title: microRNA profile of adult female Anopheles sinensis

status: Public on Sep 27 2018

city: Shanghai

first: Xinyu

last: Feng

address: No. 207 Rui Jin Er Road

department: malaria

country: China

institute: National Institute of Parasitic Diseas，Chinese Center for Disease Control and Prevention.

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigate the global miRNA expression profile of An. sinensis using illumine Hiseq 2000 sequencing.The annotation and prediction of miRNAs lays the foundation for the further functional study of An. sinensis miRNAs and will facilitate their application in vector control.

overall_design: An. sinensis (China strain) mosquito samples were pooled with TRIzol® reagent (Invitrogen) immediately following collection.Total RNA was extracted from samples for miRNAs (Takara, Dalian, China) followed manufacturer’s protocol. Small RNAs (sRNAs) libraries were made as manufacturer's instructions (Illumina Inc).The purified cDNA libraries were sequenced using the Illumina HiSeq 2000.  SRP128390  and BioProject PRJNA428608

first: Xiaojian

last: Zhou

first: Shuisen

first: Jingwen

last: Wang

first: Wei

last: Hu


title: overexpression/knockdown MEG3 in C2C12 cell lines

status: Public on Sep 28 2018

city: Beijing

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

summary: MEG3 was known as a growth suppressor in tumor cells by activating p53. Besides, MEG3 could regulate transforming growth factor-β (TGF-β) signaling pathway, which is the key regulator of skeletal myogenesis and can enhance the proliferation of myogenic cells. Previous study also showed MEG3 was highly expressed in the paraxial mesoderm and probably regulated muscle development. To investigate the potential function of MEG3 in muscle development, we detected the expression levels of protein-coding genes after MEG3 over-expression or knockdown in C2C12 cell line using microarrays.

overall_design: Identification of differentially expressed genes in C2C12 cell lines after MEG3 overexpression and knockdown

first: Kui

last: Li


title: LncRNAs expression profiling of mouse skeletal muscle at postnatal 0 and 65 days

summary: In the study presented here, we collected the longissimus dorsi samples at postnatal days 0 and  65 from ICR mice and identified the genome-wide expression level of lncRNAs.

overall_design: To identify the differentially expressed long noncoding RNA during the mouse skeletal muscle development, we analysiedthe long noncoding RNA profile of skeletal muscle at postnatal 0 and 65 days.


title: Discovery of a novel plant eIF4E-binding protein: Conserved Binding of eIF4E 1 (CBE1)

status: Public on Sep 26 2018

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

country: USA

institute: Purdue University

type: Expression profiling by high throughput sequencing

summary: Regulation of translation initiation is accomplished in diverse eukaryotes through proteins which bind to the mRNA cap-binding protein, eIF4E, and either prevent its association with eIF4G or form repressive mRNPs which exclude the translation machinery. Such mechanisms in plants, and even the presence of eIF4E-interacting proteins outside of eIF4G (and the plant-specific isoform eIFiso4G, which binds eIFiso4E) which operate in a gene regulatory manner are not known. Here we describe the Conserved Binding of eIF4E 1 (CBE1), a plant-specific protein with an evolutionarily conserved eIF4E binding motif. This protein binds eIF4E or eIFiso4E in vitro to form cap-binding complexes, and is found as a constituent of cap-binding complexes in vivo in an eIF4E-dependent manner. Mutants lacking CBE1 show dysregulation of cell cycle related transcripts, accumulating higher levels relative to wild-type plants of mRNAs encoding proteins involved in mitotic processes. These findings support CBE1 as a plant protein with the capability to form cap-binding complexes with the potential for gene regulatory activity.

overall_design: poly(A) RNA fraction was purified and sequenced from homogenized 7-day-old seedling tissue, grown under long day conditions on 1% sucrose MS plates, with three biological replicates of Col0 (wild-type) or cbe1 mutant

middle: M

first: Karen

middle: S

last: Browning


title: Oleanolic acid inhibits epithelial–mesenchymal transition of hepatocellular carcinoma by promoting iNOS dimerization

status: Public on Sep 22 2018

city: Tianjin

first: long

middle: wei

last: zhong

state: Tianjin

address: Tianjin International Joint Academy of Biotechnology and Medicine,TJAB

institute: NanKai University

summary: Oleanolic acid (OA) exhibits extensive pharmacological activities and takes significant anti-tumor effects. Its pharmacological mechanism, however, are still remained to be further clarified. In this study, we demonstrated that OA attenuated the migration and invasion abilities, resulting in the suppression of the EMT process in liver cancer cells, and inhibited the tumor growth of the PLC-bearing mice. We further proved that inducible nitric oxide synthase (iNOS) may be the potential target of OA. We confirmed that OA could promote the dimerization of iNOS, activating it and subsequently increasing the production of nitric oxide (NO). Further experiments indicated that OA promoted the nitration of specific proteins and consequently suppressed their epithelial–mesenchymal transition (EMT)-related biological functions. Furthermore, it has been confirmed that OA enhanced the anti-tumor effects of regorafenib in liver cancer treatment. These results deepened our understanding of the pharmacological mechanism of the antitumor effect OA, and the importance of NOS as a therapeutic target for liver cancer treatment.

overall_design: PLC-PRF-5 cells were treated with OA (50 μM) or DMSO for 24 h. TRIzol Reagent (Invitrogen) was then used to lyse cells and extract the total RNA.

first: Hongzhi

first: Weilong

last: Zhong


title: Compound-induced NR5A1 exon-skipping and circular-RNA expression show impaired steroidogenesis in adrenocortical cancer cells

status: Public on Sep 25 2018

city: Fukuoka

first: Kenji

last: Ohe

state: Fukuoka

address: 8-19-1, Jyonan-ku, nanakuma

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Fukuoka University

summary: Despite the intensive search for an effective drug to treat steroid-producing adrenocortical carcinomas, there are few therapeutic options. We sought whether splicing modifying compounds are effective on this devastating disease. Here, we show that a chemical compound in clinical trial, CX-4945, suppressed the expression of NR5A1 through aberrant multiple exon skipping leading to suppressed steroidogenesis and induced dysfunctional autophagy and progression to ER-stress-related apoptosis. A circular RNA of NR5A1 exons with an IRE1α-cleavage site on the ligated ends (circAd4BP HAC1-type ex1-6 RNA) is expressed in normal adrenal cortex but not in H295R adrenocortical cancer cells, and CX-4945 induced a different circular RNA of NR5A1 exons (circAd4BP ex2-4 RNA). This potential pharmacological control of abnormal steroidogenesis through NR5A1 aberrant splicing and interplay with its circAd4BP makes CX-4945 a strong candidate novel drug for the treatment of adrenocortical carcinomas.

overall_design: CX-4945-induced gene expression in H295R adrenocortical cancer cells  was compared with solvent (DMSO) treated H295R cells.

first: Tomoko

last: Tanaka

first: Yuta

last: Horita

first: Yoshihiro

last: Harada

first: Takafui

last: Yamasaki

first: Ichiro

last: Abe

first: Makito

first: Takashi

last: Nomiyama

first: Kunihisa

last: Kobayashi

first: Toshihiko

last: Yanase

first: Munechika

last: Enjoji


title: Gene expression signatures in HCC cell lines transfected with a miR-199a-3p mimic molecule

status: Public on Sep 23 2018

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: To clarify the role of miR-199a-3p in HCC, we carried out a gene expression microarray analysis using HCC cell lines (HLE and HLF) transfected with a miR-199a-3p mimic or a negative control. We found that 819 genes were downregulated (>2-fold) by miR-199a-3p in both cell lines.

overall_design: HCC cell lines HLE and HLF were transfected with a mirVana miR-199a-3p mimic (Thermo Fisher Scientific) or a mirVana miRNA mimic Negative Control (Thermo Fisher Scientific). Seventy-two hours after transfection, total RNA was extracted and gene expression signatures were analyzed.

first: Hideki

last: Wakasugi


title: Effects of DLEU1 knockdown on gene expression profiles in oral squamous cell carcinoma cells

summary: We identified DLEU1 as a long noncoding RNA (lncRNA) frequently overexpressed in oral squamous cell carcinoma (OSCC). Knockdown of DLEU1 suppressed proliferation, migration and invasion and induced cell cycle arrest and apoptosis in OSCC cells. To further clarify the molecular function of DLEU1, we carried out gene expression microarray analysis in OSCC cell lines with DLEU1 knockdown. We found that genes associated with “matrix metalloproteinases”, “apoptosis”, “cell cycle” and “MAPK signaling” were enriched among the affected genes. These results suggest that DLEU1 may play a role in the development of OSCC.

overall_design: OSCC cell lines (HSC-3, KON and Ca9-22) were transfected with a control siRNA (Sigma-Aldrich) or a siRNA targeting DLEU1 (Sigma-Aldrich) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h.

first: Koyo

last: Nishiyama


title: The Xenopus animal cap transcriptome: building a mucociliary epithelium.

city: Neuherberg-Munich

first: Pawel

last: Smialowski

address: Ingolstaedter Landstrasse 1

department: Institute of Stem Cell Research

country: Germany

institute: Helmholtz Zentrum Muenchen German Research Center for Environmental Health

summary: Here we investigate dynamics of the RNA landscape during formation of the Xenopus tropicalis larval epidermis.  To obtain RNA expression data, we used ectodermal explants (Animal Caps), which differentiate autonomously into a ciliated epidermis, highly related to the one in human airways.  Animal caps were harvested at the gastrula neurula and tailbud stage.

overall_design: Transcriptomic analysis of 3 developmental stages of embryonic epidermis development in Xenopus tropicalis. We looked at gene´s  expression and splicing isoforms expression

first: Alessandro

last: Angerilli

first: Ralph

middle: A

last: Rupp


title: Comparison of transcriptomic profiles of Pseudomonas protegens H78 and its rpoN-deleted mutant (H78ΔrpoN)

first: Xianqing

last: Huang

address: DongChuan RD, Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: Transcriptomic profiles of  Pseudomonas protegens H78 and its rpoN-deleted mutant (H78ΔrpoN), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on BGISEQ-500 (illumina).

overall_design: Two bacterial strains, Pseudomonas protegens H78 wild type strain and its rpoN-deleted mutant strain (H78ΔrpoN), each was replicated three times.


title: DOT1L inhibition blocks multiple myeloma cell proliferation through suppressing IRF4-MYC signaling

summary: Epigenetic alterations play an important role in the pathogenesis in multiple myeloma (MM), but its biological and clinical relevance is not fully understood. Here, we show that DOT1L, which catalyzes methylation of histone H3 lysine 79, is required for the survival of MM cells. Treatment with DOT1L inhibitors induced cell cycle arrest and apoptosis in MM cells, and strongly suppressed cell proliferation in vitro. Chromatin immunoprecipitation-sequencing (ChIP-seq) and microarray analysis revealed that DOT1L inhibition downregulated H3K79 dimethylation (H3K79me2) and expression levels of IRF4-MYC signaling genes in MM cells. Our data suggest that DOT1L may play an essential role in the development of MM, and DOT1L inhibition may provide a new therapy for MM treatment.

overall_design: Gene expression microarray analysis was performed in MM cells treated with SGC0946 for 6 days (RPMI-8226 and MM.1S) or 12 days (KMS-12PE).

first: Kazuya

last: Ishiguro


title: EML4-ALK transgenic mouse lung normal tissue vs. lung tumor tissue

city: Saitama

first: Norihiro

last: Kotani

institute: Saitama Medical school

summary: Gene expression profile of lung tumor tissues from EML4-ALK transgenic mouse (generous gift from Prof. H. Mano, Univ. of Tokyo) compared with lung normal tissues

overall_design: Two-condition experiment, Tumor vs. Normal tissue. Biological replicates: 3 mice tumor and normal lung tissue (mix)

first: Koichi

last: Honke


title: Gene expression data from mouse colon. AOM+DSS induced colitis. INSR fl/fl mice or villin-CRE INSR-/- mice

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: The epithelial expression of the insulin receptor in the colon is previously reported to correlate with the extent of colonic inflammation. Here, we investigated the effect of inactivating the epithelial insulin receptor in the intestinal tract, in an experimental model of inflammation-induced colorectal cancer. We report increased susceptibility to chemically-induced colitis together with potentiated colonic tumorigenesis in the knockout mice. Furthermore, we show that topically administered insulin in inflamed colons of wildtype mice reduces inflammation-induced weight loss and improves remission in a dose-dependent manner. Mice receiving rectal insulin enemas exhibited lower colitis endoscopic scores and developed significantly fewer and smaller tumors compared with the control group receiving phosphate-buffered saline only. Rectal insulin therapy can potentially be a novel treatment targeting the epithelial layer to enhance mucosal healing in the ulcerated areas. Our findings open up new possibilities for combination treatments to synergize with the existing anti-inflammatory therapies.

overall_design: 57 samples were analyzed. INSRfl/fl, untreated (10 biological replicates); INSRfl/fl AOM+DSS (10 biological replicates); villin-CRE INSR-/-, untreated (10 biological replicates); villin-CRE INSR-/- AOM+DSS (10 biological replicates), INSR fl/fl tumor AOM+DSS (8 biological replicates), villin-CRE INSR-/- tumor AOM+DSS (9 biological replicates)

first: Jørgen

first: Mohammad

last: Yassin


title: Interrupted reprogramming of Alveolar Type II cells induces progenitor-like cells that ameliorate pulmonary fibrosis

city: Toronto

first: Li

last: Guo

address: 101 College Street

country: Canada

institute: University Health Network

summary:
We describe here an interrupted reprogramming strategy to generate "induced Progenitor-Like (iPL) cells" from Alveolar Epithelial Type II (AEC-II) cells.  A carefully defined period of transient expression of reprogramming factors (Oct4, Sox2, Klf4 and c-Myc; OSKM) is able to rescue the limited in vitro clonogenic capacity of AEC-II cells, potentially by activation of a bipotential progenitor-like state.
Microarray analysis of genome-wide transcriptional changes showed the ability of AEC-II-iPL cells to return to the original phenotype

overall_design: Day0 freshly isolated AEC-II cells, cells were cultured for 2 weeks without Dox (2WND), followed by 2-week dox treamtent (2WND+2W+D, AEC-II-iPL cells), AEC-II-iPL cells with subsequent 2-week culture in Dox-free media (2WND+2W+D+2w-D), and iPS cells were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Tom

last: Waddell


title: Expression of candidate genes in Celiac Disease - Regulatory elements and their targets (part 4)

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of regulatory elements (4) and some of their targets in biopsies from duodenum.

overall_design: The sample set consisted of duodenal biopsies from 16 CD children at diagnosis (on a gluten-containing diet, with CD associated antibodies, atrophy of intestinal villi and crypt hyperplasia), and the same patients in remission after being treated with GFD for >2 years (asymptomatic, antibody negative, and normalized intestinal epithelium at that time), plus 15 tissue samples from non-celiac individuals not suffering from inflammation at the time of endoscopy used as controls.


title: Expression of candidate genes in Celiac Disease - Associated new genes and regulatory elements (part 2)

summary: Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate new genes and regulatory elements (2) in biopsies from duodenum.

overall_design: The sample set consisted of duodenal biopsies from 15 CD children at diagnosis (on a gluten-containing diet, with CD associated antibodies, atrophy of intestinal villi and crypt hyperplasia), and the same patients in remission after being treated with GFD for >2 years (asymptomatic, antibody negative, and normalized intestinal epithelium at that time), plus 15 tissue samples from non-celiac individuals not suffering from inflammation at the time of endoscopy used as controls.


title: Genome-wide analysis of gene expression in mouse pancreas tumors [FAP and aSMA depletion]

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

summary: Gene expression analysis of pancreatic tumors from genetically engineered mice (Pdx-Cre;LSL-KRASG12D;TGFBRIIf/f) with depletion of aSMA+ or FAP+ cells. The pancreas tumors were harvested and analysed for gene expression profiles comparisons.

overall_design: Total RNA was isolated from the pancreas tumors of 3 PKT FAP control mice, 3 PKT FAP depleted mice, 3 PKT aSMA control mice, 3 PKT aSMA depleted mice


city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

summary:
Midgut  gene expression after induction by 11 compounds:
each treatment was done in biological triplicate and using dye swap resulting in 6 microarrays per treatment. on each microarray a treated midgut RNA was compared to a DMSO treated midgut RNA.

indole3carbinol, xanthotoxine, 2tridecanone, clofibrate, indole, phenobarbital, quercetine, methoprene, methoxyfenozide, deltamethrine and fipronil

overall_design: Each of the 11 treatment was done in biological triplicate and using dye swap resulting in 6 microarrays per treatment. On each microarray a compound_treated midgut RNA was compared to a DMSO_treated midgut RNA

first: Gaëlle

last: Le Goff

first: Pascal

last: Barbry

first: Kevin

last: Lebrigand

first: Frederique

last: Hilliou


title: Gene expression analysis of disease-infected Pyropia tenera

city: Gongju-si

first: Soo Hyun

last: Im

address: Gongjudaehak-ro

department: Department of Biology

country: South Korea

institute: Kongju National University

summary: Disease outbreaks devastate Pyropia aquaculture farms every year. The three most common and serious diseases are Olpidiopsis blight and red-rot disease caused by oomycete pathogens and green-spot disease caused by PyroV1 virus. We hypothesized that a basic genetic profile of molecular defenses will be revealed by comparing and analyzing genetic response of Pyropia tenera against the above three pathogens.   RNAs isolated from infected thalli were hybridized onto an oligochip containing 15,115 primers designed from P. tenera ESTs. Microarray profiles of the three diseases were compared and interpreted together with histochemical observation.   Massive amounts of reactive oxygen species (ROS) were accumulated in P. tenera cells exposed to oomycete pathogens. Heat shock genes and serine proteases were the most highly upregulated genes in all infection experiments. Genes involved in RNA metabolism, ribosomal proteins and antioxidant metabolism were also highly upregulated. Genetic profiles of P. tenera in response to pathogens were most similar between the two biotrophic pathogens, Olpidiopsis pyropiae and PyroV1 virus. A group of plant R-gene homologues were specifically regulated against each pathogen.   Our results suggested that disease resistance of P. tenera consist of a general and constitutive defense and a genetic toolkit against specific pathogen.

overall_design: In this study presented here, 4 samples of Pyropia tenera were analyzed. Non disease infected P. tenera thalli was used as control and three disease infected thalli were used as treatment. RNAs isolated from non-infected and infected thalli were hybridized onto an oligochip containing 15,115 primers designed from P. tenera ESTs. Microarray profiles of each samples were compared and interpreted three times.

first: Soo-Hyun

first: Tatyana

last: Klochkova

first: Da-Jeoung

last: Lee

first: Gwang-Hoon

last: Kim


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Acss2-/- liver Transcriptomes

city: dallas

first: Zhiguang

last: Huang

state: Texas

address: 5323 Harry Hines Boulevard

institute: UTSW

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived liver transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Liver mRNA profiles of 48 hours fasted wild-type (WT) and Acyl-CoA Synthetase Short Chain Family Member 2 knockout (Acss2−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9).
Conclusions: Our study represents the first detailed analysis of liver transcriptomes of Acss2-/- mice, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Liver mRNA profiles of 48 hours fasted wild type (WT) and Acss2-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Ling

last: Cai


title: Expression data from Drosophila melanogaster wing disc - YAP/Yki  vs  YAP/Yki+dTcf/Pan-RNA RNAi conditions

status: Public on Sep 29 2018

first: Diana

last: Andrejeva

department: Faculty of Health and Medical Sciences

summary:
Determine the genes controlled by dTcf/Pan involved in tumor formation
manuscript dTcf/Pangolin suppresses growth and tumor formation in Drosophila

overall_design: 6 Total samples were analyzed at  gene-level. Differentially expressed genes between treatment groups were calculated using “Limma” package.  Adjusted p.value <0.05 and log2 fold-change ≥1 treshold was set to selec differentially expressed genes.

first: Shilin

last: Song

first: Héctor

last: Herranz


title: Psychosocial stress-induced brain atrophy and its suppression via theanine intake

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary: When mice of accelerated senescence prone 10 (SAMP10) were psychosocially stressed using male mouse’s territorial imperative, the mice exhibited higher cerebral atrophy and cognitive dysfunction than same-aged group-housing mice. The brain atrophy was examined using MRI. The volumes of various brain areas were decreased at the time of one month after confrontational housing. However, in SAMP10 mice ingesting theanine, the main amino acid in tea leaves, brain atrophy was suppressed even under confrontational housing. To investigate the function of theanine, the early response against stress was examined at the third day of confrontational housing. The level of transcription factor Npas4 that plays a role in the development of inhibitory synapses for regulating the balance between excitation and suppression was significantly increased by theanine intake. Actually, the levels of glutamate and γ-aminobutyric acid (GABA), excitatory and inhibitory neurotransmitters, were balanced in the mice ingested theanine under confrontational housing. These data suggest that theanine suppresses stress-induced damage in the brain via increased expression of Npas4 and regulation of excitement/suppression balance. In addition, SAMP10 is a useful model of stress vulnerability.

overall_design: Comparison of 4 groups: confrontation +/- and theanine +/-

first: Keiko

last: Unno


title: Expression of candidate genes in Celiac Disease - Associated new genes and regulatory elements (part 3)

first: Jose Ramon

last: Bilbao

summary: Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate new genes (2) and regulatory elements (3) in biopsies from duodenum.


title: Expression data from control or rat Giver knock-down cells treated w/o Ang II for 3 hours

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary:
Giver is a novel lncRNA found to be upregulated by Ang II stimulation in rat vascular smooth muscle cells (RVSMCs). The regulatory mechanisms of rat Giver has not been reported so far.
We used microarrays to detail Giver-mediated global gene expression and identified distinct classes of up- and down-regulated genes.

overall_design: RVSMCs were isolated from male Sprague-Dawley rats by enzymatic digestion and cultured for 2 passages before treatment. Cells were transfected with either non-targeting control siRNA (siNTC) or rat Giver siRNA for 48 hours, and then treated with either 100 nM of Angiotensin II or equivalent volume of 1x PBS for 3 hours.

first: Rama

last: Natarajan

first: Erli

last: Zhang

first: Sadhan

last: Das

first: Zhuo


title: Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription

city: Lyon

first: Pascal

last: BERNARD

address: 46 allée d'Italie

department: LBMC

institute: CNRS

summary: Condensins are genome organisers that shape chromosomes and promote their accurate transmission. Several studies have also implicated condensins in gene expression, although the mechanisms have remained enigmatic. Here, we report on the role of condensin in gene expression in fission and budding yeasts. In contrast to previous studies, we provide compelling evidence that condensin plays no direct role in the maintenance of the transcriptome, neither during interphase nor during mitosis. We further show that the changes in gene expression in post-mitotic fission yeast cells that result from condensin inactivation are largely a consequence of chromosome missegregation during anaphase, which notably depletes the RNA-exosome from daughter cells. Crucially, preventing karyotype abnormalities in daughter cells restores a normal transcriptome despite condensin inactivation. Thus, chromosome instability, rather than a direct role of condensin in the transcription process, changes gene expression. This knowledge challenges the concept of gene regulation by canonical condensin complexes.

overall_design: RNA-seq analyses of total (ribo-depleted) RNA of condensin mutants and appropriate controls.  Strand specific library  - Total (ribo-depleted) RNA - 50 Mio reads x 50 bases SE per sample - 15 samples = 3 lanes of Hiseq 4000 at ~ 250 Mio reads /lane.

first: Clémence

last: Hocquet

first: Xavier

last: Robellet

first: Laurent

last: Modolo

first: Xi-Ming

last: Sun

first: Claire

last: Burny

first: Sara

last: Cuylen-Haering

first: Esther

last: Toselli

first: Sandra

last: Clauder-Münster

first: Lars

last: Steinmetz

first: Christian

middle: H

last: Haering

first: Samuel

last: Marguerat


title: Transcriptome analysis of naïve Tregs, memory Tregs and CD161+ Tregs

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: We analyze bulk transcriptomes of three populations of human Tregs

overall_design: 200,000 naïve, memory and CD161+ Tregs were either sorted from fresh blood directly into Trizol LS (Ambion) for baseline genetic profile or cells were polyclonally activated post-sorting for 4h with Dynabeads Human T-Activator CD3/CD28 (ratio 1:1) and then lyzed in Trizol LS. RNA was isolated using RNeasy mini kit (QIAGEN) and Ovation PicoSL WTA System V2 (NuGEN Technologies) was used for reverse transcription and cDNA amplification steps. Fragmentation and labelling was performed using the Encore Biotin Module (NuGEN Technologies); all kits were employed following manufacturer’s instructions. Samples were run on GeneChip® Human Gene 1.0 ST Array (Affymetrix Ltd).

first: Giovanni

last: Povoleri


title: Expression of candidate genes in Celiac Disease - Associated genes and regulatory elements (part 1)

first: Jose Ramon

last: Bilbao

summary: Celiac disease is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate genes and regulatory elements in biopsies from duodenum.


title: Rca-T78 vs, Rca-S78

status: Public on Sep 17 2018

city: Urbana

first: Sang Yeol

last: Kim

state: IL

address: 1201 W Gregory st, ERML #197,Urbana, IL 61801

department: IGB

institute: University of Illinois Urbana-Champaign

summary: Transcription profiiling of arabidopsis transgenic Rca-T78S comparing Control WT plant (Rca-T78). Rca is Rubisco activase and Threonine78 residue of Rca is phosphorylated only in the dark. However, Serine substituted Rca (T78S) was phosphorylated even in the light. Thus, Rca-T78 or Rca-T78S expressing plants which were exposed light for an hour were harvested to check gene expression pattern

overall_design: Two condition experiments, Rca-T78S vs. Rca-T78, 4 replicates in each

first: Steven

last: Huber

first: Sang

middle: Y


title: Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

status: Public on Sep 20 2018

city: Irapuato

first: Ruairidh

middle: J H

last: Sawers

address: Km9.6 Car. N. Irapuato-Leon

country: Mexico

institute: LANGEBIO-CINVESTAV

summary:
Analysis of cell specific gene expression in mycorrhizal rice roots. Described in Roth, Chiapello et al. 2019
We used LCM to harvest arbusculated and adjacent systemic cells from mycorrhizal rice roots, along with cortical cells from mock inoculated plants

overall_design: Three replicates each were analyzed of 1) cells that contained arbuscules (A), 2) systemic cells (S) that were non-colonized but adjacent to arbusculated cells in colonized roots, 3) cells from mock (M) inoculated roots.

first: Uta

last: Paszkowski

middle: J


title: Expression data of miRNAs and mRNAs from the fetal rats with anorectal malformations

city: beijing

first: hui

last: xiao

address: yabao road 2#

institute: capital institute of pediatric

summary:
many dysregulated mRNAs as the primary factor could be play an important role in the development of anorectum
we used microarrays to reveal the global programme of gene expression underlying the development of anorectal malformations.

overall_design: The fetal rats with anorectal malformations were successfully established, the terminal hindgut was collected for RNA extraction. This represents the microRNA component only.

first: Hui

last: Xiao


title: Effect of Ibrutinib on the gene expression of CD4+ cells from patients with Peripheral T-cell lymphoma (PTCL)

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

summary: Interleukin-2-inducible T-cell kinase (ITK) has essential roles in T-cell proliferation in response to T-cell receptor stimulation and promotes Th2 and Th17 cell differentiation while suppressing Treg differentiation. ITK inhibitors have not previously been investigated for their ability to modify differentiation of either normal or malignant human CD4+ T-cells. We demonstrate that normal tonsillar CD4+ T-cell differentiation to Tfh and Th17 cells is inhibited by ITK inhibitors (ITKi) while Treg differentiation is promoted. Purified CD4+ T-cells from two cases of peripheral T-cell lymphoma demonstrated the capacity to proliferate and differentiate to Tfh, Th17 or Treg subsets in vitro. Gene expression profiling showed differences in Th-cell signature genes between normal and lymphoma cells. ITKi promoted Treg differentiation while suppressing Tfh and Th17 differentiation. The majority of CD4+ T-cells within lymph node sections did not express BCL6 compatible with the in vitro results being due to differentiation and not outgrowth already differentiated populations. The novel concept suggested by this report is that some cases of PTCL-NOS show a capacity to differentiate, which can be modified by ITKi for potential therapeutic benefit.

overall_design: Whole genome gene expression was analysed in normal and lymphoma cells with or without Interleukin-2-inducible T-cell kinase inhibitor

first: Sami

last: Mamand

first: Simon

last: Wagner

first: Spencer

last: Gibson


title: Gene expression analysis of sanroque mouse strain, a model for human follicular helper (Tfh) T-cells lymphoma

summary: Treatment of peripheral T-cell lymphoma is inadequate but investigation of their genetics demonstrated that some are derived from normal follicular helper (Tfh) T-cells. The sanroque mouse strain bears a mutation that increases Tfh cell number and heterozygous animals (Roquinsan/+) develop lymphomas similar to human Tfh lymphoma. We have begun to characterise the lymphomas by whole exome sequencing and gene expression profiling. Interleukin-2-inducible kinase (ITK) is expressed in Tfh lymphoma and ibrutinib is a small molecule inhibitor of mouse and human ITK and a potential therapeutic agent. A preclinical study of ibrutinib in established lymphoma was then carried out and showed lymphoma regression in 8/12 (67%) of mice. Using T2-weighted MRI to assess lymph node volume and diffusion weighted MRI scanning as a measure of function, we showed that treatment increased mean apparent diffusion coefficient (ADC) suggesting cell death, and that change in ADC following treatment correlated with change in lymphoma volume. We suggest that heterozygous sanroque mice produce genetically diverse Tfh cell derived lymphomas in an immunocompetent animal and are a useful model system for preclinical testing.

overall_design: Comparison of Wild type mice with Roquinsan/+ mice

first: Rebecca

last: Allchin


title: Sf9 induction with  8 compounds

first: frederique

last: hilliou

summary: Effect of 8 compounds (xanthotoxine, fipronil, clofibrate, 2tridecanone, indole3carbinol, indole, quercitine, deltamethrine) on Sf9 cell cultures genes expression. RNA from treated Sf9 cell cultures were compared to control treated (DMSO) Sf9 cell.

overall_design: each treatment was done in biological triplicate and using dye swap resulting in 6 microarrays per treatment. on each microarray a treated Sf9 RNA was compared to a DMSO treated Sf9

first: Frederique

last: Hilliou

first: Pascal

last: Barbry

first: Kevin

last: Lebrigand

first: Gaëlle

last: Le Goff


title: Sf9 induction with phenobarbital

summary: Effect of phenobarbital on Sf9 cell cultures genes expression. RNA from phenobarbital treated Sf9 cell cultures were compared to control treated (DMSO) Sf9 cell

overall_design: the treatment was done in biological triplicate and using dye swap resulting in 6 microarrays per treatment. on each microarray a treated Sf9 RNA was compared to a DMSO treated Sf9


title: The role of short telomeres in CD8 TEMRA cells (CCR7- CD45RA+) immune aging: A gene expression microarray study

status: Public on Sep 14 2018

city: Baltimore

first: Mary

last: Armanios

address: 401 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary:
Telomere shortening is universally acquired with aging in humans, but the contribution of telomere shortening to immune aging is not fully understood.  Here, we studied T cells derived from short telomere syndrome patients and compared their T cell profile and function to controls and elderly individuals who had normal age-adjusted telomere length.  The short telomere syndrome patients were all under age 40 and carried mutant telomerase or telomere genes and had telomere lengths below the 1st age-adjusted percentile.  The T cell profile of young short telomere syndrome patients resembled those that were five decades older including a depletion of naive T cell population and accumulation of terminally differentiated effector cells.  To test whether short telomeres affect the quality of these cells, we performed a gene expression microarray.  The data are summarized here. We found that although numerically expanded in both short telomere and elderly cases, the gene expression microarrays were distinct with short telomere cells predominately upregulating gene expression of DNA damage pathways and elderly T cells upregulating cell extrinsic apoptotic pathways.
The goal of the experiment is to highlight important genes and pathways that may drive immune aging in short telomere syndromes and which may also contribute to normal immune aging.

overall_design: Human CD8+ TEMRA cells were flow sorted from short telomere syndrome subjects (test group), and two control groups, young (age-matched) and old subjects. Each test and control group contained 4 individual samples, 2 female and 2 male.

first: Christa

middle: L

first: C

middle: C

last: Talbot Jr


title: Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains

status: Public on Sep 18 2018

city: New York

first: David

last: Bechhofer

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Department of Pharmacology and Systems Therapeutics

institute: Icahn School of Medicine at Mount Sinai

summary: Messenger RNA decay in Bacillus subtilis is accomplished by a combination of exoribonucleases and endoribonucleases. Intermediates in the decay process have not been readily detectable, and previous studies on mRNA decay have used a handful of highly expressed transcripts as models. Here, we use RNA‐Seq analysis to probe mRNA turnover globally. A significant fraction of messages showed differential accumulation of RNA fragments that mapped near the 5′ or 3′ end of the coding sequence, consistent with initiation of decay from either the 5′ end or from an internal cleavage site. Patterns of mRNA decay in the wild type were compared with patterns in a mutant strain lacking polynucleotide phosphorylase (PNPase), which is considered the major 3′ exonuclease activity in mRNA decay and which is one of four known 3′ exonucleases in B. subtilis. The results showed a striking dependence on PNPase for mRNA turnover in many cases, suggesting specificity in the ability of 3′ exonucleases to degrade from 3′‐hydroxyl termini. RNA‐Seq data demonstrated a sharp decrease in expression of Sigma D in the PNPase‐deletion strain. Reduction in sigD regulon expression explained the chain growth phenotype of the PNPase mutant and also predicted a defect in swarming motility.

overall_design: Examination of mRNA decay intermediates by comparison of read coverage in the 5' and 3' proximal regions from RNA sequencing experiments

first: Bo

last: Liu


title: Analysis of Staphylococcus aureus transcriptome changes in response to inhibition of Rho activity by bicyclomycin

status: Public on Sep 21 2018

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: The transcriptomes of Δrho mutant cells and of wild-type cells grown in RPMI medium with or without 40 or 80 µg/ml of BCM were analyzed using Agilent microarrays in order to analyze the effects of the Rho inhibitor bicyclomycin (BCM) treatment on antisense transcription and changes in the expression of protein coding genes. All antisense RNAs exhibiting higher levels in the rho mutant compared to the wild-type showed similar levels in BCM-treated wild-type cells (80 µg/ml BCM). In addition, microarray data revealed activation of the SaeR regulon in the presence of BCM as observed in the rho mutant.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: S. aureus HG001 and its isogenic Δrho mutant were grown in RPMI medium. At OD600 of 0.2 (early exponential phase), controls were taken and the wild-type culture was split in pre-warmed flasks for BCM treatment. After 70 min (exponential phase), rho mutant and wild-type samples (untreated and with 40 or 80 µg/ml BCM) were collected. Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.

first: Anna

last: Nagel

first: Hermann

last: Rath

first: Stephan

last: Michalik

first: Uwe

last: Völker


title: Gene expression profiling of Angioimmunoblastic T-Cell lymphoma (AITL) tumors

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

summary: Angioimmunoblastic T-Cell lymphoma (AITL) is a mature T-cell lymphoma of blood or lymph vessel immunoblasts. It is the most common subtype of T-cell lymphoma in the Western world and the second most frequent one in Asia. We sequenced nine pairs of AITL exomes and their matched normals. Frequent mutations in TET2 and RHOA were detected, and confirmed through targeted sequencing in a larger cohort of 43 samples. Gene expression profiling was performed to identify genes differentially expressed between patients with and without mutations in genes of interest.

overall_design: Microarray gene expression profiling was performed on 20 AITL tumor samples. 18 were used for further study as somatic mutations were not detecting in two samples.

first: Maarja-Liisa

last: Nairismägi

first: Weng-Khong

first: Soon-Thye

first: Bin-Tean

last: Teh


title: K120R mutation inactivates p53 by creating an aberrant splice site leading to nonsense-mediated mRNA decay

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

summary: The point mutation that substitutes lysine with arginine at position 120 of human p53 has been characterized as a missense mutation. The K120R mutation renders the p53 protein disabled for acetylation and, as a result, defective for apoptotic function, which provides a mechanistic link between the missense mutation and tumorigenesis. However, we noticed the failures of tumorigenesis in mice with the mutation, and of the related studies to notice that it has arbitrarily reflected in amino acid change through a sequence modification (AGA) of the original tumor mutation (AGG) by codon degeneracy. Unlike this modified version, we also discovered a novel splicing site the original mutation, TP53 c.359A>G, may induce. Using a human induced pluripotent stem cell line that was engineered to be homozygous for the original mutation, we here identified that the accidental splicing site generates a defective transcript variant with a frame-shifted premature termination codon which is subjected to nonsense-mediated mRNA decay. The authentic splicing still occurs but in extremely low amounts. Taken together, this mutation causes depletion of cellular p53 via defective mRNA, suggesting a new link to tumorigenesis.

overall_design: We generated p53 knockout cells or p53 mutated cells (TP53 c.359A>G) from human (fibroblasts cell line) induced pluripotent stem cells. Responsive patterns of gene expression by doxorubicin treatment was compared between these cells.

first: Sun-Ku

last: Chung


title: stem transcriptome in a triple wd40 mutant.-Gene disruption in a triple WD40 mutant.

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra16-04_3wd40 - stem transcriptome in a triple wd40 mutant. - Are cell wall genes affected in a triple WD40 mutant (LWD1xLWD2xTTG1)? - Not specified

overall_design: 2 dye-swap - genotype comparaison

first: Richard

last: Sibout

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: PIM1 and NFATC1 targets in PC-3 prostate cancer cells

status: Public on Sep 19 2018

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

summary: PC-3 cells stably transfected with PIM1 overexpressing vector and transiently transfected with wt or multi-mutant NFATC1 overexpressing vector

overall_design: To identify potential targets for the interplay between PIM1 and NFATC1, we designed microarray experiments, where mRNA expression levels were compared in PC-3 cells with or without stable overexpression of PIM1 and with or without transient overexpression of either wild-type or multi mutant NFATC1.

first: Sini

last: Eerola


title: Brassica napus high oleic acid vs. low oleic acid

city: Changsha

first: Gang

last: Xiao

address: nongda raod 1#

institute: Hunan agricultural university

summary: Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. In this study, we employed a microarray analysis with high oleic acid line and low oleic acid line from the developing seeds (27 days after flowering) of Brassica napus.

overall_design: High oleic acid line vs. low oleic acid line, 2 replicates.

first: Haiqiang

last: Zhang


title: microRNA 27b-3p modulates SYK in Pediatric Asthma Induced by Dust Mites

city: Shanghai

first: Xiao-yan

last: dong

state: Shanghai

address: NO 24, Alley 1400, West Beijing Road

department: Department of respiration

institute: Shanghai Children's Hospital

summary: The PI3K-AKT pathway is known to regulate cytokines in dust mite-induced pediatric asthma. However, the underlying molecular steps involved are not clear. In order to clarify further the molecular steps, this study investigated the expression of certain genes and the involvement of miRNAs in the PI3K-AKT pathway, which might affect the resultant cytokine-secretion. In-vivo and in-vitro ELISA, qRT-PCR, western-blot and microarrays analyses were used in this study. A down-expression of miRNA-27b-3p in dust mite induced asthma group (group D) was found by microarray analysis. This was confirmed by qRT-PCR that found the miRNA-27b-3p transcripts that regulated the expression of SYK and EGFR were also significantly decreased (p < 0.01) in group D. The transcript levels of the SYK and PI3K genes were higher, while those of EGFR were lower in the former group. Meanwhile, we found significant differences in plasma concentrations of some cytokines between the dust mite-induced asthma subjects and the healthy controls. On the other hand, this correlated with the finding that the transcripts of SYK and its downstream PI3K were decreased in HBE transfected with miRNA-27b-3p, but were increased in HBE transfected with the inhibitor in vitro. Our results indicate that the differential expression of the miRNAs in dust mite-induced pediatric asthma may regulate their target gene SYK and may have an impact on the PI3K-AKT pathway associated with the production of cytokines. These findings should add new insight into the pathogenesis of pediatric asthma.

overall_design: Twelve pairs of gender- and age-matched Group D dust mite-induced asthma children and Group N normal control children were included in the initial microarray-based discovery analysis.

first: Xiao-Yan

last: Dong

last: Zhong


title: Genome-wide H3K9me2 mapping in single deletions of the selected chromatin modulating genes, histone H3 mutants and ccp1Δepe1Δ double mutant

status: Public on Sep 12 2018

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the high-throughput profiling of H3K9me2 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 maps in single deletions of the selected chromatin modulating genes, histone H3 mutants and ccp1Δepe1Δ double mutant in fission yeast. We find that the subtelomeric heterochromatin distribution is highly variable under different genetic perturbations and small heterochromatin islands are formed at clr4 and clr2 loci in ccp1Δepe1Δ.

overall_design: Single deletions of the selected chromatin modulating genes, histone H3 mutants and ccp1Δepe1Δ double mutant were examined by anti-H3K9me2 ChIP-seq in fission yeast.

first: Xiangwei

last: He


title: Early regenerative capacity in the porcine heart

first: Giuseppe

middle: Alessandro

last: D'Agostino

address: 11 Mandalay Road

institute: Lee Kong Chian School of Medicine - NTU

summary: Background: The adult mammalian heart has limited ability to repair itself following injury. Zebrafish, newts and neonatal mice can regenerate cardiac tissue, largely by cardiac myocyte (CM) proliferation. It is unknown if hearts of young large mammals can regenerate. Methods: We examined the regenerative capacity of the pig heart in neonatal animals (ages: 2, 3 or 14 days postnatal) after myocardial infarction (MI) or sham procedure. Myocardial scar and left ventricular function were determined by cardiac magnetic resonance (CMR) imaging and echocardiography. Bromodeoxyuridine pulse-chase labeling, histology, immunohistochemistry and Western blotting were performed to study cell proliferation, sarcomere dynamics and cytokinesis and to quantify myocardial fibrosis.  RNA-sequencing was also performed. Results: After MI, there was early and sustained recovery of cardiac function and wall thickness in the absence of fibrosis in 2-day old pigs. In contrast, older animals developed full-thickness myocardial scarring, thinned walls and did not recover function. Genome wide analyses of the infarct zone revealed a strong transcriptional signature of fibrosis in 14-day old animals that was absent in 2-day old pigs, which instead had enrichment for cytokinesis genes. In regenerating hearts of the younger animals, up to 10% of CMs in the border zone of the MI showed evidence of DNA replication that was associated with markers of myocyte division and sarcomere disassembly. Conclusions: Hearts of large mammals have regenerative capacity, likely driven by cardiac myocyte division, but this potential is lost immediately after birth.

overall_design: 36 RNA-seq samples of heart biopsies from 24 pigs, including 12 sham-treated controls and the infarction zone and border zone of the myocardium from 12 additional pigs. 4 conditions (old late, young late, old early and young early) in triplicate with respective controls.

first: Lei

last: Ye

first: Sze

last: Loo

first: Chen

last: Wang

first: Li

last: Su

first: Shi

last: Tan

first: Gui

last: Tee

first: Chee

last: Pua

first: Edgar

last: Macabe Pena

first: Redmond

last: Cheng

first: Way

last: Chen

first: Desiree

last: Abdurrachim

first: Janise

last: Lalic

first: Ru

first: Teck

last: Lee

first: Jian

first: Stuart

last: Cook


title: Identification of early transcriptome-based biomarkers related to lipid metabolism in peripheral blood mononuclear cells of rats nutritionally programmed for improved metabolic health

status: Public on Sep 15 2018

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Moderate maternal calorie restriction during lactation protects rat offspring against obesity development in adulthood, due to an improved ability to handle and store excess dietary fuel. We used this model to identify early transcriptome-based biomarkers of metabolic health using peripheral blood mononuclear cells (PBMCs), an easily accessible surrogate tissue, by focusing on molecular markers of lipid handling. Male and female offspring of control and 20 % calorierestricted lactating dams (CR) were studied. At weaning, a set of pups was killed, and PBMCs were isolated for whole-genome microarray analysis. The remaining pups were killed at 6 months of age. CR gave lower body weight, food intake and fat accumulation, and improved levels of insulin and leptin throughout life, particularly in females. Microarray analysis of weaned rat PBMCs identified 278 genes significantly differentially expressed between control and CR. Among lipid metabolism-related genes, expression of Cpt1a, Lipe and Star was increased and Fasn, Lrp1 and Rxrb decreased in CR versus control, with changes fully confirmed by qPCR. Among them, Cpt1a, Fasn and Star emerged as particularly interesting.  Transcript levels of Cpt1a in PBMCs correlated with their levels in WAT and liver at both ages examined; Fasn expression levels in PBMCs at an early age correlated with their expression levels in WAT; and early changes in Star expression levels in PBMCs correlated with their expression levels in liver and were sustained in adulthood. These findings reveal the possibility of using transcript levels of lipid metabolism-related genes in PBMCs as early biomarkers of metabolic health status.

overall_design: The study was conducted on male and female Wistar rats from 16 different litters. All animals were housed under standard conditions of controlled temperature (22 _C), the normal 12 h light and 12 h dark cycle, free access to tap water and a standard chow diet (3 kcal/g, with 8 % calories from fat; Panlab, Barcelona, Spain), unless specified otherwise. Briefly, 16 virgin female Wistar rats (body weight 225–260 g) were mated with male rats (Charles River Laboratories, Barcelona, Spain). After mating, each female was placed in an individual cage. On day 1 after delivery, excess pups in each litter were removed aiming for 10 pups per dam (five males and five females, when possible). Dams were assigned to either the control (n = 11 dams) or calorie-restricted (n = 5 dams) group. Control dams were fed ad libitum with standard chow diet, while calorie-restricted dams were fed daily with a 20 % calorie-restricted diet throughout lactation, starting on day 1 after delivery until weaning (day 21) as previously described (Palou et al. 2012). During the lactating period, body weight of male and female offspring of control and calorie-restricted dams (control and CR, respectively) was followed. At weaning at age 21 days, a set of animals made up of 24 pups from control (12 males and 12 females) and 24 from CR (12 males and 12 females) group were killed by decapitation under ad libitum feeding conditions. One half of pups (n = 6/group) were used to obtain trunk blood samples for peripheral blood mononuclear cells (PBMCs) isolation. Another set of animals, 28 control pups (12 males and 16 females) and 26 CR pups (14 males and 12 females), were kept alive. They were placed two per cage, paired with another animal of the same group and fed ad libitum with a normal-fat (NF) diet (3.8 kcal/g, 10 % calories from fat, Research Diets, Inc., NJ, USA) until the age of 6 months. Body weight and food intake of those animals were followed. Moreover, at the age of 6 months (prior to sacrifice), blood samples were collected at fed state and after 12 h fasting to obtain plasma. All the animals were decapitated under ad libitum feeding conditions at the age of 6 months, and samples of trunk blood for PBMCs isolation were collected. Body length (from the tip of the nose to the anus) and body composition (by EchoMRI-700TM, Echo Medical Systems, LLC, TX, USA) were measured in control and CR animals without anesthesia when animals were 21 days and 6 months old. PBMCs were collected using heparin in NaCl (0.9%) as anticoagulant and then diluted with equal volume of balanced salt solution, and separated using Ficoll density gradient.

first: Jadwiga

last: Konieczna

first: Joana

last: Sanchez

first: Annelies

last: Bunschoten

first: Catalina

last: Pico


title: Effect of an Analgesic Drug on Necelus Pulposus Cells from Human Intervertebral Disc (IVD) Tissues

city: Isehara

first: Tomoko

last: Nakai

state: Kanagawa

department: Orthopaedic Surgery, Surgical Science

institute: Tokai University School of Medicine

summary:
Neurotropin (NTP), a non-protein extract from inflamed rabbit skin inoculated with vaccinia virus. It has been widely used in Japan to treat low back pain. The current sutudy evaluated its stimulative effect on the disc cells to enhance glycosaminoglycan synthesis, which is one of the most important functions of the cells.
Gene expression profile was exzamined in the cells treated with or without NTP in vitro.

overall_design: Cultured human nucleus pulposus cells were treated with NTP every second day for a week. Total RNA was prepared from the harvested cells, and analyzed gene expression.  RNA from the cells  cultured in the basal medium for the same time period was used as control.

first: D

last: Sakai

first: T


title: Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: The objective of this study was to profile the gene-regulatory heterogeneities of breast epithelial cells grown in an ECM-rich environment.  The approach was to use stochastic profiling (Janes et al., Nat Methods 7(4):311-7 [2010]) to collect 10-cell pools of ECM-attached cells obtained by laser-capture microdissection and measure fluctuations in the 10-cell-averaged measurements to infer heterogeneous regulatory states.

overall_design: 16 random 10-cell samples of ECM-attached MCF10A-5E cells were obtained by laser-capture microdissection and their expression fluctuations compared to 16 pool-and-split controls comprised of larger microdissected cell populations extracted and split into 10-cell equivalents before poly(A) PCR preamplifcation.

first: Joan

last: Brugge


title: Detection of new pathways involved in the acceptance and the utilization of plant-based diet in isogenic lines of rainbow trout fry

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

summary:
We  investigate mechanisms behind the response to a plant based diet at short term, by analyzing the transcriptome of 3 isogenic lines of rainbow trout (R23, AB1, A22). These families represent an interesting genetic material to work on as they have similar responses when fed marine based-diet (M diet) but highly different responses when fed a plant-based diet (V diet).
Transcriptomic analyses of whole fry revealed 1740, 1834 and 246 probes differentially expressed among the three isogenic lines. Gene ontology enrichment analysis revealed different enriched pathways. Among them, some were related to immunity and perception. Among ontologies related to metabolism only the methionine metabolism pathway was found to be significantly enriched.
First, the use of these isogenic lines of rainbow trout led to find new pathways related to plant-based diets utilization which had not been described previously. Secondly, difference in expression of genes related to immunity suggest that this function play an important role but specific effect on immune status was difficult to assess, and further investigations are needed. Finally, results suggested that mechanisms underlying the use of plant-based diets is more linked to feed intake rather than to metabolism. Research on plants components affecting feed intake should be further explored to continue to improve feed formulation and reduce the reliance of aquaculture on marine resources without affecting fish performance.

overall_design:
Transcriptomic response was studied in whole-body fry from 3 isogenic lines (R23, AB1, A22).
Just before the first feeding, fish were randomly distributed into 18 tanks supplied with natural spring water at a constant temperature of 11.4°C (6 tanks/isogenic line with on average 350 fish). For each isogenic line, three tanks received the control diet (M diet) and the three other, the plant-based diet (V diet). Feed was distributed ad libitum.
The control diet contained fish meal, fish oil and whole wheat as major ingredients (M diet). The plant-based diet (V diet) was totally devoid of marine ingredients, and contained a blend of vegetable oils (rapeseed, palm and linseed oil) and vegetable meals (faba bean, corn, soybean, wheat gluten, peas, and white lupin) added with L-Lysine and L-methionine to meet nutrient requirements of rainbow trout. The V diet also contained an attractant mix.
Sampling took place after 5  weeks of feeding (n=6/condition).

first: Mathilde

last: Dupont-Nivet

first: Françoise

last: Médale


title: Jiangya Kangxian Formula attenuates Cardiac Remodeling induced by Hypertension in Spontaneous Hypertensive Rat through modulating Mitochondrial Dysfunction

city: guangzhou

first: Kai

last: Chen

institute: TCM

summary: Kangxian formula (KXF), composed of 5 traditional Chinese distinct herbs including Panax Notoginseng, Radix Salviae, Spatholobus Suberectus Dunn, Hedysarum Multijugum Maxim and Citri Grandis Exocarpium, is a proved recipe showing promising outcomes in treating hypertension and cardiac remodeling in clinic. However, the effect of longterm treatment with KXF in such a condition and the related molecular mechanisms remain  ambiguous. Here, we evaluated the effect of KXF on the gut microbiota and the prevention of hypertension and cardiac remodeling.

overall_design: Spontaneously hypertensive rats (SHRs) administered intragastrically with KXH (KXF high-dose,9.6g/kg) or distilled water

first: Guohua

last: Zhang


title: Host chaperones can define the fitness of adaptive influenza variants

status: Public on Sep 10 2018

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: The threat of viral pandemics demands a comprehensive understanding of evolution at the host-pathogen interface. Here, we systematically show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which is conserved across human flu strains, confers resistance to the MxA antiviral-restriction factor, and critically contributed to the pathogenicity of the 1918 pandemic flu, is rendered unfit by host chaperone depletion. This fitness loss is linked to biophysical defects that chaperones cannot address when heat shock factor-I is inhibited. Thus, host chaperones can be hijacked by viruses to un-couple biophysically deleterious consequences of mutations from the benefits of immune escape. In summary, host chaperones play a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host-switching, and for the design of antiviral strategies refractory to resistance.

overall_design: Three replicates each of MDCK cells transduced with inducible inhibitor of HSF1 in the presence or absence of Doxycycline at 37 or 39 degrees C.

first: Anna

middle: I

last: Ponomarenko

first: Angela

last: Phillips

first: Kenny

first: Orr

last: Ashenberg

first: Jiayuan

last: Miao

first: Sean

last: McHugh

first: Vincent

last: Butty

first: Christopher

last: Moore

first: Jesse

middle: D

last: Bloom

first: Yu-Shan

last: Lin

first: Matthew

last: Shoulders


title: Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination (ChIP-Seq)

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

summary: Nuclear pore complex components (Nups) are involved in neural development and alterations in Nup genes are linked to human neurological diseases. However, the physiological functions of specific Nups and the underlying mechanisms involved in these processes remain elusive. Here we show that tissue-specific depletion of nucleoporin Seh1 causes dramatic myelination defects in the Central Nervous System (CNS). Seh1-deficient Oligodendrocyte Progenitor Cells (OPCs) proliferate properly, but fail to differentiate into mature oligodendrocytes, which impairs myelin production and remyelination after demyelinating injury. Genome-wide analyses show that Seh1 regulates a core myelinogenic regulatory network and depletion of Seh1 alters open chromatin configurations at its target genes. Mechanistically, Seh1 regulates OPCs differentiation by assembling Olig2 and Brd7 into a transcription complex at nuclear pores. Together, our results reveal that Seh1 is required for oligodendrocyte differentiation and myelination by promoting assembly of an Olig2-dependent transcription complex and expose nucleoporins as key players in the CNS.

overall_design: ChIP was performed on rat oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1) using antibodies against seh1 or IgG. RNA-seq was performed on mouse control or Seh1cKO immature oligodendrocytes(T3 D2). Atac-seq was performed on mouse control or Seh1cKO oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1).

first: Liang

first: Zhixiong

last: Liu


title: Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach

status: Public on Sep 11 2018

city: Basel

first: Thomas

last: Lorber

address: Schönbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

type: Genome variation profiling by genome tiling array

summary: Variable tumor cellularity can limit sensitivity and precision in comparative genomics, because differences in tumor content can result in misclassifying truncal mutations as region-specific private mutations in stroma-rich regions, especially when studying tissue specimens of mediocre tumor cellularity such as LUADs. To address this issue, we refined a nuclei flow-sorting approach by sorting nuclei based on ploidy and the LUAD lineage marker thyroid transcription factor 1 (TTF-1) and applied this method to investigate genome-wide somatic copy number aberrations (SCNA) and mutations of 409 cancer genes in 39 tumor populations obtained from 16 primary tumors and 21 matched metastases. This approach increased the mean tumor purity from 54% (range: 7-89%) of unsorted material to 92% (range: 79-99%) after sorting. Despite this rise in tumor purity, we detected limited genetic heterogeneity between primary tumors and their metastases. In fact, 88% of SCNAs and 80% of mutations were propagated from primary tumors to metastases and low allele frequency mutations accounted for much of the mutational heterogeneity. Even though the presence of SCNAs indicated a history of chromosomal instability (CIN) in all tumors, metastases did not have more SCNAs than primary tumors. Moreover, tumors with biallelic TP53 or ATM mutations had high numbers of SCNAs, yet they were associated with a low interlesional genetic heterogeneity. The results of our study thus provide evidence that most macroevolutionary events occur in primary tumors before metastatic dissemination and advocate for a limited degree of CIN over time and space in this cohort of LUADs. Sampling of primary tumors thus may suffice to detect most mutations and SCNAs. In addition, metastases but not primary tumors had seeded additional metastases in three of four patients; this provides a genomic rational for surgical treatment of such oligometastatic LUADs.

overall_design: In total, there are 39 copy number Agilent 180k SurePrint arrays, representing 16 patients with 37 LUAD tumor samples, including 35 fresh frozen tissues and 2 FFPE tissues. There are 11 patients with primary tumor and one matched metastasis (22 arrays, one for each sample), 3 patients with primary tumor and two matched metastasis (9 arrays, one for each sample), one patient with primary tumor and three matched metastasis (4 arrays, one for each sample) and one patient with multiple populations in the primary tumor and one metastasis (4 arrays, 3 for each population in the primary tumor and 1 for the metastasis).

first: Noemi

last: Andor

first: Tanja

last: Dietsche

first: Valeria

last: Perrina

first: Darius

last: Juskevicius

first: Karen

last: Pereira

first: Stephanie

middle: U

last: Greer

first: Arthur

last: Krause

first: David

last: Mueller

first: Spasenija

last: Prince

first: Didier

last: Lardinois

first: Michael

middle: T

last: Barrett

first: Christian

last: Ruiz

first: Lukas

last: Bubendorf


title: Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

institute: Université Laval

summary:
Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genome-wide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intra-provenance cross (north-north cross, 58th parallel) and an inter-provenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a wide-spread North American forest tree.
Results: A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar’s 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the inter-provenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar’s distribution, and higher photosynthetic assimilation rates and water-use efficiency at high-latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs, may in fact represent efficient adaptive variations against fast-evolving pathogens.

overall_design: A total of 34 individuals were hybridized (17 in each dye) in addition to 12 reference DNA (6 in each dye). Reference DNAs were corrected for day and batch effect and averaged within each dye. Afterwards, each sample was compared to this average representation of the reference in the opposite dye.

first: Isabelle

last: Giguère

first: Ilga

last: Porth

first: Nathalie

last: Isabel

first: John

last: MacKay


title: cinetique comparison-FUI GranoFlakes.

first: Stéphanie

last: Pateyron

summary: 4plex_maize_2015_02 - cinetique comparison - Delineation of the metabolic pathways involved in maize endosperm vitreousness. - comparaison of vitreous (outer) and floury (inner) endosperm from flint and dent maize inbred lines harvested at 15 and 20 day after pollinisation.

overall_design: 8 dye-swap - time course

last: MARION

last: Gaillard

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Exposure-induced changes of plasma mRNA expression levels in patients with panic disorder

city: Munich

first: Angelika

last: Erhardt

address: Kraepelinstraße 2-10

department: Translational Research in Psychiatry

institute: Max Planck Institute of Psychiatry

summary: Anxiety disorders including panic disorders with or without agoraphobia are the most prevalent mental disorders. Exposure is a core technique within the framework of cognitive behavioral therapy to treat phobia- and anxiety-related symptoms. The primary aim of this study was to trace specific anxiety-related plasma gene expression changes of subjects with PD at three time points in order to identify biomarkers for acute anxiety states. In this intervention, the patient is exposed to highly feared and mostly avoided situations.

overall_design: Blood samples from individuals with panic disorder (n=24) were drawn at three time points during exposure: baseline, 1 hour post-exposure and 24 hours after exposure-onset.

first: Jade

last: Martins

first: Darina

last: Czamara

first: Jennifer

last: Lange

first: Chris

middle: W

last: Turck

first: Elisabeth

last: Binder


title: Gene Expression Differences in MYC and RAS Driven Liver Cancer Transgenic

city: San Francisco

first: Andrei

last: Goga

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

summary: MYC and RAS signaling are two oncogene pathways important in human liver cancer.  We sought to model liver cancer driven by either MYC or RAS using conditional LAP-tTA crossed to either TRE-MYC or TRE-HRAS models in the FVB/N background, and to understand oncogenic signaling pathways that are distinct between each model.  Non-tumor tissue, from LAP-tTTA (LT2) mice were used as controls.  In this study, we generated tumors from either MYC or RAS driven tumors and compared global gene expression changes to each other and control samples.

overall_design: LAP-tTA (LT2) control, LAP-tTA x TRE-MYC (MYC), or  LAP-tTA x TRE-HRAS (RAS) were bred.  Tumor initiation was achieved by removing doxycycline from the diet of dual-transgenic mice to allow for MYC or HRAS oncogene expression.  Tumors were collected and flash frozen in liquid nitrogen followed by total RNA isolation and Agilent mRNA array analysis.  Four tumors or control tissues from each genotype were analyzed.


title: Transcriptomic Signature of Right Ventricular Failure in Experimental Pulmonary Arterial Hypertension: Deep Sequencing Demonstrates Mitochondrial, Fibrotic, Inflammatory and Angiogenic Abnormalities

city: Kingston

first: Stephen

last: Archer

state: Ontario

address: 94 Stuart Street

department: Medicine

institute: Queen's University

summary: Abstract: Right ventricular failure (RVF) remains the leading cause of death in pulmonary arterial hypertension (PAH). We investigated the transcriptomic signature of RVF in hemodynamically well-phenotyped monocrotaline (MCT)-treated, male, Sprague-Dawley rats with severe PAH and decompensated RVF (increased right ventricular (RV) end diastolic volume (EDV), decreased cardiac output (CO), tricuspid annular plane systolic excursion (TAPSE) and ventricular-arterial decoupling). RNA sequencing revealed 2547 differentially regulated transcripts in MCT-RVF RVs. Multiple enriched gene ontology (GO) terms converged on mitochondria/metabolism, fibrosis, inflammation, and angiogenesis. The mitochondrial transcriptomic pathway is the most affected in RVF, with 413 dysregulated genes. Downregulated genes included tfam (−0.45-fold), suggesting impaired mitochondrial biogenesis, Cyp2e1 (−3.8-fold), a monooxygenase which when downregulated increases oxidative stress, dehydrogenase/reductase 7C (Dhrs7c) (−2.8-fold), consistent with excessive autonomic activation, and polypeptide N-acetyl-galactose-aminyl-transferase 13 (Galnt13), a known pulmonary hypertension (PH) biomarker (−2.7-fold). The most up-regulated gene encodes Periostin (Postn; 4.5-fold), a matricellular protein relevant to fibrosis. Other dysregulated genes relevant to fibrosis include latent-transforming growth factor beta-binding protein 2 (Ltbp2), thrombospondin4 (Thbs4). We also identified one dysregulated gene relevant to all disordered transcriptomic pathways, Annexin A1. This anti-inflammatory, phospholipid-binding mediator, is a putative target for therapy in RVF-PAH. Comparison of expression profiles in the MCT-RV with published microarray data from the RV of pulmonary artery-banded mice and humans with bone morphogenetic protein receptor type 2 (BMPR2)-mutations PAH reveals substantial conservation of gene dysregulation, which may facilitate clinical translation of preclinical therapeutic and biomarkers studies. Transcriptomics reveals the molecular fingerprint of RVF to be heavily characterized by mitochondrial dysfunction, fibrosis and inflammation.

overall_design: RNA extracted from the right ventricle of rats exposed to monocrotaline or vehicle.

first: Francois

last: Potus

first: Charles

last: Hindmarch

first: Kimberly

last: Dunham-Snary

first: Jeff

last: Stafford


title: Next Generation Sequencing to determine HHV-6B Transcriptome in HCT patients with a recent viral reactivation

status: Public on Sep 08 2018

city: seattle

first: Serge

last: Barcy

state: WA

address: 1900 Ninth Avenue

department: SCRI

institute: Seattle Children's

summary:
Purpose: The goal of this study is to determine the expression profile of HHV-6B in whole blood samples from transplant patients with HHV-6B genomes detected in plasma

Methods: Viral mRNA profiles in whole blood samples of different transplant patients  were generated by deep sequencing using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation for U38 expression was performed using TaqMan

Results: Hierarchical clustering uncovered systematic detection of U38 mRNA transcripts in whole blood samples from all patients with a detectable HHV-6B reactivation in their plasma

Conclusions: Our study represents the first detailed analysis of viral transcriptomes associated with HHV-6B reactivation in whole blood samples generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate qualitative evaluation of mRNA content within a whole blood sample.

sample_organism:
Homo sapiens
Human betaherpesvirus 6B

platform_organism:
Homo sapiens
Human betaherpesvirus 6B

overall_design: Examine HHV-6B viral transcriptome in whole blood samples from hematopoietic transplant patients with detectable plasma viral loads determined by qPCR

first: Joshua

last: Hill

first: Minako

last: Oda

first: Ryan

last: Basom

first: Vikas

last: Peddu

first: Meei-Li

last: Huang

first: Ruth

last: Sedlak

first: Keith

middle: R

last: Jerome

first: Danielle

middle: M

last: Zerr

first: Michael

last: Boeckh


title: Characterization of the transcriptome of Haloferax volcanii with mixed RNA-Seq

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Recently a dRNA-Seq study with Haloferax volcanii has been published that led to the discovery of nearly 2800 novel transcription start sites for non-coding RNAs. However, the dRNA-Seq results are confined to the 5'-end of transcripts and does not contain any length information. Therefore, a major aim of the present RNA-Seq study was the elucidation of the lengths of the novel non-coding RNAs. A second aim was to analyze the operon structure of protein-coding genes. The recent dRNA-Seq study was confined to cultures grown under optimal conditions. It was revealed that less than half of the protein-coding genes were expressed. Therefore, the present RNA-Seq study used cultures grown under four different conditions to identify further transcripts of protein-coding genes that are not needed under optimal conditions. RNA samples from the four conditions were mixed prior to the RNA-Seq analyses (mixed RNA-Seq). The results allowed to characterize the sum of transcriptomes of H. volcanii under four conditions. Northern blot analyses were used to characterize selected examples in detail. Many important results were obtained, including the length determination of all transcripts, a genome-wide operon analysis, verification of a high fraction of antisense RNAs, and the discovery that 30% of all protein-coding transcripts have overlapping 3'-UTRs.

overall_design: Three H. volcanii cultures were grown to mid-exponential growth phase under optimal conditions, at low salt concentration, and with glucose as sole carbon source, In addition, a fourth culture was grown to stationary phase. Total RNA was isolated from all four cultures and equal fractions were mixed. RNA-Seq was performed with the mixed RNA sample. 50 million paired end reads of 150 nt length were generated.

first: Jörg

last: Soppa

first: Sebastian

last: Laass


title: Comparative gene expression profiling of pig‐derived iPSC‐like cells: Effects of induced pluripotency on expression of porcine endogenous retrovirus (PERV)

city: Hennigsdorf

first: Martina

last: Schad

address: Neuendorfstrasse 16b

institute: OakLabs GmbH

summary:
Background: Porcine induced pluripotent stem cells (piPSCs) offer an alternative strategy in xenotransplantation (XTx). As human endogenous retroviruses (HERV), particularly HERV‐K, are highly expressed in natural human stem cells, we compared the expression of porcine endogenous retroviruses (PERV) and retrotransposon LINE‐1 (L1) open reading frames 1 and 2 (pORF1 and pORF2) in different piPSC‐like cell lines with their progenitors (porcine fetal fibroblasts, pFF).
Methods: Cells reprogrammed via Sleeping Beauty‐transposed transcription factors were cultured and analyzed on a custom‐designed microarray representing the reference pig genome. Data were complemented by qRT‐PCR and reverse transcriptase (RT) assay.
Results: The expression profiles revealed that 8515 of 26967 targets were differentially expressed. A total of 4443 targets showed log2 expression ratio >1, and 4072 targets showed log2 expression ratio less than −1 with 0.05 P‐value threshold. Approximately ten percent of the targets showed highly significant expression ratios with log2 ≥4 or ≤−4. Besides this general switch in cellular gene expression that was accompanied by an altered morphology, expression of both PERV and L1 pORF1/pORF2 was significantly enhanced. piPSC‐like cells revealed a 10‐fold to 100‐fold higher transcription of the viral PERV‐A and PERV‐B envelope genes (env), viral protease/polymerase (prt/pol), and L1 elements. No functional retrovirus could be detected under these conditions.
Conclusion: Epigenetic reprogramming has functional impact on retrotransposons. Thus, the induction of pig‐derived pluripotent cells influences their PERV expression profile. Data emphasize the necessity to focus on animals, which show non‐functional endogenous viral background to ensure virological safety.

overall_design: 'a' versus 'b' analysis, 7 samples per group.

first: Ralf

last: Tönjes

first: Antonia

last: Godehardt


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (human cell lines RNA-Seq)

city: Cincinnati

first: Kakajan

last: Komurov

state: OH

address: 3333 Burnet Ave OH 45229

department: Division of Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital

summary: The nature and the role of global transcriptional deregulations in cancers are not fully understood. We report a phenotype in a significant portion of cancers characterized by widespread defects in mRNA transcription elongation (TE). Cancers with TE defects (TEdeff) were characterized by spurious transcription and defective mRNA processing, specifically in a large set of genes characterized by long genomic length, poised promoters and inducible expression. As such, signaling pathways regulated by such genes, such as interferon/JAK/STAT and TNF/NF-κB pathways, were consistently suppressed in TEdeff tumors. Remarkably, TEdeff significantly correlated with the poor response and outcome in immunotherapy, but not chemo- or targeted therapy, -treated renal cell carcinoma and metastatic melanoma patients in 4 different cohorts. Importantly, forced pharmacologic or genetic induction of TEdeff in tumor cells impaired the expression of the interferon/JAK/STAT and TNF/NF-κB pathways, and imposed resistance to the innate and adaptive anti-tumor immune responses and checkpoint inhibitor therapy in vivo. Therefore, defective TE is a novel epigenetic mechanism in the tumor arsenal of immune resistance tools, which warrants its assessment in cancer patients undergoing immunotherapy.

overall_design: RNAseq was performed on a panel of human breast cancer cell lines to illustrate transcription elongation defects existed in a subset of samples. The data was also used to illustrate that results obta

first: Vishnu

last: Modur

first: Navneet

last: Singh

first: Vakul

last: Mohanty

first: Eunah

last: Chung

first: Belal

last: Muhammad

first: Kwangmin

last: Choi

first: Xiaoting

last: Chen

first: Kashish

last: Chetal

first: Nancy

last: Ratner

first: Nathan

last: Salomonis

first: Matthew

last: Weirauch

first: Susan

last: Waltz

first: Gang

first: Lisa

last: Privette-Vinnedge

first: Joo-Seop

last: Park

first: Edith

last: Janssen


title: Real-time quantitative PCR analysis of serum from osteoporotic Mexican women

city: México City

first: Eric

middle: Gustavo

last: Ramírez-Salazar

address: Periferico Sur 4809, Arenal Tepepan, 14610 Ciudad de México

institute: INMEGEN

summary: RNA was purified from serum of osteoporotic and healthy postmenopausal mexican women using miRNeasy Serum/Plasma kit  (QIAGEN). For microRNA expression analysis we used the Human MicroRNA A+B Cards Set v3.0 TaqMan Low Density Array platform (Applied Biosystems). Analysis was performed in the Expression Suite v.1.1.3 software (Applied Biosystems).

overall_design: We made 4 pools for each studied group, pooling 150 ng of RNA of 5 samples. Hence, we have 4 pools for Normal and 4 pools for osteoporotic women.

middle: G

first: Sergio

last: Carrillo-Patiño

first: Alberto

last: Hidalgo-Bravo

first: Berenice

last: Rivera-Paredez

first: Manuel

last: Quiterio

first: Paula

last: Ramírez-Palacios

first: Nelly

last: Patiño

first: Margarita

last: Valdés-Flores

first: Jorge

last: Salmerón

first: Rafael

last: Velázquez-Cruz


title: mRNA stability as measured by thiouracil incorporation in the presence and absence of translational inhibitors

status: Public on Sep 07 2018

city: Berkeley

first: Leon

last: Chan

state: California

address: 628 Barker Hall UC Berkeley

department: Molecular Cell Biology

institute: UC Berkeley

summary: We measure the stability of mRNAs in rapidly dividing yeast by metabolic labeling with thiouracil and determine the effects on mRNA stability in the presence of various inhibitors of translation elongation and initiation.

overall_design: Measurement of transcriptome stability in 2 different yeast strains and in 5 different conditions.


title: Regulatory mechanisms of brown rot genes for responding to environmental carbon signals in Postia placenta

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

summary: Brown rot fungi evolved the unique strategy to efficiently decay wood structures and selectively extract carbohydrates, and this involved the sophistical regulation of functional genes (Zhang et al., PNAS, 2016, 113: 10968-). However, the regulatory mechanisms of brown rot genes were not well known, impeding the implication and application of brown rot machinery in biomass conversions. In this work, we systematically studied the roles of environmental carbon signals (e.g., aspen, cellobiose, glucose and no-carbon) in regulating gene expression in model brown rot fungus Postia placenta by RNA-seq. We found the complex substrate aspen (Populus sp.), but not the commonly recognized disaccharide cellobiose, was the universal inducer for Carbohydrate Active Enzymes (CAZYs) expression. Even though, cellobiose clearly induced the expression of cellulase (GH5 and GH12, endoglucanase) and xylanase (GH10, endoxylanase) (cellobiose vs. no-carbon, fold change > 4), as we reported previously (Zhang and Schilling, FGB, 2017, 106: 1-). When response to easy to use carbons, P. placenta lost the CCR effect on the main-chain cleaving CAZYs expression, but kept this repressing effect on side-chain cleaving CAZYs and AAs, which indicated a clear adaption relative to that in saprotrophic ascomycete ancestors. This “loss of CCR effect” was independent of the glucose concentrations. To explore the distinctive brown rot regulatory machinery, the gene modules subjected to inducing or CCR effects were then used to predict the regulatory motifs and transcriptional factors to build the regulatory network in P. placenta. Together, these findings will facilitate us to understand the adaptions of regulatory elements in brown rot fungi, as well as the efficient brown rot strategy.

overall_design: We sequenced mRNA from 24 samples, including treatments of four carbon souces (e.g., no carbon, glucose, cellobiose and aspen) mutiply two time points (e.g., 15 h and 72 h), to compare the gene regulations in response to variable carbon sources. Three bioreplicates were included for each treatment.

first: Jiwei

last: Zhang

first: Hugh

last: Mitchell

first: Lye

last: Markillie

first: Galya

last: Orr

middle: S

first: Matthew

last: Gaffrey


title: Gene expression of sheep epidermal stem cells and corneal epithelia cells

city: Luoyang

first: Xueyi

last: Yang

address: 6# Jiqing road

institute: Luoyang normal university

summary: Corneal epithelial cells (CECs) are required for corneal transparency and visual function, and corneal injuries may cause corneal blindness. Skin epidermal stem cells (SESCs), which share the same origin with CECs and have the potential of multi-directional differentiation are ideal seed cells for tissue engineered corneal construction to treat corneal blindness. To identify critical genes and pathways that modulate transdifferentiation from SESCs to CECs, we isolated and cultured the sheep SESCs and CECs and then compared gene expression of SESCs and CECs using microarray.

overall_design: Three epidermal stem cell lines (Use the method described by X Yang et al. 2007 and 2008) and three corneal epithelia cell lines (Use the method described by JC Jones 2011) were used in the study. Total  RNA  was  extracted  and  purified  using  miRNeasy  Mini  Kit（Cat#217004,   QIAGEN, GmBH, Germany) following the manufacturer’s instructions. The integrity of the isolated RNA was analyzed using the Agilent 2100 Electrophoresis Bioanalyzer System and found to be of sufficient quantity (13 to 21ug) and quality (RNA integrity number in the range of 9.9 to 10.0) for analysis using the Agilent sheep gene expression microarray, 8×15K.

first: Yanjie

last: Guo


title: A transcriptome analyses of Longissimus dorsi muscle in Nguni cattle finished on different feedlot diets

city: Irene

first: Dina

middle: Alida

last: Linde

state: Gauteng

address: Olifantsfontein road

department: Animal Breeding and Genetics

country: South Africa

institute: Agricultural research council

summary:
Background: The Nguni is an indigenous Bos taurus Sanga breed which is primarily used in extensive commercial and communal farming systems in South Africa. The Nguni is a small framed early maturing breed not preferred for finishing under feedlot systems, as the large framed later maturing types are favoured for high lean meat yield. In this study we aim to investigate differentially expressed genes in Longissimus dorsi muscle of Nguni cattle fed diets differing in energy levels finished under commercial feedlot conditions.
Results: Twenty Nguni and twenty Bonsmara were fed either a low (10.9 MJ ME/kg) or a high (12.00 MJ ME/kg) energy diet for 120 days. At slaughter, muscle samples were taken for RNA extraction and RNA-sequencing. A total of 2214 differentially expressed genes (DEG) were observed between the two breeds regardless of diet. For the low energy diets, 2244 DEG in the Nguni and the Bonsmara were significantly expressed, while a higher number of were differentially expression between the Nguni and Bonsmara on high energy diet (3154 DEG). A difference of 288 DEG were identified between the Nguni fed on the low and high energy diets.  Most of the fat deposition genes were upregulated in the Bonsmara (ASIP, OXT, SNAI3, FOX01, PPARGC1A), with lower levels in the Nguni.
Conclusion: Clear breed differences were found for the number and level of gene expression, while a larger variation in DEG were observed between the two diets within in the Bonsmara breed.

overall_design: The effect of 2 diets (high or low energy) on two breeds

first: M

last: Scholtz

first: E

last: van Marle-Koster


title: Transcriptomic evaluation of mismatch repair defects

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Using numerous isogenic models of mismatch repair defects we sought to understand how these defects influence global transcription

overall_design: A total of 11 cell lines were analyzed in triplicate

first: Shiaw-Yih

last: Lin


title: Expression data from ectopic expression of BDH2 in Nasopharyngeal carcinoma (NPC) cell lines

city: Nanning

first: Bo

last: Li

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

institute: Guangxi Medical University

summary:
Compare with normal nasopharyngeal epithelial cells, we found BDH2 was decreased in NPC cells, we found that BDH2 inhibited proliferation, colony formation, migration and invasion in NPC cells.
We used microarrays to identify differential genes regulated by BDH2 in NPC cell lines.

overall_design: A NPC cell line were included in the microarray analysis. the NPC cell line 5-8F was stably transfected with control vector and BDH2 expression plasmid. We had three single clones of pCMV6-Entry-5-8F. pCMV6-Entry-5-8F as control.

first: Xiaoying

last: Zhou

first: Zhe


title: RNA-seq of miR-183 knockout mouse dorsal root ganglia

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: To identify the mechanism by which the miR-183 cluster works to cause change of the fate of early dorsal root ganglion progenitor cells, we compared RNA expression in E12.5 lumbar dorsal root ganglia from the miR conditional knockout mice to control mice

overall_design: Three knockout mice and three control mice on a background mixed strain C57/Bl6 x 129/SvEv.

first: Changgeng

last: Peng

first: Patrik

last: Ernfors


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

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

overall_design: Refer to individual Series


title: Expression data from skeletal muscles of Ts1Cje and disomic C57BL/6 mice

city: UPM Serdang

first: King Hwa

last: Ling

state: Selangor

address: Faculty of Medicine and Health Sciences

department: Department of Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

summary:
To determine the gene expression profile of extensor digitorum longus (EDL) and soleus (SO) muscles of wild-type and Ts1Cje mouse model of Down Syndrome (DS).
Two types of skeletal muscles (EDL and SO) were harvested from both Ts1Cje and its disomic littermate.

overall_design: RNA was extracted for hybridization to arrays from 4 pairs of Ts1Cje and disomic C57BL/6 littermate control SO skeletal muscles and 3 pairs of Ts1Cje and disomic C57BL/6 littermate control EDL skeletal muscles.

first: Melody P-Y

last: Leong

first: King-Hwa