title: Gene expression from laser capture microdissected pancreatic cancer epithelium and stroma

status: Public on Nov 27 2018

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: This study used laser capture microdissection to obtain paired tumor epithelium and stroma RNA samples from human pancreatic ductal adenocarcinoma (PDA) frozen sections. Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to model compartment-specific gene expression density on a genome-wide scale and build an algorithm for transcriptional devonvolution (ADVOCATE). RNA sequencing of macrodissected bulk PDA sections was performed on 15 samples in order to systematically compare TruSeq and NuGEN RNA-Seq libraries and (ii) correlate histopathological and molecular assessment of tumor composition.

overall_design:
Gene expression data are presented for 65 pairs of tumor epithelium and stroma LCM samples and 15 bulk tumors using NuGEN and TruSeq library preparation, respectively.
Gene expression data are presented for 57 additional tumor stromas.

middle: C

first: Kenneth

last: Olive


title: yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_2]

status: Public on Jan 29 2019

city: Aachen

first: Chao-Chung

last: Kuo

state: NRW

address: Pauwelsstrasse 30

department: IZKF Genomics Facility

country: Germany

institute: RWTH Aachen University Hospital

type: Expression profiling by high throughput sequencing

summary:
Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes.
Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include  day2, day4, day6 and day8.
Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of  yylncRNAs identified from RNA-Seq  had a linear relationship with qRT–PCR .
Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: We have used 4 different time-point (all in duplicates), covering key stages of human  ES cell differentiation to cardiomyocytes. It includes day 2 (late mesoderm), day 4 (cardiac mesoderm), day 6 (cardiac progenitors) and day 8 (early cardiomyocytes).

first: Leo

last: Kurian

first: Stefan

last: Frank


title: Multigene biomarkers of pyrethroid exposure: preliminary experiments: 15k microarrays

status: Public on Oct 31 2018

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

country: USA

institute: US Environmental Protection Agency

summary: We describe initial development of RNA profiling-based assays for detecting pyrethroid pesticides in water. We conducted 48-hour flow-through exposures of Pimephales promelas adults and larvae to lab water and eight nominal concentrations of each of four pyrethroid insecticides: bifenthrin, cypermethrin, esfenvalerate, and (trans) permethrin. Concentration-response curves suggest steep dose responses, and LC50s below most published values. Expression microarray analysis of dissected brains from adults and whole larvae exposed to cypermethrin and bifenthrin suggests both assay formats can be used to detect these pyrethroids at concentrations well below P. promelas LC50s, and below LC50s of about 70% of aquatic metazoan species. Geneset analysis and intersections between lists of differentially expressed genes failed to identify substantial functional overlaps between these toxicants. Geneset analysis was sensitive to parameter choice, which may reflect the large number of genes analyzed relative to the number of samples, and substantial biological variability relative to effect sizes. Several identified GO terms can be rationalized based on known pyrethroid action, but implications of other highlighted GO terms are unclear.

overall_design: Adult (6 months old) and larval (48 hrs post-hatch) fathead minnow were exposed for two days to the pyrethroids bifenthrin and cypermethrin at several concentrations, in order to estimate LC50s. For each pesticide, samples exposed to two concentrations well below LC50s were selected for transcriptomic analysis and classifier development. Cross-validation was used to estimate classifier performance and compare classifiers developed using dissected adult brains with classifiers developed using whole larvae.

first: Mitchell

middle: S

last: Kostich


title: yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_1]

summary:
Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes.
Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include day 0, day 1, day 2, day 4,day 6, day 8 and day 14.
Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of  yylncRNAs identified from RNA-Seq  had a linear relationship with qRT–PCR .
Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content in the process of cardiac differentitation. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: We have used 7 different time-point (all in triplicates), covering key stages of human  ES cell differentiation to cardiomyocytes. It includes day 0 (ES cells), day 1(   early mesoderm), day 2 (late mesoderm), day 4 (cardiac mesoderm), day 6 (cardiac progenitors), day 8 (early cardiomyocytes) and day 14 (cardiomyocytes).


title: Multigene biomarkers of pyrethroid exposure: preliminary experiments: 60k microarrays

summary: We describe initial development of RNA profiling-based assays for detecting pyrethroid pesticides in water. We conducted 48-hour flow-through exposures of Pimephales promelas larvae to lab water and eight nominal concentrations of each of four pyrethroid insecticides: bifenthrin, cypermethrin, esfenvalerate, and (trans) permethrin. Concentration-response curves suggest steep dose responses, and LC50s below most published values. Expression microarray analysis of whole larvae suggests transcriptomic changes can be used to detect these pyrethroids at concentrations well below P. promelas LC50s, and below LC50s of about 70% of aquatic metazoan species. Geneset analysis and intersections between lists of differentially expressed genes failed to identify substantial functional overlaps between these toxicants. Geneset analysis was sensitive to parameter choice, which may reflect the large number of genes analyzed relative to the number of samples, and substantial biological variability relative to effect sizes. Several identified GO terms can be rationalized based on known pyrethroid action, but implications of other highlighted GO terms are unclear.

overall_design: In order to estimate LC50s, larval (48 hours post-hatch) fathead minnow were exposed for two days to several concentrations of each of four pyrethroid pesticides: bifenthrin, cypermethrin, esfenvalerate and (trans) permethrin. For each pesticide, samples exposed to two concentrations well below LC50s were selected for transcriptomic analysis and classifier development. Cross-validation was used to estimate classifier performance.


title: The miR-200b/200a/429 cluster prevents metastasis and induces dormancy in murine claudin-low mammary tumor cells

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

summary: The miR-200 family of microRNAs consisting of miR-141, miR-200a, miR-200b, miR-200c and miR-429 are key regulators of breast cancer progression. The miR200 family maintains mammary epithelial identity and downregulation of miR-200 expression drives the epithelial-to-mesenchymal transition. Re-expression of one or more miR-200 family members in tumor cells with mesenchymal characteristics may restore the epithelial phenotype and alter growth and metastatic potential. To test this, the miR-200b/200a/429 cluster was re-expressed in a murine claudin-low mammary tumor cell line, RJ423

overall_design: We carried out RNA-Seq on mouse mammary tumor cell lines derived from the MTB-IGFIR mouse model, with either re-expression of the miR200a/b/429 cluster or empty vector control. RNA was isolated from each cell line in 3 independent experiments.

first: Katrina

last: Watson

first: Robert

last: Jones

first: Anthony

last: Bruce


title: Multigene biomarkers of pyrethroid exposure: preliminary experiments

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

overall_design: Refer to individual Series


title: Translation elongation rate varies among organs and decreases with age

status: Public on Dec 31 2018

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: There has been a surge of interest towards targeting protein synthesis to treat diseases and extend lifespan. Despite the progress, few options are available to assess translation in live animals, as their complexity limits the repertoire of experimental tools to monitor and manipulate processes within organs and individual cells. It this study, we developed a labeling-free method for measuring organ- and cell-type-specific translation elongation rates in vivo. It is based on time-resolved delivery of translation initiation and elongation inhibitors in live animals followed by ribosome profiling. It also reports translation initiation sites in an organ-specific manner. Using this method, we found that the elongation rates differ more than 50% among mouse organs and determined them to be 6.8, 5.0, and 4.3 amino acids per second for liver, kidney, and skeletal muscle, respectively. We further found that the elongation rate is reduced by 20% between young adulthood and mid-life. Thus, translation, a major metabolic process in cells, is tightly regulated at the level of elongation of nascent polypeptide chains.

overall_design: Measuring translation elongation rate in three organs (heart, kidney, skeletal muscle) and two ages (15 and 72 weeks), three timepoints per each organ, 2-4 replicated per a timepoint.

middle: V

first: Zalan

last: Peterfi

first: Vadim

middle: N

last: Gladyshev


title: SENP3-mediated host defense response contains HBV replication and restores protein synthesis

status: Public on Nov 14 2018

city: Ithaca

first: Ji

last: Wan

state: NY

address: 303 Biotech 526 Campus Road

institute: Cornell University

summary: Certain organs are capable of containing the replication of various types of viruses. In the liver, infection of Hepatitis B virus (HBV), the etiological factor of Hepatitis B and hepatocellular carcinoma (HCC), often remains asymptomatic and leads to a chronic carrier state. Here we investigated how hepatocytes contain HBV replication and promote their own survival by orchestrating a translational defense mechanism via the stress-sensitive SUMO-2/3-specific peptidase SENP3. We found that SENP3 expression level decreased in HBV-infected hepatocytes in various models including HepG2-NTCP cell lines and a humanized mouse model. Downregulation of SENP3 reduced HBV replication and boosted host protein translation. We also discovered that IQGAP2, a Ras GTPase-activating-like protein, is a key substrate for SENP3-mediated de-SUMOylation. Downregulation of SENP3 in HBV infected cells facilitated IQGAP2 SUMOylation and degradation, which leads to suppression of HBV gene expression and restoration of global translation of host genes via modulation of AKT phosphorylation. Thus, The SENP3-IQGAP2 de-SUMOylation axis is a host defense mechanism of hepatocytes that restores host protein translation and suppresses HBV gene expression.

overall_design: Investigating the role of SENP3 in host cell translation upon HBV infection.

first: Rui

last: Xi

first: Kadur

middle: L

last: Murthy

first: Kuei-Ling

last: Tung

first: Cynthia

middle: D

last: Guy

first: Feng

last: Li

first: Zhuo

last: Wang

first: Xiaodong

first: Anastasia

last: Varanko

first: Nikolai

last: Rakhilin

first: Yongning

last: Xin

first: Botao

last: Liu

first: Shu-Bing

last: Qian

first: Lishan

last: Su

first: Yan

last: Han

first: Xiling

last: Shen


title: Circular RNAs in cattle muscle: developmental stage-dependent changes

status: Public on Oct 10 2018

city: Yangling

first: Hui

state: Shaanxi

address: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China

country: China

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development.

overall_design: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China.

first: Hong

last: Chen


title: A Population of Navigator Neurons is Essential for Olfactory Map Formation during Critical Period

status: Public on Oct 03 2018

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

summary: In the developing brain, heightened plasticity during the critical period enables the proper formation of neural circuits. Here we identify the “navigator” neurons, a group of perinatally born olfactory sensory neurons, as playing an essential role in establishing the olfactory map during the critical period. The navigator axons project circuitously in the olfactory bulb and traverse multiple glomeruli before terminating in perspective glomeruli. These neurons undergo a phase of exuberant axon growth and exhibit a shortened lifespan. Single cell transcriptome analyses reveal distinct molecular signatures for the navigators. Extending their lifespan prolongs the period of exuberant growth and perturbs axon convergence. Conversely, genetic ablation experiment indicates that, despite postnatal neurogenesis, only the navigators are endowed with the ability to establish a convergent map. The presence and the proper removal of the navigator neurons are both required to establish tight axon convergence into the glomeruli.

overall_design: 10X scRNA-seq was preformed on 4 samples of 4 ages of the olfactory epethelium of CD-1 mice. These ages were postanatal days 0, 3, 7, 21.

first: Yunming

last: Wu

first: Limei

last: Ma

first: Kyle

last: Duyck

first: Carter

last: Long

first: Andrea

last: Moran

first: Hayley

last: Scheerer

first: Jillian

last: Blanck

first: Allison

last: Peak

first: Andrew

last: Box

first: Anoja

last: Perera

first: C

middle: R


title: Conservation and divergence in the asexual development gene regulatory network across a genus of filamentous fungi [ChIP-seq]

status: Public on Jul 24 2018

city: Nashville

first: Antonis

last: Rokas

address: VU Station B 35-1364

department: Biological Sciences

institute: Vanderbilt University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Asexual development is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In the filamentous fungal genus Aspergillus, the production of asexual spores is primarily governed by the BrlA-AbaA-WetA central regulatory cascade. The final step in this cascade, which is controlled by the WetA protein, not only governs cellular development (i.e., the morphological differentiation of spores) but also ensures its coupling with chemical development (i.e., the coordinated production and deposition of diverse secondary metabolites, such as aflatoxins, into spores). While the wetA gene is conserved across the genus Aspergillus, the structure and degree of conservation of the BrlA-AbaA-WetA regulatory cascade and the broader wetA gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type (WT) asexual spores in three representative species spanning the diversity of the genus Aspergillus: the genetic model A. nidulans, the agricultural pest A. flavus, and the human pathogen A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascade’s first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory element, which we term the WetA Response Element (WRE). Interestingly, the WRE is found completely conserved in the non-coding region upstream of the wetA translation start site of many diverse Aspergillus genomes. In contrast, several global transcriptional regulators, most notably those in the velvet complex (veA, velB, and laeA) known to regulate the coupling between asexual development and production of secondary metabolites, show species-specific regulatory patterns. These results suggest that the BrlA-AbaA-WetA cascade’s regulatory role in cellular and chemical development of asexual spores is functionally conserved, but that the WetA-associated GRN has diverged during Aspergillus evolution. This entry is for the ChIP-seq data.

overall_design: Two ChIP experiments were carried out in Aspergillus nidulans to study the WetA protein. In the first experiment, ChIP samples that used a rabbit anti-WetA polyclonal antibody are compared to an input control. In the second experiment, a ChIP sample that used the same rabbit polyclonal anti-WetA antibody and wild type spores was compared to a ChIP sample that used the same antibody but wetA deletion spores. There are four replicates of each sample for the first experiment and there were three replicates of each sample for the second experiment.

first: Ming-Yueh

first: Matthew

middle: E

last: Mead

first: Mi-Kyung

last: Lee

first: Sun-Chang

last: Kim

first: Jae-Hyuk


title: Conservation and divergence in the asexual development gene regulatory network across a genus of filamentous fungi [RNA-seq]

summary: Asexual development is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In the filamentous fungal genus Aspergillus, the production of asexual spores is primarily governed by the BrlA-AbaA-WetA central regulatory cascade. The final step in this cascade, which is controlled by the WetA protein, not only governs cellular development (i.e., the morphological differentiation of spores) but also ensures its coupling with chemical development (i.e., the coordinated production and deposition of diverse secondary metabolites, such as aflatoxins, into spores). While the wetA gene is conserved across the genus Aspergillus, the structure and degree of conservation of the BrlA-AbaA-WetA regulatory cascade and the broader wetA gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type (WT) asexual spores in three representative species spanning the diversity of the genus Aspergillus: the genetic model A. nidulans, the agricultural pest A. flavus, and the human pathogen A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascade’s first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory element, which we term the WetA Response Element (WRE). Interestingly, the WRE is found completely conserved in the non-coding region upstream of the wetA translation start site of many diverse Aspergillus genomes. In contrast, several global transcriptional regulators, most notably those in the velvet complex (veA, velB, and laeA) known to regulate the coupling between asexual development and production of secondary metabolites, show species-specific regulatory patterns. These results suggest that the BrlA-AbaA-WetA cascade’s regulatory role in cellular and chemical development of asexual spores is functionally conserved, but that the WetA-associated GRN has diverged during Aspergillus evolution. This entry is for the RNA-seq data.

sample_organism:
Aspergillus nidulans
Aspergillus fumigatus

overall_design: For the A. fumigatus experiments, 3 technical replicates of each genotype (wild type and deletion mutant) were sequenced. For the A. nidulans experiments, 4 technical replicates of each genotype (wild type and deletion mutant) were sequenced. The A. nidulans RNA samples were paired-end in nature, making 8 total samples.


title: Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth

status: Public on Jul 16 2018

city: Yuseong-gu

first: Yoseb

last: Song

state: Daejeon

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.

overall_design: Transcription abundance and ribosomal profiling analysis of Eubacterium limosum in heterotrophic and autotrophic condition

first: Jongoh

last: Shin

first: Yujin

last: Jeong

first: Sangrak

last: Jin

first: Bong

middle: H

last: Sung

first: Dong

first: Sun

first: Suhyung

last: Cho

first: Byung-Kwan


title: Dynamic Temperature-Sensitive A-to-I RNA editing in the Brain of a Heterothermic Mammal during Hibernation

status: Public on Aug 09 2018

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: RNA editing diversifies genomically encoded information to expand the complexity of the transcriptome. In ectothermic organisms, including Drosophila and Cephalopoda, where body temperature mirrors ambient temperature, decreases in environmental temperature lead to increases in A-to-I RNA editing and cause amino acid recoding events that are thought to be adaptive responses to temperature fluctuations. In contrast, endothermic mammals, including humans and mice, typically maintain a constant body temperature despite environmental changes. Here, A-to-I editing primarily targets repeat elements, rarely results in the recoding of amino acids and plays a critical role in innate immune tolerance. Hibernating ground squirrels provide a unique opportunity to examine RNA editing in a heterothermic mammal whose body temperature varies over 30°C and can be maintained at 5°C for many days during torpor. We profiled the transcriptome in three brain regions at six physiological states to quantify RNA editing and determine whether cold-induced RNA editing modifies the transcriptome as a potential mechanism for neuroprotection at low temperature during hibernation. We identified 5,165 A-to-I editing sites in 1,205 genes with dynamically increased editing after prolonged cold exposure. The majority (99.6%) of the cold-increased editing sites are outside of previously annotated coding regions, 82.7% lie in SINE-derived repeats, and 12 sites are predicted to recode amino acids. Additionally, A-to-I editing frequencies increase with increasing cold exposure demonstrating that ADAR remains active during torpor. Our findings suggest that dynamic A-to-I editing at low body temperature may provide a neuroprotective mechanism to limit aberrant dsRNA accumulation during torpor in the mammalian hibernator.

overall_design: RNA-Seq of brain tissue from 13-lined ground squirrels at multiple homeothermic and heterothermic stages.

middle: A

first: Jay

last: Hesselberth

first: Sandra

last: Martin


title: Conservation and divergence in the asexual development gene regulatory network across a genus of filamentous fungi

first: Antonis

platform_organism:
Aspergillus nidulans
Aspergillus fumigatus


title: RNA-seq of MCF7 cell lines after EPIC1 siRNA knockdown

status: Public on May 03 2018

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

summary: In an integrated analysis of long noncoding RNA (lncRNA) epigenetic alterations in 6475 tumor samples and 781 cancer cell lines, we characterized the epigenetic landscape for 1,006 epigenetically activated and 1,117 epigenetically silenced lncRNAs across 20 cancer types. Combining bioinformatics analyses and functional validation, we identified epigenetically induced lncRNA 1 (EPIC1) as a potential oncogene. EPIC1 is epigenetically activated in 15 cancer types and correlated with poor survival of breast cancer. In EPIC1 hypermethylated cancer cell lines, its expression can be induced by demethylating agent in a time- and dose-dependent manner. Knockdown of EPIC1 inhibits MYC targets expression, leads to cell cycle arrest, inhibits colony formation, and decreases cancer cell growth in vitro and in vivo. Mechanistically, EPIC1 directly interacts with MYC 148-220 aa region through its 5’ end. Overexpression of EPIC1 increases MYC targets expression and promotes cell proliferation, which can be abolished by the MYC knockdown.

overall_design: MCF-7 cells were transfected with 40 nM siRNAs targeting EPIC1 or a control gene luciferase.  After transfection for 72 hours, total RNA was isolated and RNA libraries were prepared for sequencing.

first: Zehua

last: Wang

first: Bo

first: Min

last: Zhang


title: XPO1 inhibition antagonizes MCL via nuclear retention of IkB: Selinexor demonstrates antitumor activities in both ibr-sensitive and ibr-resistant tumor cells

status: Public on Jul 10 2018

city: Cambridge

first: Sabah

last: Kadri

address: 7 Cambridge Center

department: Computational Biology

institute: Broad institute

summary: Inhibition of BCR signaling through BTK inhibitor, ibrutinib, has generated a remarkable response in mantle cell lymphoma (MCL).  However, approximately one-third of the patients do not respond well to the drug and disease relapse on ibrutinib is nearly universal.  Alternative therapeutic strategies aimed to prevent and overcome ibrutinib resistance are needed.  We compared and contrasted the effects of selinexor, a selective inhibitor of nuclear export, with ibrutinib in six MCL cell lines that display differential intrinsic sensitivity to ibrutinib.  We found that selinexor had a broader anti-tumor activity in MCL than ibrutinib.  MCL cell lines resistant to ibrutinib remained sensitive to selinexor.  We showed that selinexor induced apoptosis/cell cycle arrest and XPO-1 knockdown also retarded cell growth.  Further, down-regulation of the NF-B gene signature, as opposed to BCR signature, was a common feature that underlies the response of MCL to both selinexor and ibrutinib. Meanwhile, unaltered NF-B was associated with ibrutinib resistance.  Mechnistically, selinexor induced nuclear retention of IB that was accompanied by the reduction of DNA binding activity of NF-B suggesting that NF-B is trapped in an inhibitory complex. Co-immunoprecipitation confirmed that p65 of NF-B and IB were physically associated.  In primary MCL tumors, we further demonstrated that the number of cells with IB nuclear retention was linearly correlated with the degree of apoptosis.  Our data highlight the role of NF-B pathway in drug response to ibrutinib and selinexor and show the potential of using selinexor to prevent and overcome intrinsic ibrutinib resistance through NF-B inhibition.

overall_design: To capture early changes in RNA transcription, JEKO1 and MAVER were treated for 6 hr with or without the inhibitors (0.4 uM for ibrutinib and 1.5 uM for selinexor) with three biological triplicates. Cells were harvested and subjected to RNA sequencing and diffrences in biological pathway perturvation were analyzed using GSEA.

first: Mei

last: Ming

first: Bingqing

last: Xie

first: Weige

first: Shruti

last: Sharma

first: Natalia

last: Maltsev

first: Pin

last: Lu

first: Y


title: Drosophila melanogaster late third instar larval ovary and gonadal fatbody polyA+ RNA-Seq profiling.

status: Public on Jun 09 2018

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Here we perform transcriptional profiling of late third instar larval ovaries and gonadal fatbody from Drosophila melanogaster w1118 flies. We designed this experiment to investigate the effect of protease treatment on dissected ovaries. We profiled ovaries without protease treatment with some fatbody still attached, fatbody alone dissected from around the ovaries, ovaries cleaned of fatbody using a papain/collagenase cocktail, and ovaries dissociated using a papain/collagenase cocktail. We then constructed polyA+ libraries and performed 50 bp stranded single end RNA-Seq.

overall_design: For each sample type we pooled 10-30 ovaries and collected biological quadruplicates. Sample types include: ovaries with some remaining fatbody (OF), fatbody dissected from around ovaries (FO), ovaries cleaned of fatbody using a papain/collagenase cocktail (OCP), and ovaries dissociated using a papain/collagenase cocktail (ODP). Within a sample type, pools of ovaries were collected at the same time, and different replicates and treatments were collected on different days. Samples were stored at -80ºC until RNA extraction and library preparation. We extracted RNA and constructed libraries simultaneously for all samples in a 96 well plate.

first: Sharvani

last: Mahadevaraju

first: Justin

middle: M

last: Fear


title: Drosophila melanogaster late third instar larval testes and gonadal fatbody RNA-seq profiling

status: Public on Jun 08 2018

summary: In order to study the effect of protease treatment on dissected testes, we performed different strategies of cleaning and dissociation on Drosophila melanogaster w1118 larval testes. We collected testes without protease treatment with fatbody just attached around the gonad, fatbody alone dissected from around the testes, testes without fatbody and testes dissociated by either by Papain or Trypsin and Collagenase cocktail. We prepared poly A+ RNA-Seq libraries and performed transcriptional profiling to generate 50 bp stranded single end reads.

overall_design: We collected late third instar larvae and dissected testes in PBS at at 22°C. Testes were pooled (see Extraction Protocol for details) and treated as one of 5 sample types: testes with fatbody just attached around the gonad (TF), fatbody from around the testes (FT), testes with fatbody removed by briefly treating with a papain cocktail (TCP), testes dissociated with a papain cocktail (TDP), and testes dissociated with a trypsin cocktail (TDT).  All samples were collected in biological quadruplicate. While pools of testes were collected at the same time, different treatments and replicates were collected on different days and stored at -80ºC until RNA extraction and library preparation. RNA extraction and library preparation were performed simultaneously for all samples in a 96 well plate (see Extraction protocol and Library Construction protocol for details).


title: Gene expression profile in porcine buccal pouch mucosal cells during long-term in vitro culture

status: Public on Apr 05 2018

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

summary:
The most experiments about buccal pouch mucosal cells were investigated in mice and hamster. In these studies we have used porcine buccal pouch mucosal cells cultured primarily in vitro to investigate the expression profile of new molecular markers of mucosal wounding, vascularization and proliferation.
In this study, we demonstrated the gene expression profile of long time primary cultured porcine buccal pouch mucosal cells.

overall_design: Mucosal cells were obtained from 9 months old crossbred landrace glits. The cells were harvested 7 days, 15 days and 30 days after beginning of culture and submited to RNA isolation and microarray analisys.

first: Marta

last: Dyszkiewicz-Konwinska

first: Artur

last: Bryja

first: Wiesława

last: Kranc

first: Joanna

last: Budna

first: Piotr

last: Celichowski

first: Maurycy

last: Jankowski

first: Bartosz

last: Kempisty


title: Valproic acid attenuates hyperglycemia induced complement and coagulation cascade gene expression

status: Public on Jan 13 2018

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Diabetes is a multifactorial disorder and epigenetics changes are increasingly appreciated to influence the development of diabetic complications. Chromatin remodeling and histone acetylation are implicated in activation of the inflammatory response. Recently, histone deacetylase (HDAC) inhibitors (HDACi) have proved to reduce the severity of inflammatory diseases. We have previously shown that chromatin alterations regulated by HDACi in HepG2 cells stimulated by hyperglycemia reduced hepatic glucose production. In this study, we examined gene expression patterns using next generation sequencing. We show the pharmacological HDAC inhibitor VPA attenuates hyperglycemia induced gene expression, highlighting the relevance of complement and coagulation cascade. These findings reveal a novel mechanism of VPA protection against hyperglycemia induced hepatic gene expression changes, which might improve the therapeutic approaches for diabetes.

overall_design: RNA-seq was performed to understand gene expression changes in HepG2 cells in response to hyperglycemia and valproic acid. Analyses were performed in triplicate.

first: Marina

middle: B

last: Felisbino

first: Ishant

last: Khurana

first: Camila

last: de Oliveira

first: Maria

last: Mello

first: Assam

last: El-Osta


title: Transcript profiling of sugar beet colonized by Rhizoctonia solani, the crown and root rot pathogen

status: Public on Dec 22 2017

city: Uppsala

first: Louise

middle: Sara

last: Andersson

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary:
Background: Sugar beet is an important root crop, accounting for 30 % of the sugar production worldwide. The long growing season make sugar beets exposed to a range of plant pathogens for longer periods than most other crops. Here, contrasting sugar beet genotypes were used for transcriptome analysis to reveal differential responses and new defense genes to Rhizoctonia solani, a soilborn fungal pathogen.
Results: After curation of primary RNA-sequencing reads, 16,768 genes deriving from 36 samples composed of two susceptible and two resistant sugar beet genotypes, three time-points (0, two and five days post inoculation), each in three replicates were subjected for analysis. Among the elevated 217 transcripts at 2 dpi, three resistance-like genes (Bv4_088600_cumk, Bv8u_204980_frqg, and Bv_44840_iifo) were activated. By employing edgeR package statistics, 660 genes were significantly different (false discovery rate < 0.05) between resistant and susceptible genotypes in their response to R. solani inoculation. A combination of eukaryotic orthologous group assignments and gene ontology enrichment analyses, revealed three Bet v I/Major latex protein homologous genes (Bv7_162510_pymu, Bv7_162520_etow, Bv_27270_xeas) in the resistant genotypes after five days of fungal challenge. Co-expression network analysis of differentially expressed sugar beet genes further identified a MYB46 transcription factor, a plant disease resistance response protein (DRR206) and a flavonoid o-methyltransferase protein. MYB46 has a key function in secondary cell wall formation and exist as a singleton in the sugar beet genome. The genome of R. solani is enriched in cell wall degrading enzyme encoding genes and it is anticipated that they represent important virulence factors. Compared to Arabidopsis thaliana, sugar beet has 2.4-fold more carbohydrate esterases and particularly large numbers (26-fold) of auxiliary activity encoding genes whose function in cell wall biosynthesis is largely unknown.
Conclusions: Based on components identified in this sugar beet transcript data set we conclude that defense responses to R. solani are attributed to a wide range of gene categories but functional information is missing to a large extent.  This calls for careful integration to avoid negative side effects to obtain optimal combinations of these traits in order to reach the long-term goal of improved resistance in sugar beet.

overall_design: Four sugar beet genotypes, three time-points and three biological replicates were sequenced.

first: Johan

last: Fogelqvist

first: Christina

last: Dixelius

first: Jonathan

last: Cohn

last: Varrelmann

first: Thomas

last: Kraft


title: Genetic complementation analysis revealed distinct contributions of the N-terminal tail of H2A.Z to epigenetic regulations

status: Public on Aug 21 2017

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

summary: The histone variant H2A.Z is one of the most evolutionally conserved histone variants. In vertebrates, two isoforms, H2A.Z.1 and H2A.Z.2, are identified and are involved in multiple epigenetic regulations. However, the role of H2A.Z in epigenetic regulations largely remains unknown especially in vertebrate. Previously, we derived tetracycline-inducible H2A.Z isofmrs double knockout (DKO) cells by using DT40 cells. With this cell, we showed that H2A.Z DKO leads to defects in mitotic progression and gene expression. To elucidate the function of H2A.Z further, we established genetic complementation system and confirmed that introducing exogenous H2A.Z complemented phenotypes of H2A.Z DKO cells. Given that acetylation of the N-terminal tail of H2A.Z reportedly contributes to significant roles in H2A.Z functions, we introduced two types of H2A.Z mutants, non-acetylable H2A.Z (5KR-H2A.Z) and chimeric H2A.Z in which its N-terminal tail is replaced with that of canonical H2A (H2A-H2A.Z), into H2A.Z DKO cells. These H2A.Z mutants complemented defects in mitotic progression. However, significant transcriptional dysregulation was observed in H2A.Z DKO cells stably expressing 5KR-H2A.Z and H2A-H2A.Z. These results suggest that the core domain and the N-terminal tail of the vertebrate H2A.Z contribute individually to mitotic progression and transcription regulation, respectively.

overall_design: DT40 wild-type (WT) cells, H2A.Z DKO cells and DKO cells stably expressing exogenous H2A.Z.1 or its mutants (5KR-H2A.Z and H2A-H2A.Z) were cultured in the presence of tetracycline for 72 hours. Total RNAs were extracted with the RNeasy mini kit (QIAGEN) according to the manufacture’s protocol. 100 ng of total RNAs was processed for microarray by using the Agilent expression array (Agilent).

first: Masayuki

last: Kusakabe

first: Ryo

last: Matsuda

first: Tetsuya

last: Hori

first: Hiroyuki

last: Oku

first: Hitoshi

last: Kurumizaka

first: Tatsuo

last: Fukagawa


title: Multisystems analysis of Mycobacterium tuberculosis reveals kinase-dependent remodeling of the pathogen-environment interface

status: Public on Mar 08 2018

first: Robert

last: Husson

state: MA

address: 300 Longwood Ave.

department: Division of Infectious Diseases

institute: Boston Children's Hospital

summary: Tuberculosis is the leading killer among infectious diseases worldwide. Increasing multi-drug resistance has prompted new approaches for tuberculosis drug development, including targeted inhibition of virulence determinants and of signaling cascades that control many downstream pathways. We used a multisystems approach to determine the effects of a potent small molecule inhibitor of the essential Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB. We observed differential phosphorylation of many proteins and extensive changes in gene expression, protein abundance, cell wall lipids and intracellular metabolites. The patterns of these changes indicate regulation by PknA and PknB of several pathways required for cell growth, including ATP synthesis, DNA synthesis and translation. These data also highlight effects on pathways for remodeling of the mycobacterial cell envelope via control of peptidoglycan turnover, lipid content, a SigE-mediated envelope stress response, transmembrane transport systems, and protein secretion systems. Integrated analysis of phosphoproteins, transcripts, proteins, and lipids identified an unexpected pathway whereby threonine phosphorylation of the essential response regulator MtrA decreases its DNA binding activity. Inhibition of this phosphorylation is linked to decreased expression of genes for peptidoglycan turnover, and of genes for mycolyl transferases, with concomitant changes in mycolates and glycolipids in the cell envelope. These findings reveal novel roles for PknA and PknB in regulating multiple essential cell functions and confirm these kinases as potentially valuable targets for new anti-tuberculosis drugs. In addition, these linked multisystems data provide a valuable resource for future targeted investigations into the pathways regulated by these kinases in the M. tuberculosis cell.

overall_design: RNA-seq for comparison of transcriptomic effects of a chemical inhibitor of Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB, to an inactive control compound. Two experiments: 1) a time course comparing active inhibitor (T4) vs. control compound (T10) in wild type M. tuberculosis H37Rv, and 2) comparison of treatment with T4 vs. T10 at 48 hours in pknD and pknL mutant strains derived from M. tuberculosis H37Rv.

first: Xavier

last: Carette

first: John

last: Platig

first: David

last: Young

first: Michaela

last: Helmel

first: Albert

middle: T

first: Zhe

last: Wang

first: Lakshmi-Prasad

last: Potluri

first: Cameron

last: Moody

first: Jumei

last: Zeng

first: Sladjana

last: Prisic

first: Joseph

last: Paulson

first: Ashoka

last: Madduri

first: Jacob

last: Mayfield

first: Christopher

last: Locher

first: Tiansheng

last: Quackenbush

first: Kyu

middle: Y

last: Rhee

first: Hanno

last: Steen


title: Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

status: Public on Mar 08 2017

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: Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. While the majority of genes (80-85%) are not differentially expressed across growth phases, other genes exhibited growth phase-dependent expression patterns. Gene expression in outgrowth phase was strongly influenced by the length of the preceding stationary phase. After 57 h in stationary phase a much larger number of genes was induced after dilution, 35% of which are known to be controlled by the alternative sigma factors RpoHI and/or RpoHII. Growth experiments with mutant strains assign an important function in stationary phase and especially in outgrowth to these sigma factors and genes for both sigma factors showed growth phase-dependent expression. Besides the known consensus sequences for the RpoH sigma factors, some new consensus sequences were identified in subsets of growth phase-dependent genes suggesting regulation by common transcription factors.

overall_design: 4 phases

first: Bernhard

last: Remes

first: Tom

last: Rische-Grahl

middle: U

first: Verena

last: Peuser

first: Gabriele

last: Klug


title: Study of ribosome dynamics after eIF5A depletion in budding yeast

status: Public on May 16 2017

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: eIF5A is an essential translation elongation factor present  in all eukaryotes, and the only known protein to follow a post-translational modification called hypusination. Here, we performed a wide analysis of ribosome dynamics in S. cerevisiae eIF5A depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441). This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Since eIF5A is an essential protein in yeast, we used two eIF5A temperature-sensitive strains containing a single Pro83 to Ser mutation (tif51A-1) and double Cys39 to Tyr and Gly118 to Asp mutations (tif51A-3) in the highly expressed gene TIF51A (HYP2) that encodes eIF5A protein (Li et al. 2011 PMID: 24923804).

overall_design: For our 5PSeq experiments we incubated the wild-type and the two eIF5A mutant cells at 37°C for 4 hours, conditions in which there is almost no drop in cell viability for both mutants but it can be observed an important reduction in eIF5A protein. We performed three independent 5PSeq experiments with each of the strains tif51A-1 (hyp2-1) and tif51A-3 (hyp2-3) and compared with two independent experiments with the isogenic wild-type BY4741 strain.

first: Paula

last: Alepuz


title: Galectin-3 Induces a Pro-degradative/inflammatory Gene Signature in Human Chondrocytes, Teaming Up with Galectin-1 in Osteoarthritis Pathogenesis

status: Public on Feb 09 2017

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: Inflammatory chemo- and cytokines and matrix-degrading proteases underlie the progression of osteoarthritis (OA). Aiming to define upstream regulators for these disease markers, we pursued initial evidence for an upregulation of members of the adhesion/growth-regulatory galectin family. Immunohistochemical localization of galectin-3 (Gal-3) in sections of human cartilage with increasing levels of degeneration revealed a linear correlation reaching a chondrocyte positivity of 60%. Presence in situ was cytoplasmic, in OA chondrocyte cultures the lectin was secreted and binding of Gal-3 yielded lactose-inhibitable surface staining. Exposure of cells to the lectin led to enhanced gene expression and secretion of functional disease markers. Genome-wide transcriptomic analysis broadened this insight to reveal a pro-degradative/inflammatory gene signature under the control of NF-κB. Fittingly, targeting this route of activation by inhibitors impaired the unfavourable response to Gal-3 binding, as also seen by shortening the lectin’s collagen-like repeat region. Gal-3’s activation profile overlaps with that of homodimeric galectin-1 (Gal-1) and also has distinctive (supplementing) features. Tested at subsaturating concentrations in a mixture, we found cooperation between the two galectins, apparently able to team up as driving forces in OA pathogenesis. In summary, our results suggest that a network of endogenous lectins acts as upstream master regulator in OA.

overall_design: For microarray experiments, osteoarthritic chondrocytes were isolated from four female patients (59-68 years). Following starvation, cells were incubated in the presence of 50 µg/ml recombinant Galectin-3 for 24 h. For each donor population, untreated cells were included as control. In total, 8 samples were analyzed.

first: Daniela

last: Weinmann

first: Karin

last: Schlangen

first: Sabine

last: André

first: Sebastian

last: Schmidt

first: Sonja

last: Walzer

first: Bernd

last: Kubista

first: Reinhard

last: Windhager

first: Stefan

last: Toegel

first: Hans-Joachim

last: Gabius


title: Pronounced Strain-Specific Chemosensory Receptor Gene Expression in the Mouse Vomeronasal Organ

status: Public on Dec 05 2017

first: Congrong

last: Yu

summary: Our study reports strain specific expression and abensce of sexual dimorphic expression in mouse vomeronasal epithelial tissue

overall_design: High throughput sequencing of 32 mice Vomeronasal epithelial tissues with eight samples per strain C57/B6, 129SVEV, SJL, SWR and 4 samples per male and female within each strain

first: Kyle

last: Duyck

first: Vasha

last: DuTell

first: Limei

last: Ma

first: Ariel

last: Paulson

first: C


title: Integrated transcriptomics and metabolomics profiling delineates early molecular correlates of immunity to herpes zoster vaccination in humans

status: Public on Aug 18 2017

city: Atlanta

first: Thomas

last: Hagan

state: GA

address: 954 Gatewood Road

department: Emory Vaccine Center

institute: Emory University

summary: The goal of this study is to characterize the human immune responses to the live attenuated Herpes zoster vaccine Zostavax, to understand the molecular and cellular mechanisms that lead to antibody production and T cell induction, and to understand the difference between young and elderly healthy adults. The overall data collection included antigen specific assays, flow cytometric profiling of innate and adaptive cell populations, measurement of serum cytokines, and transcriptomic and metabolomics signatures. Zostavax induced robust antigen-specific antibody responses, and significant T cell responses. A number of gene pathways were upregulated after vaccination. Using our previously developed blood transcription modules, we also identified transcriptomic correlates to antibody response. Furthermore, this study revealed strong association between PBMC transcriptomics and plasma metabolomics. Integrative analysis of orthogonal datasets from metabolomics, transcriptomic and immune profiling facilitated a temporal reconstruction of Zostavax induced biological networks culminating in antibody responses , and the delineation of novel molecular correlates of vaccine immunity.

overall_design: A longitudinal study of Zostavax® vaccination was conducted on healthy adults, between August 2011 and November 2013.  Seventy-seven people were enrolled at Atlanta, Georgia and Denver, Colorado, USA. The cohort contained two age groups: 33 subjects considered to be young adults between the age of 25~40, and 44 subjects as elderly between the age of 60~79 years . The subject’s blood was collected at baseline, days 1, 3, 7, 14, 28, 90 and 180 post-vaccination. Throughout the course of study, we measured Zostavax specific antibody titers, B and T cell populations, as well as various cell populations involved in innate immunity, including dendritic cell (DC) and monocyte subsets. Cytokines were assayed by a 27-plex Luminex platform. Varicella zoster viremia was measured by real-time PCR and nested PCR reactions. We profiled transcriptomics of PBMCs, and high-resolution mass spectrometers to obtain metabolomics of plasma from subjects at baseline and on days 1-7 post-vaccination.

first: Shuzhao

last: Li

first: Helder

last: Nakaya

first: Bali

last: Pulendran


title: An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype

city: Taipei

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary: Although clinical features, cytogenetics, and mutations are widely used to predict prognosis in patients with acute myeloid leukemia (AML), further refinement of risk stratification is necessary for optimal treatment, especially in cytogenetically normal (CN) patients. We sought to generate a simple gene expression signature as a predictor of clinical outcome through analyzing the mRNA arrays of de novo CN-AML patients. Among 43 treatment response-related genes, expression of 11 genes was significantly associated with overall survival (OS) in univariate Cox regression analysis in 104 patients who received standard intensive chemotherapy. We integrated the z-transformed expression levels of these 11 genes to generate a risk scoring system. Higher risk scores were significantly associated with shorter OS (median 17.0 months vs. not reached, P<0.001) in ours and 3 other validation cohorts. In conclusion, we developed a simple mRNA expression signature for prognostication in CN-AML patients. This prognostic biomarker will help refine the treatment strategies for this group of patients.

overall_design: Cryopreserved bone marrow cells were obtained from 104 de novo AML patients with normal karyotype. Each sample was analyzed with Illumina HumanHT-12 V4.0 expression beadchip.

first: Hwei-Fang

last: Tien


title: Small RNA interactome revealed through crosslinking of the degradosome

status: Public on Feb 14 2017

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. To identify functionally important sRNA-target RNA interactions we applied crosslinking and sequencing of hybrids (CLASH) to the core degradosome component RNase E in EHEC. RNase E was shown to bind to many classes of RNA, confirming the wide distribution of degradosome targets. These included several hundred sRNA-mRNA duplexes, and the distribution of non-templated oligo(A) tails indicated that the sRNA target RNase E-mediated cleavage at these interaction sites. Functional repression of target mRNAs was confirmed for the core sRNA RyhB, and the pathogenicity-associated sRNA Esr41. In the case of Esr41, three confirmed target mRNAs participate in iron accumulation and the ∆esr41 strain showed increased growth under conditions of iron limitation. We conclude that CLASH can be used to identify functional targets for bacterial sRNAs.

overall_design: The endoribonuclease, RNase E, was affiity tagged with a His-FLAG tag. Cultures were UV irradiated with 1800 mJ of UV-C and harvested. RNA-protein complexes were purified using M2-anti-FLAG resin and eluted but incubating with TEV protease to release the FLAG tag. RNAs were trimmed using RNase T1/A and bound to Ni-NTA resin under denaturing conditions. Complexes were washed, 5' and 3' ends phophorylated and dephophorylated respectively and RNA linkers ligated. Complexes were eluted and cDNA libraries prepared from recovered RNAs. cDNA were PCR amplified and gel extracted before Illumina HiSeq2500 sequencing. Sequence files were analysed using the hyb package and pyCRAC software.

middle: J

first: Grzegorz

last: Kudla

first: David

middle: P

last: Gally

last: Tollervey


title: Lung gene expression

status: Public on Aug 01 2016

city: Boston

first: Romy

last: Christmann

state: MASSACHUSETTS

address: 715 Albany Street E5

institute: Boston University School of Medicine

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Expression of miRNA from lung tissue from Systemic Sclerosis patients with interstitial lung disease (SSc-ILD)  and healthy controls.

summary:
Objective: MicroRNAs (miRNAs) control key elements of mRNA stability and likely contribute to the dysregulated lung gene expression observed in systemic sclerosis associated interstitial lung disease (SSc-ILD). We analyzed the miRNA gene expression of tissue and cells from SSc-ILD patients. A chronic lung fibrotic murine model was used.
Methods: RNA was isolated from lung tissue of 12 SSc-ILD patients and 5 control lungs. High-resolution computed tomography (HRCT) was performed at baseline and 2-3 years after treatment. Lung fibroblasts and PBMCs were isolated from healthy controls and SSc-ILD patients. miRNA and mRNA were analyzed by microarray, quantitative polymerase chain reaction, and/or Nanostring; pathway analysis was performed by DIANA-miRPath v2.0 software. Wild-type and miR-155 deficient (miR-155ko) mice were exposed to bleomycin.
Results: Lung miRNA microarray data distinguished patients with SSc-ILD from healthy controls with 185 miRNA differentially expressed (q<0.25). DIANA-miRPath revealed 57 KEGGs pathways related to the most dysregulated miRNAs. miR-155 and miR-143 were strongly correlated with progression of the HRCT score. Lung fibroblasts showed only mild expression of miR-155/miR-21 after several stimuli. miR-155 PBMC expression strongly correlated with lung function tests in SSc-ILD. miR-155ko mice developed milder lung fibrosis,  survived longer, and showed a weaker lung induction of several genes after bleomycin exposure compared to wild-type mice.
Conclusions: miRNAs are dysregulated in lungs and PBMCs of SSc-ILD patients. Based on mRNA-miRNA interaction analysis and pathway tools, miRNAs may play a role in the progression of the disease. Our findings suggest that targeting miR-155 might provide a novel therapeutic strategy for SSc-ILD.

overall_design: Lung biopsies taken from open lung biopsy from SSc-ILD patients (n=15 samples) and from cancer free control patients (n=5) during ressection of the lung tumor.

first: Percival

last: Sampaio-Barros


title: mRNA expression profile in murine bone marrow-derived macrophages that were isolated from calpain-6 wild-type and deficient mice

status: Public on Jun 29 2016

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

department: Biochemistry

institute: Showa University School of Medicine

summary: Transcriptional profiling of calpain-6-deficient murine bone marrow-derived macrophages comparing with calpain-6 wild-type macrophages. Total RNA was extracted from the pooled cells.

overall_design: Two-condition experiment, wild-type macrophages vs. calpain-6-deficiennt macrophages. The cells were derived from four mice, and were pooled for analysis.


title: Down-regulation of miR-200a-3p, targeting C-terminal binding protein-2 (CtBP2), is involved in hypoproduction of IL-2 in SLE-derived T cells

status: Public on Sep 23 2016

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

summary: Systemic lupus erythematosus (SLE) damages multiple organs by producing various autoantibodies. Insufficient interleukin-2 (IL-2) production causes decreased regulatory T cells and permits expansion of autoreactive T cells in the development of SLE. We here show that decreased miR-200a-3p causes IL-2 hypoproduction through directly recruiting ZEB1 or ZEB2 and CtBP2 (ZEB1/ZEB2-CtBP2) complex in SLE T cells. First, we performed RNA sequencing with Illumina Hiseq to obtain the candidate miRNAs and mRNAs involved in the pathogenesis of SLE. We found that miR-200a-3p was significantly downregulated, while its putative targets, ZEB2 and CtBP2 were upregulated in CD4+ T cells in MRL/lpr lupus model mice compared with those of C57BL/6J control mice. ZEB1 and ZEB2 compose ZEB family and suppress various genes including IL-2 by recruiting CtBP2. IL-2 plays a critical role in immune tolerance and IL-2 defect has been recognized in SLE pathogenesis. Therefore, we hypothesized that decreased miR-200a-3p cause IL-2 defect through ZEB1/ZEB2-CtBP2 complex in SLE CD4+T cells. Overexpression of miR-200a-3p induced IL-2 production though downregulating ZEB1, ZEB2 and CtBP2 in EL4 cell lines. We further revealed that miR-200a-3p promote IL-2 expression by reducing the bindings of suppressive ZEB1/ZEB2-CtBP2 complex on NRE-A of IL-2 promoter in SLE murine T cells. Interestingly, ZEB1/ZEB2-CtBP2 complex on NRE-A (a negative regulatory element) were significantly upregulated after phorbol-12-myristate-13-acetate and ionomycin (PMA/Iono) stimulation in lupus T cells. Our findings provide a new insight for the epigenetic regulation of IL-2 defect in SLE.

overall_design: To identify the new candidate miRNAs involved in the pathogenesis of SLE, we performed Illumina Hiseq to analyze the expression of miRNA and mRNA of CD4+ T cell isolated from spleens in MRL/lpr-Tnfrsf6lpr  (MRL) mice and C57BL/6J (B6) mice. Both mice are female, 16 weeks old. For Illumina analysis, we used one mouse of MRL mice and two mice of B6 mice.

first: Eri

last: Katsuyama

first: Katsue

middle: S

last: Watanabe


title: Identification of loci and signaling pathways associated with ITP using pooling genome-wide association study in Han Chinese

status: Public on Jan 12 2016

city: Nanchang

first: Yanmei

last: Xu

state: Jiangxi

address: No.1 Min De Road

department: Department of Clinical Laboratory

institute: the Second Affiliated Hospital of Nanchang University

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

summary: Immune thrombocytopenia (ITP) is an autoimmnue bleeding disorder characterized by low platelet count. To identify susceptibility loci for disease progression of ITP, we performed this genome-wide association study using DNA pools of 200 ITP cases and 200 controsl in Han Chinese. Performing GWAS on pools of DNA samples is an effective strategy to reduce the costs of studies and pooling DNA has been shown to be an efficient method to select candidate susceptibility loci for follow-up by individual genotyping.

overall_design: Illumina HumanOmniZhongHua-8 v1.0 BeadChip array were performed for DNA pools, which were constructed by pooling 50ng DNA from each participant. Two independent pools were created: case group was 200 sporadic ITP in Han Chinese, control group was 200 healthy subjects which age-, sex, race-matched with cases. Equimolar amounts of each DNA sample were then added to either the case or control pool. Two chips (each pool was replicated in triplicate) were finished according to the manufacturer's instruction.

first: Xiaozhong

last: Wang

first: Libin

last: Deng

first: Jing

first: Wentao

last: Yang

first: Bo

last: Huang

last: Liu

last: Zhang


title: Genome-wide chromosomal conformation elucidates regulatory relationships in human brain development and disease

status: Public on Oct 20 2016

city: Chapel Hill

first: Hyejung

last: Won

state: North Carolina

address: 116 Manning Dr.

department: Genetics

institute: UNC

summary: The demonstration that chromatin exhibits a complex 3 dimensional organization, whereby short and long distance physical interactions correspond to complex gene regulatory processes has opened a new window on understanding the functional organization of the human genome. Recently, chromatin remodeling has also been causally implicated in several neurodevelopmental disorders, including autism and schizophrenia. However, it remains unclear whether knowledge of chromosome organization in a tissue specific manner might inform our understanding of gene regulation in brain development or disease. Here we determined the genome-wide landscape of chromosome conformation during early human cortical development by performing Hi-C analysis in the mitotically active and post mitotic laminae of human fetal brain. We integrate Hi-C data with transcriptomic and epigenomic data and utilize chromosome contact information to delineate physical gene-gene regulatory interactions for non-coding regulatory elements. We show how these data permit large-scale functional annotation of non-coding variants identified in schizophrenia GWAS and of human specific enhancers. These data provide a rubric that illustrates the power of tissue-specific annotation of non-coding regulatory elements, as well as novel insights into the pathogenic mechanisms of neurodevelopmental disorders and the evolution of higher cognition.

overall_design:
Hi-C data of fetal cortical anlage from three individuals. SRA: SRP066745, BioProject ID: PRJNA304334, dbGaP: phs001190.v1.p1.

*Raw reads are available through dbGaP (phs001190.v1.p1).*

first: Daniel

last: Geschwind


title: NextGen Consortium: GENESiPS Study: Identifying the Gene Networks of Insulin Resistance

status: Public on Dec 28 2016

city: Stanford

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

summary:
RNA-seq transcriptome profiling of human induced pluripotent stem cells to characterize gene expression variation across individuals and within multiple iPSC lines from the same individual
The purpose of this study was to analyze the potential differential responses to HMGCR inhibition of insulin sensitive versus insulin resistant human iPSC lines.

overall_design:
Donor erythroblast or activated T-cells were reprogrammed with a Sendai viral vector coding for reprogramming factors.  IPSC lines were propagated for ~9 passages before RNA sequencing

**Please note that addtional sample records (GSM5100626- GSM5100649) have been included on Feb 22, 2021;
Human iPSC lines are incubated in the presenceof Atorvastatin and gene expression changes are measured through RNAseq.

first: Ivan

last: Carcamo-Orive

first: Josh

first: Marc

last: Henrion


title: Time Course of Adults Vaccinated with Influenza TIV Vaccine during 2011/12 Flu Season

status: Public on Jan 05 2016

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans.
Whether such signatures are similar across multiple seasons, and in diverse populations is unknown. We applied systems approaches to study immune responses in young and, elderly subjects vaccinated with the seasonal influenza vaccine across 5 consecutive seasons.

overall_design: During the 2011 Influenza season, healthy adults were vaccinated with TIV, and blood samples isolated at days 0, 3, 7 post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.

first: H

middle: I

first: B

last: Pulendran


title: Epigenetic regulation in the elderly over time

status: Public on Sep 02 2016

city: Denmark

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

type: Methylation profiling by genome tiling array

summary: DNA methylation levels in whole blood measured over a ten years follow up in an elderly birth cohort of 86 samples

overall_design:
For each sample, whole blood was drawn in year 1997 and in year 2007
Follow-up design: Same participant was measured over time in 1997 and 2007

first: Lene

last: Christiansen


title: Time Course of Adults Vaccinated with Influenza TIV Vaccine during 2010/11 Flu Season (FluCenter cohort)

status: Public on Dec 16 2015

overall_design: During the 2010 Influenza season, healthy adults were vaccinated with TIV, and blood samples isolated at days 0, 3, 7 post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.


title: Time Course of Adults Vaccinated with Influenza TIV Vaccine during 2010/11 Flu Season (HIPC cohort)

overall_design: During the 2010 Influenza season, healthy adults were vaccinated with TIV, and blood samples isolated at days 0, 1, 3, 7, 14 post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.


title: Galectin-1 couples glycobiology to inflammation in osteoarthritis through the activation of an NF-κB-regulated gene network

status: Public on Mar 01 2016

first: Markus

last: Jeitler

summary: Osteoarthritis is a degenerative joint disease that ranks among the leading causes of pain, adult disability, shortening of working life, and socioeconomic costs worldwide. The mechanisms underlying osteoarthritis pathogenesis are yet to be fully elucidated, thus limiting current disease management and treatment. Galectin-1 is an endogenous carbohydrate-binding protein central to adhesion via glycan-bridging, glycoconjugate-mediated signaling, cell proliferation, differentiation, apoptosis, cancers, and host-pathogen interactions. The chondrocyte glycophenotype, which can act as a system of counter-receptors for galectin binding, is compromised in osteoarthritis. We here investigated Galectin-1 and associated gene network's role in human osteoarthritis pathogenesis. Immunohistochemical analysis showed that Galectin-1 associates with osteoarthritic cartilage and subchondral bone histopathology and severity (p<0.0001, n=29 patients). Glycan-dependent Galectin-1 binding to osteoarthritic chondrocytes' cell surface led to marked upregulation of matrix metalloproteinases and activation of NF-κB. Biochemical, molecular and genome-wide analyses showed that Galectin-1 strongly activates a large inflammatory gene network (p<10-16). Bioinformatic analyses of gene promoters up-regulated by Galectin-1 unveiled an overwhelming NF-κB signaling signature. Inhibition of any of several components of the NF-κB pathway using dedicated inhibitors led to dose-dependent impairment of Galectin-1-mediated transcriptional activation. This study identifies for the first time Galectin-1 as an activator of clinically relevant inflammatory-response genes co-regulated by NF-κB. Since inflammation is critical to cartilage degeneration in osteoarthritis, this report is also first to put glycobiology at the center-stage of osteoarthritic cartilage degeneration. Finally, this is the first report to uncover a Galectin-1 gene signature and associated gene network in any biological setting or species.

overall_design: For microarray experiments, osteoarthritic chondrocytes were isolated from five male patients (47-78 years). Following starvation, cells were incubated in the presence of 50 µg/ml recombinant Galectin-1 for 24 h. For each donor population, untreated cells were included as control. In total, 10 samples were analyzed.

first: Stefan

last: Toegel

first: Daniela

last: Bieder

first: Sabine

last: André

first: Sona

last: Walzer

first: Martin

last: Bilban

first: Catharina

last: Chiari

first: Reinhard

last: Windhager

first: Christoph

last: Krall

first: Idriss

last: Bennani-Baiti

first: Hans-Joachim

last: Gabius


title: Identification of genes involved in the anti-inflammatory effects of berberine in DNP-activated mouse MC/9 mast cells

status: Public on Dec 22 2015

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Atopic dermatitis is a common chronic inflammatory skin disease characterized by infiltration of inflammatory cells, extensive pruritus and a clinical course of symptomatic flares and remissions. Berberine (BER), a naturally occurring isoquinoline alkaloid, has many pharmacological effects including inhibition of protein synthesis, cell cycle arrest, and anti-inflammatory activities. However, a detailed molecular mechanism underling the anti-inflammatory action of BER in inflammatory cells is unclear.
Here, to identify genes involved in the anti-inflammatory effects of BER in DNP-activated mouse MC/9 mast cells, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: Mouse MC/9 mast cells were treated with BER (10 microM), DNP (anti-DNP IgE, Sigma; 500 microg/ml) or a combination of BER and DNP. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Mouse Genome 430 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Yoko

last: Yoshihisa


title: Time Course of Adults Vaccinated with Influenza TIV Vaccine during 2009/10 Flu Season

first: Helder

last: Nakaya

overall_design: During the 2009 Influenza season, healthy adults were vaccinated with TIV, and blood samples isolated at days 0, 3, 7 post-vaccination. Microarrays were performed using total RNA extracted from the peripheral blood mononuclear cells of vaccinees.

first: H


title: Transcriptomic profiling of human placental trophoblasts in response to Enterococcus faecalis invasion

status: Public on Dec 03 2015

first: qianglai

last: tan

address: 235 Nanjing Donglu

institute: State Key Laboratory of Food Science and Technology

summary: Analysis of the molecular mechanisms of the interaction between E. faecalis and host placental barrier at gene expression level. The hypothesis tested in the present study was that E. faecalis influence the ranscriptomic profiling of human placental trophoblasts. Results provide important information of the response of human placental trophoblasts to E. faecalis, such as Several representative terms of the differentially expressed genes are involved in apoptosis, stress and stimulus response, placenta and embryonic development, immune response, and cell adhesion.

overall_design: Total RNA obtained from human placental trophoblasts subjected to 4 hours in vitro E. faecalis compared to untreated control.

first: Qianglai

first: Hua

last: Wei


title: Time Course of Adults Vaccinated with Influenza TIV Vaccine 2009-2012


title: Comparison of TLR4-stimulated mouse microglia from wildtype and CD14ko strains

status: Public on Oct 23 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The analysis reveals the importance of CD14 in microglial responses to pathogen- and damage-associated  molecular patterns, based on stimulations with lipopolysaccharide (LPS) and fiibronectin (FN). The data show a dose- and agonist-dependent involvement of CD14. Lack of CD14 impairs responses to low-dose challenegs with LPS, whereas high-dose challenegs are affected to a much lesser degree. For FN, CD14 deficiency causes a major impairment of the response capacity.

overall_design: Mouse microglia from wt and cd14-/- strains were stimulated with 0.1 and 10 ng/ml of LPS or with 100 µg/ml of mouse FN for 3 h. Untreated cells served as the controls. Each condition was based on three independent cell preparations as wells a processing.

first: Hana

last: Janova

first: Uwe-Karsten

last: Hanisch

last: Salinas-Riester


title: Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways

status: Public on Oct 01 2015

city: Bethesda

first: Shaad

middle: M.

last: Ahmad

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

institute: National Heart Lung and Blood Institute

summary: Cardiogenesis involves multiple biological processes acting in concert during development, a coordination achieved by the regulation of diverse cardiac genes by a finite set of transcription factors (TFs).  Previous work from our laboratory identified the roles of two Forkhead TFs, Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu) in governing cardiac progenitor cell divisions by regulating Polo kinase activity.  These TFs were also implicated in the regulation of numerous other cardiac genes.  Here we show that these two Forkhead TFs play an additional and mutually redundant role in specifying the cardiac mesoderm (CM):  eliminating the functions of both CHES-1-like and jumu in the same embryo results in defective hearts with missing hemisegments.  Our observations indicate that this process is mediated by the Forkhead TFs regulating the fibroblast growth factor receptor Heartless (Htl) and the Wnt receptor Frizzled (Fz), both previously known to function in cardiac progenitor specification:  CHES-1-like and jumu exhibit synergistic genetic interactions with htl and fz in CM specification, thereby implying function through the same genetic pathways, and transcriptionally activate the expression of both receptor-encoding genes.  Furthermore, ectopic overexpression of either htl or fz in the mesoderm partially rescues the defective CM specification phenotype seen in embryos doubly homozygous for mutations in jumu and CHES-1-like.  Together, these data emphasize the functional redundancy that leads to robustness in the cardiac progenitor specification process mediated by Forkhead TFs regulating the expression of signaling pathway receptors, and illustrate the pleiotropic functions of this class of TFs in different aspects of cardiogenesis.

overall_design:
GFP-positive cells were profiled from Stage 11-early Stage 12 Drosophila embryos of the following three genotypes:
Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP
twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157
twi-GAL4 UAS-2EGFP

first: Pritha

last: Bhattacharyya

first: Neal

last: Jeffries

first: Stephen

last: Gisselbrecht

first: Alan

last: Michelson


title: Gene expression data from acetaminophen-induced toxicity in human hepatic in vitro systems and clinical liver samples

status: Public on Nov 04 2015

city: Brussels

first: Robim

last: Rodrigues

address: Laarbeeklaan 103

department: IVTD

country: Belgium

institute: Vrije Universiteit Brussel

summary:
In this study we conducted transcriptomics analyses of: (i) liver samples from patients suffering from acetaminophen-induced acute liver failure (n=3) and from healthy livers (n=2) and (ii) hepatic cell systems exposed to acetaminophen, including their respective vehicle controls. The investigated in vitro systems are: HepaRG cells, HepG2 cells and a novel human skinpostnatal stem cell-derived model i.e. human skin-precursors-derived hepatocyte-like cells (hSKP-HPC).
Clinical samples were obtained after surgical removal of the explant liver of patients diagnosed with ALF due to acetaminophen intoxication and treated by orthotopic liver transplantation (n=3).  Samples from healthy livers were obtained from individuals deceased from brain damage (n=2).

overall_design: Different samples of hSKP, HepG2 and HepaRG were obtained from the same cell batch of each cell system. All cells were exposed for 24 hours to their corresponding sub cytotoxic concentrations (IC10): IC10(hSKP-HPC)=18mM; IC10(HepaRG)=13mM; IC10(HepG2)=2mM. Experiments were conducted in triplicate.

first: Olivier

last: Govaere

first: Tania

last: Roskams

first: Tamara

last: Vanhaecke

first: Vera

last: Rogiers

first: Joery

last: De Kock


title: Genome-wide mapping of Zea maize TSSs

city: East Lansing

first: Erich

last: Grotewold

state: Michigan

address: 603 Wilson Rd

department: Department of Biochemistry and Molecular Biology

institute: Michigan State University

summary:
Genome-wide mapping of the TSS in root and shoot from two maize lines B73 and A632
Genome-wide locations and dynamics of maize core promoters obtained from the experimental establishment of the TSSs coordinates. The work derived from this data it is the first genome-wide atlas of core promoters and its dynamic generated for an important crop species.

overall_design: Four samples each one with biological replicates. Comparisons were done between B73 and A632 for each of the tissues and between tissues for each line

first: Maria

middle: K

last: Mejia-Guerra

first: Wei

last: Li

first: Narmer

middle: F

last: Galeano

first: Mabel

last: Vidal

first: Jonh

last: Gray

first: Andrea

last: Doseff


title: Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [Affymetrix]

status: Public on Jul 15 2015

city: Sangareddy

first: Ashish

last: Misra

state: Telangana

address: Kandi

department: Biotechnology

country: India

institute: Indian Institute of Technology Hyderabad

summary: Transcriptome analysis of samples from Non-silencing, RBFOX2 and CPSF3 knockdown cells. Our analysis shows the role of CPSF-SYMPK in regulation of global alternative splicing.

overall_design: We analyzed 9 samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Three techinical replicates were performed.

first: Jianhong

last: Ou

first: Lihua

last: Zhu

first: Michael

middle: R

last: Green


title: The gene expression of numerous SLC transporters is altered in the immortalized hypothalamic cell line N25/2 following amino acid starvation

status: Public on Sep 30 2015

city: Uppsala

first: Robert

last: Fredriksson

address: Husargatan 3

department: Neurosceince

institute: Uppsala University

summary:
The immortalized mouse hypothalamic cell line N25/2 was treated with medium containing amino acids or medium lacking all amino acids for 1, 2, 3, 5 or 16 hours, and the gene expression was measured for 28270 genes using microarray.
Numerous transporters from the SLC family were transcriptionally regulated in response to changed amino acid levels.

overall_design: Singlet's were run in in each treatment group (controls vs. starved cells) for all times (1, 2, 3 and 16 hours), except for 5 hours with four replicates in each treatment group.

first: Sofie

middle: V

last: Hellsten


title: Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [iCLIP-Seq]

summary: iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies.

first: L

first: M


title: Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

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

overall_design: Refer to individual Series


title: Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [RNA-Seq]

summary: RNA-seq analysis of samples from Non-silencing, RBFOX2 and CPSF2 knockdown cells

overall_design: We analyzed 6 samples using the Illumina HiSeq 2000. Sequence data was processed by DexSeq. Two biological replicates were performed for Non-silencing, RBFOX2 and CPSF2 knockdown cells


title: Renal systems biology of patients with systemic inflammatory response syndrome

status: Public on Jul 01 2015

city: Albuquerque

first: Raymond

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

summary: A systems biology approach was used to comprehensively examine the impact of renal disease and hemodialysis (HD) on host response during critical illness. We examined the metabolome, proteome, and transcriptome of 150 patients with critical illness, stratified by renal function. Plasma metabolite values showed greater changes as renal function declined, with the greatest derangements in patients receiving chronic HD. Specifically, 6 uremic retention molecules, 17 other protein catabolites, 7 modified nucleosides, and 7 pentose phosphate sugars increased as renal function declined, consistent with decreased excretion or increased catabolism of amino acids and ribonucleotides. Similarly, the proteome showed increased levels of low-molecular weight proteins and acute phase reactants. The transcriptome revealed a broad-based decrease in mRNA levels among HD patients. Systems integration revealed an unrecognized association between plasma RNASE1 and several RNA catabolites and modified nucleosides. Further, allantoin, N1-methyl-4-pyridone-3-carboxamide, and n-acetylaspartate showed inverse correlations with the majority of significantly down-regulated genes. In conclusion, renal function broadly affected the plasma metabolome, proteome, and peripheral blood transcriptome during critical illness. These changes were not effectively mitigated by hemodialysis. These studies suggest several novel mechanisms whereby renal dysfunction contributes to critical illness.

overall_design: We sequenced peripheral blood RNA of 133 representative subjects with systemic inflammatory response syndrome that had Acute Kidney Injury (AKI) or Hemodialysis (HD). No injury (AKI0; n= 58); AKI Stage 1 (AKI1; n= 36); AKI stage 2 and 3 (AKI23; n= 17); HD (N=22).

first: Neil

middle: A

last: Miller


title: Bisulfite-seq from Neurospora crassa a wild type (WT) strain grown in minimum medium, a dim-3 strain grown in minimum medium, and a dim-3 strain grown with supplemented histidine

status: Public on Mar 22 2015

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

type: Methylation profiling by high throughput sequencing

summary: We report the placement of cytosine methylation from the filamentous fungus Neurospora crassa in wild type and dim-3 strains by bisulfite-sequencing.  Compared to a wild type strain, the dim-3 strain has a global reduction in cytosine methylation, and this reduction in cytosine methylation is exacerbated by the supplementation of histidine to the growth medium.  This global reduction in cytosine methylation results from a causative mutation in importin alpha (NUP-6), a component of the nuclear transport machinery, which severely reduces the level of the heterochromatic mark H3K9me3. NUP-6(dim-3) compromises the heterochromatic localization of several components of the DCDC, a histone H3K9 methyltransferase complex, which in turn reduces the level of Heterochromatin Protein-1 (HP1) found at heterochromatin and compromises the direct interaction between HP1 and the DNA methyltransferase dim-2. To determine whether the reduced level of cytosine methylation, as assayed by Southern blotting heterochromatic regions following digestion of genomic DNA with methylation-sensitive restriction endonucleases, is globally reduced at the A:T rich, repetitive DNA comprising heterochromatin, we performed Bisulfite-seq on a dim-3 strain (grown either in minimal medium or medium supplemented with histidine) and compared that to a wild type strain (grown in minimum medium; histidine does not reduce the levels of cytosine methylation in a wild type strain, as assayed by Southern blotting).

overall_design: Examination of cytosine methylation, as determined by bisulfite treatment, of two strains (a wild type strain and a dim-3 strain; the dim-3 strain was grown in two different conditions)

middle: D

last: Rountree

first: Eric

last: Selker


title: Integrative analysis of haplotype-resolved epigenomes across human tissues

status: Public on Feb 18 2015

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: Allelic differences between the two sets of chromosomes can affect the propensity of inheritance in humans, but the extent of such differences in the human genome has yet to be fully explored.  Here, we delineate allelic chromatin modifications and transcriptomes amongst a broad set of human tissues, enabled by a chromosome-span haplotype reconstruction strategy1. The resulting haplotype-resolved epigenomic maps reveal extensive allele bias in the transcription of human genes as well as chromatin state, allowing us to infer cis-regulatory relationships between genes and their control sequences. These maps also uncover a new class of cis regulatory elements and detail activities of repetitive elements in various human tissues. The rich datasets described here will enhance our understanding of the mechanisms controlling tissue-specific gene expression programs.

overall_design: One replicate of Hi-C experiment in four human tissues with four different individuals (Thymus STL001, Aorta STL002, Leftventricle STL003, and Liver STL011).

first: Anthony

last: Schmitt

first: Danny

last: Leung

first: Bing

last: Ren


title: Perinatal malnutrition in male mice influences gene expression in the next generation offspring: Potential role of epigenetics.

status: Public on Feb 01 2015

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

country: Spain

institute: IDIBAPS

summary: Perinatal nutritional imbalances may have long-lasting consequences on health and disease, increasing risk of obesity, insulin resistance, type 2 diabetes or cardiovascular disease. This idea has been conceptualized in the Developmental Origins of Health and Disease Hypothesis (DOHaD).     In addition, there is evidence that such early-programmed phenotypes can be transmitted to the following generation(s). It is proposed that, environmentally induced, transmission of disease risk is mediated by epigenetic mechanisms.

overall_design:
The aim of this study was to determine whether patterns of gene expression in the first generation offspring are also present in the following generation offspring, via the paternal lineage. Paternal transmission of patterns of gene expression strongly suggest epigenetic inheritance of disease risk.
Liver tissue was obtained from the follwing experimental groups: a) control male mice, b) adult male mice previously exposed to 50% caloric restriction in utero (IUGR), c) adult male mice overfed during lactation (ON), d) adult male offspring from control mice, e) adult male offspring from IUGR mice and f) adult male offspring from ON mice.RNA was extracted and processed for further hybridization on Affymetrix microarrays (GeneChip Mouse Genome 430 2.0 (Affymetrix, Santa Clara, CA)).

first: Josep

middle: C

last: Jimenez-Chillaron

middle: G


title: The chromatin modifier CHD8 targets autism risk genes during human neurodevelopment

status: Public on Jan 21 2015

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

summary: Whole-exome sequencing studies have implicated chromatin modifiers and transcriptional regulators in autism spectrum disorder (ASD) through the identification of de novo loss of function mutations in affected individuals. Many of these genes are co-expressed in mid-fetal human cortex, suggesting ASD risk genes converge in regulatory networks that are perturbed in ASD during neurodevelopment. To elucidate such networks we mapped promoters and enhancers bound by the chromodomain helicase CHD8, which is strongly enriched in ASD-associated de novo loss of function mutations, using ChIP-seq in mid-fetal human brain, human neural stem cells (hNSCs), and embryonic mouse cortex. We find that CHD8 targets are strongly enriched for ASD risk genes that converge in ASD-associated co-expression networks in human midfetal cortex. CHD8 knockdown in hNSCs results in significant dysregulation of ASD risk genes targeted by CHD8, as well as additional genes important for neurodevelopment, including members of the Wnt/β-catenin signaling pathway. Integration of CHD8 binding data with genetic and gene co-expression data in ASD risk models provides support for additional ASD risk genes. Together, our results suggest that loss of CHD8 function contributes to ASD through regulatory perturbation of other ASD risk genes during human cortical development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Two biological replicates for each ChIP with appropriate Input control
Four biological replicates for each condition in knockdown experiments (Ctrl construct, Chd8 target C, and Chd8 target G)

No raw data are provided for human samples (GSM1381214-GSM1381221) due to patient confidentiality issue. Human alignments were anonymized by removing sequence information and provided as aligned bam files instead

first: James

last: Noonan


title: Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery


title: Recombination initiation maps of individual human genomes

status: Public on Nov 17 2014

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and to generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here we present the first high-resolution map of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors dictate the efficiency of DSB formation. Furthermore, we find that in human males, the frequency of DSB formation is the primary determinant of crossover rate. Patterns of sequence polymorphisms around meiotic DSB hotspots provide evidence for both GC-biased gene conversion and for a mutagenic role of DSB repair and/or recombination. Finally, we provide compelling evidence that the aberrant repair of meiotic DSBs is a driver of human genomic disorders.

overall_design: Detection of meiotic double strand breaks in testis of several human male individuals.

first: Florencia

last: Pratto

first: Pavel

last: Khil

first: Fatima

last: Smagulova

first: Galina

last: Petukhova

first: Rafael-Daniel

last: Camerini-Otero