA analysis of ionizing radiation related basal cell carcinoma

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

institute: Bundeswehr Institute for Radiobiology

type: Genome variation profiling by genome tiling array

summary: gDNA from patient samples with multiple basal cell carcinomas and possible exposure to ionizing radiation was hybridized Vs. GM12878 gDNA to assess CNAs. We aimed to find a possible common aberration pattern related to ionizing radiation or a rare metastasis.

overall_design: 6 cancer samples (BCC) Vs. GM12878 control gDNA

middle: V


title: Tissue and circulating microRNA co-expression analysis reveals potential involvement of miRNAs in the pathobiology of frontal fibrosing alopecia [blood]

status: Public on Sep 04 2017

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

institute: King's College London

summary: Frontal fibrosing alopecia (FFA), a clinical variant of follicular lichen planus, is a predominantly postmenopausal, immune-mediated, inflammatory, primary lymphocytic cicatricial alopecia. FFA mainly involves the scalp, facial hair and eyebrows but also affects other body regions. MicroRNAs (miRNAs) have emerged as potential candidates of pathobiologic, diagnostic and therapeutic interest in chronic inflammatory, fibrotic and autoimmune diseases. To explore miRNAs in FFA for their disease relevance we isolated plasma from venous blood from 10 biopsy-proven treatment-naïve FFA cases and 10 matched controls and undertook miRNA expression analysis using the Human Fibrosis miRNA PCR Array (Qiagen). A separate cohort of 7 active FFA cases and 7 matched healthy controls were ascertained for tissue microRNA analysis and all 14 scalp-biopsy-extracted microRNA samples were subjected to microarray analysis on Affymetrix GeneChip miRNA 4.0 arrays. We generated a list of communities for the two skin tissue networks (cases and controls) and identified cluster centres (exemplars) as representative miRNAs of each community. Twenty exemplars in the control network were significantly enriched in the plasma (control) dataset compared to 27 for FFA. Amongst these, there were 17 miRNAs common in both networks, 9 of which were representative in the FFA disease phenotype. Random Forest analysis suggested that 4 circulating miRNAs (hsa-let-7d-5p, hsa-miR-18a-5p, has-miR-20a-5p and hsa-miR-19a-3p) can discriminate between FFA and controls. Our study of skin and plasma miRNA co-expression highlights circulating miRNAs of potential predictive value as biomarkers that should now be validated in larger cohorts.

overall_design: RT-PCR for miRNA in plasma from healthy controls or FFA patients.

first: Christos

last: Tziotzios

first: Chrysanthi

last: Ainali

first: Susan

last: Holmes

first: Fiona

last: Cunningham

first: Su

middle: M

last: Lwin

first: Ioulios

last: Palamaras

first: Kapil

last: Bhargava

first: Janice

last: Rymer

first: Catherine

last: Stefanato

first: Niall

last: Kirkpatrick

first: Sergio

last: Vano-Galvan

last: Petridis

first: David

last: Fenton

first: Michael

last: Simpson

first: Alexandros

last: Onoufriadis


title: Gene expression profiling of HepG2 cells after treatment with Brefeldin A

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

summary: To investigate the effects of the Golgi disruptor on liver cancer cells, we explored a global gene expression of HepG2 cells after treatment with Brefeldin A.

overall_design: HepG2 cells were treated with DMSO or Brefeldin A, followed by gene expression profiling using microarray.

first: Yoichi

last: Furukawa


title: Influence of irradiated PBMCs on both ex vivo cell proliferation of natural killer cells and change in cellular property

first: Jutta

last: Kollet

summary: The harnessing of natural killer cells (NK cells) as adoptive anti-cancer therapy relies on sufficient numbers of functional NK cells. The use of autologous peripheral blood mononuclear cells (PBMCs) from respective allogeneic donors to boost NK cell proliferation ex vivo, has shown to be a suitable strategy to obtain high NK cell numbers for clinical applications. However, the mechanisms underlying the effect of PBMCs on NK cell proliferation have not been completely characterized. Thus, in this study, we performed a thorough analysis of the influence of autologous PBMCs on NK cell proliferation.   We used irradiated autologous CD56-negative PBMCs stimulated with OKT3 that induced significantly increased expansion of purified CD56+CD3- NK cells, already after 5 days of culture (3.2 mean fold, n= 9) compared to standard cultures with only IL-2 supplement (1.3 mean fold n=90 proliferation, as observed when NK cells were cultured separately from the PBMCs through a permeable membrane. Depletion of B cells had no influence on the enhancement of NK cell proliferation, observing no changes in terms of fold expansion or cytokine profile, exemplified by high levels of TNF-α, IFN-γ, IL-6 and GM-CSF. In contrast the absence of T cells or monocytes reduced dramatically the proliferation of NK cells and abrogated cytokine production. Moreover, we analyzed differences in gene expression between proliferating and non-proliferating NK cells within this co-culture set up, to sought to determine changes in signalling pathways or phenotype related to a high proliferative status. The transcriptome analysis indicated that actively proliferating NK cells developed a differential activation response towards the stimuli provided during the co-culture compared to non-proliferating NK cells. In particular, differences in phenotype, expression of mitogen-activated protein kinases and zinc finger transcription factors could be demonstrated. In summary, our findings give rise to improve ex vivo expansion protocols of NK cells for future clinical applications.

overall_design: A total of 15 samples were included in the study. Briefly, three different samples of natural killer (NK) cells were obtained from 5 different donors. These three samples from each donor consisted on freshly isolated NK cells (resting, day 0), 5-days highly proliferating NK cells (proliferating) and 5-days non-proliferating NK cells (non-proliferating). 5-days cultured NK cells were obtained from the same sample of NK cells co-culture with respecitve autologous irradiated feeder cells. On day 0 NK cells were labeled with a cell trace dye, and on day 5, after exclusion of dead cells and gating on CD3negative/CD56+ cells, proliferating and non-proliferating NK cells (CD3negative/CD56+ cells) were sorted according to the cell trace dye brightness. Therefore proliferating NK cells are defined as dim due to a higher dilution of the dye after several number of cell divisions completed, and non-proliferating NK cells are defined as bright due to a lower dilution of the dye and higher brightness thereof.

first: Maria

last: Delso-Vallejo

first: Ulrike

last: Koehl

first: Volker

last: Huppert


title: Gene Expression Profiling Reveals Novel Candidate Markers of Ovarian Carcinoma Intraperitoneal Metastasis

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary:
Epithelial ovarian cancer (EOC) has the highest mortality among gynecological carcinomas. The lack of specific markers for prognostic determination of EOC progression hinders the search for novel effective therapies.
The aim of the present study was (i) to explore differences in expressions of ATP-binding cassette and solute carrier transporter genes, genes associated with drug metabolism and cell cycle regulation between control ovarian tissues, primary epithelial ovarian carcinomas (EOC) and intraperitoneal EOC metastases; (ii) to investigate associations of gene expression level with prognosis of patients with intraperitoneal metastases.

overall_design: Transcript levels of 62 genes were determined by quantitative real-time PCR in 44 primary EOCs, 29 intraperitoneal EOC metastases and in 14 control ovarian tissues. PPIA, UBC, and YWHAZ were used as reference genes for data normalization.

first: Katerina

last: Elsnerova

first: Radka

last: Vaclavikova


title: Investigation of gene expression of Pseudomonas putida (NBAII RPF 9) under abiotic stress [heat]

status: Public on Aug 31 2017

city: Bangalore

first: Rajagopal

last: Rangeshwaran

state: Karnataka

address: Bellary Road

department: Molecular Entomology

institute: National Bureau of Agricutural Insect resource

summary: To undestand the mechanism involved in abitoic stress tolerance of P. Putida (NBAII-RPF 9) the bacterium was grown in liquid LB media overnight and further subjected to heat shock at 45 degrees in incubated shaker for one hour seperately. The cultures were pelleted with centrifuged for total RNA. The RNA was hybridised in 8X15K Agilent array and image analysis carried out with Agilent Microarray scanner

overall_design: Pseudomonas putida grown was grown in Luria Bertani media and subjected heat shock (45 degrees). Respective controls were used for comparison.

first: R

first: Karkera

last: Ashwitha


title: Investigation of gene expression of Pseudomonas putida (NBAII RPF 9) under abiotic stress [salt]

summary: To undestand the mechanism involved in abitoic stress tolerance of P. Putida (NBAII-RPF 9) the bacterium was grown in liquid LB media overnight and further subjected to saline shock of (1M NaCl) for one hour seperately. The cultures were pelleted with centrifuged for total RNA. The RNA was hybridised in 8X15K Agilent array and image analysis carried out with Agilent Microarray scanner.

overall_design: Pseudomonas putida grown was grown in Luria Bertani media and subjected to saline shock (1.5M NaCl). Respective controls were used for comparison..


title: PCR array analysis of the heart of Wild Type (WT) and Ebi3 deficient mice infected for 7 days with Trypanosoma cruzi

city: Toronto

first: Tiago

last: Medina

address: 101 College Street

institute: University Health Network

summary: WT and Ebi3 deficient mice were intraperitoneally infected or not with 1,000 forms of trypomastigotes of T. cruzi Y strain for 7 days, and fragments of the heart tissues of non-infected and infected animals were obtained for RNA extraction. Samples were examined by qPCR assay according to RT²ProfilerPCRArrayTM kit of Mouse Innate Immune Responses & Adaptive (PAMM 052Z - Qiagen) on the ABI StepOnePlusTM equipment.

overall_design: PCR array gene expression profiling. Heart fragments from five animals of each group were used, and the amount of RNA was normalized prior to gene expression analysis

first: Oliveira

last: Gabriela

first: Medina

last: Tiago


title: The Distinct Transcriptional and Metabolic Profiles Associate with Empathy in Spiritual/Religious Trained Buddhists: A Pilot Study of Shingon Esoteric Buddhism Priests

status: Public on Aug 23 2017

city: Itabashi

first: Junji

last: OHNISHI

state: Tokyo

department: Department of Food and Nutrition

country: Japan

institute: Tokyo Kasei University

summary: The microarray analyses revealed that the “priest-type” transcripts included up-regulated genes of type I interferon innate anti-viral responses (MX1, RSAD2, IFIT1, IFIT3, IFI27, IFI44L, and HERC5), and down-regulated genes of C17orf97 (ligand of arginyltranseferase 1), hemoglobin γA (HBG1), keratin associated protein (KRTAP10-12), and sialic acid Ig-like lectin 14 (SIGLEC14) at baseline.

overall_design: Ten qualified Shingon Esoteric Buddhist priests and 10 age-matched healthy controls were recruited.  Subjects provided peripheral blood samples for the analysis of gene expression

last: Ohnishi

first: Shigeko

last: Sakamoto

first: Miyo

last: Hori

first: Seiji

last: Nakamura

first: Tomoko

last: Sasaoka

first: Eriko

first: Masakazu

last: Tanatsugu

first: Kazuo

last: Murakami

first: Satoshi

last: Ayuzawa


title: Scalable generation of Schwann cell precursors from human pluripotent stem cells

status: Public on Aug 15 2017

city: Daejeon

first: Han-Seop

last: Kim

address: Gwahak-ro

department: Stem Cell Research Laboratory, Immunotherapy Convergence Research Center,

country: South Korea

institute: KRIBB

summary: Schwann cells (SCs) are an absolute prerequisite for development of effective treatment of myelin disorders and nerve injuries. However, human sources of functional, myelinating SCs are extremely limited. Here, we have developed a novel, efficient strategy for producing directly an unlimited supply of functional human SCs via successful derivation of expandable Schwann cell precursors (SCPs) from human pluripotent stem cells (hPSCs) (hPSC-SCPs). Functional and molecular characteristics of SCs from hPSC-SCPs (hPSC-SCP-SCs) appeared to be similar to those of authentic Schwann cells. As a novel therapeutic target, transplanted hPSC-SCP-SCs effectively promoted axonal regeneration through directly myelinating regenerated-axons in sciatic nerve injured mice. Here, we present hPSC-SCPs and hPSC-SCP-SCs as an outstanding resource to use for investigating human Schwann cell pathology and biology and for translational approaches to PNS and CNS repair and regeneration.

overall_design: These data include global gene expression of 13 samples including 4 kinds of SCP, 4 kinds of SC, 2 kinds of neural crest stem cells (NCSC), 2 kinds of iPSC and 1 kind of hESC (H9).

first: Yee

middle: S

last: Cho

first: Han

first: Jungwoon

last: Lee


title: Genome-wide microRNA expression profiling in placentae from frozen-thawed embryo transfer (FET)

status: Public on Aug 16 2017

city: Sendai

first: Hitoshi

last: Hiura

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

department: Obstetrics and Gynecology

institute: Tohoku University Graduate School of Medicine

summary: Frozen-thawed embryo transfer (FET) is increasingly available for the improvement of the success rate of assisted reproductive technologies other than fresh embryo transfer (ET). There have been numerous findings that FET provides better obstetric and perinatal outcomes. However, the birth weight of infants conceived using FET is heavier than that of those conceived via ET. In addition, some reports have suggested that FET is associated with perinatal diseases such as placenta accreta and pregnancy-induced hypertension and a decrease in the sex ratio of male infants. These phenotypic alterations are caused by epigenetic alterations. MicroRNAs (miRNAs) are one of epigenetic modifications and dysregulation of miRNAs due to the environment in utero leads to placenta-associated diseases in infants and subsequently chronic diseases later in life. In this study, we compared miRNA expression profiles in the placentas originated from intracytoplasmic sperm injection and FET (ICSI-FET), intracytoplasmic sperm injection and ET (ICSI-ET) and from intracytoplasmic sperm injection and FET (ICSI-FET), intracytoplasmic sperm injection and ET (ICSI-ET) and spontaneous pregnancies (SP).

overall_design: To investigate miRNAs contribute various phenotypes of frozen–thawed embryo transfer (FET), we carried out comprehensive analysis for the miRNA profiling of human term placenta from intra-cytoplasmic sperm injection and frozen–thawed embryo transfer (ICSI-FET), intra-cytoplasmic sperm injection and fresh embryo transfer (ICSI-ET) and spontaneous pregnancies (SP).

first: Norio

last: Kobayashi

first: Hiroaki

last: Okae

first: Naoko

last: Miyauchi

first: Hiroyuki

last: Kikuchi

last: Yoshida

first: Takahiro

last: Arima


title: Muscle-released exosomes modulate gene expressions in beta-cells in mice

status: Public on Jul 14 2017

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: Exosomes are cell-released bioactive nanovesicles now considered as new partners in the inter-organ cross-talks. The possibility that skeletal muscle (SkM)-derived exosomes act as a mode of systemic communication has been described. Thus, in this study we have tested the hypothesis that through the exosomal route, muscle might transmit specific signals during insulin-resistance.

overall_design: Methods: Muscle from mice submitted to an high fat diet or a control diet were dissected. These muscles were incubated in media and exosomes released were purified. Exosomes released from high fat diet muscle (EXO-HP)  and from standard diet muscle (EXO-STD) were collected by ultracentrifugation. Then MIN6 (pancreatic cell line) were treated with either EXO-HP or EXO-STD. RNA was extracted and global transcriptomic analysis was performed.

first: Sophie

last: Rome

first: Emmanuelle

last: Meugnier


title: Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [miRNA expression]

status: Public on Jul 28 2017

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

country: USA

institute: leslie cope

summary: Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube.  Serous tubal intraepithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. The most significant focal DNA SCNAs were shared between cases with and without STIC lesions. RNA sequence and miRNA data did not identify any clear separation between cases with and without STIC lesions.  HGSCs had molecular profiles more similar to normal fallopian tube epithelium than ovarian surface epithelium or peritoneum. The data suggest that the molecular features of HGSCs with and without associated STIC lesions are mostly shared, indicating a common biologic origin, likely to be the distal fallopian tube among all cases.

overall_design: In this study, 96 previously untreated high-grade serous carcinoma samples were selected to have half with STIC lesions and half without.  Molecular assays were performed that included RNAseq, microRNA expression, and copy number variation.

first: Douglas

last: Levine

first: Leslie

last: Cope


title: Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VII

status: Public on Aug 25 2017

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

institute: National Cancer Institute

summary:
Purpose:  This study uses a high-throughput glycan microarray to evaluate the immunological evolution of antibodies to the glyco-antigen GD2.  The goal is to determine germline and affinity mature antibody specificity and affinities/
Results:  Affinity mature anti-GD2 antibodies 3F8 and ch14.18 had high affinity and were highly specific for the target GD2.  Germline antibodies were also hihgly specific and had surprisingly high affinity.
Conclusion: Antibodies to GD2 evolved from highly specific germlines.  Highly specific germlines may be critical in evading autoimmunity issues.

platform_organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Trypanosoma cruzi
Pandalus borealis
Oncorhynchus nerka
Gallus gallus
Homo sapiens
Sus scrofa domesticus
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Human immunodeficiency virus 1
Ceratonia siliqua
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

overall_design: Germline variable regions of 3F8 and ch14.18 were determined.  Germline and affinity mature antibody DNA were synthesized and transfected into HEK293 cell lines.  Secreted antibodies were purified from supernatant using affinity chromatography.  Antibodies were evaluated on multiple assay platforms, including glycan microarrays, protein microarrays, and cell binding assays.

first: Eric

last: Sterner

first: Megan

last: Peach

first: Marc

last: Nicklaus

first: Jeffrey


title: Genotyping of Single Nucleotide Polymorphisms (SNP) in photosynthetic genes of Sorghum bicolor

status: Public on Aug 10 2017

city: Ames

first: Maria

middle: Guadalupe

last: Salas Fernandez

state: IA

address: 1126E Agronomy Hall

department: Agronomy

institute: Iowa State University

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring  conditions that occur at northern latitudes, usually coupled with excessive light, and that greatly affects the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for eight photosynthesis and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28°C/24°C), cold (15°C/15°C)  and recovery (28°C/24°C). Cold stress significantly reduced the photosynthetic capacity of sorghum plants and a total of 204 genomic regions were discovered associated with at least one trait in a particular treatment or in the time integrated response to cold.
If no GBS markers were available for the targeted candidate genes, new SNPs were developed and genotyped using a SNPtype™ Assay (Fluidigm) on the Fluidigm BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm.

overall_design: 98 SNPtype™ Assay were designed to genotype 24 photosynthesis-related genes in 359 diverse sorghum accessions. 82 SNPs were finally genotyped in all accessions using BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm.

first: Diego

last: Ortiz

first: Jieyun

last: Hu

middle: G