title: Transcriptome analysis of rhesus monkey germinal vesicle and failed-to-mature oocytes

country: USA

summary: Oocyte maturation defects are one contributing factor in unexplained female infertility.  Failure of some oocytes to undergo germinal vesicle breakdown or progress to second meiotic metaphase in response to an ovulatory stimulus can limit the number of high quality oocytes available for assisted reproduction.  Understanding the molecular mechanisms that underlie oocyte maturation failure may lead to novel methods for increasing the number of high quality oocytes available for assisted reproduction, as well as providing new insight into the basic biology of oocyte maturation.  Using RNA sequencing, we compared the transcriptome of rhesus monkey oocytes that failed to mature (FTM) in response to an ovulatory stimulus in vivo to normal germinal vesicle and metaphase II stage oocytes.

overall_design: Transcriptomes of rhesus monkey oocytes that failed to mature (FTM) in response to an ovulatory stimulus in vivo, normal germinal vesicle, and metaphase II stage oocytes were compared using RNAseq.

first: Meghan

middle: L

last: Ruebel

first: Peter

middle: Z

last: Schall

first: Kailey

middle: A

last: Vincent

first: Benjamin

last: Goheen

first: Catherine

last: VandeVoort

first: Keith

middle: E

last: Latham


title: Environmental stress to Ethiopia indigenous chicken breeds induce immune signaling response among transcriptomic changes in heart, breast muscle and spleen tissues

status: Public on Sep 13 2018

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

country: South Korea

institute: National Institute of Animal Science

type: Expression profiling by high throughput sequencing

summary: Ethiopia indigenous chicken breeds are typically divided into low and high altitude chicken breeds. Firstly, representative city of low altitude such as Awash is an altitude of around 950 meters above sea level and have a climate which is humidity and high temperature with 37℃ between May and June. Secondly, representative city of high altitude such as Addis Ababa is the capital of Ethiopia in eastern Africa and this city is an altitude of over 2,400 meters above sea level and has a climate which is generally comparable with the average annual temperature of around 16℃. These chicken breeds are adapted to the environmental (climate, temperature and altitude) on the city. Moreover, in Awash, chicken breed is more adapted to heat resistance. So we generated RNA sequencing (RNA-seq) data of Ethiopia indigenous chicken breeds such as low altitude chicken breed (adapted heat) and high altitude chicken breed (Non-adapted heat) to compare the gene expression profiling induced by heat stress (HS). Therefore, we identified 13 hub differentially expressed genes (DEGs) using cuffdiff within cufflinks, which validated by real-time quantitative-PCR (qRT-PCR) in Kenya chicken breed for biological and technical validation. These hub DEGs were subjected to pathway enrichment, protein/protein interaction, and the partial correlation coefficient with information theory (PCIT) to determine their involvement in heat stress and immune response. Our findings suggest that not only hub DEGs but also many others DEGs may play a role in heat stress and immune response.

overall_design: Whole mRNA sequencing profiles of heart, breast muscle and spleen tissues

first: Jong-Eun

last: Park

first: Jun-Mo

last: Kim

first: Woncheoul


title: MicroRNA profiling associated with muscle growth in modern broilers compared to an unselected chicken breed

status: Public on Sep 07 2018

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

type: Non-coding RNA profiling by high throughput sequencing

summary: We recently performed global gene expression in the breast muscles of modern broiler and foundation line chickens. In this study, we have peformed miRNA expression analyses in the same tissues to identify muscle specific miRNAs that could be regulatory factors for muscle growth and feed efficiency in chickens.

overall_design: Breast muscle samples were collected from six birds each from pedigree male broiler and Barred Plymouth Rock chickens. Small RNA was purified and small RNA sequencing was done using illumina 1*50 bp single end read method.

first: Byungwhi

middle: C


title: Transcriptome analysis of rhesus monkey MII oocytes

status: Public on Sep 06 2018

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University


title: MicroRNA profiling in male rat germ cells after chronic cyclophosphamide treatment

status: Public on Sep 05 2018

city: Montreal

first: Anne Marie

middle: Lucie

last: Downey

state: Quebec

address: 3655 Promenade Sir William Osler, Room 115

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: Although numerous miRNAs have been identified in the testis, their roles in regulating the highly specific events that occur in the different germ cell types throughout spermatogenesis remain largely unknown. Furthermore, whether male germ cell miRNA expression is altered in response to or as a consequence of exposure to a toxic agent is unknown. Here we examine miRNA expression profiles in pachytene spermatocytes and round spermatids obtained from control rats and from rats treated with a chronic low dose of cyclophosphamide, a male germ cell toxicant. We observed that pachytene spermatocytes and round spermatids display vastly different miRNA expression profiles, reflecting their different developmental stages and possibly influencing the cellular response to toxic insult. Chronic low dose cyclophosphamide treatment altered the miRNA profiles in both pachytene spermatocytes and round spermatids. Target prediction analyses revealed that miRNAs altered by cyclophosphamide treatment may be involved in the response to cellular stress and damage. However, many are also involved in processes that are crucial for proper germ cell development. This study suggests that pachytene spermatocytes and round spermatids display distinct miRNA profiles that can be altered by cyclophosphamide treatment. The observed changes may be part of a response and repair mechanism to cyclophosphamide-induced damage or a dysregulation that disrupts normal germ cell development.

overall_design: Pachytene spermatocytes and round spermatids from rats treated chronically with cyclophosphamide were isolated and profiled for changes in gene expression.

first: Anne

middle: M

first: Barbara

middle: F

last: Hales

first: Bernard

last: Robaire


title: Methylglyoxal modification of TrkB enhances synaptic plasticity in prefrontal cortex and promotes resilience to chronic stress

city: Yangling

first: Yingxue

last: Fu

state: Shaanxi

address: Taicheng Road 3

country: China

institute: Northwest A&F University

summary: Major depressive disorder (MDD) is a severe psychiatric illness that affects about 16 percent of the global population. Despite massive efforts, unravelling the pathophysiology of MDD and developing effective treatments is still a huge challenge. Here, we report a novel therapeutic axis of methylglyoxal (MGO)/tropomyosin receptor kinase B (TrkB) for treating MDD. As an endogenous metabolite, MGO was demonstrated directly binding to the extracellular domain of TrkB, provoking its dimerization and autophosphorylation. This rapidly enhances the expression of brain-derived neurotrophic factor (BDNF) and forms a BDNF-positive feedback loop. Low-dose treatment of MGO effectively promotes the hippocampal neurogenesis and exhibits sustained antidepressant effects in chronic unpredictable mild stress rat models. In addition, the modulation on MGO concentration by overexpression or inhibition of Glyoxalase 1 (GLO1) has been demonstrated associated with depression behaviors in rats. Furthermore, we also identified a natural product luteolin and its derivative lutD as potent inhibitors of GLO1 and explored their precise binding modes. Our findings reveal a novel regulatory mechanism underlying MDD and depict principles for the rational design of new antidepressants targeting GLO1.

overall_design: Adult Sprague-Dawley (SD) male rats (180 - 200 g) were group-housed with standard laboratory bedding and conditions (12-h light/dark cycle, 22 ± 1°C, ad libitum access to food and water) for 1 week prior to the experiments. All rats were randomly assigned to three experimental groups, i.e., non-stress control + saline (SAL); stress (CMS) + SAL; stress (CMS) + drugs (5 mM/kg/day of MGO or 10 mg/kg/day of luteolin). To avoid the possible bias induced by the behavioral tests, the rats in each group were divided into two sets (n = 10 per set). The first set provided tissue samples used for morphological analysis, western blotting and qRT-PCR analyses, while the second one was adopted for behavioral assessments. During the last 3 weeks of the CMS protocol, rats were injected ip daily with drugs.

first: Ziyin

last: Wu


title: Linear isoforms of the long noncoding RNA CDKN2B-AS1 regulate the c-myc-enhancer binding factor RBMS1

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
To identify genes that are regulated from the lncRNA ANRIL (EXON19), we designed inducible short hairpin RNA constructs and stable integrated them into HEK cells
Changes of gene expression after induction were determined at 48h and 96h by genome-wide mRNA expression analysis.

overall_design: Tetracycline stimulated shRNA silencing of ANRIL in T-Rex 293 HECK and T-Rex HeLa cells at defined time points.

first: R

last: Häsler


title: OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice [ncRNA-seq]

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNA sequences. Here, we investigated the contribution of OsDCL1 to innate immunity in rice. Activation-tagged dcl1a mutants (dcl1a-Ac) showed enhanced susceptibility to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi. Susceptibility to pathogen infection in dcl1a-Ac plants was associated with weaker induction of defence gene expression. Plant growth and development were not affected in dcl1a-Ac plants in the absence of pathogen challenge. To analyse the impact of OsDCL1a activation on the host transcriptome, we compared the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants. OsDCL1a activation misregulated genes involved in detoxification of reactive oxygen species (ROS) and accumulation of O2•- in leaves. Consequently, dcl1a-Ac plants were more sensitive to oxidative stress caused by methyl viologen treatment.  Notably, transcriptome analysis revealed downregulation of diterpenoid phytoalexin biosynthetic genes in dcl1a-Ac, the expression of these genes also being weakly induced during pathogen infection in these plants. Finally, OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. Our findings support that OsDCL1a plays an important role in regulating innate immunity in rice.

overall_design: 2 different replicates of small RNA seq from mock and M. oryzae inculated rice leaves are included in this study. They correspond to wild type and DCL1a activation mutants.

last: Baldrich

first: Raquel

last: Salvador-Guirao

first: Yue-Ie

last: Hsing

first: Kazunori

last: Okada

first: Blanca

last: San Segundo


title: OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice

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

overall_design: Refer to individual Series


title: Gene expression profile of human bone marrow-derived mesenchymal stem cells (BMSC) treated with fucosyltransferase 6 (FTVI) or fucosyltransferase 7 (FTVII)

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary:
Background. The regenerative and immunomodulatory properties of human mesenchymal stem cells (hMSC) have raised great hope for their use in cell therapy. However, when intravenously infused, hMSCs fail to reach sites of tissue injury. Fucose addition in α-(1,3)-linkage to terminal sialyllactosamines on CD44 creates the molecule known as hematopoietic cell E-/L-selectin ligand (HCELL), programming hMSC binding to E-selectin that is expressed on microvascular endothelial cells of bone marrow (BM), skin, and at all sites of inflammation. Here we describe how this modification on BM-derived hMSC (BM-hMSCs) can be adapted to good manufacturing practice (GMP) standards.
Methods.  BM-hMSC were expanded using xenogenic-free media and exofucosylated using α-(1,3)-fucosyltransferases VI (FTVI) or VII (FTVII). Enforced fucosylation converted CD44 into HCELL, and HCELL formation was assessed by western blot, flow cytometry, and cell binding assays.  Untreated (unfucosylated), buffer-treated and exofucosylated BM-hMSC were each characterized by immunophenotype , differentiation potential and cell viability and fucosylation stability were assessed at room temperature and at 4°C.  Safety was assessed by microbiological testing, karyotype, and c-Myc mRNA expression, and potential effects on genetic reprogramming and in cell signaling were analyzed by gene expression microarrays and receptor tyrosine kinase (RTK) phosphorylation arrays.
Results. Our protocol efficiently generates HCELL on clinical-scale batches of BM-hMSC.  Exofucosylation yields stable HCELL expression for 48 hours at 4°C. Exofucosylation preserved full cell viability and identity, without changing gene expression or RTK phosphorylation.
Discussion. The described exofucosylation protocol using xenogenic-free reagents enforces HCELL expression on hMSC endowing potent E-selectin binding without affecting cell viability or native phenotype. This described protocol is readily scalable for GMP-compliant clinical production.

overall_design: Human bone marrow-derived mesenchymal stromal cells (BMSC) from 2 healthy donors, 2 retinitis pigmentosa (RP) patients, and 3 osteoporotic (OSP) patients  were treated in vitro with fucosyltransferase 6 (FTVI) or  fucosyltransferase 7 (FTVII) during 1 hr, or mock-treated, then reseeded in culture flasks and cultured for 24 hr. Equimolar RNA amounts from 5 untreated BMSC were pooled, labelled with cy3, and used as reference sample. Each of the mock-treated, FTVI-treated, or FTVII-treated samples was labelled with cy5 and used as a test sample. The reference sample and the test samples were hybridized together onto Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (technology 39494), scanned in an Agilent G2565CA DNA Microarray Scanner using the Agilent Scan Control software, processed with the Agilent Feature Extraction software, and analyzed using the GeneSpring GX software.

first: María Dolores

last: López-Lucas

first: José María

last: Moraleda-Jiménez


title: OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice [RNA-seq]

overall_design: 2 different replicates of RNA seq from mock and M. oryzae inculated rice leaves are included in this study. They correspond to wild type and DCL1a activation mutants.


title: Altered microRNA expression profiles are involved in Storage Lesions of Apheresis Platelet

status: Public on Sep 20 2018

city: Guangzhou

first: Zhaohu

last: Yuan

address: Panfu road 1, Yuexiu District, Guangzhou

institute: Guangzhou First People’s Hospital

summary: Investigation of miRNA expression level changes of human platelets stored for 2, 5 and 8 days，and to explore the mechanism of storage lesions of human platelets.

first: Qianyu

first: Yaming

last: Wei

first: Xiaojie

last: Chen


title: P. aeruginosa PAO wildtype Cy3 PA3898 mutant Cy5

status: Public on Sep 16 2018

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

summary: We present here a transcriptional regulator, PA3898, which controls biofilm formation and multidrug efflux-pumps in P. aeruginosa. A mutant of this regulator significantly reduced the ability of P. aeruginosa to produce biofilm in vitro, and affected its in vivo fitness and pathogenesis in Drosophila melanogaster and BALB/c mouse lung infection models. Transcriptome analysis revealed that PA3898 modulates essential virulence genes/pathways, including multidrug efflux-pumps and phenazine biosynthesis.

overall_design: PAO1 wildtype versus PA3898 mutant both grown in LB media. cDNA samples were hybridized onto P. aeruginosa 70mer duplicate array (GEO accession number GPL10633).

first: Yun

last: Heacock-Kang


title: EpCAM-Aptamer Toxin Conjugates for targeting tumors

city: Chennai

first: Narayanan

last: Janakiraman

state: Tamil nadu

address: College Road

department: Nanobiotechnology

country: India

institute: Vision Research Foundation

summary:
Neocarzinostatin (NCS) is an anti-tumor DNA damaging agent. Conjugating NCS with EpCAM Aptamer will direct the toxin pay loads to the EpCAM positive cancer cells as a targeted therapy
We used microarrays to detail the global gene expression to understand the pathways involved in EpCAM-mediated NCS drug delivery in breast cancer cells.

overall_design: MCF-7 breast cancer cells were cultured and treated with Neocarzinostatin and Neocarzinostatin-EpCAM Aptamer conjugate for the duration of 24h. RNA was extracted from cells and hybridized onto Affymetrix Human PrimeView arrays. To understand the changes in the transcriptome, we have included untreated MCF-7 cells (Controls; C1, C2) along with treated cells (N1, N2, NC1, NC2).

first: Prasanna

middle: k

last: Athyala

first: Srujana

last: Chitipothu


title: Gene expression in B16-OVA cells transfected with/without double-stranded DNA

status: Public on Sep 04 2018

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary:
Transfected double strand DNA were required for the efficient activation of STING to activate innate immune cytokine.
We used microarrays to evaluate the innate immune cytokine expression in B16-OVA cells transfected with double strand DNA.

overall_design: We transfected 90mer double strand DNA into B16 ova cells for 6 hours and evaluated gene expression profile.

first: Glen

middle: N

last: Barber

first: Jeonghyun

last: Ahn


title: Gene array analysis of WT and SKO macrophages following engulfment of irradiated HEK 293 cells with/without double-stranded DNA

summary:
The ability of dying cells to activate antigen presenting cells (APCs) is carefully controlled to avoid unwarranted inflammatory responses. Here we show that engulfed cells only containing cytosolic dsDNA species (viral or synthetic) or cyclic di-nucleotides (CDNs) are able to stimulate APCs, via extrinsic STING-signaling.
HEK293 cells containing double strand DNA robustly induced the production of cytokines in macrophages that was dependent on extrinsic STING signaling within the macrophage.

overall_design: HEK293 cells were transfected by double-strand DNA for 3 hours and irradiated by UV (120mJ/cm). After 24 hours, the irradiated HEK293 cells were fed to WT or SKO macrophages for 6 hours.


title: Genome-wide gene expression profiles of 14 paired (normal and varicose) vein samples from the patients with varicose vein disease.

city: Novosibirsk

first: Mariya

middle: Alexandrovna

last: Smetanina

address: 8 Lavrentiev Avenue

country: Russia

institute: Institute of Chemical Biology and Fundamental Medicine SB RAS

summary: To identify genes whose products are involved in the formation of a pathological phenotype of varicose veins, we attempted to analyze the transcriptome of their constituent cells and compare it to the transcriptome of normal veins from the same patient. We identified a number of genes of extracellular matrix remodeling and cell-cell communication significantly changing gene expression status in disease condition.

overall_design: 7 pairs (14) of RNA samples of varicose and normal veins were tested on the gene expression beadchips.


title: Profiles of 20 paired (normal and varicose) vein samples from the patients with varicose vein disease

type: Methylation profiling by genome tiling array


title: Genome-wide DNA methylation profiles of 20 paired (normal and varicose) vein samples from the patients with varicose vein disease.

summary: To identify genes involved in the formation of a pathological phenotype of varicose veins, we attempted to analyze the methylome of their constituent cells and compare it to the methylome of normal veins from the same patient. We identified a number of genes of extracellular matrix remodeling and cell-cell communication whose methylation status was significantly changed in disease condition.

overall_design: Bisulphite converted DNA from the 10 pairs (20) of samples of varicose and normal veins were tested on the methylation beadchips.


title: Comparative transcriptome analyses provide insights into the adaptation mechanisms to acute salt stresses in juvenile Sinonovacula constricta

status: Public on Sep 03 2018

city: Ningbo

first: Zhaoshou

last: Ran

state: Zhejiang

address: Fenghua Road 818, Jiangbei Districta

department: Institute of Marine Science

institute: Ningbo University

summary: Sinonovacula constricta is an economically important bivalve species in China, Korea and Japan. It widely resides in estuarine and coastal areas where salinity fluctuates rapidly. However, little is known about its adaptation mechanisms to acute salt stresses. To address this, we establish nine cDNA libraries (triplicate each treatment) from juvenile S. constricta, which were subjected to low salinity (5 psu), optimal salinity (15 psu, the control) and high salinity (25 psu) for 6 h, respectively. Illumina sequencing generated 478,587,310 clean reads totally, which were assembled into 427,057 transcripts of 246,672 unigenes. Compared with the control, 1259 and 2163 differentially expressed genes (DEGs) were identified under acute low and high salt stresses, respectively. GO and KEGG enrichment analyses of DEGs suggested that several key metabolic modulations were mainly responsible for the acute salt stresses. Based on the significantly highlighted KEGG pathways, some key DEGs were identified and discussed in details, including cysteine sulfinic acid decarboxylase, alanine transaminase, glutamine synthetase, glutamate dehydrogenase, nitric-oxide synthase, arginase, betaine-homocysteine S-methyltransferase, serine racemase, L-serine ammonia-lyase, phosphoserine phosphatase, glutamate 5-kinase, glutamate-5-semialdehyde dehydrogenase, ornithine-oxo-acid transaminase, ornithine decarboxylase, stearoyl-CoA desaturase, carnitine O-palmitoyltransferase 1, serine/threonine-protein kinase, NF-kappa-B, NF-kappa-B inhibitor alpha, phosphoenolpyruvate carboxykinase and carbohydrate response element binding protein. Furthermore, some potential osmolytes were speculated. In summary, this study would not only provide insights into the adaptation mechanisms to acute salt stresses in juvenile S. constricta, but also facilitate to better understand the physical and biochemical performances of this bivalve species involved in acute salt stresses. Moreover, the transcriptome data obtained here greatly enriched the genetic information of S. constricta, which would be valuable for promoting its molecular biology researches.

overall_design: Juvenile S. constricta were first subjected to low salinity (5 psu), optimal salinity (15 psu, the control) and high salinity (25 psu) for 6 h respectively. Subsequently, samples in whole organism were used to establish 9 cDNA libraries (triplicate each group) by Illumina sequencing.

first: Bin

last: Ma

first: Xiaorong

last: Xu

first: Jilin

first: Kai

last: Liao

first: Jiayi

last: Cao

first: Xiaojun

last: Yan


title: Extrinsic Phagocyte-Dependent STING-Signaling Dictates the Immunogenicity of Dying Cells


title: Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp.

status: Public on Sep 01 2018

city: Jena

first: Falk

last: Hillmann

address: Adolf-Reichwein-Straße 23

department: Evolution of Microbial Interactions

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

sample_organism:
Candida albicans
Nakaseomyces glabratus
Candida parapsilosis
Planoprotostelium fungivorum


title: Integration of genome-wide DNA methylation and transcription uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis [gene expression]

city: Dallas

first: Quan

last: Li

state: TX

address: 6001 Forest Park Rd

department: Immunology

institute: UTSW

summary: The identified MeDEGs may represent novel candidate factors which lead to the abnormal activation of immune regulatory pathways in the pathogenesis of SSc. They may also be used as diagnostic biomarkers for SSC and clinical complications

overall_design: Genome-wide mRNA transcription and global DNA methylation analysis were performed on PBMC from 18 SSc patients and 19 matched normal controls (NC) using Illumina BeadChips

first: Hongling

last: Zhu

first: Chengsongg

first: Wentaog

last: Mi

first: Taog

last: Chen

first: Hongjung

last: Zhao

first: Xiaoxiag

last: Zuo

first: Huig

last: Luo

first: Quan-Zheng


title: Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp. (here: C. albicans and C. glabrata)

summary: We investigated different escape and defense strategies of Candida glabrata and Candida albicans against the natural fungivorous predator Protostelium aurantium using dual RNA-Seq. While C. albicans was found to be very succesfull in preventing from amoeba recognition, C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity. Trophozoites of the amoeba Protostelium aurantium were fed seperately with the two fungal species and samples for RNA isolation were taken at time points 0 min (control), 30 min and 60 min. At indicated time points samples were shock frozen and used for RNA isolation. Samples for RNAseq were taken at time points 0 min (control), 30 min and 60 min. RNA samples from identical timepoints for C. albicans and C. glabrata were pooled for RNA sequencing. We investigated different escape and defense strategies of Candida spp. against natural fungivorous predator. While C. parapsilosis underwent rapid predation and intracellular killing of the yeast, C. albicans was found to be very succesfull in preventing from amoeba recognition. C. glabrata in turn, was rapidly taken up but remained undigested with a comparably low transcriptional activity.

sample_organism:
Candida albicans
Nakaseomyces glabratus
Planoprotostelium fungivorum

overall_design: Analysis of nine samples in total. Three time points (0min, 30min and 60min) with three replicates each. The three 0min samples are the control samples.

first: Silvia

last: Radosa

first: Jörg

last: Linde


title: Tissue-specific transcriptomic profiling of opium poppy (Papaver somniferum)

city: Xi'an

first: Li

last: Guo

address: 28 Xianning West Road

institute: Xi'an Jiao Tong University

summary: To facilitate genome annotation, we performed RNA sequencing of seven different opium poppy tissues (leaf, petal, stamen, capsule, stem, fine root, tap root).

overall_design: On the first day of anthesis material was sampled from the following seven tissue types using a subset of plants: fine roots, tap root, leaves (the two uppermost ones), stem (the 2 cm long part just underneath the capsule), capsule, petals and stamens. Five days after the onset of anthesis stem and capsule materials were collected from another subset of plants. These plants had been manually pollinated on the first day of anthesis and had shed their petals at the time of sampling.

first: Thilo

last: Winzer

first: Ian

last: Graham


title: Analysis of lncRNAs for the characterization of the response to neoadjuvant chemoradiotherapy

city: Genova

first: Lorenzo

last: Ferrando

address: Viale Benedetto XV

department: Department of Internal Medicine

country: Italy

institute: University of Genoa

summary: We investigated the role of lncRNAs to predict the response to preoperative tretament in locally advanced rectal adenocarcinoma

overall_design: We collected 30 samples of locally advanced rectal adenocarcinoma. Response to neoadjuvant treatment was considered positive in 18 samples, while 12 samples showed negative response.

first: Gabriele

last: Zoppoli

first: Gabriella

last: Cirmena

first: Anna

last: Garuti


title: Transcriptome of the ansamitocin producer Actinosynnema pretiosum ATCC 31280

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

summary: To explore gene expression and search for the ansamitocin resistant genes during fermentation, total RNA of the ansmitocin high producer NXJ-24 and the wildtype strain ATCC31280 were extracted and sequenced. The gene expression values from day 1 to day 5 of NXJ-24 and day 5 of ATCC31280 were compared. 6 genes were considered most likely to be the ansamitocin transporter genes.

overall_design: Exploration of the expression profile of genes during ansamitocin production and search for ansamitocin resistant genes.

first: Xinjuan

last: Ning

first: Linquan

last: Bai


title: Interaction of soil amoeba Protostelium aurantium with three pathogenic yeasts Candida spp. (here: C. parapsilosis)

first: Falk

last: Hillmann

summary: We investigated different escape and defense strategies of Candida parapsilosis against the natural fungivorous predator Protostelium aurantium using dual RNA-Seq. Trophozoites of the amoeba Protostelium aurantium were fed with C. parapsilosis and samples for RNA isolation were taken at time points 0 min (control), 30 min and 60 min. At indicated time points samples were shock frozen and used for RNA isolation. C. parapsilosis underwent rapid predation and intracellular killing of the yeast

sample_organism:
Candida parapsilosis
Planoprotostelium fungivorum


title: HLJ1 is an endogenous Src inhibitor that suppresses cancer progression through dual mechanisms

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
HLJ1 acts as a prognosis marker and associates with overall survival of patients with non-small-cell lung cancer. This study sought to investigate the specific contribution of HLJ1 to neoplastic diseases.
We used microarrays to identify the HLJ1-affected signaling pathways.

overall_design: CL1-0 cells were infected with scramble shRNA or HLJ1 shRNA (shHLJ1) lentiviruses for 24 hours and then cells were treated with 0.75 μg/ml puromycin to select for puromycin-resistant pooled clones. The extracted RNAs from these clones were analyzed by expression arrays.

first: Ching-Hsien

last: Chen

first: Wen-Hsin

last: Chang

first: Kang-Yi

last: Su

first: Qi-Sheng

last: Hong

first: Yi-Jing

last: Hsiao

first: Hong-Chen

first: Reen

last: Wu

first: Pan-Chyr

last: Yang

first: Jeremy

middle: J


title: Expression data from Arabidopsis thaliana (Col-0) exposed to Arsenic, Hypoxia and their combination

city: Bielefeld

first: Vijay

last: Kumar

address: University Street 25

institute: Bielefeld University

summary:
Plants often face combinatorial stresses in their natural environment. Here arsenic (As) toxicity was combined with hypoxia (Hpx) in the roots of Arabidopsis thaliana as it often occurs in nature. The present work aimed to explore the effects of single and combined hypoxia and As stress applied at realistic stress levels to hydroponically grown A. thaliana.
Arsenic as well as hypoxic growth conditions generate a characteristic signaling pattern, a significant part of which is mediated by ROS. The current study utilized the microarray to determine the overlapping signalling pattern and changes in gene expression for the defined stress combinaton compared to individual stresses.

overall_design: Roots of Arabidopsis thaliana (Col-0; WT), grown hydroponically for 32d were exposed to either 250 µM As (AsV; Na2HAsO4) alone or in combination with hypoxic nutrient media and also hypoxia alone. The plant material was harvested after 7d of treatment and root samples were used for RNA extrcation and subsequent hybridization on Affymetrix microarray chips. Three completely independent biological replicates were analyzed for each treatment (C1, C2, C3: Control; As1, As2, As3: Arsenic; Hpx1, 3, 5: Hypoxia; Hpx2, 4, 6: Hypoxia + Arsenic)

first: Karl-Josef

last: Dietz


title: Microarray expression data derived  from ovaries of women with Polycystic Ovary Syndrome and Female to Male Transexual individuals after treatment with Testosterone

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

summary:
This microarray analysis identified differentially regulated expression of 326 genes (p value=<0.05 and fold change of +/-2). Based on these genes, a biological LH network was generated consisting molecules where the significance of the association was measured by Fisher's exact test.
We used microarray gene expression analysis to dissect the LH-induced gene expression in the ovaries of PCOS women.

overall_design: RNA was isolated from ovary biopsies of PCOS women and TSX individuals to investigate LH induced gene expression.

first: S

last: Gielen

first: J

middle: S

last: Laven

first: PJ

last: van der Spek

first: A

first: B

last: de Hoon


title: Cellulose perturbation has broad impacts on resource allocation in Arabidopsis thaliana putatively mediated by glycine rich peptides

city: Guelph

first: Malcolm

last: Campbell

state: Ontario

address: 50 Stone Road East

institute: University of Guelph

summary: The interplay between plant chemistry and architecture was investigated using a pharmacological approach combined with mutant analysis. Due to the high abundance and essential role of cellulose in plant development and function, it was hypothesized that perturbation of cellulose biosynthesis would have far-reaching effects on plant chemistry and resource allocation. The impact of cellulose disruption was studied through comprehensive multiphase-NMR (CMP-NMR) using the Arabidopsis thaliana cellulose synthase mutant ectopic lignification1 (eli1). CMP-NMR confirmed several known metabolic impacts of cellulose disruption including increased lignification, increased starch production, and a shift from crystalline to amorphous cellulose. It also revealed unexpected metabolic impacts such as increased methanol production, increased seed-derived lipid content, and the presence of the peptide pentaglycine, which had not been previously observed in plants. It was further hypothesized that the metabolic impacts of cellulose disruption are mediated by one or more signal molecules that would be elevated in cellulose synthase mutants such as eli1. The presence of one or more signal molecules in eli1 that induce a lignification response was confirmed by exposing wild-type seedlings to ground tissue from eli1. Treatment of wild-type seedlings with pentaglycine suggested that the peptide may be at least partially responsible for mediating this response. A case is made for glycine rich proteins (GRPs) as the source of pentaglycine in vivo, and for wall associated kinases (WAKs) as receptors that trigger either developmental or defence responses through differential binding of intact GRPs and oligoglycine peptides.

overall_design: Examination of two different genotypes (wild type and eli1) in the absence and presence of glucose, with two biological replicates

first: Heather

last: Wheeler

first: Ronald

last: Soong

first: Denis

last: Courtier-Murias

first: Adolfo

last: Botana

first: Blythe

last: Fortier-McGill

first: Andre

last: Simpson


title: GATA2 mutant transduction of murine hematopoietic stem cells

city: Toulouse

first: Eric

last: DELABESSE

address: 1 avenue Irène Joliot-Curie

country: France

institute: Institut Universitaire de Cancérologie de Toulouse, site Oncopôle CHU de Toulouse

overall_design:
C57BL/6 8-week female were treated with 5-fluorouracil (5-FU) at 150mg/kg 6 days prior to bone marrow cell harvesting. The bone marrow cells were infected with MIE, WT and R396Q retroviral particles. GFP-positive cells were sorted after 72h of culture. Total RNA was extracted using Rneasy plus MiniKit (Qiagen) and its quality was assessed with the RNA Screen Tape on Agilent 2200 Tapestation Bioanalyzer (Agilent Technologies). RNA samples were purified and prepared according to the manufacturer's protocol using the Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) and hybridized on Affymetrix GeneChip Mouse Exon 1.0 ST arrays. Probe-signal intensities were normalized and summarized using the robust multiarray average (RMA) method with the Affymetrix’s Expression Console software.
3 controls (MIE), 3 GATA2 wild type, 3 GATA2 R396Q

last: Delabesse

first: Nais

last: Prade


title: Real-time quantitative PCR analysis of Normal and Cancerous Prostate Cells [RT-PCR]

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: To validate a panel of selected genes expression in prostate cancer, we performed expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP using qPCR.

overall_design: RNA was extracted from prostate cancer (LNCaP) and normal (PrEC) cells and selected genes differential expression was quantified using qPCR.

first: Hugh

last: French

first: Aaron

last: Statham

first: Susan

last: Clark


title: Transcriptomic analysis of engineered and improved Pichia pastoris for S-adenosyl-l-methionine (SAM) production

city: Nanning

first: Xiulin

last: Qin

state: Guangxi

address: 100 Daxue Road

department: College of Life Science and Technology

institute: Guangxi university

summary: SAM is the principal methyl group donor in all living organisms, and has attracted much interest in clinical research. We improved SAM production in engineered P. pastoris strain GS115/DS56 by overexpression of the recombinant methionine adenosyltransferase (MAT) gene DS56, and further enhanced SAM prduction in G12-CBS by downregulation of the cystathionine β-synthase (CBS) gene CYS4 with a weak promoter G12. We performed the pairwise transcriptome comparisons between high-producing (HP) and low-producing (LP) strains, in order to understand the impact of SAM accumulation on the P. pastoris physiology and to identify genome-wide targets for further improving SAM production.

overall_design: A twelve array study using total RNA recovered from the LP control strain GS115/3.5K, and the HP strains GS115/DS56 and G12-CBS grown in shake flask at 72 h after methanol induction in the presence of L-Met, as well as from the strain G12-CBS just before L-Met feeding after methanol induction for 24 h. Each chip measures the expression levels of 5777 genes (8 probes per gene).

first: Jinagchao

last: Qian


title: miRNA expression data from sun-exposed and sun- protected skin of young (18-25 years) and old (>70 years) females

status: Public on Aug 31 2018

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary:
In this study we explored the effects of chronological and photoageing on the miRNome of human skin. To this end, miRNA expression was analysed in biopsies collected from sun-exposed (outer arm) and sun-protected (inner arm) skin from fair-skinned (phototype II/III) healthy female volunteers of two age groups: young, 18-25 years and aged, >70 years. Strict inclusion criteria were used for photoageing scoring and for chronological ageing. Microarray analysis revealed that chronological ageing had minor effect on the human skin miRNome. In contrast, photoageing had a robust impact on miRNAs, and a set of miRNAs differentially expressed between sun-protected and sun-exposed skin of the young and aged groups was identified.
We have performed miRNome analysis (using microarray) on RNA isolated from sun-exposed and sun-protected skin of young and old females

overall_design: Matched/paired biopsies from sun-exposed and sun-protected zones of anatomically close locations from the same individual were collected and total RNA was isolated for miRNA-microarray analysis.

first: Magnus

last: Karlsson

first: Claire

last: Marionnet

first: Françoise

last: Bernerd

first: Audrey

last: Gueniche

first: Charles

last: El Rawadi

first: Mona

last: Ståhle

first: Enikö

last: Sonkoly

first: Lionel

last: Breton

first: Andor

last: Pivarcsi


title: Comparison of variant calling pipelines using Illumina CanineHD BeadChip array as the truth dataset

city: Darlington

first: Tracy

last: Chew

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

institute: University of Sydney

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

summary: Next generation sequencing platforms have become essential tools for understanding DNA in a wide range of contexts. Their success heavily relies on the accuracy, sensitivity and specificity of methods used to discern differences between the reference genome and genomes under investigation. Here we compare the relative performances of five popular single nucleotide variant callers with and without their associated recommended hard filtering criteria. We compare: FreeBayes; the Genome Analysis Toolkit’s Haplotype Caller and Unified Genotyper; SAMtools; and VarScan. We tailor this comparison to suit smaller projects with modest sample numbers (n = 10) and coverage (~10X) to fill a current gap in the literature. Other comparison studies are generally applicable only to larger projects in model species, where there is access to large amounts of sequencing data and curated callsets for base and variant quality score recalibration. We estimated the accuracy, sensitivity and specificity of each pipeline according to the genotype concordance rate and number with the “truth” dataset for 10 canine samples. The truth dataset was defined as genotypes obtained from the CanineHD BeadChip array. Whole genome sequencing data was performed on the Illumina HiSeq2000 or HiSeq2500 platform as 100-101 base pair, paired end reads to an average sample coverage of 10.3X. Apart from GATK Haplotype Caller, applying recommended hard filters did not improve the performance of genotyping concordance at the tested levels of minimum coverage. The default VarScan pipeline with no additional filters applied (VarScan uses SAMtools mpileup, without base alignment quality computation) generally outperformed other callers in terms of accuracy, sensitivity and specificity. The results of this study demonstrate that hard filtering of variant calls from low-powered genome studies can impair accuracy, sensitivity and specificity of callsets and provides some benchmark performance metrics on a range of low coverage levels.

overall_design: We whole genome sequenced and genotyped using the Illumina CanineHD BeadChip array 12 individual samples. After quality control, we used Illumina CanineHD BeadChip array genotypes as the truth dataset and measured concordance rates between variant calling pipelines to the truth dataset.  This series contains only the 'truth'  BeadChip dataset.  The whole genome sequence project is available in BioProject: PRJNA477886.

last: Wade

first: Bianca

last: Haase

first: Cali

last: Willet


title: Sensory domain of the cell cycle kinase CckA regulates the differential DNA binding of the master regulator CtrA in Caulobacter crescentus

city: Thiruvananthapuram

first: Sharath

last: Narayanan

state: Kerala

address: CET campus

department: Biology

institute: IISER

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We show the role of CckA kinase in controlling the differential DNA binding activity of CtrA

overall_design: Comparative ChIP-Seq analysis of CtrA occupancy in WT cckA and cckA(L228P) genetic backgrounds.

first: Lokesh

last: Kumar

first: Sunish

last: Radhakrishnan


title: Short-term inhalation exposure to copper oxide nanoparticles induces gene expression changes associated with inflammation and cell proliferation in rat bronchoalveolar epithelium

city: Ottawa

first: Andrew

last: Williams

address: 50 Colombine Dr

institute: Health Canada

summary: Copper oxide nanoparticles (CuO NPs) are considered for various technological and consumer applications, leading to growing concerns for potential human hazards resulting from inhalation. Recent studies have revealed a dose-dependent toxicity of CuO NPs in rats following short-term inhalation exposure. Here, we utilized transcriptomics approaches to further investigate the responses in rats exposed via inhalation for five consecutive days to two doses of CuO NPs, 3.3 (low dose, LD) and 13.2 (high dose, HD) mg/m3, with collection of lung tissues on days 6 (1 day post-exposure) and 28 (i.e., after a 22-day post-exposure recovery period). Histopathology confirmed an acute inflammatory response that was resolved during the post-exposure phase. Global gene expression analyses yielded about 1,000 differentially expressed genes in HD rats and 200 in LD on day 6, and less than 20 after the recovery period. Pathway analysis indicated cell proliferation/survival and inflammation as the main processes triggered by exposure and identified epithelial cell transforming protein 2 (Ect2) as a potential gene of interest implicated in cell proliferation. Indeed, ECT2 was upregulated in exposed lungs and was localized in the cytoplasm of alveolar epithelial cells in HD rats, in hyperplasic foci identified based on the Ki67 antigen, a marker of cell proliferation. Monocyte chemoattractant protein 1 (MCP-1, also known as CCL2), with an important role in the regulation of inflammatory processes and cell proliferation, was also upregulated and this was confirmed immunohistochemically. Finally, we could not find any evidence for aberrant DNA methylation of inflammation-associated genes in response to CuO NP exposure. In summary, the current findings suggest that airborne CuO NPs cause an acute response that translates into inflammation and cellular proliferation in bronchoalveolar epithelium, with upregulation of neoplasia-related factors even after a short-term exposure.

overall_design: This experiment examined lung tissues from Wistar Unilever outbred rats (strain HsdCpb:WU) exposed to 6 hour equivalent doses of 3.3 and 13.2 mg NPs / m3 of copper oxide nanoparticles by nose only inhalation according to the OECD test Guideline 403 for Acute Inhalation Toxicity Test. Rats were exposed to five consecutive days and lung tissues were sampled on day 1 after the last exposure (referred to as T6) and day 22 post-exposure (referred to as T28). Control animals were exposed to air only. Each treatment group consisted of 5 animals. Exposure and sample collection were conducted at the National Institute for Public Health (RIVM) at Bilthoven, The Netherlands, under permit number 201300190. Experimental procedures were in accordance with the European directive on the protection of animals for scientific purposes (Directive 2010/63/EU).

first: Sabina

last: Halappanavar


title: Role for ABCI20 in regulating seed maturation

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

summary:
We analyzed the monsome and polysome associated transcripts of mutant abci20 compared to Col-0 seeds
The aim was to investigate the role of ABCI20 for its role in regulating seed dormancy and longevity.

overall_design: Transcript level on both total mRNA and polysomal RNA of abci20 and Col-0 seeds were evaluated. For each RNA fraction, three replicates were used.

first: Bing

last: Bai

first: Jan

last: Cordewener

first: Twan

last: America

first: Johannes

last: Hanson


title: Transcriptomic study in mog1 yeast mutant

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: The goal of the project was to study the effects on transctiptome of some mutations related with SAGA complex

overall_design:
Cells were grown in YPD at 30ºC to 0.5 OD600. At that OD cells were spun-down and collected. Each sample was done in triplicates.

Please note that each sample record represents three replicates (more details in the sample description field).

first: José

last: Pérez-Ortín

first: María

last: Pérez-Martínez

first: Paula

last: Oliete-Calvo

first: Susana

last: Rodríguez-Navarro


title: Expression profile of immortalized mesothelial cells with or without activated TAZ

city: Aichi

first: Akihiro

last: Matsushita

address: 1-1 Kanokoden, Chikusa-ku, Nagoya

department: Division of Cancer Biology

country: Japan

institute: Aichi Cancer Center Research Institute

summary: Transcriptional profiling of HOMC-D4 immortalized mesothelial cell lines expressing wild type TAZ or activated S89A mutant TAZ

overall_design: Immortalized mesothelial cells expressing wild type TAZ vs.  immortalized mesothelial cells expressing  TAZ S89A mutant

first: T

last: Sato

first: A

first: Y

last: Sekido


title: Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [gene expression]

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: Breast cancer is a heterogeneous disease described in well-recognized biological subtypes. Particularly, gene expression profiling has revealed 5 intrinsic subtypes of breast cancer characterized by different biological and clinical features. The diversity of the intrinsic subtypes across human population has been limited described, and there is few information about the genomic architecture of breast tumors in Mexican or Hispanic populations. In this study, we performed PAM50 assay, based in Affymetrix microarray profiling of 128 fresh frozen tumors from Mexican Latino Hispanic population, to describe the overall distribution of subtypes, and characterize the relation to clinicopathologic characteristics. As well, we correlated the mRNA expression patterns with specific copy number alterations (CPA), in order to analyze their role in breast tumors. A total of 100 blood-tumor samples were assayed using Affymetrix 6.0 SNP arrays; segmentation analysis and GISTIC were performed to identify focal amplifications or deletions. The distribution of PAM50 intrinsic subtypes in our cohort was computed to be 44% luminal A, 20% luminal B, 12.0% HER2-enriched, 12% basal-like, and 12% normal-like. Study comparison with the literature mainly TCGA and METABRIC (most of the patients came from Caucasian population), as well as LACE (which describe a population study) show a similar distribution of the intrinsic subtypes within Hispanic and Caucasian populations. Interestingly, basal-like subtype is less represented than in African-American race. The sum of sensitivity and specificity between the clinicopathologic and intrinsic subtype categories across 4 groups (excluding normal-like) was 50% and 87.5%, respectively. Differentially expression profiles within the subtypes reveal a set of genes altered in each group with biological relevance to stablish the phenotypical characteristics of each subtype. Our analyses confirmed the already reported copy number data. Importantly, many of the copy number profiles correlated with mRNA subtype. With this analysis we can conclude that breast cancer intrinsic subtypes have been reproduced in Mexican population contributing to the description of the PAM50 subtypes among multiple ethnic groups based on a gene expression assay. Our observation based in the integrative genomic analysis of mRNA expression and CPA allowed us to define gene circuits and phenotypic characteristics that can explain the heterogeneity of breast cancer subtypes.

overall_design: Breast cancer tumors were collected at the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) during the surgical procedure in adjuvant. Two training pathologist carefully performed a histopathological review to define percentage of tumoral cells. Also, immunochemistry markers (ER-, PR- and Her2-) were analyzed. Thus tumors with at least 70% of tumoral cells were processed (N=124). Total RNA was extracted and hybridize on Affymetrix miRNA microarrays. To define PAM50 subtypes Parker algorithm was computed.

first: R

last: Rebollar-Vega

first: S

last: Romero-Córdoba

last: Rodríguez-Cuevas

last: Maffuz-Aziz

last: Hidalgo-Miranda


title: PAMP-induced secreted peptide 1, PIP1 (At4g28460) and PIP2 (At4g37290) are negative modulators of immunity in Arabidopsis thaliana

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: Transcriptomic responses in Arabidopsis thaliana to PIP1 and PIP2 peptide

overall_design: Two weeks old seedlings were treated either with 100 nM PIP1 or PIP2 peptide (treated), while control plants were treated with MQ water and 0.02% Silwet L-77. Whole rosettes were harvested 3 hours after treatment using 3 biological replicaes per treatment.

first: Javad

last: Najafi

first: Rannveig

last: Viste

first: Ane

middle: K

last: Vie

first: Imre

last: Somssich

first: Torfinn

last: Sparstad

first: Tore

last: Brembu

first: Atle

last: Bones


title: Genome-wide analysis of the role of S276 phosphorylation of p65-NFkappaB on the regulation of gene expression in response to EGF or IL-1 treatment.

city: Cleveland

first: George

last: Stark

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

country: USA

institute: Cleveland Clinic Lerner Research Institute

summary: Genome-wide gene expression levels of were measured by microarray in wildtype (WT) or S276A-p65 HMECs treated with or without 100 ng/mL EGF or 10 ng/mL IL-1 for 4 h.

overall_design: To interrogate the role of S276 phosphorylation in NF-kappaB genomic regulation in response to EGF or IL-1 stimulation, using the gene editing approach CRISPR, we introduced the genetic mutation S276A in the RELA gene in HMECs by means of HDR repair of the Cas9-induced DSB.

first: Josephine

last: Dermawan

middle: R


title: Theissenolactone C inhibits lipopolysaccharide-induced TAK-1/IKK signaling and improves septic injuries in vivo

city: Taipei

last: Hsiao

address: No. 250, Wu-Hsing Str

department: Pharmacology

institute: Taipei Medical University

summary: Sepsis is a common leading cause of death and evolves to multi-organ injury. Clinical studies show that endotoxin lipopolysaccharide (LPS) acts as an exogenous pyrogen and produces many types of mediators involved in septic shock. In vivo and in vitro, LPS can induce the expression of pro-inflammatory mediators in human monocytes, such as proteinases, cytokines and inducible nitric oxide synthase (NOS). The released cytokines, such as tumor necrosis factor (TNF)-α, interleukin (IL)-6 and IL-1β, play important roles in sepsis or chronic infection. These cytokines could also enhance the matrix metalloproteinases (MMP) production in monocytes, which leads to serious tissue structure destruction. Theissenolactone C (LC53) is derived from the Taiwan strains Xylariaceae (Xylariaceae) Theissenia cinerea. In this study, microarray technology was first applied to detect the possible regulated genes in LPS-activated human monocytic cells (THP-1) under pretreatment of LC53. We also found LC53 obviously decreased LPS-induced extracellular MMP-9, TNF-α and IL-6 levels in THP-1 cells within 24 hours. It inhibited LPS-induced intracellular MMP-9 protein and mRNA expression. In signaling studies, LC53 could block the LPS-induced degradation of IκBα, p65 translocation, and NF-κB regulated gene reporter activity. It also decreased the phosphorylation of IKKα/β while not affected the TAK1 and p38 phosphorylation. In vivo studies showed LC53 could improve the cecum shrinkage, decrease plasma TNF-α/IL-6 levels, and lower the hepatic iNOS/MMP-9 expression in LPS-induced mice endotoxemia model. Theissenolactone C may be a promising potential therapeutic agent which might be through its inhibition on TAK1/TAB2/3/IKK pathway for endotoxemia injuries.

overall_design: Three samples of RNA are analyzed. THP-1 cells were stimulated with 50 ng/ml LPS for 8 hours (LPS group). Cells were pretreated with LC53 (5 μM) for 15min and subsequently stimulated with 50 ng/ml LPS for 8 hours (LC53 group). Resting group is untreated anything.

first: Yung-Chen

last: Chou

first: Yu-Chieh

last: Lee

first: Che-Jen

first: Chi-Li

last: Chung

first: Jing-Shiun

last: Jan

first: Chiu-Yun

last: Chang

first: Tzong-Huei


title: Protein microarray epitope mapping of monoclonal antibody 5H2 raised by human immunization with the 4CMenB vaccine formulation containing the fusion antigen NHBA-NMB1030.

status: Public on Aug 30 2018

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

institute: GSK Vaccines

summary: The aim of the study was to determine the epitope targeted by 5H2 human Fab directed against NHBA and the crossreactivity aginst a panel of nine different NHBA long and short peptide variants (p2, p3, p5, p10, p17, p20, p21, p24, p29). 5H2 were diluted at 1:2000 and incubated on a non-commercial Protein Microarray platform printed with NHBAp2  specific recombinant protein fragments and full length NHBA of different variants.

overall_design: A panel of  recombinant fragments of different length spanning the entire sequence of  NHBAp2 and NHBAp3 plus different nine different NHBA long and short peptide variants (p2, p3, p5, p10, p17, p20, p21, p24, p29) were printed in 8 replicates on a no-commercial Protein Microarray. All fragments were expressed in E. coli as either glutathione S-transferase-, His-tagged or TRX-fusions, purified from the cytoplasmic fraction as soluble forms. Human IgG (at 8 different concentration points) was distributed in each array copy as control. HuFab 5H2 was profiled for anti-Human IgG specific analysis of reactivity to the spotted proteins.


title: Bone marrow neutrophils regulate multiple myeloma by releasing DNA

city: Philadelphia

first: Cindy

last: Lin

state: PA

address: 3601 Spruce Street

institute: Wistar Institute

summary:
Development of Multiple Myeloma is associated with an accumulation of myeloid derived suppressor cells (MDSCs ) - cells that are morphologically and phenotypically similar to neutrophils (PMN-MDSC) and monocytes (M-MDSC), but are distinct in their functional and biochemical characteristics as well as in their ability to suppress immune responses.
In our study, we found that both neutrophils and PMN-MDSCs equally promoted MM survival and decreased MM cell sensitivity to chemotherapy. Therefore, we used a microarray to elucidate the mechanism of the protective effect of neutrophils on myeloma cells.

overall_design: DP42 murine myeloma cells were cultured alone or together with mouse B-cells (control) or neutrophils for 24 hours. The cells were subsequently separated using FACs and RNA was extracted using Trizol

first: Indu

last: Ramachandran

first: Yulia

last: Nefedova


title: Cardiac maturation process from human iPSCs

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary:
To improve the maturity of iPSC-cardiomyocytes, we addressed the cell type specification of iPSC-cardiomyocytes by microarray and analyzed in detail about cardiac maturation process.
We compared gene expression between samples, and extracted several key genes for cardac maturation and check the function of these genes.  We show that a number of genes expression correlate with cardiac maturation process, and found surface markers to discriminate differentiated cardiomyocytes from other immature cells.

overall_design: mRNA profiles of differentiated iPSC-cardiomyocytes at several differentiation stages. Additionally, we checked the function of several important genes for cardiac maturation, which were extracted from microarray data.

first: S

last: Funakoshi

first: Y

last: Yoshida


title: Amphiregulin-producing pathogenic memory T helper-2 cells instruct eosinophils to secrete Osteopontin and facilitate airway fibrosis

status: Public on Aug 21 2018

city: Chiba

first: Yuki

last: Morimoto

state: Chiba

address: 1-8-1, Inohana, Chuoku

department: Graduate school of Medicine

institute: Chiba University

summary: Memory helper T cells provide long-lasting host defeMemory helper T cells provide long-lasting host defense against microbial pathogens, while distinct subpopulations of memory T cells drive chronic inflammatory diseases such as asthma.  Asthma is a chronic allergic inflammatory disease with airway remodeling including fibrotic changes.  The immunological mechanisms that induce airway fibrotic changes in allergic inflammation remain unknown.  We found that Interleukin-33 (IL-33) enhanced Amphiregulin production by the IL-33 receptor, ST2hi memory T helper-2 (Th2) cells.  Amphiregulin-epidermal growth factor receptor (EGFR)-mediated signaling directly reprogramed eosinophils to an inflammatory state with enhanced production of Osteopontin, a key profibrotic immunomodulatory protein.  IL-5-producing memory Th2 cells and Amphiregulin-producing memory Th2 cells appeared to cooperate to establish lung fibrosis.  The analysis of polyps from patients with eosinophilic chronic rhinosinusitis revealed fibrosis with accumulation of Amphiregulin-producing CRTH2hiCD161hiCD45RO+CD4+ Th2 cells and Osteopontin-producing eosinophils.  Thus, the IL-33-Amphiregulin-Osteopontin axis directs fibrotic responses in eosinophilic airway inflammation and is a potential target for the treatment of fibrosis induced by chronic allergic disorders. against microbial pathogens, while distinct subpopulations of memory T cells drive chronic inflammatory diseases such as asthma.  Asthma is a chronic allergic inflammatory disease with airway remodeling including fibrotic changes.  The immunological mechanisms that induce airway fibrotic changes in allergic inflammation remain unknown.  We found that Interleukin-33 (IL-33) enhanced Amphiregulin production by the IL-33 receptor, ST2 hi memory T helper-2 (Th2) cells.  Amphiregulin-epidermal growth factor receptor (EGFR)-mediated signaling directly reprogramed eosinophils to an inflammatory state with enhanced production of Osteopontin, a key profibrotic immunomodulatory protein.  IL-5-producing memory Th2 cells and Amphiregulin-producing memory Th2 cells appeared to cooperate to establish lung fibrosis.  The analysis of polyps from patients with eosinophilic chronic rhinosinusitis revealed fibrosis with accumulation of Amphiregulin-producing CRTH2hiCD161hiCD45RO+CD4+ Th2 cells and Osteopontin-producing eosinophils.  Thus, the IL-33-Amphiregulin-Osteopontin axis directs fibrotic responses in eosinophilic airway inflammation and is a potential target for the treatment of fibrosis induced by chronic allergic disorders.

overall_design: Amphiregulin producing cells, eosinophils and lung treated with HDM are assessed by RNA-seq.

first: Kiyoshi

last: Hirahara

first: Masahiro

last: Kiuchi

first: Tomoko

last: Wada

first: Tomomi

last: Ichikawa

first: Toshio

last: Kanno

first: Mikiko

last: Okano

first: Kota

last: Kokubo

first: Atsushi

last: Onodera

first: Daijyu

last: Sakurai

first: Yoshitaka

last: Okamoto

first: Toshinori

last: Nakayama


title: Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation [RNA-seq]

status: Public on Aug 28 2018

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

institute: Osaka University

summary: It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

overall_design: Allele-specific RNA-seq analysis of mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1. The MEFs were obtained from B6-JF1 F1 males crossed with B6 females carrying Xist-deltaA mutation.

last: Sakakibara

first: Chikashi

last: Obuse

first: Takashi

last: Sado


title: Genes reflect the common recent history of the Uralic-speaking populations

status: Public on Aug 13 2018

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

summary: We genotyped 135 new samples (121 samples from 10 Uralic-speaking and 14 samples from 8 non-Uralic-speaking populations) and combined these data with previously published data to characterize the population structure of Uralic-speaking populations in the context of their geographic neighbours across Eurasia

overall_design:
135 samples were analysed with the Illumina Human610-Quad, HumanHap650Yv3, Human660W-Quad and HumanOmni1-Quad Genotyping BeadChips and are described herein.

Please note that
[1] The following samples represent the 'non-Uralic-speaking' samples;
German7, Gagauz10, Poland135, Poland148, Poland149, Poland150, Poland151, C_Russian1012, C_Russian1006, latvian51E3, swede_V49245, Tatar1003, Tatar1008, buryat_V43501

[2] the processed (*Matrix_processed.txt) and raw data (*Matrix_signal_intensities.txt) is provided as Series supplementary file as indicated in the corresponding sample description field.

[3] The following published data was included in the overall study;
PMID18292342, PMID20148029 (GSE22494), PMID20531471 (GSE21478), PMID21917723 (GSE37342), PMID23782551 (GSE46828), PMID24256729 (GSE50727), PMID25079123, PMID25898006 (GSE66157), PMID26332464 (GSE71049)

first: Kristiina

last: Tambets

first: Mait

last: Metspalu

first: Richard

last: Villems


title: Genetic characterization of macrophages from induced sputum of asthma and COPD patients

status: Public on Aug 09 2018

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Background: Macrophages are important cells in pathogenesis of obstructive lung diseases including asthma and chronic obstructive pulmonary disease (COPD). The aim of the study was a multivariate, genetic, comparative analysis of macrophages from patients with asthma and COPD.
Methods: Macrophages were isolated from induced sputum (IS) by magnetic bead separation. Transcriptomic measurements were carried out using Affymetrix Human Gene 2.1 ST ArrayStrip in 17 samples: 8 asthma (4 ICS naive , 4 ICS treated), 4 COPD and 5 control samples. The expression of the most significantly differentiating genes was evaluated by real time PCR in 34 samples (15 patients with asthma, 11 patients with COPD and 17 controls).
Results: USP53 was the only gene differentially expressed (p adjusted clue =0.09) in the comparison between ICS naïve and ICS treated asthma. The PCR verification showed increased expression of BTF3, CDS2, DNAJC13, DDX5, GNAI2, SCGB1A1, SIRPB1, TRAF3IP, USP53, WDR49 in the asthma compared to COPD group. The changed gene expression profile of macrophages were characterized mostly by gene ontology terms linked with cell motility, cilium function, cell junction and adhesion organization.
Conclusions: Gene expression profiling of sputum macrophages revealed distinct molecular capacity in asthma and COPD. The role of sputum macrophages in the pathophysiology of obstructive lung diseases is probably connected with biological processes associated with their motility, cilium dysfunction and cell junction organization.

overall_design: The microarray experiments were performed using 17 samples: 8 asthma (4 untreated , 4 treated with ICS), 4 COPD and 5 control samples (4 non-smoker, 1 smoker)

first: Magdalena

last: Paplinska-Goryca

first: Paulina

last: Misiukiewicz

first: Patrycja

last: Nejman-Gryz

first: Katarzyna

last: Górska

first: Małgorzta

last: Proboszcz

first: Rafał

last: Krenke


title: Muscle Ring Finger-1 regulation of right-sided heart transcriptional responses to hypoxia in vivo.

status: Public on Aug 24 2018

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To determine the role of cardiomyocyte muscle ring finger-1 (MuRF1) in vivo, we employed whole genome microarray expression profiling as a discovery platform to identify genes differentially regulated by MuRF1 using MuRF1-/- and alphaMHC (cardiomyocyte-specific) MuRF1 transgenic mice in a model of pulmonary hypertension-induced right sided heart failure. Mice were placed in hypoxia chambers set at 10.0% oxygen (partial pressure of oxygen roughly 65 mmHg in Albuquerque) and monitored both by the digital feedback control system (Biospherix, Colorado) as well as by a secondary O2/CO2 monitor (O2Cap, OxiGraf, Inc.; Mountain View, CA). The hypoxia exposure lasted 3 weeks with twice-weekly cage changes and standard 12 h light:dark cycle. Multiple genes from the microarray expression profile were quantified in the same RNA samples by real-time PCR to confirm their expression.

overall_design: Hypoxia-induced pulmonary hypertension and right heart failure was induced over 3 weeks of mice being placed in a hypoxia chamber with 10.0% oxygen (partial pressure of oxygen approximately 65 mm Hg in Albequerque, NM). Three biological replicates of each condition (hypoxia) and genotype were used from independent experiments.

first: John

last: Cidlowski

first: Monte

last: Willis


title: Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation

status: Public on Aug 01 2018

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Background:  In the Lophotrochozoan superphylum, few organisms have the capacity for rapid  testing of gene function and single-cell transcriptomics as the freshwater planarian.  The species Schmidtea mediterranea in particular has become a powerful model to  study adult stem cell biology and mechanisms of regeneration. Despite this,  systematic attempts to define gene complements and their annotations are lacking,  restricting comparative analyses that detail the conservation of biochemical pathways  and identify lineage-specific innovations.  Results:  In this study we compare several transcriptomes and define a robust set of 35,232  transcripts. From this, we perform systematic gene annotations and undertake a  genome-scale metabolic reconstruction for S. mediterranea. Cross-species  comparisons of gene content identify both conserved, lineage-specific, and expanded  gene families, which may contribute to the regenerative properties of planarians. In  particular, we find that TRAF and cadherin gene families have been greatly expanded  in planarians. We further provide a single-cell RNA-sequencing analysis of 2000 cells,  revealing both known and novel cell-types defined by unique signatures of gene  expression. Amongst these were a novel mesenchymal cell population as well as a cell  type involved in eye regeneration. Integration of our metabolic reconstruction further  reveals the extent to which a given cell types have adapted energy and nucleotide  biosynthetic pathways to support their specialized roles.  Conclusions:  In general, S. mediterranea displays a high level of gene and pathways conservation  with other model systems, rendering it as a viable model to study the roles of these  pathways in stem cell biology and regeneration.

overall_design: Wildtype animals were mechanically dissociated in Calcium-magnesium free media (CMF) with 1% BSA and stained with calcein to label live cells. Calcein-positive cells were collected by FACS. Cells were barcoded and cDNA libraries were prepared in nanoliter droplets using Drop-seq. The cDNA library pool was sequenced to a total depth of 480 million paired-end reads on an Illumina NextSeq500.

first: Swapna

last: Lakshmipuram

first: Alyssa

last: Molinaro

first: Nicole

last: Lindsay-Mosher

last: Parkinson


title: Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling

status: Public on Jul 05 2018

city: Haifa

first: Ayala

last: Shiber

address: Emerson building, Technion City

country: Israel

institute: Technion, Israel institute of technology

summary: Folding of newly synthesized proteins to the native state is a major challenge within the crowded cellular environment, since non-productive interactions can lead to misfolding, aggregation and degradation1. Cells cope with this challenge by coupling synthesis with polypeptide folding and by employing molecular chaperones to safeguard folding already cotranslationally2. However, little is known about the final step of folding, the assembly of polypeptides into complexes, although most of the cellular proteome forms oligomeric assemblies3. In prokaryotes, a proof-of-concept study showed that assembly of heterodimeric luciferase is an organized cotranslational process, facilitated by spatially confined translation of the subunits encoded on a polycistronic mRNA4. In eukaryotes, however, fundamental differences such as rarity of polycistronic mRNAs and different chaperone constellations raise the question whether assembly is also coordinated with translation. Here we provide a systematic and mechanistic analysis of protein complex assembly in eukaryotes using ribosome profiling. We determined the in vivo nascent subunits interactions of 12 hetero-oligomeric protein complexes of Saccharomyces cerevisiae at near-residue resolution. We find 9 complexes assemble cotranslationally; the 3 complexes that do not show cotranslational interactions are regulated by dedicated assembly chaperones5-7. Cotranslational assembly often occurs uni-directionally, with one fully synthesized subunit engaging its nascent partner subunit(s), thereby counteracting its aggregation propensity. The onset of cotranslational subunit association coincides sharply with full exposure of the nascent interaction domain at the ribosomal tunnel exit. The action of the ribosome-associated Hsp70 chaperone Ssb8 is coordinated with assembly. Ssb transiently engages partially synthesized interaction domains, then dissociates before the onset of partner subunit association, presumably to prevent premature assembly interactions. Our study shows that cotranslational subunit association is a prevalent mechanism for hetero-oligomers assembly in yeast and indicates that translation, folding and assembly of protein complexes are integrated processes in eukaryotes.

overall_design: Investigating the interaction of 26 individual complex subunits with nascent polypeptide chains in yeast.

first: Kristina

last: Döring

first: Ulrike

last: Friedrich

first: Kevin

last: Klann

first: Dorina

last: Merker

first: Mostafa

last: Zedan

first: Frank

last: Tippmann

first: Günter

last: Kramer

first: Bernd

last: Bukau


title: Cardiolipin Synthesis Governs Systemic Energy Homeostasis through Thermogenic Fat Mitochondria

status: Public on Jul 19 2018

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we show that synthesis of the mitochondrial phospholipid cardiolipin is an indispensable driver of thermogenic fat function. Cardiolipin biosynthesis is robustly induced in brown and beige adipose upon cold exposure. Mimicking this response by overexpressing cardiolipin synthase (Crls1) enhances energy consumption in mouse and human adipocytes. Crls1 deficiency diminishes mitochondrial uncoupling in brown and beige adipocytes and elicits a nuclear transcriptional response through ER stress-mediated retrograde communication. Cardiolipin depletion in brown and beige fat abolishes adipose thermogenesis and glucose uptake and renders animals strikingly insulin resistant. We further identify a rare human CRLS1 variant associated with insulin resistance and show that adipose CRLS1 levels positively correlate with insulin sensitivity. Thus, adipose cardiolipin is a powerful regulator of organismal energy homeostasis through thermogenic fat bioenergetics.

overall_design: Genome-wide profiling of mRNA from brown adipose tissue (BAT) of five different mice of either wild-type (WT) or with knockout of CRLS1 (KO)

first: Elahu

middle: G

last: Sustarsic

first: Isabel

last: Forss

first: Zachary

last: Gerhart-Hines


title: Expression data from rice roots treated with N starvation for 1 h

status: Public on Jun 30 2018

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary:
We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by N starvation (1 h) in rice roots.
Transcriptomic analysis of rice roots revealed that the expression of 288 genes was differentially regulated (144 up, 144 down) by N starvation (1 h).

overall_design: Total RNA extracted from roots of 10-day-old rice seedlings grown in Yoshida's hydroponic solution (+N) and treated with N starvation for 1 h (-N) was used for microarray analysis. RNA samples from three biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.

first: C

last: Kan

first: M


title: Dynamics of genome alterations in Crohn’s disease associated colorectal carcinogenesis

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary: To determine the pattern of copy number alterations that characterizes Crohn’s disease associated colorectal carcinomas (CD-CRCs), we performed array-based comparative genomic hybridization (aCGH) of CD-CRCs. As control group, we used histomorphologically similar sporadic mucinous colorectal adenocarcinomas. To gain insight into the dynamics of copy number alterations in CD associated colorectal tumor development, we additionally analyzed non-dysplastic, i.e., normal or inflamed, mucosa samples and dysplastic lesions from CD-CRC patients by aCGH. This revealed the gain of chromosome arm 5p as a distinctive feature of CD related colorectal carcinogenesis, while the overall pattern of copy number changes in CD-CRC was similar to sporadic mucinous CRC, including gains of chromosomes and chromosome arms 7, 8, 13 and 20q, and losses of 5q, 8p, 17p and 18q.

overall_design: We analyzed 73 tissue samples by aCGH. These comprised CD-CRCs (n = 32), dysplastic lesions (n = 3), inflamed mucosa samples (n = 7), histologically normal mucosa samples (n = 4), lymph node metastases (n = 2) and a local recurrence (n = 1) along with sporadic mucinous CRCs (n = 24). Biological replicates: 73.

first: Yuelin

last: Zhu

first: Daniela

last: Hirsch

first: Thomas

last: Ried

first: Timo

last: Gaiser


title: Role of SmcHD1 in the establishment of the epigenetic states required for the maintenance of X chromosome inactivation

first: Koji

last: Nagao

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

overall_design: Refer to individual Series


title: Human Extrafollicular CD4+ T Helper Cells Help Memory B Cells Produce Immunoglobulins

status: Public on Jun 29 2018

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: Follicular helper T (Tfh) cells are necessary for germinal center B cell maturation during primary immune responses; however, the T cells that promote humoral recall responses via memory B cells are less well defined. We herein characterize a human tonsillar CD4+ T cell subset with this function. These cells are similar to Tfh cells in terms of expression of the chemokine receptor CXCR5 and the inhibitory receptor PD-1, interleukin (IL)-21 secretion, and expression of the transcription factor BCL6; however, unlike Tfh cells that are located within the B cell follicle and germinal center, they reside at the border of the T cell zone and the B cell follicle in proximity to memory B cells, a position dictated by their unique chemokine receptor expression. They promote memory B cells to produce antibodies via CD40 ligand, IL-10, and IL-21. Our results reveal a unique extrafollicular CD4+ T cell subset in human tonsils, which specialize in promoting T cell-dependent humoral recall responses.

overall_design: We sorted four different CD4 T cell subgroups and extracted mRNA from each subgroup. The four subgroups are CD45RA+ T cells, T effector memory cells,  T follicular helper cells and PSGL-1 high PD-1 high CXCR5 high T cells. The samples were obtained from three separate tonsils, and triplicates were made for the last two subgroups per each tonsil, generating a total of nine replicates for the last two subgroups.

first: Sang

middle: T

last: Kim

first: Jin

middle: Y

last: Choi

first: Begona

last: Lainez

first: Patrick

last: Gallagher

first: Vincent

middle: P

first: David

last: Karas

first: Eric

middle: D

last: Baum

first: Jennifer

last: Setlur

first: Joseph

last: Craft


title: Transcriptomic and epigenetic signatures of hepatocellular carcinoma and intrahepatic cholangiocarcinoma derived from oncogenically transformed murine hepatocytes

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

institute: Institut Pasteur


title: Acute and delayed transcriptomics changes in 3D LUHMES exposed to rotenone

status: Public on Jun 27 2018

city: Baltimore

first: Lena

last: Smirnova

address: 615 N. Wolfe St

department: Environmental Health & Engineering

institute: Johns Hopkins University

summary:
To date, most in vitro toxicity testing has focused on acute effects of compounds at high concentrations. This testing strategy does not reflect real-life exposures, which might contribute to long-term disease outcome. We used a 3D-human dopaminergic in vitro LUHMES cell line model to determine whether effects of short-term rotenone exposure (100 nM, 24 h), are permanent or reversible. A decrease in complex I activity, ATP, mitochondrial diameter and neurite outgrowth were observed acutely. After compound removal, complex I activity was still inhibited, however, ATP levels were increased, cells were electrically active and aggregates restored neurite outgrowth integrity and mitochondrial morphology. We identified significant transcriptomic changes after 24 h which were not present 7 days after wash-out. Our results suggest that testing short-term exposures in vitro may capture many acute effects which cells can overcome, missing adaptive processes and long-term mechanisms. Additionally, to study cellular resilience, cells were re-exposed to rotenone after wash-out. Pre-exposed cells maintained higher metabolic activity than controls and presented a different expression pattern in genes previously shown to be altered by rotenone. NEF2L2, ATF4 and EAAC1 were downregulated upon single hit on day 15, but unchanged in pre-exposed aggregates. DAT and CASP3 were only altered after re-exposure to rotenone while TYMS and MLF1IP were downregulated in both single-exposed and pre-exposed aggregates. In summary, our study shows that a human cell-based 3D model can be used to assess cellular adaptation, resilience and long-term mechanisms relevant to neurodegenerative research.
In this study acute and delayed effects of rotenone on transcriptome in 3D LUHMES were assessed by microarray. The goal was to characterize perturbations in gene expression immediately after exposure to rotenone and identify whether these perturbations persist after compound wash-out and recovery period

overall_design: LUHMES were differentiated in 3D and exposed to 50 or 100 nM rotenone on day 7 of differentiation for 12 or 24 hours. After the exposure half of the samples were collected for RNA isolation and in half of the samples rotenone was washed-out and cells were incubated for another 7 days until day 15. On day 15 the rest of the samples were collected for RNA isolation. Microarray gene expression analysis was performed on both groups of samples and normalized to the corresponding DMSO control in the group. Three replicates (wells) per sample were generated.

first: Andre

last: Kleensang


title: Identification and validation of single sample breast cancer radiosensitivity gene expression predictors [Nanostring custom assay data]

status: Public on Jul 01 2018

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

institute: Lund University

summary:
Purpose  To develop a radiosensitivity gene expression assay to predict the response to adjuvant radiotherapy (RT) after breast conserving surgery (BCS) in breast cancer.    Patients and methods  Fresh frozen primary tumors from 336 patients operated with BCS with or without RT were collected. Patients were split in a discovery cohort (N=172) and a validation cohort (N=164). Genes predicting ipsilateral breast tumor recurrence (IBTR) in an Illumina HT12 v4 whole transcriptome analysis were combined with genes from the literature (248 genes in total) to develop a targeted radiosensitivity assay on the Nanostring nCounter platform. Single sample predictors (SSPs) for IBTR based on a k-top scoring pairs algorithm were trained stratified for estrogen receptor (ER) status and RT. Two previously published profiles (radiosensitivity index, RSI, and radiosensitivity score, RSS) were also tested in our data     Results   The SSPs were prognostic for IBTR in ER+RT- patients (AUC 0.67, p=0.005), ER+RT- patients (AUC=0.89, p=0.015) and ER-RT+ patients (AUC=0.78, p<0.001). Among ER+ patients, radiosensitive tumors had an excellent effect of RT (p<0.001), while radioresistant tumors had no effect of RT (p=0.4) and a high risk of IBTR (55% at 10 years). Our SSPs developed in ER+ tumors and the RSS correlated with proliferation, while SSPs developed in ER- tumors correlated with immune response. RSI negatively correlated with both proliferation and immune response.    Conclusions  Our targeted SSPs were prognostic for IBTR and has the potential to stratify patients for RT. The biology behind models may explain the different performance in subgroups of breast cancer.
Purpose
To develop a radiosensitivity gene expression assay to predict the response to adjuvant radiotherapy (RT) after breast conserving surgery (BCS) in breast cancer.
Patients and methods
Fresh frozen primary tumors from 336 patients operated with BCS with or without RT were collected. Patients were split in a discovery cohort (N=172) and a validation cohort (N=164). Genes predicting ipsilateral breast tumor recurrence (IBTR) in an Illumina HT12 v4 whole transcriptome analysis were combined with genes from the literature (248 genes in total) to develop a targeted radiosensitivity assay on the Nanostring nCounter platform. Single sample predictors (SSPs) for IBTR based on a k-top scoring pairs algorithm were trained stratified for estrogen receptor (ER) status and RT. Two previously published profiles (radiosensitivity index, RSI, and radiosensitivity score, RSS) were also tested in our data
Results
The SSPs were prognostic for IBTR in ER+RT- patients (AUC 0.67, p=0.005), ER+RT- patients (AUC=0.89, p=0.015) and ER-RT+ patients (AUC=0.78, p<0.001). Among ER+ patients, radiosensitive tumors had an excellent effect of RT (p<0.001), while radioresistant tumors had no effect of RT (p=0.4) and a high risk of IBTR (55% at 10 years). Our SSPs developed in ER+ tumors and the RSS correlated with proliferation, while SSPs developed in ER- tumors correlated with immune response. RSI negatively correlated with both proliferation and immune response.
Conclusions
Our targeted SSPs were prognostic for IBTR and has the potential to stratify patients for RT. The biology behind models may explain the different performance in subgroups of breast cancer.

overall_design:
Total RNA was extracted from fresh frozen breast cancer tissue and analyzed with a custom design Nanostring nCounter assay.
Please note that the 'final_nano_data (SUPPLEMENTAL FILE).csv' file contains  the finally filtered and processed data.


title: Screening microRNA-196 targets in 11q23-translocation acute myeloid leukemia reveal mechanisms maintaining leukemia stemness with therapeutic potential [Gene 1.0 ST]

city: Cincinnati

first: H. Leighton

last: Grimes

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: microRNA are aberrantly expressed in acute myeloid leukemia (AML), and clinically may have diagnostic, prognostic, and therapeutic value. We identify one such microRNA, miR-196b, is essential for MLL-AF9 leukemia initiation and maintenance. To discover how miR-196b contributes to leukemogenesis, we utilized multiple unbiased approaches that identified and functionally screened miR-196b target activity in AML. Our studies resolved how conflicting networks of miRNA-regulated targets are integrated during leukemogenesis. This work uncovered two miR-196b direct targets, the cell cycle regulator Cdkn1b (p27Kip1) and Polycomb group member Phc2, that independently cooperate with MLL-AF9 to promote leukemogenesis by regulating stem cell transcriptional programs. Finally, we found that therapeutic disruption of miR-196b direct targeting of Cdkn1b suppresses leukemogenesis.

overall_design: Identify the AML-relevant miR-196b direct targets using a biotinylated miRNA mimic as bait to capture biotinylated miR-containing RISC complexes with assoicated mRNA targets. Associated mRNA targets are then puified using the biotin-streptavidin system and identified by microarray.

first: Sara

middle: E

last: Meyer

first: Andrew

middle: M

last: Rogers

first: Emily

last: Orr

first: John

last: Doench

first: Bruce

last: Aronow

first: Ashish

last: Lal

first: Judy

last: Lieberman

first: Edwina

last: McGlinn

first: Nathan

last: Salomonis

first: H

middle: L


title: Transcriptomic signature of hepatocellular carcinoma and intrahepatic cholangiocarcinoma derived from oncogenically transformed murine hepatocytes after stable knock-down of Tbx3 or Prdm5

summary: Primary liver cancer represents a major health problem. It comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), which differ markedly with regards to their morphology, metastatic potential and therapy response. Yet, molecular actors and tissue context that commit transformed hepatic cells towards HCC or ICC are largely unknown. Here, we report that the hepatic microenvironment epigenetically shapes lineage commitment in mosaic mouse models of liver tumourigenesis. While a necroptosis associated hepatic cytokine microenvironment determines ICC outgrowth from oncogenically transformed hepatocytes, hepatocytes harbouring identical oncogenic drivers give rise to HCC if surrounded by apoptotic hepatocytes. Epigenome and transcriptome profiling of murine HCC and ICC singled out Tbx3 and Prdm5 as major microenvironment-dependent and epigenetically regulated lineage commitment factors, a function conserved in humans. Together, our study provides unprecedented insights into lineage commitment in liver tumourigenesis and explains molecularly why common liver damaging risk factors can either lead to HCC or ICC.

overall_design: We established clonal cell lines from focal in vivo electroporation derived ICC and hydrodynamic tail-vein injection derived HCC (both driven by c-Myc and NrasG12V, pCaMIN vector). One single cell clone from each cell line was stably transfected with vectors harbouring doxycyclin inducible shRNA cassettes and a GFP reporter protein as well as a puromycin resitance gene via retroviral infection. For each cell line we used one control shRNA (shRen) and two independent shRNAs targeting Tbx3 (HCC) or Prdm5 (ICC). Each infection experiment was repeated two times.

first: Lars

last: Zender

first: Marco

last: Seehawer

first: Florian

last: Heinzmann

first: Pierre-Francois

last: Roux

first: Gregory

last: Dore

first: Nir

last: Rozenblum


title: Regeneration in the pituitary after cell-ablation injury: time-related aspects and molecular analysis

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: We recently showed that the mouse pituitary holds regenerative competence. Young-adult GHCre/iDTR mice, expressing diphtheria toxin (DT)-receptor in growth hormone (GH)-producing cells, regenerate the cells ablated by 3-day DT treatment (3DT) up to 60% after 5 months. The pituitary's stem cells were found to participate in this restoration process. Here, we characterized this regenerative capacity in relation to age and recovery period, and started to search for underlying molecular mechanisms. Extending the recovery period (to 19 months) does not result in higher regeneration levels. In addition, the regenerative competence disappears at ageing, coinciding with a reduction in pituitary stem cell number and fitness. Surprisingly, prolonging the DT treatment period in young-adult mice to 10 days (10DT) completely blocks the regeneration. The stem cell compartment still reacts by promptly expanding, and retains in vitro stem cell functionality. To obtain a first view on molecular grounds underlying reparative capacity and/or failure, the stem cell-clustering side population (SC-SP) was analyzed by whole-genome expression analysis. A number of stemness factors and components of the Notch, Shh, Wnt, epithelial-mesenchymal transition (EMT) and Hippo pathways are higher expressed in the SC-SP of the regenerating pituitary (after 3DT) when compared to the basal gland and to the non-regenerating pituitary (after 10DT). Taken together, the regenerative capacity of the pituitary is limited both in age-related terms and final efficacy, and appears to rely on stem cell-associated pathway activation. Dissection of the molecular profiles may eventually identify targets to induce or boost regeneration in situations of (injury-related) pituitary deficiency.

overall_design: Gene expression profile was compared of -/iDTR (ctrl) and GHCre/iDTR of female (independent 2 samples) mouse pituitaries treated with diphteria toxin for 3 (3DT) or 10 (10DT) days. The Nonsca1high (SC-SP) was sorted using FACS and total RNA was isolated.

first: Christophe

last: Willems

first: Qiuli

last: Fu

first: Hugo

last: Vankelecom


title: Transcriptomic signature of hepatocellular carcinoma and intrahepatic cholangiocarcinoma derived from oncogenically transformed murine hepatocytes

status: Public on Jun 28 2018

first: Oliver

last: Bischof

overall_design: We established clonal cell lines from focal in vivo electroporation derived ICC and hydrodynamic tail-vein injection derived HCC (both driven by c-Myc and NrasG12V, pCaMIN vector).


title: Yra1-bound R loops cause orientation-independent transcription-replication collisions and telomere instability

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary: R loops are an important source of genome instability largely due to its negative impact on replication progression. Yra1/ALY is an abundant RNA-binding factor conserved from yeast to humans and required for mRNA export, but its excess cause lethality and genome instability. Here, we show that Yra1 binds RNA-DNA hybrids in vitro and when artificially overexpressed is recruited to chromatin in an RNA-DNA hybrid-dependent manner stabilizing R loops and converting them into replication obstacles in vivo. Importantly, excess of Yra1 increases R loop-mediated genome instability caused by transcription-replication collisions regardless of whether they are co-directional or head-on. It also induces telomere shortening and senescence, consistent with a defect in telomere replication. Our results indicate that R loops form transiently in cells regardless of replication and, after stabilization by excess Yra1, they compromise genome integrity, in agreement with a two-step model of R loop-mediated genome instability. This work opens new perspectives to understand transcription-associated genome instability in repair-deficient cells, including tumoral cells.

overall_design: RNA:DNA hybrid immunoprecipitation sequencing (DRIP-seq) in wild-type yeast cells

first: J

middle: F

last: Lafuente-Barquero

first: A