title: Promoter targeted histone acetylation of chromatinized parvoviral genome is essential for infrection progress

status: Public on Feb 11 2016

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

summary: The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that at late infection parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e. histone H3 lysine acetylation (H3K27ac). The H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized parvoviral genome, particularly the two viral promoters were rich in H3K27ac. Histone acetyltransferase (HAT) inhibitorefficiently interfered with expression of viral proteins and infection progress. Altogether, our data suggest that acetylation of histones on parvoviral DNA is essential for viral gene expression and completion of viral life cycle.

overall_design:
Examination of H3K27 acetylation in CPV infected and non-infected NLFK (Norden laboratory feline kidney) cells.

Please note that the result in this study, considering the sequencing, is the fact that the viral genome is chromatinized. Processed data in this case would be the aligned read percentages in control cells (of which 0% aligns to parvoviral genome) and infected cells (of which ~9% only aligns to parvoviral genome and not to the cat genome), which is basically the output of the read aligner software without further processing steps (no peaks or regions were identified for the associated publication). Therefore no processed data was provided, and an exception to GEO processed data requirement was made.

first: Elina

last: Mäntylä

first: Kari

last: Salokas

first: Vesa

last: Aho

first: Pekka

last: Mäntysaari

first: Lassi

last: Palmujoki

first: Olli

last: Kalliolinna

first: Teemu

middle: O

last: Ihalainen

first: Einari

last: Niskanen

first: Jussi

last: Timonen

first: Keijo

last: Viiri

first: Maija

last: Vihinen-Ranta


title: mRNA expression profiles in Wilms tumor subtypes

status: Public on May 11 2016

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

summary: The aim of the study was to identify differentially expressed mRNAs in different Wilms tumor subtypes and correlate them to miRNA expression profiles of the same tumor samples.

overall_design: Comparison of mRNA expression profiles in Wilms tumor of different subtypes (total n=28) compared to normal kidney tissue (n=4)


title: RNA-Seq of Ctcfl transgenic mouse ES cells

status: Public on Aug 19 2015

city: new haven

first: James

last: McGrath

state: CT

address: 333 cedar st

department: comparative Medicine

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Ctcfl, a paralog of Ctcf, also known as BORIS (Brother of Regulator of Imprinted Sites), is a testis expressed gene whose function is largely unknown. As a cancer testis antigen, it is often expressed in tumor cells and also seen in two benign human vascular malformations, juvenile angiofibromas (JA) and infantile hemangiomas (IH). To better understand the function of Ctcfl we created tetracycline-inducible Ctcfl transgenic mice. We show that when Ctcfl expression is induced during embryogenesis, it results in intrauterine growth retardation, developmental eye malformations, multi-organ pathologies, vascular defects, and early neonatal lethality. This phenotype resembles prior mouse models which perturb the TGFB pathway. Embryonic stem cells with the Ctcfl transgene reproduce the same phenotype in ES cell: tetraploid chimeras. RNA-Seq of the Ctcfl ES cells revealed 14 genes, including a number of transcription factors/ co-activators, and signal transduction pathway genes that are significantly deregulated by Ctcfl expression. Bioinformatics analysis revealed the TGFB pathway to be most affected by embryonic Ctcfl expression. We propose that our transgenic mice reiterate a developmental program normally reserved for spermatogenesis that results in multiple organ pathology when expressed in embryogenesis as a result of the TGFB pathway dysregulation. Understanding of the phenotypic consequence of Ctcfl expression in non-testicular cells and elucidating downstream targets of Ctcfl has the potential to explain its role as a cancer testis antigen (CTA) and its involvement in two, if not more, human vascular malformations.

overall_design: Two mouse ES cell lines, one with an inducible Ctcfl transgene and one without the transgene, were compared by RNA Seq.  Both cell lines were grown for 48 hours either with or without doxycycline, to induce Ctcfl transgene expression.  Therefore there were 4 RNA samples sequenced in each experiment and the experiment was repeated twice.  The results of both experiments were combined for the statistical analysis.  14 genes were found to be significantly altered in expression with induction of the Ctcfl transgene.  When the non-transgenic ES cell line was compared with and without doxycycline in the culture medium there were no significant changes in gene expression.

first: Leyla

last: Sati

first: Caroline

last: Zeiss

first: Krishna

last: Yekkal

first: Ramazan

last: Demir


title: Genome-Wide Pharmacogenomic Study on Methadone Maintenance Treatment Identifies SNP rs17180299 and Multiple Haplotypes on CYP2B6, SPON1, and GSG1L Associated with Plasma Concentrations of Methadone R- and S-enantiomers in Heroin-Dependent Patients

status: Public on Feb 19 2016

city: Miaoli County

first: Yu-Li

last: Liu

address: 35 Keyan Road, Zhunan

department: Center for Neuropsychiatric Research

country: Taiwan

institute: National Health Research Institutes

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

summary: Methadone maintenance treatment (MMT) is commonly used for controlling opioid dependence, preventing withdrawal symptoms, and improving the quality of life of heroin-dependent patients. A steady-state plasma concentration of methadone enantiomers, a measure of methadone metabolism, is an index of treatment response and efficacy of MMT. Although the methadone metabolism pathway has been partially revealed, no genome-wide pharmacogenomic study has been performed to identify genetic determinants and characterize genetic mechanisms for the plasma concentrations of methadone R- and S-enantiomers. This study was the first genome-wide pharmacogenomic study to identify genes associated with the plasma concentrations of methadone R- and S-enantiomers and their respective metabolites in a methadone maintenance cohort. After data quality control was ensured, a dataset of 344 heroin-dependent patients in the Han Chinese population of Taiwan who underwent MMT was analyzed. Genome-wide single-locus and haplotype-based association tests were performed to analyze four quantitative traits: the plasma concentrations of methadone R- and S-enantiomers and their respective metabolites. A significant single nucleotide polymorphism (SNP), rs17180299 (raw p = 2.24 × 10-8), was identified, accounting for 9.541% of the variation in the plasma concentration of the methadone R-enantiomer. In addition, 17 haplotypes were identified on SPON1, GSG1L, and CYP450 genes associated with the plasma concentration of methadone S-enantiomer. These haplotypes accounted for approximately one-fourth of the variation of the overall S-methadone plasma concentration. The association between the S-methadone plasma concentration and CYP2B6, SPON1, and GSG1L were replicated in another independent study. A gene expression experiment revealed that CYP2B6, SPON1, and GSG1L can be activated concomitantly through a constitutive androstane receptor (CAR) activation pathway. In conclusion, this study revealed new genes associated with the plasma concentration of methadone, providing insight into the genetic foundation of methadone metabolism. The results can be applied to predict treatment responses and methadone-related deaths for individualized MMTs.

overall_design: The genomic DNA of 360 Han Chinese MMT patients at discovery stage and 78 Han Chinese MMT patients at replication stage were isolated from leukocytes by using a Puregene kit (Gentra Systems, Minneapolis, MN). The DNA concentration was measured and adjusted to 15–20 ng/μL by using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE). All samples were genotyped at the National Center of Genomic Medicine (Taipei, Taiwan) by using the Axiom Genome-Wide CHB 1 Array (Affymetrix, Inc., San Diego, CA) following the manufacturer’s protocols (http://www.affymetrix.com). The genotype calling was performed using the Genotyping Console 4.0 with default parameters (http://www.affymetrix.com).

first: Sheng-Chang

last: Wang


title: Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast.

status: Public on Feb 04 2016

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

institute: National Institute of Information and Communications Technology

summary: In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its SRI domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser2 and Ser5 (CTD-S2,5-P). H3K36me2 recruits the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P–dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 did not. Clr6 complex II appeared not to be responsible for heterochromatic silencing. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insight into the multiple roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.

overall_design: Gene expression profile at exponentially-growing phase.in the fission yeast deletion mutants of set2.

first: Shota

last: Suzuki

first: Hiroaki

last: Kato

first: Yutaka

first: Yuji

last: Chikashige

first: Yasushi

last: Hiraoka

first: Hiroshi

last: Kimura

first: Koji

last: Nagao

first: Chikashi

last: Obuse

first: Shinya

last: Takahata

first: Yota

last: Murakami


title: Cell-specific microRNA expression patterns in TB patients and household contacts

status: Public on Aug 24 2015

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and microRNA expression was measured using microarrays.

overall_design: House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.

first: Maria

last: Esterhuyse

first: Hans-Joachim

last: Mollenkopf


title: Gene expression profiles of epithelial and mesenchymal cells extracted from heterotypic ex vivo co-cultures or monocultures

status: Public on Sep 26 2015

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary:
Stromal-epithelial interactions play a fundamental role in tissue homeostasis, controlling cell proliferation and differentiation. Not surprisingly, aberrant stromal-epithelial interactions contribute to malignancies. The goals and objectives of this study were 1.) to characterize and validate the molecular identity of human primary epithelial and stromal/mesenchymal breast cells maintained long-term in novel ex vivo culture conditions in serum free medium. 2.) To analyze changes in gene expression profiles of normal human primary epithelial and stromal/mesenchymal breast cells upon long-term ex vivo co-culture when compared to corresponding monocultures 3.) To study the dynamic reciprocity between normal human primary epithelial and stromal/mesenchymal breast cells. 4.) To identify critical molecular pathways and biomarkers controlling epithelial and/or stromal cell growth and quiescence.
Human primary epithelial progenitor cells and mesenchymal stem cells bearing fluorescent tags were either co-cultured in novel ex vivo culture conditions on ECM coated meshes in serum free medium (M5) or cultured as monocultures in the same conditions for 30 days. The cultures were then dissociated and epithelial and stromal/mesenchymal cells from either co-cultures or monocultures separated by FACS. Gene expression profiling of epithelial or stromal/mesenchymal cells was performed.  Clean gene expression profiles from three different epithelial and stromal/mesenchymal cell extracts either grown in co-cultures or monocultures were successfully obtained.

overall_design: Three complete biological replicates of heterotypic co-cultures and corresponding monocultures were set up in parallel. In order to take account of the biological variability tissues from donors in three different age groups (16-25, 26-40, >40) were included in the study. Epithelial progenitor cells were isolated from cleaned epithelial tissue from reduction mammoplasties of tree different donors (MP9, MP13, MP15) immediately infected in suspension with Lentivirus containing an EGFP (Enhanced Green Fluorescent Protein) expression cassette. Adipocyte tissue derived mesenchymal stem cells (hAMSCs) were isolated from cleaned breast fat tissue from reduction mammoplasties of tree different donors (MP22, MP28, MP29) and were immediately infected in suspension with Lentivirus containing a DsRed2 (Red fluorescent Protein) expression cassette. After selection, spheres were dissociated and single cell suspensions prepared. For heterotypic co-cultures, EGFP tagged epithelial progenitor cells were randomly aggregated with DsRed2 tagged hAMSCs (MP9&MP29, MP13&MP22, MP15&MP28). For monocultures the three corresponding epithelial progenitor cell isolates (MP9, MP13, MP15) or hAMSC isolates (MP29, MP22, MP28) were aggregated alone. The aggregates of each condition were then added on top of ECM coated meshes and serum free medium (M5) was regularly supplemented and changed during the whole ex-vivo culture period. After 30 days the cultures were dissociated with mild proteinase/EDTA (HyQtase, Thermo Scientific) treatment for 20 min. Cells remained thereafter on ice and FACS sorts were performed immediately to isolate viable epithelial or stromal cells, based on their fluorescent protein tag. 300 cells of each condition were directly sorted in 100ul TRIZOL in cooled tubes. The samples were immediately frozen on dry ice and stored at -70°C prior to RNA extraction. A total of 12 samples were successfully hybridized on Gene 1.0 AFFYMETRIX human gene chips: Co-culture derived epithelial cells (ESe, Arrays 4, 8, 12), co-culture derived stromal cells (ESs, Arrays 3, 7, 11), monoculture derived epithelial cells (Ee, Arrays 2, 6, 10) and monoculture derived stromal cells (Ss, Arrays 1, 5, 9).

first: Stephan

last: Duss

first: Erik

last: Cabuy

first: Mohamed

last: Bentires-Alj


title: Cellular economy in fission yeast cells continuously cultured at limited nitrogen resources

status: Public on Oct 22 2015

first: Atsushi

last: Matsuda

summary: In ribosome biogenesis, a large fraction of ribosomes is used for producing ribosomal proteins. Here, we deal with the question what fraction of ribosomes should be allocated for synthesis of ribosomal proteins to optimize the cellular economy for growth. We define the "r-fraction" as the fraction of mRNA of the ribosomal protein genes out of the total mRNA and simulated how the amount of the total protein is affected by the r-fraction. Then, we empirically measured the amount of protein and RNA in fission yeast cells cultured at a high or low nitrogen source. In the cells cultured at a low nitrogen source, the r-fraction decreased from 0.46 to 0.42 with a 40% reduction of rRNA, but the reduction of the total protein was smaller at 30%. These results indicate that the r-fraction is internally controlled to optimize the efficiency of protein synthesis at a limited cellular cost.

overall_design: Gene expression profile at exponentially-growing phase in the fission yeast cultured at low nitrogen condition.

first: Shin'ichi

last: Arakawa

first: Kenji

last: Leibnitz

first: Chihiro

last: Tsutsumi

first: Chie

last: Mori

first: Hiroko

last: Osakada

first: Masayuki

last: Murata

first: Tokuko

last: Haraguchi


title: Gene expression profiles of epithelial and mesenchymal cell populations extracted from normal human breast tissue

summary:
Stromal-epithelial interactions play a fundamental role in tissue homeostasis, controlling cell proliferation and differentiation. The goals and objectives of this study were 1.) To generate gene expression profiles and identify signatures of freshly isolated, non-cultured, luminal epithelial or basal epithelial and CD10 positive or negative stromal cell populations from the human breast. 2.) Use the generated signatures to characterize and validate the molecular identity of human primary epithelial and stromal/mesenchymal breast cells maintained long-term in novel ex vivo culture conditions in serum free medium (previous study in our lab)
Breast tissue from three different reduction mammoplasties was dissociated and single cells were labeled with antibodies against lineage markers (CD31, CD45 CD235ab), CD10, EpCAM, CD49f and DAPI.  Different cell populations were identified, separated and sorted with a fluorescence activated cell sorter. Gene expression profiling of luminal epithelial (EpCAM+, CD49f+/-), basal epithelial (EPCAM-, CD49f+), CD10 negative and CD10 positive stromal cells was performed and distinct gene expression signatures for the four cell populations were identified.

overall_design: A total of 12 samples were analyzed. To obtain three complete biological replicates, breast tissue from three different reduction mammoplasties (MP9, MP13, MP15) was dissociated and single cells were labeled with fluorescent antibodies prior to cell sorting. Four distinct cell populations (two epithelial and two stromal) were identified and gated. 300 cells of each of the four cell populations were sorted directly in 100ul TRIZOL for all three donor tissues. The samples were immediately frozen on dry ice and stored at -70°C prior to RNA extraction. Gene expression profiles of luminal epithelial cells (EpCAM+, CD49f+/-), basal epithelial (EPCAM-, CD49f+), CD10 negative and CD10 positive stromal cells were successfully obtained for all three reduction mammoplasties.

first: Magdalena

last: Guzowska

first: Stéphane

last: Thiry


title: Diffuse Large B-Cell Lymphoma Classification System That Associates Normal B-Cell Subset Phenotypes With Prognosis

status: Public on Mar 24 2015

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary:
Purpose
Current diagnostic tests for diffuse large B-cell lymphoma use the updated WHO criteria based on biologic, morphologic, and clinical heterogeneity. We propose a refined classification sys-tem based on subset-specific B-cell–associated gene signatures (BAGS) in the normal B-cell hierarchy, hypothesizing that it can provide new biologic insight and diagnostic and prognostic value.

Patients and Methods
We combined fluorescence-activated cell sorting, gene expression profiling, and statistical modeling to generate BAGS for naive, centrocyte, centroblast, memory, and plasmablast B cells from normal human tonsils. The impact of BAGS-assigned subtyping was analyzed using five clinical cohorts (treated with cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP], n _ 270; treated with rituximab plus CHOP [R-CHOP], n _ 869) gathered across geo-graphic regions, time eras, and sampling methods. The analysis estimated subtype frequencies and drug-specific resistance and included a prognostic meta-analysis of patients treated with first-line R-CHOP therapy.

Results
Similar BAGS subtype frequencies were assigned across 1,139 samples from five different co-horts. Among R-CHOP–treated patients, BAGS assignment was significantly associated with overall survival and progression-free survival within the germinal center B-cell–like subclass; the centrocyte subtype had a superior prognosis compared with the centroblast subtype. In agreement with the observed therapeutic outcome, centrocyte subtypes were
estimated as being less resistant than the centroblast subtype to doxorubicin and vincristine. The centroblast subtype had a complex genotype, whereas the centrocyte subtype had high TP53 mutation and insertion/deletion frequencies and expressed LMO2, CD58, and stromal-1–signature and major histocompatibility complex class II–signature genes, which are known to have a positive impact on prognosis.

Conclusion
Further development of a diagnostic platform using BAGS-assigned subtypes may allow pathogenetic studies to improve disease management.

overall_design: Global gene expression data combined with B-cell subpopulation

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Steffen

last: Falgreen

middle: S

first: Malene

middle: K

last: Kjeldsen

first: Alexander

last: Schmitz

first: Anders

middle: E

last: Bilgrau

first: Zijun

middle: Y

last: Xu-Monette

first: Ling

last: Li

first: Kim

last: Bergkvist

middle: B

last: Laursen

first: Marie

last: Rodrigo-Domingo

first: Sara

middle: C

last: Marques

first: Sophie

last: Rasmussen

first: Mette

last: Nyegaard

first: Michael

last: Gaihede

last: Moeller

first: Richard

middle: J

last: Samworth

first: Rajen

middle: D

last: Shah

first: Preben

last: Johansen

first: Tarec

last: El-Galaly

first: Ken

middle: H

last: Young

first: Hans

last: Johnsen


first: Julie

last: Bødker

overall_design: Global gene expression data of diagnostic samples of diffuse large B-cell lymphoma (DLBCL)

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Steffen

last: Falgreen

first: Malene

last: Kjeldsen

last: Schmitz

last: Bilgrau

first: Maria


title: Gene expression profile analysis of conditional Mll2 knockout germinal center B cells and littermate controls

status: Public on Sep 13 2015

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Somatic mutations of the MLL2 methyltransferase gene represent a common genetic lesion in multiple cancer types. In diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) (collectively, over 70% of all lymphoma diagnoses), these mutations are highly recurrent and appear early during transformation, possibly in pre-malignant precursors. Here we show that FL- and DLBCL-associated MLL2 mutations impair its enzymatic activity and lead to diminished global H3K4 methylation in normal germinal-center (GC) B cells and DLBCL, consistent with the enrichment of MLL2 binding at enhancer and promoter regions marked by mono- and tri-methylation. Conditional deletion of Mll2 early during B cell development, but not after initiation of the GC reaction, leads to increased percentages and numbers of GC B cells, which feature a distinct transcriptional profile defined by the enrichment of cell-cycle regulatory and B-cell receptor signaling genes. Consistently, Mll2-deficient B cells exhibit proliferative advantage and accumulation in the S phase of the cell cycle, which is influenced by the number of cell divisions.  While GC-specific loss of Mll2 was not sufficient to initiate malignant transformation, compound Mll2-deficient/BCL2-transgenic mice displayed an increased incidence of clonal lymphoproliferations resembling the features of human FL and DLBCL. These findings suggest that early MLL2 loss favors BCL2-induced lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells.  Eradication of MLL2-deficient cells may represent a rational therapeutic approach targeting early tumorigenic events.

overall_design: Murine germinal center B cells (B220+CD95+PNA+) were sorted from the spleen of conditional Mll2 knock-out, Mll2 heterozygous and Mll2 wild type mice (crossed with CD19-Cre or Cg1-Cre deletor strains) and sacrificed at day 12 after  immunization with sheep red blood cells (SRBC)(n=3 mice per genotype). Total RNA was extracted from single cell suspensions and processed according to the Ovation RNA Amplification System and Encore® Biotin Module protocols (both from NuGEN). Samples were analyzed on Affymetrix Mouse Genome 430 2.0 arrays.

first: Jiyuan

last: Zhang


title: Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors

status: Public on Dec 08 2014

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: Quorum sensing (QS) is a process of cell-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence in Vibrio cholerae, the causative agent of the disease cholera. Differential RNA-sequencing (dRNA-seq) analyses of wild-type V. cholerae and a locked low cell density QS-mutant strain identified a total of 7641 transcriptional start sites (TSS) with ~40% initiated in the antisense direction. Genome-wide TSS mapping combined with phylogenetic comparisons enabled re-annotation of 129 genes from the NCBI database. 107 of the transcripts we identified do not appear to encode proteins suggesting they could specify non-coding RNAs. We focused on one such transcript that we name VqmR. vqmR is located upstream of the vqmA gene that encodes a DNA-binding transcription factor. Mutagenesis and microarray analyses demonstrate that VqmA activates vqmR transcription; that vqmR encodes a regulatory RNA, and VqmR directly controls at least eight mRNA targets including the rtxBA toxin genes and the vpsT transcriptional regulator of biofilm production. We show that VqmR inhibits biofilm formation through repression of vpsT. Together, these data provide the first global annotation of the V. cholerae transcription landscape and they highlight the importance of post-transcriptional regulation for collective behaviors in this human pathogen.

overall_design: Global mapping TSS in V. cholerae

first: Kai

last: Papenfort


title: The chicken immature erythrocyte transcriptome

status: Public on Jan 01 2016

city: Winnipeg

first: James

middle: Ronald

last: Davie

state: Manitoba

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary: Transcriptional regulation is impacted by multiple layers of genome organization. Here, we  identified and mapped out all the transcriptionally active chromosomal domains in the chicken  immature erythrocyte genome, including the known β- and α-globin domains, by combining a  powerful chromatin fractionation method with next generation DNA and RNA sequencing.

overall_design: Two biological replicates of total RNA were sequenced to characterize genes in chicken erythrocyte cells

first: Sanzida

last: Jahan

first: Wayne

last: xu

first: Shihua

last: He

first: Carolina

last: Gonzalez

first: Geneviève

middle: P

last: Delcuve

middle: R


title: Identification of novel gene signatures in patients with atopic dermatitis complicated by eczema herpeticum

status: Public on Aug 18 2015

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
Background:  A subset of patients with atopic dermatitis (AD) is prone to disseminated herpes simplex virus (HSV) infection, i.e. eczema herpeticum (ADEH+). Biomarkers that identify ADEH+ are lacking.
Objective: To search for novel ADEH+ gene signatures in peripheral blood mononuclear cells (PBMCs).
Methods: A RNA-sequencing (RNA-seq) approach was applied to evaluate global transcriptional changes using PBMCs from ADEH+ and AD without a history of EH (ADEH-). Candidate genes were confirmed by qPCR or ELISA.
Results:  ADEH+ PBMCs had distinct changes to the transcriptome when compared to ADEH- PBMCs following HSV-1 stimulation: 792 genes were differentially expressed at a false discovery rate (FDR) < 0.05 (ANOVA), and 15 type I and type III interferon (IFN) genes were among the top 20 most down-regulated genes in ADEH+.  We further validated that IFN-α and IL-29 mRNA and protein levels were significantly decreased in HSV-1 stimulated PBMCs from ADEH+ compared to ADEH- and normal. Ingenuity pathway analysis (IPA) demonstrated that the up-stream regulators of type I and type III IFNs, IRF3 and IRF7 was significantly inhibited in ADEH+ based on the down-regulation of their target genes. Furthermore, we found that gene expression of IRF3 and IRF7 were significantly decreased in HSV-1 stimulated PBMC from ADEH+ subjects.
Conclusions: PBMCs from ADEH+ have a distinct immune response following HSV-1 exposure compared to ADEH- .  Inhibition of the IRF3 and IRF7 innate immune pathways in ADEH+ may be the important mechanisms for increased susceptibility to disseminated viral infection.

overall_design: Expression profiles of PBMCs were taken from 5 AD patients with a history of disseminated herpes simplex virus (HSV) infection, i.e. eczema herpeticum (ADEH+) and 6 AD patients who don’t have a history of disseminated HSV infection (ADEH-).  PBMC samples from each subject were divided in two and were treated with and without HSV-1 virus for 21 hours before processing for total RNA.

first: Lianghua

last: Bin

middle: G

first: Ryan

last: Heiser

first: Joanne

last: Streib

first: Brittany

last: Richers

first: Cliff

last: Hall

first: Donald

last: Leung


title: Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

status: Public on Aug 22 2015

first: January

last: Weiner

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Cell-specific gene expression patterns in TB patients and household contacts

summary: Monocytes and granulocytes were isolated from blood of TB patients and household contacts. RNA was isolated and gene expression was measured using microarrays.

first: Maria

last: Esterhuyse

first: Hans-Joachim

last: Mollenkopf


title: Human Airway Smooth Muscle Transcriptome Changes in Response to Asthma Medications

status: Public on Jan 01 2014

city: Philadelphia

first: Blanca

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
Rationale: Asthma is a chronic inflammatory airway disease. The most common medications used for its treatment are β2-agonists and glucocorticosteroids, and one of the primary tissues that these drugs target in the treatment of asthma is the airway smooth muscle. We used RNA-Seq to characterize the human airway smooth muscle (HASM) transcriptome at baseline and under three asthma treatment conditions.
Methods: The Illumina TruSeq assay was used to prepare 75bp paired-end libraries for HASM cells from four white male donors under four treatment conditions: 1) no treatment; 2) treatment with a β2-agonist (i.e. Albuterol, 1μM for 18h); 3) treatment with a glucocorticosteroid (i.e. Dexamethasone (Dex), 1μM for 18h); 4) simultaneous treatment with a β2-agonist and glucocorticoid, and the libraries were sequenced with an Illumina Hi-Seq 2000 instrument. The Tuxedo Suite Tools were used to align reads to the hg19 reference genome, assemble transcripts, and perform differential expression analysis using the protocol described in https://github.com/blancahimes/taffeta

overall_design: mRNA profiles obtained via RNA-Seq for four primary human airway smooth muscle cell lines that were treated with dexamethasone, albuterol, dexamethasone+albuterol or were left untreated.

first: Quan

last: Lu


title: Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast

status: Public on Jul 27 2015

first: Atsushi

last: Matsuda

summary: It is generally believed that silent chromatin is condensed and transcriptionally active chromatin is decondensed. However, little is known about the relationship between condensation levels and gene expression. Here we report condensation levels of interphase chromatin in the fission yeast Schizosaccharomyces pombe examined by super-resolution fluorescence microscopy. Unexpectedly, silent chromatin was observed to be less condensed than the euchromatin. Furthermore, the telomeric silent regions were flanked by highly condensed chromatin bodies, or “knobs”. Knob regions span approximately 50 kb of sequence devoid of methylated histones. Knob condensation was independent of HP1 homolog Swi6 and other gene silencing factors. Disruption of methylation at lysine 36 of histone H3 (H3K36) eliminated knob formation and gene repression at the subtelomeric and adjacent knob regions. Thus, epigenetic marks atH3K36 play crucial roles in the formation of a unique chromatin structure and in gene regulation at those regions in S. pombe.

overall_design: Gene expression profile at exponentially-growing phase in the fission yeast deletion mutant of set2 and histone H3 mutant K36R, K36A.

first: Yuji

last: Chikashige

first: Da-Qiao

last: Ding

first: Chizuru

last: Ohtsuki

first: Chie

last: Mori

first: Haruhiko

last: Asakawa

first: Hiroshi

last: Kimura

first: Tokuko

last: Haraguchi

first: Yasushi

last: Hiraoka


title: RNA-seq analysis of germline stem cell removal and loss of SKN-1 in C. elegans

status: Public on Jul 21 2015

city: Quechee

first: Michael

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

summary: In C. elegans, ablation of germline stem cells (GSCs) extends lifespan, but also increases fat accumulation and alters lipid metabolism, raising the intriguing question of how these effects might be related.  Here we show that a lack of GSCs results in a broad transcriptional reprogramming, in which the conserved detoxification regulator SKN-1/Nrf increases stress resistance, proteasome activity, and longevity.  SKN-1 also activates diverse lipid metabolism genes and reduces fat storage, thereby alleviating the increased fat accumulation caused by GSC absence.  Surprisingly, SKN-1 is activated by signals from this fat, which appears to derive from unconsumed yolk that was produced for reproduction.  We conclude that SKN-1 plays a direct role in maintaining lipid homeostasis, in which it is activated by lipids.  This SKN-1 function may explain the importance of mammalian Nrf proteins in fatty liver disease, and suggests that particular endogenous or dietary lipids might promote health through SKN-1/Nrf.

overall_design:
Samples were prepared from ~5,000 synchronized, L1 arrested day-one adult animals cultured at 25°C.  Worms were synchronized by sodium hypochlorite (bleach) treatment, as previously described (Porta-de-la-Riva et al., 2012).  Bleach solution (9 mL ddH2O; 1 mL 1 N NaOH; 4 mL Clorox bleach) was freshly prepared before each experiment.  Worms were bleached for 5 minutes, washed 5x in M9, and arrested at the L1 stage at 25°C in M9 containing 10 µg/mL cholesterol.  Feeding RNAi was started at the L1 stage.  This approach only partially reduces skn-1 function, but allows analysis of larger samples than would be feasible with skn-1 mutants, which are sterile (Bowerman et al., 1992).  Because these animals were not treated with FUdR, the WT adults contained an intact germline and eggs.  As is explained in the Results section, we therefore confined our analysis to genes that were overrepresented in glp-1(ts) animals, which lack eggs and most of the germline, and established a high-confidence cutoff for genes that were upregulated by GSC absence as opposed to simply being expressed specifically in somatic tissues.  RNA was extracted using the same protocol for qRT-PCR samples.  Purified RNA samples were DNase treated and assigned a RIN quality score using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Only matched samples with high RIN scores were sent for sequencing.  Single read 50 bp RNA sequencing with poly(A) enrichment was performed at the Dana-Farber Cancer Institute Center for Computational Biology using a HiSeq 2000 (Illumina, San Diego, CA).

FASTQ output files were aligned to the WBcel235 (Feb 2014) C. elegans reference genome using STAR (Dobin et al., 2013).  These files have been deposited at the Gene Expression Omnibus (GEO) with the accession number GSE63075.  Samples averaged 75% mapping of sequence reads to the reference genome.  Differential expression analysis was performed using a custom R and Bioconductor RNA-seq pipeline (http://bioinf.wehi.edu.au/RNAseqCaseStudy/) (Gentleman et al., 2004; Anders et al., 2013; R Core Team, 2014).  Quantification of mapped reads in the aligned SAM output files was performed using featureCounts, part of the Subread package (Liao et al., 2013, 2014).  We filtered out transcripts that didn’t have at least one count per million reads in at least two samples.  Quantile normalization and estimation of the mean-variance relationship of the log-counts was performed by voom (Law et al., 2014).  Linear model fitting, empirical Bayes analysis and differential expression analysis was then conducted using limma (Smyth, 2005).  To identify genes that are upregulated in a SKN-1-dependent manner by GSC loss, we sought genes for which glp-1(ts) expression was higher than WT, and for which glp-1(ts);skn-1(-) expression was reduced relative to glp-1(ts).  To test for this pattern, if a gene’s expression change was higher in the comparison of glp-1(ts) vs. WT and lower in the comparison of glp-1(ts);skn-1(-) vs. glp-1(ts), then we calculated the minimum (in absolute value) of the t-statistics from these two comparisons, and assessed the significance of this statistic by comparing to a null distribution derived by applying this procedure to randomly generated t-statistics.  We corrected for multiple testing in this and the differential expression analysis using the false discovery rate (FDR) (Benjamini and Hochberg, 1995).  Heatmaps were generated using heatmap.2 in the gplots package (Warnes et al., 2014).

Functional annotations and phenotypes were obtained from Wormbase build WS246.  SKN-1 transcription factor binding site analysis of hits was conducted with biomaRt, GenomicFeatures, JASPAR, MotifDb, motifStack, MotIV, and Rsamtools (Sandelin et al., 2004; Durinck et al., 2005; Durinck et al., 2009; Lawrence et al., 2013; Ou et al., 2013; Mercier and Gottardo, 2014; Shannon, 2014).  JASPAR analysis was performed with the SKN-1 matrix MA0547.1 using 2 kb upstream sequences obtained from Ensembl WBcel235 (Staab et al., 2013).  modENCODE SKN-1::GFP ChIP-seq analysis of hits was performed using biomaRt, ChIPpeakAnno, IRanges, and multtest (Durinck et al., 2005; Durinck et al., 2009; Gerstein et al., 2010; Zhu et al., 2010; Niu et al., 2011; Lawrence et al., 2013).  SKN-1::GFP ChIP-seq peaks were generated by Michael Snyder’s lab.  We used the peak data generated from the first 3 larval stages: L1 (modENCODE_2622; GSE25810), L2 (modENCODE_3369), and L3 (modENCODE_3838; GSE48710).  Human ortholog matching was performed using Wormbase, Ensembl, and OrthoList (Shaye and Greenwald, 2011).  Gene lists were evaluated for functional classification and statistical overrepresentation with Database for Annotation, Visualization and Integrated Discovery (DAVID) version 6.7 (Dennis et al., 2003).

first: Jonathan

middle: M

last: Dreyfuss

first: T

last: Blackwell


title: Gene expression data from serial samples of follicular lymphoma (FLSB - follicular lymphoma serial biopsies)

status: Public on Jan 07 2014

city: Oslo

first: Marianne

last: Brodtkorb

address: Ullernchausseen 70

department: Institute for Cancer Research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

summary: Transformation of follicular lymphoma (FL) to a more aggressive disease is associated with rapid progression and death. Existing molecular markers for transformation are few and their clinical impact is limited. Here, we report on a whole-genome study of DNA copy numbers and gene expression profiles in serial FL biopsies. We identified 698 genes with high correlation between gene expression and copy number and the molecular network most enriched for these cis-associated genes. This network includes 14 cis-associated genes directly related to the NFκB pathway. For each of these 14 genes, the correlated NFκB target genes were identified and corresponding expression scores defined. The scores for six of the cis-associated NFκB pathway genes (BTK, IGBP1, IRAK1, ROCK1, TMED7-TICAM2 and TRIM37) were significantly associated with transformation. The results suggest that genes regulating B-cell survival and activation are involved in transformation of FL

overall_design: Expression profiles were obtained from 81 biopsies origniating from 41 patients diagnosed with follicular lymphoma using Affymetrix HG U133 Plus 2.0 Gene Chip. Of these, 49 biopsies were from 24 patients with subsequent transformation to higher-grade lymphoma (DLBCL) (43 with histological diagnosis FL and 6 with DLBCL) and 32 biopsies were from 17 patients without any signs transformation

first: Ole

last: Lingjærde

first: Kanutte

last: Huse

first: Gunhild

last: Trøen

first: Mait

last: Hystad

first: Vera

middle: I

last: Hilden

first: June

last: Myklebust

first: Ellen

last: Leich

first: Andreas

last: Rosenwald

first: Jan

last: Delabie

first: Harald

last: Holte

first: Erlend

last: Smeland


title: Expression data from neural stem cells treated with endotherial progenitor-derived soluble protein

status: Public on Apr 01 2015

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

summary: Endogenous neural stem cells reside in the mammalian brain during development and within special niche microenvironments during adulthood. We discovered that endothelial progenitor cell-secreted factors promote the self-renewal of adult mouse NSCs in vivo and identified this protein as ECF-L. We also analyzed molecular signalling networks caused by ECF-L in neural stem cells using global gene expression analysis.

overall_design: Neural stem cells were isolated and expanded from adult mouse brain. Neural stem cells were cultured in the presence or absence of ECF-L in the MHM medium. After the designed period of ECF-L treatment, cells were harvested and RNA was extacted, followed by DNA microarray analysis.

first: Jun

last: Namiki

first: Hideyuki

last: Okano


title: Affymetrix SNP array data for squamous cell carcinoma of base of tongue and healthy individuals samples

status: Public on Aug 14 2014

city: Campinas

first: Benilton

middle: Sa

last: Carvalho

state: Sao Paulo

address: Tessália Vieira de Camargo, 126

department: Medical Genetics

country: Brazil

institute: Universidade Estadual de Campinas

summary:
Base of tongue squamous cell carcinoma (BTSCC) is a common tumor of oropharynx worldwide. In addition, BTSCC is a lethal disease and its treatment results in significant disability. Considerable importance is given in lifestyle, particularly tobacco and alcohol use, in cases of BTSCC. It was postulated that BTSCC arises if the ability to metabolize carcinogens, to repair DNA damage and to control cell signaling and cell cycle are defective in individuals with continued exposure to benzo(a)pyrene, ethanol and acetaldehyde. Since these abilities are inherited and vary among human beings, healthy individuals may be at distinct risks for BTSCC.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

overall_design: SNP analysis of Affymetrix 5.0 SNP arrays was performed for 49 BTSCC samples and 49 controls (healthy individuals) which were used as references.

first: Gustavo

last: Lourenco


first: Rasmus

middle: Froberg

last: Brøndum

department: Department of Haematology

summary:
This SuperSeries is composed of the SubSeries listed below:
GSE56313 and GSE56314

Purpose
Current diagnostic tests for diffuse large B-cell lymphoma use the updated WHO criteria based on biologic, morphologic, and clinical heterogeneity. We propose a refined classification sys-tem based on subset-specific B-cell–associated gene signatures (BAGS) in the normal B-cell hierarchy, hypothesizing that it can provide new biologic insight and diagnostic and prognostic value.

Patients and Methods
We combined fluorescence-activated cell sorting, gene expression profiling, and statistical modeling to generate BAGS for naive, centrocyte, centroblast, memory, and plasmablast B cells from normal human tonsils. The impact of BAGS-assigned subtyping was analyzed using five clinical cohorts (treated with cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP], n _ 270; treated with rituximab plus CHOP [R-CHOP], n _ 869) gathered across geo-graphic regions, time eras, and sampling methods. The analysis estimated subtype frequencies and drug-specific resistance and included a prognostic meta-analysis of patients treated with first-line R-CHOP therapy.

Results
Similar BAGS subtype frequencies were assigned across 1,139 samples from five different co-horts. Among R-CHOP–treated patients, BAGS assignment was significantly associated with overall survival and progression-free survival within the germinal center B-cell–like subclass; the centrocyte subtype had a superior prognosis compared with the centroblast subtype. In agreement with the observed therapeutic outcome, centrocyte subtypes were
estimated as being less resistant than the centroblast subtype to doxorubicin and vincristine. The centroblast subtype had a complex genotype, whereas the centrocyte subtype had high TP53 mutation and insertion/deletion frequencies and expressed LMO2, CD58, and stromal-1–signature and major histocompatibility complex class II–signature genes, which are known to have a positive impact on prognosis.

Conclusion
Further development of a diagnostic platform using BAGS-assigned subtypes may allow pathogenetic studies to improve disease management.


title: Mediator directs co-transcriptional heterochromatin assembly by RNAi-dependent and -independent pathways.

status: Public on Aug 31 2013

first: Atsushi

last: Matsuda

summary:
Background: Heterochromatin at the pericentromeric repeats in fission yeast is assembled and spread by an RNAi-dependent mechanism, which is coupled to the transcription of non-coding RNA from the repeats by RNA polymerase II. In addition, Rrp6, a component of the nuclear exosome, also contributes to heterochromatin assembly and is coupled to non-coding RNA transcription. The multi-subunit complex Mediator, which directs initiation of RNA polymerase II-dependent transcription, has recently been suggested to function after initiation in processes such as elongation of transcription and splicing. However, the role of Mediator in the regulation of chromatin structure is not well understood.

Results: We investigated the role of Mediator in pericentromeric heterochromatin formation and found that deletion of specific subunits of the head domain of Mediator compromised heterochromatin structure. The Mediator head domain was required for Rrp6-dependent heterochromatin nucleation at the pericentromere and for RNAi-dependent spreading of heterochromatin into the neighboring region. In the latter process, Mediator appeared to contribute to efficient processing of siRNA from transcribed non-coding RNA, which was required for efficient spreading of heterochromatin. Furthermore, the head domain directed efficient transcription in heterochromatin.

Conclusions: These results reveal a pivotal role for Mediator in multiple steps of transcription-coupled formation of pericentromeric heterochromatin. This observation further extends the role of Mediator to co-transcriptional chromatin regulation.

overall_design: Gene expression profile at exponentially-growing phase.in the fission yeast deletion mutants of pmc6, med20 and dcr1.

first: Eriko

last: Oya

first: Hiroaki

last: Kato

first: Yuji

last: Chikashige

first: Chihiro

last: Tsutumi

first: Yasushi

last: Hiraoka

first: Yota

last: Murakami


title: Impaired neutrophil recruitment in CXCL5 knockout mice during Mtb infection

status: Public on Sep 02 2014

first: January

last: Weiner

summary: Comparison of Mycobacterium tuberculosis infection in WT mice strain C57BL/6 (WT) and the CXCL5 knockout (KO)

overall_design:
Two color arrays with dye swaps, RNA harvested at day 0 (d00, no infection) and day 21 (d21); 5 mice per experimental group. RNA from each experimental group was pooled.
The e0, e8, e9 and eX are internal experimental run/labels of equivalent biological replications of the experiments.

first: Hans

last: Mollenkopf

first: Geraldine

last: Nouailles


title: Stability of meiosis-specific messenger RNA provides a novel paradigm for the regulation of meiosis

status: Public on Jul 06 2006

summary:
Compared to mitosis, much remains to be elucidated about molecular regulation of meiosis, although increasing light has been shed recently on its signal transduction, cell cycle regulation and chromosome dynamics. Here we show that some transcripts required exclusively for meiosis in fission yeast, such as mei4 mRNA encoding a transcription factor or rec8 mRNA encoding a cohesin subunit, are highly unstable if expressed during the mitotic cell cycle. These transcripts carry a cis-acting region responsible for the mitotic instability, which we name DSR. A YTH-family protein encoded by the mmi1 gene is essential for manifestation of their instability. Deletion of mmi1 impairs cell growth severely, apparently due to detriments brought by untimely expression of meiotic messages. Microarray analysis using a temperature-sensitive mmi1 mutant has revealed that at least a dozen of meiosis-specific transcripts are governed by the DSR-mmi1 system. Thus, regulation of mRNA stability appears to play a crucial role in differentiating the mitotic and the meiotic cell cycles.
Keywords: Keywards: Time course, Temperature-sensitive mutant, mmi1

overall_design:
Gene expression profile in the absence or presence of the fission yeast mmi1 gene function.
Type of experiment: Comparing between vegetatively-growing control cells and cells in each experimental condition.
Experimental factor: Time course after the shift to the restrictive temperature with mmi1-ts3 mutant cells or wild-type control cells.
Quality control steps taken: All experiments were repeated twice in each condition.

first: Yuriko

last: Harigaya

first: Hirotsugu

last: Tanaka

first: Akira

last: Yamashita

first: Kayoko

last: Tsutsumi

first: Yoshinori

last: Watanabe

first: Masayuki

last: Yamamoto


title: Gene expression and distribution of Swi6 in partial aneuploids of the fission yeast Schizosaccharomyces pombe

status: Public on Dec 01 2007

type:
Expression profiling by array
Genome variation profiling by array

summary:
Imbalances of gene expression in aneuploids containing an abnormal number of chromosomes cause a variety of growth and developmental defects. Aneuploid cells of the fission yeast Schizosaccharomyces pombe are inviable, or very unstable, during mitotic growth. However, S. pombe haploid cells bearing a small portion (less than 20%) of the third chromosome can grow stably as a partial aneuploid. We compared the gene expression profiles of partial aneuploid strains with those of the normal haploid strain using DNA microarray analysis. The expression of genes in disomic or trisomic cells was found to increase approximately in proportion to their copy number. We also found that some genes in the monosomic regions of partial aneuploid strains changed their expression level despite there being no change in copy number. We initially speculated that this change in gene expression was a secondary effect resulting from increased expression of the genes in the disomic or trisomic regions. However, even in an aneuploid strain that bears a minichromosome containing no protein coding genes, genes located within about 50kb of the telomere showed similar increases in expression. This result indicates that the change in expression of the genes in the telomere-adjacent region is not a secondary effect of the increased gene dosage. Examining the distribution of the heterochromoatin protein Swi6 using DNA microarray analysis, we found that binding of Swi6 within ~50kb from the telomere occurred less in partial aneuploid strains compared to euploid strains. These results suggest that additional chromosomes in aneuploid strains could lead to imbalances in gene expression through derepression of heterochromatin.
Keywords: Type of experiment: Comparing between  partial aneuploid strains and normal haploid strains.

overall_design: Gene expression profile and distribution of Swi6 in partial anueploids bearing mini chromosomes of the fission yeast Schizosaccharomyces pombe

first: Kasumi

last: Okamasa

first: Jun-ichi

last: Nakayama

first: Osami

last: Niwa

first: Tokuko

last: Haraguchi


title: miR-34 regulates JARID1A expresion (SK-N-BE2)

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary: p53 inactivation occurs only rarely in neuroblastoma, although miR-34, a transcriptional target of p53, is often deleted in neuroblastoma, suggesting  another way in which p53 signaling might be impaired. In this study we show that miR-34 directly targets and downregulates the Polycomb Repressive Complex 2 (PRC2) and its associated histone demethylase, JARID1A, in a p53-dependent manner,

overall_design: 4 samples were transfected with miRNA control or miR-34a, miR-34b, miR-34c into SK-N-BE2 cells.

first: Jun

last: Yang

first: Andrew

last: Davidoff


title: Meiotic proteins Bqt1 and Bqt2 tether telomeres to promote the bouquet arrangement of chromosomes in fission yeast

status: Public on Apr 20 2006

first: Atsushi

last: Matsuda

summary:
In many organisms, meiotic chromosomes are bundled at their telomeres to form a bouquet arrangement. The bouquet formation plays an important role in homologous chromosome pairing and therefore progression of meiosis. As meiotic telomere clustering occurs in response to mating pheromone signaling in fission yeast, we looked for factors essential for bouquet formation among genes induced under mating pheromone signaling. This genome-wide search identified two novel proteins, Bqt1 and Bqt2, that connect telomeres to the spindle-pole body (SPB; the centrosome equivalent in fungi). Neither Bqt1 nor Bqt2 alone functions as a connector, but together the two proteins form a bridge between Rap1 (a telomere protein) and Sad1 (an SPB protein). Significantly, when both Bqt1 and Bqt2 are ectopically expressed in mitotic cells, they also form a bridge between Rap1 and Sad1. Thus, a complex including Bqt1 and Bqt2 is essential for connecting telomeres to the SPB.
Keywords: Keywards: Time course, Nitrogen starvation, Mating pheromone, P-factor.

overall_design:
Gene expression profile under nitrogen starvation in the absence or presence of mating pheromone in fission yeast.
Type of experiment: Comparing between vegetatively-growing control cells and cells in each experimental condition.
Experimental factor: Time course after nitrogen starvation in the presence or absence of P-factor.
Quality control steps taken: All experiments were repeated twice in each condition.

first: Yuji

last: Chikashige

first: Chihiro

first: Miho

last: Yamane

first: Yasushi

last: Hiraoka


title: Distinctive responses to nitrogen starvation in the dominant active mutants of the fission yeast Rheb GTPase.

status: Public on Sep 29 2009

summary: Rheb, a ras-like small GTPase conserved from human to yeast, controls Tor kinase and plays a central role in regulation of cell growth depending on extracellular conditions. Fission yeast Rheb regulates amino acid uptake as well as response to nitrogen starvation. In this study we generated two mutants of Rheb, rhb1-DA4 and rhb1-DA8, and characterized them genetically. V17A mutation within the G1 box defined for the ras-like GTPases was responsible for rhb1-DA4, and Q52R I76F within the switch II domain for rhb1-DA8. In fission yeast, two events, induction of a meiosis initiating gene mei2+ and cell division without cell growth, are a typical response to nitrogen starvation. Under nitrogen-rich conditions, Rheb stimulates Tor kinase, which, in turn, suppresses the response to nitrogen starvation. While amino acid uptake was prevented by both rhb1-DA4 and rhb1-DA8 in a dominant fashion, the response to nitrogen starvation was prevented only by rhb1-DA4. rhb1-DA8 thereby allowed genetic dissection of the Rheb-dependent signaling cascade. We postulate that Rheb in fission may have two downstream elements, Tor kinase for regulation of the response to nitrogen starvation and the other element for regulation of amino acid uptake.

overall_design:
Gene expression profile under nitrogen starvation  in fission yeast.
Type of experiment: Comparing between vegetatively-growing control cells and cells 3 hrs after nitrogen starvation.
Experimental factor: Gene expression profile after nitrogen starvation in the rhb1-D4 or rhb1-D8 cells.
Quality control steps taken: All experiments were repeated more than twice except for the tsc2D which was previously reported.
Keywards:  Nitrogen starvation, rhb1-D4, rhb1-D8

first: Tomoka

last: Murai

first: Yukiko

last: Nakase

first: Keiko

last: Fukuda

first: Tomohiro

last: Matsumoto


title: The CCR4-NOT Complex Is Implicated in the Viability of Aneuploid Yeasts

status: Public on Jun 27 2012

summary: To identify the genes required to sustain aneuploid viability, we screened a deletion library of non-essential genes in the fission yeast Schizosaccharomyces pombe, in which most types of aneuploidy are eventually lethal to the cell.  Aneuploids remain viable for a period time and can form colonies by reducing the extent of the aneuploidy.  We hypothesized that a reduction in colony formation efficiency could be used to screen for gene deletions that compromise aneuploid viability.  Deletion mutants were used to measure the effects on the viability of spores derived from triploid meiosis and from a chromosome instability mutant.  We found that the CCR4-NOT complex, an evolutionarily conserved general regulator of mRNA turnover, and other related factors, including poly(A)-specific nuclease for mRNA decay, are involved in aneuploid viability.  Defective mutations in CCR4-NOT complex components in the distantly related yeast Saccharomyces cerevisiae also affected the viability of spores produced from triploid cells, suggesting that this complex has a conserved role in aneuploids.  In addition, our findings suggest that the genes required for homologous recombination repair are important for aneuploid viability.

overall_design: Gene expression profile at exponentially-growing phase.in the fission yeast deletion mutants of the CCR4-NOT complex protein genes.

first: Yoshie

last: Tange

last: Kurabayashi

first: Bunshiro

last: Goto

first: Kwang-Lae

last: Hoe

first: Dong-Uk

last: Kim

first: Han-Oh

last: Park

first: Jacqueline

last: Hayles

last: Tsutumi

first: Fumiaki

last: Yamao

first: Paul

last: Nurse


title: Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.

status: Public on Apr 01 2009

first: Atsushi

last: Matsuda

summary:
Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon
usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was
not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.

overall_design: Relative amounts of mRNA for each ORF were measured by DNA microarray using genomic DNA as a reference, and the copy number of mRNA was calculated using an estimate of the total mRNA number in the cell as 100,000 copies.

first: Kenichi

last: Kawamata

first: Tokuko

last: Haraguchi

last: Chikashige


title: Expression data from donor lungs of cardiac death and brain death donors

status: Public on Nov 12 2009

city: Seoul

first: Chang-Hyun

last: Kang

address: Yeongun-dong, Chongro-gu

country: South Korea

institute: Seoul National University Hospital

summary:
Lung donation after cardiac death (DCD), in contrast to donation after brain death (DBD), is a promising and increasingly common method to help relieve the shortage of donor organs. However, the pathogenetic consequences of retrieved lungs after DCD vs. DBD have not been clarified.
We aimed to study the differential gene expression profiles in lungs of DCD and DBD patients.

overall_design: DCD patients were matched with DBD lung transplant cases from a prospectively maintained database. The number of tissue samples included in this study was 6 pre- and 5 post-transplant in DCD and 12 pre- and 12 post-transplant in DBD for a total number of 35 lung tissue samples.

first: Chang

first: Masaki

last: Anraku

first: Marcelo

last: Cypel

first: Masaaki

last: Sato

first: Jonathan

last: Yeung

first: Sina

middle: A

last: Gharib

first: Andrew

middle: F

last: Pierre

first: Marc

last: de Perrot

first: Tom

middle: W

last: Waddell

first: Mingyao

last: Liu

first: Shaf

last: Keshavjee


title: Age-dependent decline in lung regeneration with loss of clonogenicity and myofibroblastic differentiation of lung fibroblasts

status: Public on Mar 16 2011

city: North Grafton

first: Julia

last: Paxson

state: MA

address: 200 Westboro Road

department: Clinical Sciences

institute: Tufts Cummings School of Veterinary Medicine

summary: While aging leads to a reduction in the capacity for regeneration after pneumonectomy (PNX) in most mammals, this biological phenomenon has not been characterized over the lifetime of mice. We measured the age-specific (3, 9, 24 month) effects of PNX on physiology, morphometry, cell proliferation and apoptosis, global gene expression, and lung fibroblast phenotype and clonogenicity in female C57BL6 mice. The data show that only 3 month old mice were fully capable of restoring lung volumes by day 7 and total alveolar surface area. By 9 months, the rate of regeneration was slower (with incomplete regeneration by 21 days), and by 24 months there was no regrowth 21 days post-PNX. The early decline in regeneration rate was not associated with changes in alveolar epithelial cell type II (AECII) proliferation or apoptosis rate. However, significant apoptosis and lack of cell proliferation was evident after PNX in both total cells and AECII cells in 24 mo mice. Analysis of gene expression at several time points (1, 3 and 7 days) post-PNX in 3 versus 9 month mice was consistent with a myofibroblast signature (increased Tnc, Lox1, Col3A1, Eln and Tnfrsf12a) and more alpha smooth muscle actin (αSMA) positive myofibroblasts were present after PNX in 9 month than 3 month mice.

overall_design: Microarray analyses of mRNA expression patterns were performed on lung tissue from 9 month versus 3 month mice, before and after PNX. First, gene expression was compared in whole lungs tissues of young (3 month) vs. middle age (9 month) animals obtained at surgery (left, control lung). Second, the global gene expression responses of 3 vs. 9 mo mice were compared after PNX (1, 3 and 7 days) in the right lung. For each animal in the surgical study, the left (excised) lung lobe was used as a control for the corresponding right lung at the end of the study. This design was intended to increase the statistical power for detecting differences in gene expression by comparing pre- and post-PNX lung tissue from the same biological pools (2 animals/pool, 3 pools per group).

first: Chis

last: Parkin


title: Mutations of multiple genes deregulate the NF-kB pathway in diffuse large B cell lymphoma

status: Public on Apr 10 2009

first: Laura

last: Pasqualucci

summary:
Diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma in adulthood, comprises multiple biologically and clinically distinct subtypes including germinal center B cell-like (GCB) and activated B cell like (ABC) DLBCL. Gene expression profile studies have shown that its most aggressive subtype, ABC-DLBCL, is associated with constitutive activation of the NF-kB transcription complex. However, except for a small fraction of cases, it remains unclear whether NF-kB activation in these tumors represents an intrinsic program of the tumor cell of origin or a pathogenetic event. Here we show that >50% of ABC-DLBCL and a smaller fraction of GCB-DLBCL carry somatic mutations at multiple genes, including negative (TNFAIP3/A20) and positive (CARD11, TRAF2, TRAF5, MAP3K7/TAK1 and TNFRSF11A/RANK) regulators of NF-kB. Of these, the A20 gene, which encodes for a ubiquitin-modifying enzyme involved in termination of NF-kB responses, is the most commonly affected one, with ~30% of the patients displaying biallelic inactivation by mutations and/or deletions, suggesting a tumor suppressor role. Less frequently, missense mutations of TRAF2 and CARD11 produce molecules with significantly enhanced ability to activate NF-kB. Thus, our results demonstrate that NF-kB activation in DLBCL is caused by genetic lesions affecting multiple genes, whose loss or activation may promote lymphomagenesis by leading to abnormally prolonged NF-kB responses.
We show that most ABC-DLBCL and a smaller fraction of GCB-DLBCL display genetic lesions affecting multiple NFkB pathway genes, with A20 representing the most frequently mutated gene
Keywords: Phenotypic characterization of human DLBCL.

overall_design: DLBCL biopsies from 73 patients were collected from the archives of the Departments of Pathology at Columbia University and Weill Cornell Medical College. Total RNA was extracted from frozen tumor biopsies and processed according to Affymetrix standard protocols. Purified tonsillar geminal center, naive and memory B cells  (5 samples each from different individuals) were purified by magnetic cell separation as described in Klein et al, PNAS 2003. The dataset includes also: 38 Follicular lymphoma biopsies and 5 lymphoblastoid cell lines.

first: Katia

last: Basso


title: Gene expression analysis of B-NHL from λMYC, λMYC/IµHABCL6, λMYC/AIDKO and λMYC/IµHABCL6/AIDKO mouse models

status: Public on Nov 01 2007

summary:
Most human B cell lymphomas (B-NHL)  are derived from germinal centers (GCs), the structure where B-cells undergo class switch recombination (CSR) and somatic hypermutation (SHM) and are selected for high-affinity antibody production. The pathogenesis of B-NHL is associated with distinct genetic lesions, including chromosomal translocations and aberrant somatic hypermutation, which appear to arise from mistakes occurring during CSR and SHM. To ascertain the role of CSR and SHM in lymphomagenesis, we crossed three oncogene-driven (MYC, BCL6, MYC/BCL6) mouse models of B cell lymphoma with mice lacking activation-induced cytidine deaminase (AID), the enzyme required for both processes.
We show that AID deficiency prevents BCL6-dependent, GC-derived B-NHL, while it has no impact on the formation of MYC-driven, pre-GC lymphomas. Accordingly, abrogation of AID is associated with the disappearance of both CSR- and SHM-mediated structural alterations, including cMYC-IgH chromosomal translocations and aberrant SHM. These results demonstrate that AID is required for GC-derived lymphomagenesis, providing direct support to the notion that errors in AID-mediated antigen-receptor gene modification events represent major contributors to the pathogenesis of human B-NHL.
Keywords: Phenotypic characterization of tumors developing in oncogene-driven mouse models of lymphomas

overall_design: Nodal B-NHL from 5 MYC, 7 MYC/AIDKO, 12 MYC/HABCL6 and 6 MYC/HABCL6/AIDKO mice were analyzed in this study. Total RNA was extracted from frozen tumor biopsies and processed according to Affymetrix standard protocols

first: Riccardo

last: Dalla-Favera


title: Two-step, Extensive Alterations in the Transcriptome from G0 Arrest to Cell Division in Schizosaccharomyces pombe

status: Public on Mar 31 2007

first: Atsushi

last: Matsuda

summary:
Body cells in multi-cellular organisms are in the G0 state, in which cells are arrested and terminally differentiated. To understand how the G0 state is maintained, the genes that are specifically expressed or repressed in G0 must be identified, as they control G0. In the fission yeast Schizosaccharomyces pombe, haploid cells are completely arrested under nitrogen source starvation with high viability. We examined the global transcriptome of G0 cells and cells on the course to resume vegetative growth. Approximately 20% of the transcripts of ~5000 genes increased or decreased more than 4-fold in the two-step transitions that occur prior to replication. Of the top 30 abundant transcripts in G0, 23 were replaced by ribosome- and translation-related transcripts in the dividing vegetative state. Eight identified clusters with distinct alteration patterns of ~2700 transcripts were annotated by Gene Ontology. Disruption of 53 genes indicated that 9 of them were necessary to support the proper G0 state. These 9 genes included two C2H2 zinc finger transcription factors, a cyclin-like protein implicated in phosphorylation of RNA polymerase II, two putative autophagy regulators, a G-protein activating factor, and two CBS domain proteins, possibly involved in AMP-activated kinase.
Keywords: Keywards: Time course, Nitrogen starvation, G0 state, Nitrogen replenishment, Nutrient signal, Cell cycle, Cell proliferation

overall_design:
Gene expression profile during the resumption of cell growth and division from the nitrogen-starved G0 state in fission yeast.
Type of experiment: Comparing the growth-resuming cells in each experimental condition with cells at nitrogen-starved G0 state. Also compairing the vegetatively-growing cells with nitrogen-starved G0 cells.
Experimental factor: Time course after nitrogen replenishment.
Quality control steps taken: Experiments were not repeated. The time course data mostly showed gradual and successive alteration. Little contradiction were apparent among them. Northern hybridization analysis was done on 56 genes for confirmation. (35 cases showed consistent results.)

first: Mizuki

last: Shimanuki

first: Soo-Yoel

last: Chung

first: Yuji

last: Chikashige

first: Yosuke

last: Kawasaki

first: Lisa

last: Uehara

first: Chihiro

last: Tsutsumi

first: Mitsuko

last: Hatanaka

first: Yasushi

last: Hiraoka

first: Koji

last: Nagao

first: Mitsuhiro

last: Yanagida


title: A defect in protein farnesylation suppresses a loss of fission yeast tsc2

status: Public on Jun 13 2006

summary:
Human Tsc1 and Tsc2 genes predispose to Tuberous Sclerosis Complex (TSC), a disorder characterized by the widespread of benign tumors. Tsc1 and Tsc2 proteins form a complex and serve as a GAP (GTP activating protein) for Rheb, a GTPase regulating a downstream kinase, mTor. The fission yeast genome contains tsc1+ and tsc2+, homologs of human Tsc1and Tsc2, respectively. In this study we analyzed gene expression profile in a genome-wide scale and found that deletion of either tsc1+ or tsc2+ affects gene induction upon nitrogen starvation. Three hours after nitrogen depletion genes encoding permeases and genes required for meiosis are less induced. Under the same condition, retrotransposons, G1-cyclin (pas1+) and a gene normally repressed by glucose (inv1+) are more induced. We also demonstrate that a mutation (cpp1-1) in a gene encoding aβ-subunit of a farnesyl transferase can suppress most of the phenotypes associated with deletion of tsc1+ or tsc2+. When a mutant of rhb1+ (homolog of human Rheb), which bypasses the requirement of protein farnesylation, was expressed, the cpp1-1 mutation could no longer suppress, indicating that deficient farnesylation of Rhb1 contributes to the suppression. Based on these results, we discuss the TSC-pathology and possible improvement in chemotherapy for TSC.
Keywords: Keywards:  Nitrogen starvation, Dtsc1. Dtsc2

overall_design:
Gene expression profile under nitrogen starvation  in fission yeast.
Type of experiment: Comparing between vegetatively-growing control cells and cells 3 hrs after nitrogen starvation
Experimental factor: Time course after nitrogen starvation in the presence or absence of Tsc1 or Tsc2
Quality control: Northern hybridization analysis was done on mei2, inv1, tf2 for confirmation.

first: Yukiko

last: Nakase

first: Keiko

last: Fukuda

first: Daisuke

last: Morita

first: Shinpei

last: Kawamoto

first: Mari

last: Ohnuki

first: Tomohiro

last: Matsumoto