title: microRNAs profiling of amniotic fluid: evidence of the synergism of microRNAs in directing axon guidance during development

city: Hangzhou

first: Ting

middle: ting

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Neuroscience and Anatomy

institute: Zhejiang University School of Medicine

summary: Amniotic fluid is critical for the development of foetus, which provides the appropriate conditions for foetus growth. Besides its presumed traditional roles of providing movement place and protecting from crushing, amniotic fluid is considered to have more important roles in the nervous development of foetus respecting nervous related compositions and close contact with the skin of foetus. Peripheral nervous sensory system is the feeling basis for the body with neuritis anchoring on the surface of skin. The effect of amniotic fluid on the development of peripheral sensory nervous system is unknown. To disclose the relationship between amniotic fluid and peripheral sensory nervous system, we profiled microRNAs dynamic expression in amniotic fluid during the stages of E13, E15 and E17. The cluster analysis results showed that there were significantly two different expression profiles of microRNAs during this development stage. The followed informatics analysis results showed that these two groups of microRNAs synergistically regulate the axon guidance process. Axon tracing by fluorogold and co-labelled immunofluorescence results indicated that there was a direct interaction between amniotic fluid and peripheral sensory nervous system in axon guidance. Taken together, our work is helpful to understand the development of peripheral sensory nervous system of foetus.

overall_design: In this study, microRNAs in amniotic fluid cells were harvested at the stages of E13, E15 and E17 mice, then microRNAs expression profiles were performed on miRCURY microarrays. The following bioinformatics analysis, qRT-PCR and axon tracing results showed that there is a close relationship between microRNAs of amniotic fluid and the development of peripheral sensory nervous system.

middle: T

first: Shu

last: Ling


title: Transcriptional profiling the 150 kb linear plasmid of Borrelia turicatae implicates an important role in vector colonization and establishing mammalian infection.

status: Public on Feb 09 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

summary: As vector-borne pathogens transit between the arthropod and vertebrate, adaptation is key for survival as each host varies and initiates unique defense mechanisms. An environmental signal that relapsing fever (RF) and Lyme causing spirochetes detect is the change of temperature between vector and mammal, yet incomplete genomes have hindered progress in understanding the genetic constituents expressed during tick colonization. We conducted a combined transcriptional and genomic sequence analysis to further assemble the ~150 kb linear plasmid (lp150) of Borrelia turicatae, a causative agent of RF borreliosis. Contiguous sequences (contigs), which were originally generated by Sanger sequencing, contained open reading frames (ORFs) identified to be up-regulated by the spirochetes when grown under tick-like conditions compared to the mammal. To aid in assembling the contigs, a PacBio RS I Single Molecule Real-Time DNA sequencing approach was used, given extended nucleotide reads over several thousand base pairs. A 36 kb locus was identified toward the 3‘ end of lp150, and expression of the ORFs was verified in the tick and mammal. We report the most complete version of lp150, and this study indicates that the plasmid likely facilitates vector colonization and establishing early mammalian infection

platform_organism:
Borrelia hermsii
Francisella tularensis
Coxiella burnetii
Rickettsia prowazekii
Burkholderia mallei
Brucella suis

overall_design: Borrelia turicatae at 35ºC vs. 25ºC  vs. blood

first: Hannah

middle: K

last: Wilder

first: Sandra

last: Raffel

first: Alan

last: Barbour

first: Stephen

middle: F

last: Procella

first: Daniel

first: Benjamin

last: Vaisvil

first: Vinayak

last: Kapatral

middle: P

last: Schmitt

first: Tom

middle: G

last: Schwan

first: Job

middle: E

last: Lopez


title: Development of colorectal cancer miRNA expression signatures from expression profiles of embryonic development, precancer progression and cancer samples

city: Beijing

first: Kaitai

last: Zhang

state: Beijing

address: NO. 17, Pan Jiayuan South, Chao Yang District

department: Department of Etiology and Carcinogenesis

country: China

institute: Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences

summary: To further development of our gene expression signature for survival prediction, we conducted expression profiles of embryonic development, precancer progression and cancer samples.

overall_design: Developing colon was obtained from 16 cases of abortion in Maternal & Child Health Care Hospital of Hai Dian between 2007 and 2009. The samples included whole embryos (WE) at 3 to 5 postovulatory weeks (PWs), early embryonic colons (EEC) at 8 to 10 PWs and middle embryonic colons (MEC) at 14 to 22 PWs.Normal colorectal mucosae samples were collected from patients with hemorrhoids who received surgical excision in the Department of Colon and Rectal Surgery of Beijing Shi Ji Tan Hospital between 2009 and 2010.

first: An

last: Ning

first: Zhang

last: Kaitai


title: Differential expression produced by Pdrg1 gene silencing in rat hepatoma H35 cells

city: Madrid

first: Maria Angeles

last: Pajares

address: Arturo Duperier 4

department: Metabolismo y Señalizacion Celular

country: Spain

institute: Instituto de Investigaciones Biomedicas Alberto Sols (CSIC-UAM)

summary: RTqPCR results suggested a relevant role for Pdrg1 in rat hepatoma H35 cells, where its expression was dramatically enhanced. Hence, these cells were chosen as a suitable model for stable Pdrg1 silencing. For this purpose, H35 cells were transfected with appropriate shRNA plasmids against Pdrg1 and stable clones isolated. Among those exhibiting reproducible behavior, clones CN-10 (negative control), 3-44 (shRNA3) and 4-18 (shRNA4) were selected for further analysis. Pdrg1 expression analyzed by RT-qPCR was reduced by 50% and 70% in 3-44 and 4-18 clones, respectively, as compared to CN-10. RNAs of CN-10, 3-44 and 4-18 clones, as well as, RNA of an enriched pool of shRNA3 transiently transfected cells (shRNA3T) were used for expression analysis using Agilent one-color microarrays. Genes exhibiting changes ≥2-fold with FDR<0.05, according to LIMMA analysis, were identified. Pathway analysis was performed with BioProfiling using data of 114 genes (74 upregulated and 40 downregulated) exhibiting similar behavior in the three silenced samples. Selected genes, at least two of pathways with p≤0.02, were used for verification of expression changes by RT-qPCR, together with Pdrg1.

overall_design: Silencing of rat Pdrg1 expression was carried out by transfection of rat hepatoma H35 cells with SureSilencing shRNA plasmids (SaBioscience) containing sequences designed for this purpose and a negative control sequence. Stable clones for the negative control (CN), shRNA3 and shRNA4 plasmids were obtained by selection using G418 up to 4 mg/ml. This procedure rendered approximately 200 stable clones for each plasmid, from which one of each was selected [CN-10, shRNA3 (3-44) and shRNA4 (4-18)] for further experiments. Four biological replicates of these stable clones  and a transiently transfected shRNA3 H35 enriched pool (shRNA3T), were independently hybridized for each transcriptomic comparison.

first: Maria

middle: A

first: Claudia

middle: D

last: Perez

first: Franciso

middle: J

last: Pérez-Zúñiga

first: Francisco

last: Portillo

first: Edel

last: Reytor

last: Garrido


title: Temporal profiling and network analysis of rhythmic gene expression and novel functional gene annotation in the water flea, Daphnia pulex

city: Notre Dame

first: Jacqueline

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary:
We analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 48 hr time period using a cosine-fitting algorithm. Additionally, using a comprehensive network modeling and analysis approach, we go beyond the standard statistical analyses of the gene expression data. By doing so, we identified novel co-regulated rhythmic genes that have similar network topological as well as functional annotations as rhythmic genes identified by the statistical analyses but that cannot be identified by cosine-fitting alone. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus complementing the current limited functional annotation data. Our results revealed extensive 24 hr rhythms in gene expression patterns.
Moderate longitudinal study of circadian rhythm with twelve 4-hour period measurements collected over the course of 48 hours. See Supplimental Image - Modified Loop Design.png

overall_design: Periodic measures were compared in a nearly saturated modified loop design with N-period time point compared with N+4-hour period time point, followed by N-period time point compared with N+12-hour period time point. The loop is closed with N+4-hour period time point compared with N-period time point and N+12-hour period time point compared with N-period time up to the 3rd cycle.

first: Samuel

middle: S

last: Rund

first: Boyoung

last: Yoo

first: Camille

last: Alam

first: Taryn

last: Green

first: Melissa

last: Stephens

first: Erliang

last: Zeng

first: Aaron

last: Sheppard

first: Giles

last: Duffield

first: Tijana

last: Milenković

first: Michael

last: Pfrender


title: Real-time quantitative PCR analysis of MAPK cascade genes in brachypodium distachyon of different tissues and under multiple stresses

city: Shanghai

first: Zhaoqing

last: Chu

address: 3888 Chenhua Road, Songjiang

institute: Shanghai Chenshan Plant Science Research Center, CAS

summary: MAPK cascades genes responding to 14 stresses were screened using qPCR. All samples were repeated with 3 times and ACTIN was regarded as house keeping gene.  The stresses included heavy metal treatments, environmental factors, phytohormones and biotic treatments.

overall_design: qPCR gene expression profiling. The 20d-seedlings were used and the 3µg of total RNA were sysnthesis for cDNA by using PrimeScript Reverse Transcriptase (TAKARA).

first: Min

last: Jiang


title: Mouse livers: control vs miR-155 transgenic mice

city: Guangzhou

first: Lin

last: Xiaolin

address: Tonghe

department: Southern Medical University

institute: Cancer reseach institute

summary: Transcriptional profiling of mouse livers comparing control mice with miR-155 transgenic mice that overexpression of miR-155 in the liver

overall_design: Two-condition experiment, control  vs miR-155 transgenic mice livers. Biological replicates: 3 control, 3  transgenic, independently grown and harvested. One replicate per array.

first: Dong

last: Xiao

first: Xiaolin

last: Lin


title: Liver gene expression profiles of  interferon therapy in chronic hepatitis B Patients (Exon)

city: Taichung

first: Tzu-Hung

last: Hsiao

address: 1650 Taiwan Boulevard Sect. 4

department: Department of Medical Research

country: Taiwan

institute: Taichung Veterans General Hospital

summary: With 350 million carriers worldwide who may suffer from serious sequelae, including hepatocellular carcinoma, chronic hepatitis B virus (CHB) infection remains an important health issue. Current antiviral therapies hardly eradicate the virus. Therefore, there are still imperative need to develop new therapeutic strategies and predictors for treatment response to cure the disease and avoid futile treatment. By taking the advantage of having the paired liver biopsy samples of IFNalpha responders before/after treatment and pretreatment samples from responders and non-responders, we could characterize the intrahepatic expression profiles associated with necroinflammatory activity and the profiles/signature potentially predictive of response to IFNalpha therapy for CHB in this study.

overall_design: RNA was extracted from pairedliver tissues for gene expression analysis.  The gene expression profiles of seven paired liver biopsy samples of IFNalpha responders before/after treatment and other 3 pre- treatment samples were obtained by Affymatrix U133plus2 microarray. We also pooled samples of 11 responders  and 11 non-responders to perform affymatrix EXON ST 1.0 array.

first: Hui-Lin

last: Wu

first: Chun-Jen

last: Liu


title: Neisseria gonorrhoeae drg::cm versus wild type and Neisseria gonorrhoeae drg::dam versus wild type

city: Warsaw

first: Monika

middle: Julita

last: Adamczyk-Poplawska

address: Miecznikowa 1

country: Poland

institute: University of Warsaw

summary: Transcriptional profiling of N. gonorrhoeae comparing wild type cells to cells with inactivated by chloramphenicol cassette (cm) dam replacing gene (drg) or wild type cells comparing to cells with inserted dam gene. The Goal was to study the role of drg or dam presence in overall expression profile.

overall_design: Two-condition experiment, wild type cells vs. mutant cells . Biological replicates: 4 control replicates, 4 mutant replicates.

first: Agnieszka

last: Kwiatek


title: Autoantibody Profiles in Collagen Disease Patients with Interstitial Lung Disease

city: Sagamihara

first: Hiroshi

last: Furukawa

address: 18-1 Sakuradai, Minami-ku

country: Japan

institute: Sagamihara Hospital, National Hospital Organization

summary: Auto-antibody (Ab) profiles between acute-onset diffuse ILD (AoDILD) and stable states of 25 collagen disease patients were compared to screen biomarkers or pathogenic auto-Abs.

overall_design: Auto-Ab levels in pooled sera were compared between the AoDILD and stable states with ProtoArray.

first: Shigeto

last: Tohma


title: Real-time quantitative PCR analysis of Brachypodium distachyon

summary:
96 BdbZIPs responding to 14 stresses were screened using qPCR. All samples were repeated with 3 times and GAPDH was regarded as house keeping gene.
The stresses included heavy metal treatments, environmental factors and phytohormones

first: Xiang


title: Gene expression induced by blue light stimulation to oyster mushroom mycelia

city: Kami-ina

first: Masanobu

last: Kojima

state: Nagano

address: 8304 Minami-minowa

department: Bioscience and Biotechnology

institute: Shinshu University

summary:
Photoresponse mechanism of oyster muchroom mycelia was studied using a custom microarray prepared on the basis of the genome information (Pleurotus ostreatus PC15 v2.0) in JGI Genome Portal.
Blue light stimulation to the mycelia caused the up-regulation and down-regulation of genes expression. Particulary, the genes coding rate-controlling enzymes in glycolysis, pentose phosphate, and sikimic acid pathways were up-regulated to accumulate shikimic acid dramatically.

overall_design: In this study, the time course of gene expression in oyster mushroom mycelia caused by blue light stimulation using light emitting diodes (LED) was analyzed at 0, 0.5, 1, 3, 6, 12, 24, 36 h.


title: Hypoxia and fin regenerating Zebrafish fins: Normoxic regenerating control fins (blastema) vs hypoxic blastema (3 days following fin amputation in presence of CoCl2)

city: PESSAC

first: Abdel-Majid

last: Khatib

address: av des Facultes

country: France

institute: INSERM

summary: Transcriptional profiling of zebrafish rergenerating fins comparing normoxic renenerating fins and hypoxic regenerating fins (3 days following fin amputation)

overall_design: Two-condition experiment, normoxic regenerates (Blastema) vs. hypoxic regenerating fins (3 days following fin amputation)

first: Geraldine

last: Siegfried


title: Zebrafish fins: normoxic Controls vs. hypoxic fins

summary: Transcriptional profiling of zebrafish fins comparing control fins and hypoxic fins (cobalt chloride (CoCl2, 1 mM)

overall_design: Two-condition experiment, normal fins vs hypoxic fins


title: A novel action mechanism for MPT0G013, a derivative of arylsulfonamide, inhibits tumor angiogenesis through up-regulaiton of TIMP3 expression

city: Taipei

first: Chih-Ya

last: Wang

address: No. 1, Sect. 1, Jen-Ai Road

department: Pharmacological Institute

institute: National Taiwan University

summary: Tissue inhibitors of metalloproteinases 3 (TIMP3) were originally characterized as inhibitors of matrix metalloproteinases (MMPs), acting as potent antiangiogenic proteins. In this study, we demonstrated that the arylsulfonamide derivative MPT0G013 has potent antiangiogenic activities in vitro and in vivo via inducing TIMP3 expression. Treatments with MPT0G013 significantly inhibited endothelial cell functions, such as cell proliferation, migration, and tube formation, as well as induced p21 and cell cycle arrest at the G0/G1 phase. Subsequent microarray analysis showed significant induction of TIMP3 gene expression by MPT0G013, and siRNA-mediated blockage of TIMP3 up-regulation abrogated the antiangiogenic activities of MPT0G013 and prevented inhibition of p-AKT and p-ERK proteins. Importantly, MPT0G013 exhibited antiangiogenic activities in in vivo Matrigel plug assays, inhibited tumor growth and up-regulated TIMP3 and p21 proteins in HCT116 mouse xenograft models. These data suggest potential therapeutic application of MPT0G013 for angiogenesis-related diseases such as cancer.

overall_design: Two groups are analyzed, including CTL group and MPT0G013-treated group

first: Jing-Ping

last: Liou

first: An-Chi

last: Tsai

first: Mei-Jung

last: Lai

first: Yi-Min

first: Hsueh-Yun

last: Lee

first: Jing-Chi

first: Shiow-Lin

last: Pan

first: Che-Ming

last: Teng


title: The C10orf10 protein profiling of breast cancer specimens based on a tissue array

city: Chongqing

first: jianjun

last: li

address: No. 29, Gaotanyan Street, Shapingba District

institute: Department of Oncology, Southwest Hospital

summary: Expression levels of C10orf10 protein were obtained for a series of 100 breast cancer tumor specimens.

overall_design: Immunohistochemical staining was performed using the antibody against C10orf10 (1:50; Santa Cruz Biotechnology,sc-162735). The staining was evaluated for the tumor cells. The immunostaining was considered positive when ≥10% of the tumor cells being immunoreactive. The percentage of positive cells, as the extent of immunostaining, was quantified classified into 5 groups under microscope: <10% positive cells for 0; 10% to 25% for 1; 26% to 50% for 2; 51% to 75% for 3 and ≥ 76% for 4. The intensity of staining was graded as negative (scored as 0), weak (1), moderate (2) or strong (3) positivity. The two pathologists independently reviewed all core biopsies. The sum of the percentage of positive staining and the intensity was used to define expression levels.

first: Junjiang

last: Deng

first: Yan

last: Dong

first: Chong

last: Li

first: Wenwei

last: Zuo

first: Gang

last: Meng

first: Chengping

last: Xu

first: Jianjun


title: Zebrafish 2.25 dpf embryos: controls vs. med14 mutants

city: Toronto

first: Ian

middle: Cameron

last: Scott

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Childen

summary:
Transcriptional profiling of 2.25 dpf (days post fertilzation) zebrafish embryos comparing wildtype (control) to med14 (mediator complex subunit 14) mutants.
Goal was to determine the extent to which transcription was affected in med14 mutants by analyzing global gene expression.

Background: Mediator is an evolutionarily conserved multi-subunit complex that physically links the RNA polymerase II transcriptional machinery to enhancer bound regulatory factors. While classically described as a core component of the transcriptional machinery, recent evidence suggests that Mediator may have context-dependent roles. In particular, a requirement for Mediator in the maintenance of embryonic and induced pluripotent stem cells has been noted. However, the in vivo consequences of loss of function of many Mediator subunits are unknown.
Results: We identified med14, which encodes a Mediator subunit, as the gene affected in the zebrafish logelei (log) mutant. log mutants displayed a morphological arrest by 2 days of embryonic development. Surprisingly, microarray analysis showed that transcription was not broadly affected in log mutants. Transplanted log cells placed into a wild-type environment were able to survive into adulthood, suggesting a lack of global transcriptional defects in Med14-deficient cells. RNAi knockdown of the single med14 ortholog in planarians demonstrated that med14 was required for adult stem cell maintenance and regeneration. A broader assay of Mediator subunits revealed that many were required for stem cell maintenance in planarians. Multiple stem/progenitor cell populations were observed to be reduced or absent in zebrafish med14 mutant embryos, with embryonic fin regeneration defects also evident.
Conclusions: Taken together, our results show a critical, evolutionarily conserved, function for Med14 (and perhaps Mediator in general) in evolutionarily conserved in vivo stem cell maintenance and regeneration, distinct from a ubiquitous role in transcription.

overall_design: Two-condition experiment, control vs. mutant: 2 Biological replicates

first: Jeffrey

last: Burrows

middle: C


title: Expression profiling of zebrafish fin regeneration: role of hypoxia

first: Abdel-Majid

last: Khatib

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

overall_design: Refer to individual Series


title: Mock treated vs. Colletotrichum acutatum Infected Camarosa strawberry crowns.

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: Transcriptome Response of Strawberry (Fragaria × ananassa) cultivar Camarosa  to Colletotrichum acutatum Infection.

overall_design: Two-condition experiment, ‘Camarosa’ infected vs. ‘Camarosa’ uninfected. Biological replicates: 3 biological replicates, randomly paired infected-uninfected

first: Amil-Ruiz

last: Francisco

first: Gadea

last: Jose


title: Construction of a subtracted gDNA microarray for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

city: Bundoora

first: Mian-Chee

last: Gor

state: Victoria

address: Plenty Road

department: School of Applied Sciences

country: Australia

institute: RMIT University

summary: Breeding day-neutral strawberry (Fragaria x ananassa Duchesne) is pivotal to extend fruit-bearing season and increase the efficiency of production. However, genetic improvement of day-neutrality by the means of molecular marker technologies remains slow due to genome complexity of octoploid strawberry. This study employs an innovative approach by integrating the Subtracted Diversity Array (SDA) technology and Bulked Segregant Analysis (BSA) to facilitate the identification of molecular markers associated with day-neutrality in octoploid strawberry. A Fragaria Discovery Panel (FDP) containing 287 features specific to strawberry genome was constructed as a platform for rapid screening of DNA polymorphism between one short day (SD) strawberry DNA bulk and three day-neutral (DN) bulks varrying in flowering strength. Differential array hybridisation patterns between the DN and SD bulks revealed a novel molecular marker, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. Interestingly, a 12 bp deletion was observed within the FaP2E11 sequence cloned from SD genotypes but not DN genotypes. As cytokinin is required to induce flowering, this result indicates that full sequence of FaP2E11 and the sequence with deletion are allelic variants linked to the low enzyme activity CKX1 and the wild type alleles, respectively.

overall_design: To selectively capture flowering associated sequences specific to strawberry, genomic DNA subtraction was performed between a pool of five strawberry genotypes and nine non-angiosperm species using Suppression Subtractive Hybridisation (SSH) technique. A total of 287 subtracted fragments were used to construct a strawberry-specific Subtracted Diversity Array (SDA). Validation of the array revealed a high subtraction efficiency (99%), indicating that the subtracted fragments are strawberry-specific. To investigate the ability of SDA for marker-trait association, three segregating populations: (1) DN ‘01-061-311’ x SD ‘Juliette’, (2) DN ‘01-061-311’ x DN ‘05-069-63’ and (3) DN ‘01-061-311’ x DN ‘05-069-194’ were chosen for BSA based on flowering habits of parental genotypes. The DNA of the individuals derived from the F1 populations were pooled into four bulks: strong day-neutral (DN1), intermediate day-neutral (DN2), weak day-neutral (DN3) and short day (SD) according to flowering strength. Each DNA bulk was hybridised separately onto the SDA. All hybridisations were performed with six technical replicates and two biological replicates to ensure microarray reproducibility, resulting in 12 data points per feature.

first: Edwin

last: Pang

first: Nitin

last: Mantri


title: Harnessing Noxa Demethylation to overcome Bortezomib resistance in Mantle Cell Lymphoma

city: New York

first: Samir

last: Parekh

state: NY

address: 1470 Madison Ave, 5th FL, Room 114

department: Hematology and Medical Oncology

institute: Icahn School of Medicine at Mount Sinai

summary: Bortezomib (BZM) is the first proteasome inhibitor approved for relapsed Mantle Cell Lymphoma (MCL) with durable responses seen in 30%-50% of patients. The biological basis for differences in response to BZM is not completely understood. Our previous work demonstrated marked differences in methylation between primary MCL and normal B cells. We hypothesized that a subset of aberrantly methylated genes may be modulating BZM response in MCL patients. We examined genome-wide DNA methylation profiles in MCL patient treated with BZM using a NimbleGen array platform. DNA methylation analysis revealed a striking promoter hypomethylation in MCL patient samples following BZM treatment. Pathway analysis of differentially methylated genes identified molecular mechanisms of cancer as a top canonical pathway enriched among hypomethylated genes in BZM treated samples. Noxa, a pro-apoptotic Bcl-2 family member essential for the cytotoxicity of BZM, was significantly hypomethylated and induced following BZM treatment. Therapeutically, we could demethylate Noxa and induce anti-lymphoma activity using BZM and the DNA methytransferase inhibitor Decitabine (DAC) and their combination in vitro and in vivo in BZM resistant MCL cells. Noxa depletion by RNA interference protected MCL cells from death by these agents. These findings suggest a role for dynamic Noxa methylation for therapeutic benefit of BZM. Potent and synergistic cytotoxicity between BZM and DAC in vitro and in vivo supports a strategy for using epigenetic priming to overcome BZM resistance in relapsed MCL patients. Our data demonstrate that genomic methylation profiling can provide mechanistic insights to guide novel therapeutic approaches.

overall_design: Unbiased genome-wide analysis of DNA methylation from paired pre- and 96-hour post- Bortezomib treatment samples obtained from 6 patients newly diagnosed with leukemic mantle cell lymphoma (MCL).

first: Violetta

last: Leshchenko

first: Pei-Yu

last: Kuo

first: Zewei

last: Jiang

first: Marc

last: Weniger

first: Jessica

last: Overbey

first: Wyndham

middle: H

last: Wilson

first: Adrian

last: Wiestner


title: CGH analysis of mouse embryonic stem cells trisomic for chromosome 6, 8, 11,12 and 15

first: Meili

last: Zhang

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

type: Genome variation profiling by genome tiling array

summary: Aneuploidy, an uneven number of chromosomes, leads to severe developmental defects in mammals and is also a hallmark of cancer. However, whether aneuploidy is a driving cause or a consequence of tumor formation remains controversial. Paradoxically, existing studies based on aneuploid yeast and mouse fibroblasts have shown that aneuploidy is usually detrimental to cellular fitness. Here, we examined the effects of aneuploidy on mouse embryonic stem cells. Using a novel genetic scheme, we generated a series of aneuploid cell lines that each carries an extra copy of single chromosomes and then characterized the traits shared by these cell lines. All the aneuploid cell lines had rapid proliferation rates and enhanced colony formation efficiencies. They were less dependent on growth factors for self-renewal and showed a reduced capacity to differentiate in vitro. Moreover, xenografted aneuploid stem cells formed teratomas more efficiently, with features of neoplastic progression. These findings demonstrate that aneuploidy enhances the self-renewal capacities of stem cells and reduces their differentiation abilities.

overall_design: Array comparative genomic hybridization (aCGH) was performed to detect the DNA copy number variants of the trisomic mES cells on a genome-wide scale. For Ts6, Ts8, Ts11 and Ts15 ES cells, we used the wild-type AB1 mES cells (129 S7/SvEvBrd, male) as reference. For Ts8-JM8 and Ts12-JM8 ES cells, we usedJM8A3 mES cells (C57BL/6N, male) as reference. The copy number variants of all the cell lines were analyzed by NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Arrays (Build MM9) with an average probe spacing of 3.5 kb.

first: Yuyan

last: Jia

first: Guang

last: Liu

first: Shuhui

last: Song

first: Li

last: Cheng

first: Allan

last: Bradley

first: Yue

last: Huang


title: Pharmacologic disruption of agr quorum sensing in Staphylococcus aureus promotes host defense against skin and soft tissue infections

city: Hamilton

first: Dan

last: Sturdevant

address: 903 S 4th street

institute: NIH

summary: Drug discovery for novel anti-infectives is essential to meet the global health threat of antibiotic resistant bacterial infections, including those caused by Staphylococcus aureus1,2. Because ~90% of S. aureus infections involve skin and soft tissues (SSTIs)3,4, we hypothesized that developing anti-virulence therapeutics5,6 for SSTIs could minimize pressure on resistance development while sparing conventional antibiotics for control of systemic infections. We identified a small molecule inhibitor that disrupted signaling by a quorum sensing operon, agr, associated with human SSTIs7,8 without affecting agr-independent growth.

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: quorom sensing, wild type vs. agr mutant, savirin treatment

first: Erin

last: Sully

first: Natalia

last: Malachowa

first: Bradley

middle: O

last: Elmore

first: Susan

middle: M

last: Alexander

first: Jon

last: Femling

first: Brian

last: Gray

first: Frank

middle: R

last: DeLeo

first: Alexander

last: Horswill

first: Michael

last: Otto

first: Ambrose

middle: L

last: Cheung

first: Bruce

last: Edwards

first: Larry

last: Sklar

first: Pamela

last: Hall

first: Hattie

last: Gresham


title: Arabidopsis thaliana Wild-type vs. mutant sdg2

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

institute: IBMP-CNRS

summary: Transcriptional profiling of Arabidopsis wild-type (Col0) control seedlings with corresponding mutant seedlings is performed using Aligent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K).

overall_design: 15-day-old seedlings of wild-type Col0 control _vs_ 15-day-old seedlings of mutant sdg2-1. Three biological replicates. One replicate per array.

first: Alexandre

last: Berr

first: Anne

last: Molitor

first: Donghong

last: Chen


title: Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

institute: Institut national de la santé et de la recherche médicale-INSERM

summary:
Long-term allograft survival generally requires lifelong immunosuppression. Rarely, recipients display spontaneous operational tolerance with stable graft function in the absence of immunosuppression. The lack of biological markers of this phenomenon precludes identification of potentially tolerant patients in which immunosuppression could be tapered and hinders the development of new tolerance inducing strategies. The objective of this study was to identify minimally invasive blood biomarkers for operational tolerance and utilize these biomarkers to determine the frequency of this state in immunosupressed patients with stable graft function. Blood gene expression profiles from 75 renal transplant patient cohorts (operational tolerance/acute and chronic rejection/stable graft function on immunosuppression) and 16 healthy individuals were analyzed. A subset of samples was used for microarray analysis where three-class comparison of the different groups of patients identified a tolerant footprint of 49 genes. These biomarkers were applied for prediction of operational tolerance by microarray and real-time PCR in independent test-groups. 33/49 genes correctly segregated tolerance and chronic rejection phenotypes with 99% and 86% specificity. The signature is shared with 1/12 and 5/10 stable patients on triple immunosuppression and low dose steroid monotherapy respectively. The gene signature suggests a pattern of reduced co-stimulatory signaling, immune quiescence, apoptosis and memory T cell responses. This study identifies in the blood of kidney recipients a set of genes associated with operational tolerance that may have utility as a minimally-invasive monitoring tool for guiding immunosuppression titration. Further validation of this tool for safe immunosuppression minimization in prospective clinical trials is warranted.
67 samples were analyzed, no replicates included:  1. TOL (n = 12). patients with long-term stable graft function, without immunosuppression for at least 2 years  2. MIS (n = 10). Patients with stable graft function on steroid monotherapy (<10 mg/day) for 4.6. Calcineurin inhibitors and CellCept were removed in these patients because of previous posttransplant lymphoproliferative disease (n = 6), cancer (n = 2), or uncontrolled infectious disease (n = 2).  3. STA (n = 12). Patients with stable kidney graft function at >5 years posttransplantation while under mycophenolate mofetil or azathioprine and maintenance steroids with (n = 5) or without (n = 7) an associated calcineurin inhibitor.  4. AR (n = 14). Patients experiencing rapid decline (>20% from baseline) in graft function and biopsy-proven AR.  5. CR (n = 11). Patients having a progressive degradation of their renal function (creatinine clearance of <60 ml per min per 1.73 m2 and/or proteinuria of >1.5 g/day) and histological signs CR.  6. N (n = 8). These subjects all had normal blood formulae and no infectious or other concomitant pathology for at least 6 months before the study.

overall_design: 67 PBL (Peripheral Blood Leukocytes) samples from 6 groups (TOL, MIS, STA, AR, CR, N) were analyzed by microarray.

first: Sophie

last: Brouard

first: Elaine

last: Mansfield

first: Christophe

last: Braud

first: Li

last: Li

first: Magali

last: Giral

first: Szu-chuan

last: Hsieh

first: Dominique

last: Baeten

first: Meixia

last: Zhang

first: Joanna

last: Ashton-Chess

first: Cecile

last: Braudeau

last: Dupont

first: Annaik

last: Pallier

last: Moreau

first: Stephanie

last: Louis

first: Catherine

last: Ruiz

first: Oscar

last: Salvatierra

first: Jean-Paul

last: Soulillou

first: Minnie

last: Sarwal


title: 5-Fluorouracil-induced intestinal mucositis via nuclear factor-κB activation

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: 5-Fluorouracil (5-FU) is a commonly used drug for the treatment of malignant cancers. However, approximately 80% of patients undergoing 5-FU treatment suffer from gastrointestinal mucositis. The aim of this report was to identify the critical molecule involved in 5-FU-induced intestinal mucositis. Our data showed that 5-FU induced inflammation in the small intestine, characterized by the increased intestinal wall thickness and crypt length and the decreased villus height. Network analysis of 5-FU-affected genes by transcriptomic tool showed that the expression of genes was regulated by nuclear factor-κB (NF-κB), and NF-κB was the central molecule in the 5-FU-regulated biological network. NF-κB activity was activated by 5-FU in the intestine, which was judged by bioluminescence imaging and immunohistochemical staining. However, 5-aminosalicylic acid (5-ASA) inhibited 5-FU-induced NF-κB activation and proinflammatory cytokine production. Moreover, 5-FU-induced histological changes were improved by 5-ASA. In conclusion, our findings suggested that NF-κB was the critical molecule associated with the pathogenesis of 5-FU-induced mucositis, and inhibition of NF-κB activity ameliorated the mucosal damage caused by 5-FU.

overall_design: Male mice were injected intraperitoneally with 5-FU (100 mg/kg). Two days later, intestines were collected for RNA extraction. 3 5-FU-treated replicates and 3 mock replicates.

first: Tin-Yun

last: Ho


title: Scleral miRNA profiles in adult and fetal eyes

city: Berkeley

first: Ravikanth

last: Metlapally

address: 588 Minor Hall

institute: UC Berkeley

summary: Introduction: In human eyes, ocular enlargement/ growth, reflects active scleral extracellular matrix remodeling. miRNAs are small non-coding RNAs that regulate gene expression by base pairing with target sequences, and serve as nodes of signaling networks. We hypothesized that the sclera, like most tissues, expresses miRNAs, some of which modulate genes regulating ocular growth. In this study, the scleral miRNA expression profile of rapidly growing human fetal eyes was compared with that of stable adult donor eyes using high-throughput microarray and quantitative PCR analyses.  Results: Human sclera expressed several miRNAs. Microarray comparison of adult and fetal samples revealed many to be differentially expressed (p<0.01, min p= 6.5x10^11), with increased expression of collagen specific mir-214, let-7c, let-7e, mir-103, mir-107, and mir-98 in fetal sclera subsequently confirmed (1.5 to 4 fold changes, p<0.01). For both adult and fetal samples, no significant differences in miRNA expression profiles of sclera from posterior and peripheral ocular regions were observed.   Conclusion: This is the first study to catalogue miRNA expression in human sclera. The sclera expresses several miRNAs, some of which show age-related differential regulation, higher in rapidly growing fetal eyes, consistent with a role in ocular growth regulation. These findings may be useful for linking scleral miRNA expression with potential manipulation in disorders such as scleral ectasia/ axial myopia.

overall_design: Scleral samples from normal human fetal (24 wk) and normal adult donor eyes (n=4 to 6, each group) were obtained, and RNA extracted. Genome-wide miRNA profiling was performed using the Agilent miRNA microarray platform. miRNA target predictions were obtained using Microcosm, TargetScan and PicTar algorithms.


title: CGH of Drosophila Follicle Cell Amplicons in double-strand break repair mutants

status: Public on Feb 08 2017

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
CGH of stage 13 amplifying follicle cells to measure changes in replication fork progression in double-strand break repair mutants
Comparative genomic hybridization was performed to compare amplification gradients of stage 13 follicle cells from several double-strand break repair mutants to wild type (OrR) gradients. Two-three replicates were done for each genotype.

overall_design: Stage 13 egg chamber genomic DNA from each genotype was measured relative to diploid genomic DNA from 0-2 hour wild-type (OrR) embryonic DNA.

first: Jessica

last: Alexander

first: Kelly

last: Beagan

first: Mitch

last: McVey


title: Expression data from epidermis specific phytochrome B or global phytochrome B line comparing to phyB-9 mutant.

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

summary: Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.

overall_design: ML1pro:PHYBGFP/phyB-9 and PHYBpro:PHYBGFP/phyB-9 and phyB-9 seeds were grown in continuous red condition (11.4 μmol·m−2·s−1) and then, sampled for RNA extraction. Total 4 biological replicates were used for the microarray

first: G


title: Transcriptome analysis of Al stress response genes (Al stress induced genes and repressed genes) in Arabidopsis

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Comparison of gene expression pattern of Al response genes between the two Arabidopsis genotypes, wild type (Columbia-0) and the AvSAMS1-expressing transformant

overall_design: Two-condition experiment, Al treated plants vs. untreated plants. Biological replicates: 2 replicates in wild types, 2 transgenic lines.

first: Bunichi

last: Ezaki


title: Expression data from root tips of Medicago truncatula wild type and ngr mutant

city: Ardmore

first: Rujin

last: Chen

state: OK

address: 2510 Sam Noble Pkw

department: Plant Biology Division

institute: The Samuel Roberts Noble Foundation, Inc.

summary:
Root gravitropic response involves signal perception, signal transduction, asymetric auxin transport and differential cell elongation in the root tip. However, the regulatory mechanisms remain largely unknown.
We used microarray to compare transcript profiles in the root tip samples of wild type and ngr mutant.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Medicago truncatula wild type and ngr mutant derived from fast neutron bombardment (FNB) mutagenesis were grown in an aeroponic system for five days. Three centimeter-long root tips were collected for RNA isolation and microarray experiments.

first: Ashvery

last: Laxmi

first: Yuhong

last: Tang


title: Methylation RIKEN-cohort

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

summary:
BACKGROUND:
Obesity is associated with changes in fat cell gene expression and metabolism. What drives these changes is not well understood. We aimed to explore fat cell epigenetics, i.e., DNA methylation, as one mediator of gene regulation, in obese women. The global DNA methylome for abdominal subcutaneous fat cells was compared between 15 obese case (BMI 41.4?±?4.4 kg/m(2), mean?±?SD) and 14 never-obese control women (BMI 25.2?±?2.5 kg/m(2)). Global array-based transcriptome analysis was analyzed for subcutaneous white adipose tissue (WAT) from 11 obese and 9 never-obese women. Limma was used for statistical analysis.
RESULTS:
We identified 5529 differentially methylated DNA sites (DMS) for 2223 differentially expressed genes between obese cases and never-obese controls (false discovery rate <5 %). The 5529 DMS displayed a median difference in beta value of 0.09 (range 0.01 to 0.40) between groups. DMS were under-represented in CpG islands and in promoter regions, and over-represented in open sea-regions and gene bodies. The 2223 differentially expressed genes with DMS were over-represented in key fat cell pathways: 31 of 130 (25 %) genes linked to "adipogenesis" (adjusted P?=?1.66?×?10(-11)), 31 of 163 (19 %) genes linked to "insulin signaling" (adjusted P?=?1.91?×?10(-9)), and 18 of 67 (27 %) of genes linked to "lipolysis" (P?=?6.1?×?10(-5)). In most cases, gene expression and DMS displayed reciprocal changes in obese women. Furthermore, among 99 candidate genes in genetic loci associated with body fat distribution in genome-wide association studies (GWAS); 22 genes displayed differential expression accompanied by DMS in obese versus never-obese women (P?=?0.0002), supporting the notion that a significant proportion of gene loci linked to fat distribution are epigenetically regulated.
CONCLUSIONS:
Subcutaneous WAT from obese women is characterized by congruent changes in DNA methylation and expression of genes linked to generation, distribution, and metabolic function of fat cells. These alterations may contribute to obesity-associated metabolic disturbances such as insulin resistance in women.

overall_design: Abdominal subcutaneous adipose needle biopsies were obtained from women (n=56) with a wide variation in BMI. From the biopsies we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA),  labelled RNA to Affymetrix miRNA arrays, and bisulphite converted DNA to Illumina Infinium HumanMethylation27 beadchips using standardised protocols (Affymetrix Inc., Illumina Inc.) . Subsequent analyses of gene expression was performed using the Affymetrix GeneChip Operating Software version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100. Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2. Subsequent analyses were performed using Genome Studio Methylation Module 1.0 (Illumina Inc.)

first: Niklas

last: Mejhert

first: Erik

last: Arner

first: Peter


title: Renal fibrosis mRNA classifier: validation in experimental lithium-induced interstitial fibrosis in the rat kidney

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

summary:
Metzincins and related genes (MARGS) play important roles in ECM remodeling in fibrotic conditions.
In this investigation, gene expression was examined in a rat model to investigate whether the previously described MARGS based fibrosis classifier had diagnostic value in an experimental rat model of lithium-induced renal fibrosis

overall_design: Male Wistar rats (n=12) were divided into 2 groups (n=6) One group was given a diet containing lithium (40 mmol/kg food for 7 days, followed by 60mmol/kg food for the rest of the experimental period, while a control group (n=6) was fed a normal diet. After six months, animals were sacrificed and the renal cortex and medulla of both kidneys removed for analysis. For microarray investigation, 24 GeneChip® Affymetrix Rat Exon 1.0 ST arrays were used. Statistically relevant genes (p-value<0.05, fold change>1.5, t-test) were further examined.

first: Aaron

last: Jeffs

first: Andreas

last: Scherer

first: John

last: Leader

first: Catherine

first: Jennifer

last: Bedford

first: Hans-Peter

last: Marti

first: Robert

last: Walker


title: Detection of genes from five gene expression panels (GEPs) in breast tumor samples using NanoString nCounter analysis

city: Pittsburgh

first: Rekha

last: Gyanchandani

state: PA

address: 204 Craft Avenue

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

summary: The aim of this study was to examine the effect of intra-tumor heterogeneity (ITH) on detection of genes within gene expression panels (GEPs), and the subsequent ability to predict prognostic risk. Multiplexed barcoded RNA analysis was used to measure the expression of 141 genes from five GEPs (Oncotype Dx, MammaPrint, PAM50, EndoPredict, and BCI) in breast cancer tissue sections and tumor-rich cores from 71 ER positive node-negative tumors. Tumor regions with high Ki67 and/or low PR were also used to punch cores, potentially representing aggressive areas of a tumor. In addition to examining the effect of ITH on measurement of GEPs, the effect of ITH on prediction of prognosis in the Oncotype Dx assay was also assessed.

overall_design: For each patient, the FFPE block that was used for the clinical Oncotype Dx test was selected, and a 5µM section, and a 0.6mm core from a tumor-rich representative part of the block was cut.  Additional cores were cut from tumors that had foci of high Ki67 (n=26), low PR (n=13), or both (n=5). In total, 181 samples were processed for NanoString nCounter analysis.

first: Yan

last: Lin

first: Hui-Min

first: Kristine

last: Cooper

first: Daniel

last: Normolle

first: Adam

last: Brufsky

first: Michael

last: Fastuca

first: Whitney

last: Crosson

first: Steffi

last: Oesterreich

first: Nancy

last: Davidson

first: Rohit

last: Bhargava

first: David

last: Dabbs

first: Adrian

middle: V

last: Lee


title: Effect of STAT3 Knockdown on Gene Level Expression Profiling of hepatic stellate LX-2 Cells in response to TGF-b treatment

status: Public on Feb 07 2017

city: Bethesda

first: Ying

last: Zhang

state: MD

address: 37 Convent Dr, Room 2056B

department: Center for Cancer Research

institute: National Cancer Institute

summary:
Transcriptome analysis of RNAs extracted from 2 hour-TGF-b-treated or untreated LX-2 cells with or without STAT3 knockdown
We prepared RNA from the following groups: NS 0h: untreated cells with control non-silencing (NS) siRNA; NS 2h: 2-hour TGF-b treated cells with control NS siRNA; siSTAT3 0h: untreated cells with STAT3 siRNA; siSTAT3 2h:  2-hour TGF-b treated cells with STAT3 siRNA. The gene expression profiles were compared, and we found  202 genes were upregulated (fold > 1.5) upon TGF-b treatment in control NS siRNA transfected LX-2 cells. Among them, 128 genes were clasified as TGF-b-induced and STAT3 -dependent genes as their response to TGF-b decreased more than 40% upon STAT3 depletion (126 genes) or fold between NS control and siSTAT3 in the absence of TGF-b was > 1.5 (2 genes).  The results showed that STAT3 plays an important role in regulating TGF-b target genes.

overall_design: We analyzed LX-2 cells (control NS, siSTAT3) with or without TGF-b treatment (0h, 2h) using the Affymetrix GeneChip® Human Gene 2.0 ST Array platform. No techinical replicates were performed.

first: Liuya

last: Tang


title: Immunosuppressive Drug-Free Operational Immune Tolerance in Human Kidney Transplant Recipients: Blood Gene Expression Analysis  Tolerance in Human Kidney Transplant Recipients.

last: BARON

summary:
Survival of solid organ grafts depends on life-long immunosuppression, which results in increased rates of infection and malignancy. Induction of tolerance to allografts would represent the optimal solution for controlling both chronic rejection (CR) and side effects of immunosuppression. Although spontaneous ‘‘operational tolerance’’ can occur in human kidney transplantation, the lack of noninvasive peripheral blood biological markers of this rare phenomenon precludes the identification of potentially tolerant patients in whom immunosuppression could be tapered as well as the development of new tolerance inducing strategies. Here, the potential of high throughput microarray technology to decipher complex pathologies allowed us to study the peripheral blood specific gene expression profile and corresponding EASE molecular pathways associated to operational tolerance in a cohort of human kidney graft recipients. In comparison with patients with CR, tolerant patients displayed a set of 343 differentially expressed genes, mainly immune and defense genes, in their peripheral blood mononuclear cells (PBMC), of which 223 were also different from healthy volunteers. Using the expression pattern of these 343 genes, we were able to classify correctly >80% of the patients in a cross-validation experiment and classified correctly all of the samples over time. Collectively, this study identifies a unique PBMC gene signature associated with human operational tolerance in kidney transplantation.
250 samples were analyzed, replicates included: some patients from the TOL and CR groups were sampled twice with an interval between the two different time points of at least 16 months (mean 25.8 months, range 16–31 months). All the samples were analyzed in duplicate or quadruplicate.  1. TOL (n = 21). patients with stable graft function (blood creatinemia<150 mmol/L, proteinuria<1 g/24 h) for at least 1 year (mean 6.4 years,range 1.6–17.2 years) after complete interruption of immunosuppressive therapy.  2. STA (n = 190). Patients with stable kidney graft function under immunosuppressive therapy.   3. CR (n = 31). Patients having a progressive degradation of their renal function (blood creatinemia ≥150 mmol/L, proteinuria ≥1 g/24 h). CR was diagnosed on a graft biopsy according to the updated Banff criteria. CR was defined by histological signs of chronic allograft arteriopathy (arterial intimal fibrosis with mononuclear cell infiltration) and/or transplant glomerulopathy with glomerular double contours.  4. HV (n = 8). Subjects having normal blood formulae and no infectious or other concomitant pathology for at least 6 months before the study.

overall_design: 250 PBMC (Peripheral Blood Mononuclear Cells) samples from 4 groups (TOL, STA, CR, HV) were analyzed by microarray.

first: Christophe

last: Braud

first: Dominique

last: Baeten

first: Magali

last: Giral

first: Annaïck

last: Pallier

first: Joanna

last: Ashton-Chess

first: Cecile

last: Braudeau

first: Catherine

last: Chevalier

first: Alice

last: Lebars

first: Jean

last: Léger

first: Anne

last: Moreau

first: Eugenia

last: Pechkova

first: Claudio

last: Nicolini

first: Jean-Paul

last: Soulillou

first: Sophie

last: Brouard


title: miRNA profiling of C3H/HeJ mice with and without spontaneous alopecia areata

status: Public on Feb 03 2017

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

summary:
Our goal was to identify miRNA expression patterns that correlated with spontaneous onset of autoimmune alopecia in C3H/HeJ mice compare to normal haired controls.
Skin from 3 mice with or without spontaneous AA were taken for the study.

overall_design: 5 Biological samples were taken from each mouse.

first: M

last: Tavazoie

first: A

last: Christiano


title: Expression data from CD4+ T cells isolated from inguinal lymph nodes 7 days post MOG immunization

status: Public on Feb 01 2017

city: Solna

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

institute: Karolinska Institute

summary:
We isolated CD4+ T cells from draining lymph nodes 7 days post EAE from
DA rats treated with vitamin D supplemented, vitamin D deprived or regular diet

overall_design: EAE was induced with MOG in age matched DA rats. After isolation of CD4+ T cells with FACS, RNA was isolated and subjected to microarray analysis. We were interested in the effect of vitaimin D on the transcriptome of CD4+ T cells. Thus we did microarray analysis on 3 different groups: DA rats treated with vitamin D supplemented, vitamin D deprived or regular diet

first: Z

last: Adzemovic

last: Jagodic


title: Analysis of miRNA pattern in mesenchymal stem/stromal cells derived from amniotic fluid (AF-MSCs) versus differentiated AF-MSCs into Adipocyte-Like cells (AL).

city: Athens

first: Maria

middle: G

last: Roubelakis

address: Michalakopoulou 176

department: School of Medicine

country: Greece

institute: National and Kapodistrian University of Athens

summary: Identification of the expression pattern of miRNAs of AF-MSCs compared with differentiated AF-MSCs into adipocyte-like cells (AL cells). Significantly, the miRNAs that were found to be more than 2 fold up- or down-regulated on one or more slides were considered as differentially expressed candidates. The miRNA profile revealed 13 differentially expressed miRNAs between AF-MSCs and AL cells. MiR-26a was identified in high expression levels in AL cells indicating a critical role in the process of adipogenesis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two different types of cells were used: (i) AF-MScs: Two different clones (AF-MSCs 3, AF-MSCs 9) (ii) AL cells: two different clones (Adipo 1, Adipo 2). Hybridization Slide 1: AF3+AF9 / Adipo 1+Adipo 2, Hybridization Slide 2: Adipo 1+Adipo 2/ AF3+AF9

first: Ourania

last: Trohatou

first: Dimitra

last: Zagoura


title: Real-time quantitative PCR analysis of healthy and HCV-infected Child-B cirrhotic patients

city: san diego

first: mario

last: chojkier

state: ca

address: 3350 la jolla village drive

department: Medicine

institute: UCSD

summary: Samples from healthy controls where compared to samples from Child-B cirrhotic patients

overall_design: QT-PCR was performed using equal amounts of RNA from each subject's blood buffy coat

first: Martina

last: Buck

first: Mario

last: Chojkier

first: Daniela

last: Traykova


title: Ruminiclostridium thermocellum DSM 1313 strain adhE*(EA) expression arrays

city: Oak Ridge

first: Jason

last: Whitham

address: 1 Bethel Valley Rd Bld 1505 Rm 366 MS 6038

institute: Oak Ridge National Labs

summary:
Ruminiclostridium thermocellum DSM 1313 strain adhE*(EA) expression was studied along with  ∆hydG and ∆hydG∆ech mutants strains deposited under GSE54082. All strains have been described in a study entitled Elimination of hydrogenase post-translational modification blocks H2 production and increases ethanol yield in Clostridium thermocellum. Biswas, et .al. Biotechnology for Biofuels 2015 8:20
Ruminiclostridium (Clostridium) thermocellum is a leading candidate organism for implementing a consolidated bioprocessing (CBP) strategy for biofuel production due to its native ability to rapidly consume cellulose and its existing ethanol production pathway. C. thermocellum converts cellulose and cellobiose to lactate, formate, acetate, H2, ethanol, amino acids, and other products. Elimination of the pathways leading to products such as H2 could redirect carbon flux towards ethanol production. Rather than delete each hydrogenase individually, we targeted a hydrogenase maturase gene (hydG), which is involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes by assembling the active site. This functionally inactivated all three Fe-Fe hydrogenases simultaneously, as they were unable to make active enzymes. In the ∆hydG mutant, the [NiFe] hydrogenase-encoding ech was also deleted to obtain a mutant that functionally lacks all hydrogenase. The ethanol yield increased nearly 2-fold in ∆hydG∆ech compared to wild type, and H2 production was below the detection limit. Interestingly, ∆hydG and ∆hydG∆ech exhibited improved growth in the presence of acetate in the medium. Transcriptomic and proteomic analysis reveal that genes related to sulfate transport and metabolism were up-regulated in the presence of added acetate in ∆hydG, resulting in altered sulfur metabolism. Further genomic analysis of this strain revealed a mutation in the bi-functional alcohol/aldehyde dehydrogenase adhE gene, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities, whereas the wild type strain can only utilize NADH. This is the exact same adhE mutation found in ethanol-tolerant C. thermocellum strain E50C, but ∆hydG∆ech is not more ethanol tolerant than the wild type. Targeting protein post-translational modification is a promising new approach to target multiple enzymes simultaneously for metabolic engineering. This GEO study pertains to expression profiles generated for C. thermocellum DSM 1313 strain adhE*(EA)

overall_design: A six array study using total RNA recovered from Clostridium thermocellum DSM 1313 adhE*(EA) 27405 cultures. Cells were harvested at an OD 0.4-0.5 from cultures grown in the presence of additional 5mM acetate and compared to untreated controls. Three biological replicates were performed for treated and untreated cultures.

first: Biswas

last: Ranjita

first: Charlotte

last: Wilson

first: Dawn

last: Klingeman

first: Adam

last: Guss

first: Steven

last: Brown


title: Copy number profiling of synchronous primary and metastasis of invasive breast cancer

status: Public on Jan 31 2017

city: Pieve Emanuele

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: We sought to define the repertoire of genetic alterations in synchronous primary and metastasis of invasive breast cancer

overall_design: In this study, we subjected up to two anatomically distinct diagnostic biopsies of primary breast cancers and up to two anatomically distinct diagnostic biopsies of their synchronous metastatic deposits from patients who presented with de novo metastatic disease and who had not received any local or systemic therapy to gene copy number analysis and high-depth whole exome sequencing. DNA from the second diagnostic biopsy of the primary breast cancer and the second diagnostic biopsy of the metastatic deposit for the cases for which samples were available was hybridized on the molecular inverse probe assay using the OncoScan® FFPE Express custom service (Affymetrix, Santa Clara, CA).

middle: K

first: Jorge

last: Reis-Filho

first: Britta

last: Weigelt


title: Whole transcriptome profiling of Human Hepatoma culture Huh7.5 and Huh7.5M

city: HYDERABAD

first: KRISHNAN

middle: HARINIVAS

last: HARSHAN

address: HABSIGUDA

country: India

institute: CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY

summary: Huh7.5 cells, when grown in presence of 1-2mg/ml of Geneticin, generarated colonies with cells that were morphologically distinct from the parental cells. These cells were substantially smaller in size, had spindle like features and grew faster. They expressed mesenchymal markers and were named as Huh7.5M cells.

overall_design: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray

first: Dhiviya

last: Vedagiri

first: Sana

last: Parveen

first: Krishnan

last: Harshan


title: Angiocrine Bmp2 signaling in murine liver controls normal iron homeostasis

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Microvascular endothelial cells (EC) display a high degree of phenotypic and functional heterogeneity among different organs. Organ-specific EC control their tissue microenvironment by angiocrine factors in health and disease. Liver sinusoidal EC (LSEC) are uniquely differentiated to fulfil important organ-specific functions in development, under homeostatic conditions, and in regeneration and liver pathology. Recently, Bmp2 has been identified by us as an organ-specific angiokine derived from LSEC. To study angiocrine Bmp2 signaling in the liver, we conditionally deleted Bmp2 in LSEC using EC subtype-specific Stab2-Cre mice. Genetic inactivation of hepatic angiocrine Bmp2 signaling in Stab2-Cre;Bmp2fl/fl (Bmp2LSECKO) mice caused massive iron overload in the liver, and increased serum iron levels and iron deposition in several organs similar to classic hereditary hemochromatosis. Iron overload was mediated by decreased hepatic expression of hepcidin, a key regulator of iron homeostasis. Thus, angiocrine Bmp2 signaling within the hepatic vascular niche represents a constitutive pathway indispensable for iron homeostasis in vivo that is non-redundant with Bmp6. Notably, we demonstrate that organ-specific angiocrine signaling is essential not only for the homeostasis of the respective organ, but also for the homeostasis of the whole organism.

overall_design: Primary hepatocytes were isolated from three different mice and stimulated with BMP2 for 24 hours.

first: Philipp-Sebastian

last: Koch

first: Cyrill

last: Géraud


title: Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse [DNA methylation]

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

institute: Centro de Investigación del Cáncer de Salamanca

type: Methylation profiling by genome tiling array

summary:
Multiple myeloma (MM) remains incurable despite the introduction of novel agents and a relapsing course is observed in the majority of patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from 17 MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the lost of lesions present at diagnosis, and DNA losses were significantly more frequent at relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly impact the gene expression of these samples, provoking a particular deregulation of IL-8 pathway. On the contrary, no relevant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although different statistical approaches were used to uncover genes whose abnormal expression at relapse was regulated by DNA methylation, only two genes significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative methylation-expression correlation. A deeper analysis demonstrated that DNA methylation was involved in regulation of SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were not apparently preceded by alterations in corresponding DNA. Taken together, these results showed that genomic heterogeneity, both at the DNA and RNA level, is a hallmark of MM transition from diagnosis to relapse.
Please note that an a first step all analyses were carried out independently in each series, being the number of samples of 40 in methylation, 38 in SNP and 34 in expression series. In the next step, association studies were performed only in the overlapping samples, being 34 matching samples between expression and methylation and 32 samples between expression and SNP data.

overall_design: Twenty paired bone marrow samples were obtained at diagnosis and relapse (n = 40). A CD138 positive PC isolation using the AutoMACs automated separation system was carried out in all the BM samples. DNA was extracted from samples frozen in RLT-Plus buffer using commercially available kits (Allprep Kit, Qiagen, Valencia, CA) and hybridized following manufacturer’s protocol.

first: Patryk

last: Krzeminski

first: Luis

middle: A

last: Corchete

first: Juan

last: García

first: Lucía

last: López-Corral

first: Encarna

last: Fermiñán

first: Eva

first: Ana

last: Martín

first: Jesús

last: Hernández-Rivas

first: Ramón

last: García-Sanz

middle: F

last: San Miguel

first: Norma


title: Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse [DNA copy number]

overall_design: Nineteen paired bone marrow samples were obtained at diagnosis and relapse (n = 38). A CD138 positive PC isolation using the AutoMACs automated separation system was carried out in all the BM samples. DNA was extracted from samples frozen in RLT-Plus buffer using commercially available kits (Allprep Kit, Qiagen, Valencia, CA) and hybridized following manufacturer’s protocol.


title: 12plex_pea_2013_02_f-Water stress and seed filling in pea

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 12plex_pea_2013_02 - 12plex_pea_2013_02_f - What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)         - Pea plants (genotype Cameor) were subjected to a moderate water stress at the beggining of the seed filling period (12 Days After Pollination) of the second flowering node for a period of 8 days. Samples were collected from Well Watered (WW) plants at the beginning of the stress imposition (point A, T=0), and from Water-Stressed (WS) and WW control plants at the end of the drought period (point B, T=+8). Samples named SEED consisted of seeds from the pod of the second flowering node (seed-WW-A, seed-WW-B and Seed-WS-B). Samples named LEAF consisted of the leaves and stem sections from the two vegetative nodes below the first flowering node (leaf-WW-A, Leaf-WW-B and Leaf-WS-B). Each sample consited of a pool of 3 individual plants and 4 repetitions per condition were carried out.

overall_design: 12 dye-swap - treated vs untreated comparison

first: Dao-xiu

last: Zhou

first: Stephanie

last: Huguet

first: Vanessa

last: Vernoud

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Sequential rather than coincident molecular mechanisms govern the combinatorial control logic underlying pathogen-responsive gene expression programs

city: Cambridge

first: Christine

middle: S

last: Cheng

address: 7 Cambridge Center

institute: Broad Institute of MIT and Harvard

summary: Combinatorial control of gene expression is presumed to be mediated by molecular interactions between coincident transcription factors (TFs). While information on the genome-wide locations of TFs is available, the genes they regulate and whether they function combinatorially often remain open questions. Here, we developed a mechanistic, rather than statistical, modeling approach to elucidate TF control logic from gene expression data. Applying this approach to hundreds of genes in 85 datasets measuring the transcriptional responses of murine fibroblasts and macrophages to cytokines and pathogens, we found that stimulus-responsive TFs generally function sequentially in logical OR gates or singly. Logical AND gates were found between NFB-responsive mRNA synthesis and MAPKp38-responsive control of mRNA half-life, but not between temporally coincident TFs. Our analyses identified the functional target genes of each of the pathogen-responsive TFs and prompts a revision of the conceptual underpinnings of combinatorial control of gene expression to include sequentially acting molecular mechanisms that govern mRNA synthesis and decay.

overall_design: Total RNA extracted from primary mouse embryonic fibroblasts were subjected to stimulation with LPS, TNF, PDGFb, IFNb

first: Alexander

last: Hoffmann


title: miRNA expression in kidney Thick Ascending Limb in Hypersodic diet treated rats (H samples) vs normal diet rats (N samples)

city: Naples

first: Massimo

last: Mallardo

address: Via Sergio Pansini, 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples Federico II°

summary: 3 H samples vs 3 N samples Each sample was made by 3 pooled animals

overall_design: The overall experiment included 6 chips (3 Normal diet and 3 Hypersodic diet)

first: Giovanbattista

last: Capasso


title: Expression data for wildtype CD4+ T cells cells differentiated in Tr1 conditions for 2 hours

status: Public on Jan 27 2017

city: Boston

first: Asaf

last: Madi

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

summary: Type 1 regulatory T (Tr1) cells are induced by the interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. Here, we show that the transcription factors IRF1 and BATF are induced early during treatment with IL-27 and are required for the differentiation and function of Tr1 cells in vitro and in vivo . Epigenetic and transcriptional analyses reveal that both transcription factors influence chromatin accessibility and expression of genes required for Tr1 cell function. IRF1 and BATF deficiencies uniquely alter the chromatin landscape, suggesting that these factors serve a pioneering function during Tr1 cell differentiation.

overall_design: 2 hrs microarray data for Tr1 differentiation (IL27 + anti-TGFb)

first: Vijay

last: Kuchroo


title: Gene expression of mice PDL , WT and Mkx KO (10 weeks and 4 weeks)

status: Public on Jan 17 2017

city: TOKYO

first: Naoki

last: Koda

address: 1-5-45 Yushima, bunkyo-dist.

department: systems biomedicine

institute: TMDU

summary:
The periodontal ligament (PDL), which connects the teeth to the alveolar bone, is essential for periodontal tissue homeostasis. Although the significance of the PDL is recognized, molecular mechanisms underlying PDL function are not well-known. We report that Mohawk homeobox (Mkx), a tendon-specific transcription factor, regulates PDL homeostasis by preventing its degeneration. Mkx is expressed in the mouse PDL at the age of 10 weeks and 12 months. In Mkx-/- mice, age-dependent expansion of the PDL at the maxillary 1st molar (M1) furcation area was observed. Transmission electron microscopy (TEM) revealed that Mkx-/- mice presented collagen fibril degeneration in PDL with age, while the collagen fibril diameter gradually increased in Mkx+/+ mice. PDL cells lost their shape in Mkx-/- mice, suggesting changes in PDL properties. Microarray and quantitative polymerase chain reaction (qPCR) analyses of Mkx-/- PDL revealed an increase in osteogenic gene expression and no change in PDL- and inflammatory-related gene expression. Additionally, COL1A1 and COL1A2 were upregulated in Mkx-overexpressing human PDL fibroblasts, whereas osteogenic genes were downregulated. Our results indicate that Mkx prevents PDL degeneration by regulating osteogenesis.
Mohawk transcription factor is essential for homeostasis of the periodontal ligament by regulating osteogenic changes with age.

overall_design: PDL were prepared from wild type and Mkx knockout mice for RNA extraction and hybridization on Agilent technologies.

first: Hiroshi

last: Asahara


title: Characterization of gene expression changes in IRF4-deficient DT40 B cells

status: Public on Jan 01 2017

city: Turku

first: Paulina

last: Budzynska

address: Kiinamyllynkatu 13

country: Finland

institute: University of Turku

summary: The aim of experiment was to study on genome-wide level IRF4 target genes in chicken DT40 B cell line, by comparizon of gene expression profiles of IRF4-deficient DT40 cells with WT IRF4 DT40 cells .

overall_design: Total RNA from untreated IRF4-deficient DT40 B cells was compared with total RNA from untreated WT IRF4 cells

first: Asta

last: Laiho


title: Catalogue of genomic alterations in uterine cervical carcinoma of Indian patients.

status: Public on Dec 27 2016

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

institute: Saroj Gupta Cancer Centre & Research Institute

summary: To identify genomic alterations in uterine cervical carcinoma of Indian patients. Cancer of the uterine cervix (CACX) is the fourth most frequent carcinoma among women worldwide. In India, it accounts for approximately 132,000 new cases and 74,000 deaths annually contributing to nearly 1/3rd of the global cervical cancer deaths. Although, several etiological factors such as use of oral contraceptives, precocious marriage, multiparity, smoking etc. are seen to modify the risk of CACX, but infection by high risk human papillomavirus (hrHPV) is thought to be the major cause. Interestingly, long latency period for malignant outcome in only a subset of HPV-infected women indicates involvement of additional chromosomal alterations.Since the first report of changes in chromosomal content of CACX, several genome-wide studies reported frequent chromosomal gain of 3q (3q24–29), 1q (1q22–q23, 1q25.3–q32.1) and 5p (5p12–p13) and loss of 3p (3p12–23), 11q (11q22.3–25) and 4p (4p16.3–p16.1). But no study was done to catalogue the precise genomic alterations in CACX of Indian patients. To the best of our knowledge, for the first time the present study revealed precise chromosomal aberrations with differential frequency in Indian CACX patients (n=11). Among these alterations, frequent (>50%) amplifications of distinct chromosomal loci were as follows: 1p36.11-1p31.1, 1q21.1-1q44, 3q13.13-3q29, 5p15.33-5p12, 8q24.3, 16q22.2, 19q13.13-19q13.2, Xp22.33-Xp11.21 and Xq11.2-Xq12. While recurrent (>35%) loss at chromosomal loci, 2q34-2q37.3, 4p16.3-4p12, 4q21.3, 8p23.3, 8p23.2, 8p11.22, 11q14.1-11q25, 13q13.3-13q14.3, and 19p13.3 were also observed. All CACX patients showed precise amplification of chromosome 3 at coordinates 3q25.2-3q26.1 (chr3:154427429-162796745), 3q26.1-3q26.31 (chr3:162901354-175146595) and 3q26.32-3q29 (chr3:175208719-198094926). Highest (72%) loss of chromosomal loci 11q24.3-11q25 (chr11:128926744-135034169) was seen.

overall_design: Agilent two-color CGH+SNP experiment,Organism: Human ,Agilent Human CGH+SNP 2X400K Array (AMADID: 028081)

first: Anirban

last: Roychowdhury

first: Sudip

last: Samadder

first: Chinmay

last: Panda


title: The regulation roles of lncRNAs in the development of glioblastoma

status: Public on Dec 23 2016

city: Beijing

first: shuang

last: liu

address: No.6, Fucheng Road, Haidian district

institute: Navy general hospital

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

summary: lncRNA and mRNA expression between human GBM and paired normal brain tissues were compared using microarray.

overall_design: Identification of differentially expressed (DE) lncRNAs and genes in GBM compared to matched normal samples.

first: Shuang

last: Liu


title: Gene expression analysis of Wild-type and lncKdm2b-deficient ES cells

status: Public on Dec 24 2016

first: Buqing

last: Ye

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Investigation of differentially expressed genes in lncKdm2b-deficient ES cells

overall_design: A two chip study using wild-type and lncKdm2b-deficient ES cells. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

first: Benyu

first: Zusen

last: Fan


title: UGT2B17 Expedites Castration-Resistant Prostate Cancer Progression through Promoting Ligand-independent AR Signaling

status: Public on Dec 02 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: This microarry study provides novel insights into the role of UGT2B17 in prostate cancer progression

overall_design: To gain insights into UGT2B17 modulated gene expression alteration in castration resistant prostate cancer cells

first: Haolong

last: Li

first: Ning

last: Xie

first: Ruiqi

last: Chen

first: Mélanie

last: Verreault

first: Ladan

last: Fazli

first: Martin

last: Gleave

first: Olivier

last: Barbier

first: Xuesen

last: Dong


title: Galectin-1 suppression delineates a new therapeutic strategy for myeloma-induced angiogenesis

status: Public on Nov 27 2016

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Galectin-1 (Gal-1) is a lectin, involved in several processes related to cancer, including immunosuppression, angiogenesis, hypoxia, and metastases. Actually, the Gal-1 expression profile in multiple myeloma (MM) and its pathophysiological role in MM–induced angiogenesis and tumoral growth is unknown. Firstly, we found that Gal-1 was expressed by malignant plasma cells in MM patients and that its expression was up-regulated upon hypoxic treatment (1% of O2). Moreover the stable knock-down of Hypoxia Inducible Factor-1α (HIF-1α) in MM cells significantly downregulated Gal-1 expression. Thereafter, we performed Gal-1 inhibition by lentivirus shRNA anti-Gal-1 in human myeloma cell lines (HMCLs) showing that its suppression did not affect cell proliferation and survival but modified their transcriptional profiles either in hypoxia or hypoxia condition. Interestingly pro-angiogenic genes including MMP9 and CCL2 were downregulated and those anti-angiogenic SEMA3A and CXCL10 were up-regulated by Gal-1 inhibition in MM cells. Data were also validated by Real time PCR and at protein level. Consistently we found that Gal-1 suppression in MM cells significantly decreased their pro-angiogenic proprieties by an in vitro assay. These evidences were confirmed in mice injected either subcutaneously or intratibially with HMCLs carrying a stable infection with shRNA anti-inhibition of Gal-1 or with the control vector cell line. Gal-1 suppression in both models showed a significant reduction in the tumoral burden and microvascular density compared to the control mice. Moreover, Gal-1 suppression induced smaller lytic lesions on x-ray in the intratibially model. Overall, our data indicate that Gal-1 is a new potential therapeutic target in MM.

overall_design: Total RNA samples from JJN3 anti-Gal-1 and JJN3 scramble, after 48h of normoxic or hypoxic conditions and 48h of re-oxygenation process were analyzed on GeneChip® HG-U133 Plus 2.0 arrays (Affymetrix; Santa Clara, CA). Anti-Gal-1 was compared to scramble JJN3 sample in normoxic, hypoxic or re-oxygenation conditions, respectively, to find specific differentially expressed genes in each experimental condition.

first: Paola

last: Storti

first: Valentina

last: Marchica

last: Ferri

first: Daniela

last: Guasco

first: Gaetano

last: Donofrio

first: Irma

last: Airoldi

first: Katia

last: Todoerti

first: Rebecca

last: Silberman

first: Judith

first: Wei

last: Zhao

first: Eugenia

last: Martella

first: Cristina

last: Mancini

first: Nicoletta

last: Campanini

first: Marina

last: Bolzoni

first: Antonino

last: Neri

first: Douglas

last: Noonan

first: Pier

last: Petronini

first: Franco

last: Aversa

first: David

last: Roodman

first: Nicola

last: Giuliani


title: GPCR endocytosis confers uniformity in responses to chemically distinct ligands

status: Public on Nov 30 2016

city: San Francisco

first: Nikoleta

last: Tsvetanova

state: CA

address: 600 16th street

country: USA

institute: University of California, San Francisco

summary:
This study shows that chemically and pharmacodynamically distinct agonists acting on the same GPCR can produce indistinguishable cellular responses and that this uniformity is conferred by endosomal signaling
The ability of chemically distinct ligands to produce different effects on the same G protein-coupled receptor (GPCR) has interesting therapeutic implications but, if excessively propagated downstream, would introduce biological 'noise' compromising cognate ligand detection We asked if cells have the ability to limit the degree to which chemical diversity imposed at the ligand-GPCR interface is propagated to the downstream signal We carried out an unbiased analysis of the integrated cellular response elicited by two chemically and pharmacodynamically diverse β-adrenoceptor agonists, isoproterenol and salmeterol We show that both ligands generate an identical integrated response, and that this stereotyped output requires endocytosis We further demonstrate that the endosomal β2-AR signal confers uniformity on the downstream response because it is highly sensitive and saturable Based on these findings, we propose that GPCR signaling from endosomes functions as a biological noise filter to enhance reliability of cognate ligand detection

overall_design: This study includes a total of 6 microarray experiments, each condition is done in triplicate

first: Michelle

last: Trester-Zedlitz

first: Billy

middle: W

last: Newton

first: Jeffrey

last: Johnson

first: Nevan

middle: J

last: Krogan

first: Mark

last: von Zastrow


title: Expression data from Arabidopsis thaliana leaves treated with BrvC

status: Public on Nov 22 2016

city: Olomouc

first: Ondrej

last: Plihal

address: Slechtitelu 27

country: Czech Republic

institute: CRH, Palacky University

summary:
Brevicompanines are natural products isolated from the culture filtrate of the fungus Penicillium brevicompactum. They showed plant growth regulating properties in several species including lettuce, rice or Arabidopsis thaliana.
We used microarrays to gather information about the reprogramming of gene transcription when Arabidopsis leaves were treated with Brevicompanine C (BrvC) that showed significant activity in plant growth assays.

overall_design: 30-days old Arabidopsis leaves were treated with 50 M BrvC for 6 h or 48 h or left untreated (DMSO only) and subsequently used for RNA extraction and hybridization on Affymetrix microarrays.

first: Radova

last: Lenka

first: Plihal

last: Ondrej


title: Analysis of TCERG1 depletion by exon arrays

status: Public on Nov 21 2016

city: Granada

first: Carles

last: Suñé Negre

address: Avenida del conocimiento S/N

department: Molecular Biology

country: Spain

institute: Instituto Parasitología y Biomedicina López-Neyra

summary: TCERG1 is a highly conserved human protein implicated in interactions with the transcriptional and splicing machinery. To investigate TCERG1 function, we survey genome-wide changes in transcript and exon levels upon TCERG1 knockdown in HEK293T cells. Our data revealed that TCERG1 regulates different types of alternative spliced events, indicating a broad role in the regulation of alternative splicing.

overall_design: Eight samples were analyzed, comprising two conditions, siEGFP (EG) and siTCERG1 (CA). Four independent experiments were carried out for each condition.

first: Juan

middle: P

last: Muñoz-Cobo

last: Suñé


title: Genome wide expression profile of ada1 and gcn5 deletion strains in Saccharomycescerevisiae

status: Public on Dec 01 2016

city: Fukui

first: kazuma

last: kamata

address: 3-9-1 Bunkyo

department: Applied Chemistry Biotechnology

institute: University of Fukui

summary:
Ada1, Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex component, was isolated as boundary factor that separated silenced chromatin and euchromatin by previous screening, and Ada1 maintains SAGA complex integrity. SAGA complex is one of a histone modification complex that has multiple functions contributing to transcriptional activation. In Saccharomyces cerevisiae, silencing is occurred by Sir protein complex, which deacetylates histones and form high-order chromatin structure. Gcn5, SAGA complex component, has histone acetyltransferase activity, which is considered that antagonize to silencing by the screening.
Ada1 and Gcn5 might have different functions in SAGA complex, we performed microarray analysis to find different functions of gene regulations by using ada1Δ and gcn5Δ strains. As the results, Ada1-regulated genes include more than halves of Gcn5-regelated genes, which occupied only a part of Ada1 regulated genes. These suggest that the differences of contribution to SAGA functions. When SAGA complex have a loss of Ada1, almost function was lost. On the other hand, Gcn5 play a role only as acetyltransferase in SAGA complex.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: All strain cells were grown at 30C in 5ml YPD media with shaking. Total RNAs were collected at exponential phase (optimal density of 0.7) using acid phenol-chloroform extraction method and hybridized on Affymetrix microarrays.

first: K

last: Kamata

last: Shinmyozu

first: J

last: Nakayama

first: M

last: Hatashita

first: H

last: Uchida

last: Oki


title: Transcriptome analysis of Lactococcus garvieae strain 8831 grown at 13ºC and 18ºC

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

summary: Transcritome profiling of the fish pathogen Lactococcus garvieae strain 8831 in response to growth temperature

sample_organism:
Lactococcus garvieae
Lactococcus garvieae 8831
Lactococcus garvieae 21881

overall_design: Reference design experiment with samples of Lactoccocus garvieae 8831 grown at 13ºC and 18ºC. Three biological replicates. The results were referenced to a equimolar mixture of L. garvieae strains 8831 and 21881 grown at 29ºC.

first: Monica

first: Alicia

last: Gibello

first: Maria

last: Blanco

first: Mercedes

last: Reguera-Brito

first: Victoria

last: Lopez-Alonso

first: Jose

last: Fernández-Garayzabal

first: Guillermo

middle: H

last: Lopez-Campos


title: Inferring gene networks for strains of Dehalococcoides highlights conserved relationships between genes encoding core catabolic and cell-wall structural proteins

status: Public on Nov 14 2016

city: Ithaca

first: Cresten

last: Mansfeldt

address: 220 Hollister Hall

institute: Cornell University

summary: Transcriptional profiling of Dehalococcoides mccartyi in the commercially available KB-1™ consortia comparing control standard TCE batch fed culture to treatments either introducing the culture to a standard batch feeding, stressful condition, or continous feed rate.

overall_design: All experimental cultures were run in the red channel against the batch fed control in the green. Two dye swaps of the standard control were also run.

first: Gretchen

last: Heavner

first: Laura

last: Hug

first: Elizabeth

last: Edwards

first: Ruth

last: Richardson


title: Expression data of vrn2/- emf2/+  and wild-type ovules and seeds

status: Public on Nov 15 2016

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

type: Expression profiling by genome tiling array

summary: Polycomb Group proteins belonging to the Polycomb Repressive Complex 2 (PRC2) repress seed coat development before fertilization. Removal of PRC2 function in the integuments initiates autonomous seed coat development. We used microarrays to identify those genes that are under PRC2 control and become derepressed in mutants deficient for the PRC2 genes VRN2 and EMF2. Since vrn2 emf2 double mutants have strong developmental aberrations, we used the mutant combination vrn2/- emf2/+ .

overall_design: WT (Ler) and double mutant vrn2/- emf2/+ plants were emasculated at 1-2 days prior to anthesis. Two days after emasculation half of the WT plants were hand-pollinated. Unfertilized ovules and young seeds were dissected from the siliques at 4 DAE and 2 DAP, respectively.

first: Pawel

last: Roszak

first: Claudia

last: Köhler


title: Functional profiling of formaldehyde in yeast

status: Public on Nov 09 2016

city: Gainesville

first: Chris

last: Vulpe

state: FL

address: 2187 Mowry Drive, Building 470, Room 113, PO Box 110885

institute: University of Florida

summary: Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. In this study, a functional toxicogenomics approach was utilized in the model eukaryotic yeast Saccharomyces cerevisiae to identify genes and cellular processes modulating the cellular toxicity of FA. Our results demonstrate mutant strains deficient in multiple DNA repair pathways were sensitive to FA. The SKI complex and its associated factors, which regulate mRNA degradation by the exosome, were also required for FA tolerance..

overall_design: Pools of homozygous diploid deletion mutants (n = 4,607 strains) were grown in formaldehyde at 3 concentrations for 5 and 15 generations (5g, 15g). Each strain has a deletion in a different gene. In each strain, the gene was replaced by a deletion cassette containing a antibiotic resistance gene and two BARCODES, up and down tags (Please see Giaever et al, 2002, Nature). These tags in the DNA are specific to each strain. We pool all deletion strains and grow them under a selective condition; extract DNA; amplify barcodes using universal primers and hybridize to arrays containing complementary sequences to the up and down tags. In this way, we can look at growth of each of the strains. Our strategy is to analyze separately the up and down tags. Therefore, for each array (CEL file), we generate two data files, one for all ups and another one for all downs. In these files, the list of genes are the same but the data come from different set of probes, up or down. The values are log2 averages of replicate probes for the same tag. These pre processed files were used to identify strains with differential growth in formaldehyde by comparing to control arrays.

first: Matthew

last: North

first: Brandon

middle: D

last: Gaytan

first: Carlos

last: Romero

first: Vanessa

middle: Y

last: De La Rosa

first: Alex

last: Loguinov

first: Martyn

middle: T

last: Smith

first: Luoping

last: Zhang


title: microRNA array analysis for seaching IGBP1-targeting microRNA in lung adenocarcinoma

status: Public on Nov 11 2016

city: Tsukuba-shi

first: Taiki

last: Sato

state: Ibaraki

address: Tennodai

institute: University of Tsukuba

summary: Immunoglobulin (CD79a) binding protein 1 (IGBP1) is universally overexpressed in lung adenocarcinoma and exerts an anti-apoptotic effect by binding to PP2Ac. However, the molecular mechanism of IGBP1 overexpression is still unclear. In the present study, we used a microRNA (miRNA) array and TargetScan Human software to detect IGBP1-related miRNAs that regulate IGBP1 expression.

overall_design: microRNA array was performed using IGBP1-positive small invasive adenocarcinoma of lung and IGBP1-negative minimally invasive adenocarcnoma of lung


title: Apoptosis-related gene expression profiling in hematopoietic cell fractions of MDS patients

status: Public on Nov 07 2016

city: Nijmegen

first: Niccolo

last: Mariani

address: Geert Grooteplein Zuid 8

country: Netherlands

institute: Radboudumc

summary: Quantification of apoptosis-related genes in bone marrow HSPCs from MDS patients compared to healthy donor by microfluidic cards

overall_design: Bone marrow from MDS patients and healthy controls was collected. The expression of 380 different apoptosis-related genes was measured simultaneously by real-time PCR employing a 384 Microfluidic Card (Applied Biosystems). cDNA obtained from the CD34+, CD71+ and CD13/33+ cell fractions was analyzed. The relative expression of the apoptosis-related genes was calculated by measuring the housekeeping gene GAPDH.

first: Saskia

last: Langemeijer

first: Joop

last: Jansen


title: Transcriptomic profiling maps anatomically patterned subpopulations among single embryonic cardiac cells [qPCR]

status: Public on Nov 10 2016

city: Pittsburgh

first: Guang

last: Li

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: Embryonic gene expression intricately reflects anatomical context, developmental stage, and cell type. To address whether the precise spatial origins of cardiac cells can be deduced solely from their transcriptional profiles, we established a genome-wide expression database from 118, 949, and 1166 single murine heart cells at embryonic days (e)8.5, 9.5, and 10.5, respectively. We segregated these cells by type using unsupervised bioinformatic analysis and identified novel chamber-specific genes. Using a random forest algorithm, we reconstructed the spatial origin of single e9.5 and e10.5 cardiomyocytes with 92.0+/-3.2% and 91.2+/-2.8% accuracy respectively (99.4+/-1.0% and 99.1+/-1.1% if a +/-1 zone margin is permitted) and predicted the second heart field distribution of Isl1-lineage descendants. When applied to Nkx2-5-/- cardiomyocytes from murine e9.5 hearts, we showed their transcriptional alteration and lack of ventricular phenotype. Our database and zone classification algorithm will enable the discovery of novel mechanisms in early cardiac development and disease.

overall_design: Single-cell qPCR of mouse embryonic day 10.5 (e10.5) cardiac cells with probes to distinguish cell type and anatomical origin. The embryonic hearts were dissected into 9 zones: right atrium (RA), left atrium (LA), atrioventricular canal (AVC), left ventricle (LV), left septum (LS), right septum (RS), proximal outflow tract (PO), and distal outflow tract (DO). Four 96x96 Fluidigm dynamic arrays (#BMKM-96.96) were used to profile expression of 81 genes in 374 single GFP+ cells isolated from each of the 9 cardiac zones in e10.5 Nkx2-5Cre/+;ROSA26mTmG/+ mouse embryos based on GFP expression. This experiment serves as a validation of the anatomical context prediction algorithm described in the referenced publication

first: Adele

last: Xu

first: Sean

last: Wu