Transcriptome profiling of aSaccharomyces cerevisiaemutant with a constitutively activated Ras/cAMP pathway

2003 ◽  
Vol 16 (1) ◽  
pp. 107-118 ◽  
Author(s):  
D. L. Jones ◽  
J. Petty ◽  
D. C. Hoyle ◽  
A. Hayes ◽  
E. Ragni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Microarray Analysis ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Biological Significance ◽  
Altered Expression ◽  
Wall Functions ◽  
Constitutive Activation ◽  
Camp Pathway

Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Δ mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of ∼11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway.

scholarly journals SnoRNA microarray analysis reveals changes in H/ACA and C/D RNA levels caused by dyskerin ablation in mouse liver

2010 ◽  
Vol 429 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Jingping Ge ◽  
Seth D. Crosby ◽  
Michael E. Heinz ◽  
Monica Bessler ◽  
Philip J. Mason
Keyword(s):  
Microarray Analysis ◽  
Mouse Liver ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Microarray Platform ◽  
Protein Component ◽  
Small Nucleolar Rnas ◽  
Ribosome Synthesis ◽  
Nucleolar Rnas ◽  
Host Genes

snoRNAs (small nucleolar RNAs) are key components of snoRNP (small nucleolar ribonucleoprotein) particles involved in modifying specific residues of ribosomal and other RNAs by pseudouridylation (H/ACA snoRNAs) or methylation (C/D snoRNAs). They are encoded within the introns of host genes, which tend to be genes whose products are involved in ribosome biogenesis or function. Although snoRNPs are abundant, ubiquitous and their components highly conserved, information concerning their expression during development or how their expression is altered in diseased states is sparse. To facilitate these studies we have developed a snoRNA microarray platform for the analysis of the abundance of snoRNAs in different RNA samples. In the present study we show that the microarray is sensitive and specific for the detection of snoRNAs. A mouse snoRNA microarray was used to monitor changes in abundance of snoRNAs after ablation of dyskerin, an H/ACA snoRNA protein component, from mouse liver, which causes a decrease in ribosome production. H/ACA snoRNAs were decreased in abundance in these livers while, unexpectedly, C/D snoRNAs were increased. The increase in C/D snoRNAs corresponded with an increase in the abundance of the mRNAs transcribed from snoRNA host genes, suggesting the increase may be part of a cellular response to defective ribosome synthesis.

scholarly journals Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks

2016 ◽  
Vol 113 (26) ◽  
pp. E3676-E3685 ◽  
Author(s):  
Nicholas A. Willis ◽  
Chunshui Zhou ◽  
Andrew E. H. Elia ◽  
Johanne M. Murray ◽  
Antony M. Carr ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Damage ◽  
Dna Replication ◽  
Fission Yeast ◽  
Dna Damage Response ◽  
Cellular Response ◽  
Genome Stability ◽  
Biological Significance ◽  
S Phase ◽  
Damage Response

The cellular response to DNA damage during S-phase regulates a complicated network of processes, including cell-cycle progression, gene expression, DNA replication kinetics, and DNA repair. In fission yeast, this S-phase DNA damage response (DDR) is coordinated by two protein kinases: Rad3, the ortholog of mammalian ATR, and Cds1, the ortholog of mammalian Chk2. Although several critical downstream targets of Rad3 and Cds1 have been identified, most of their presumed targets are unknown, including the targets responsible for regulating replication kinetics and coordinating replication and repair. To characterize targets of the S-phase DDR, we identified proteins phosphorylated in response to methyl methanesulfonate (MMS)-induced S-phase DNA damage in wild-type, rad3∆, and cds1∆ cells by proteome-wide mass spectrometry. We found a broad range of S-phase–specific DDR targets involved in gene expression, stress response, regulation of mitosis and cytokinesis, and DNA replication and repair. These targets are highly enriched for proteins required for viability in response to MMS, indicating their biological significance. Furthermore, the regulation of these proteins is similar in fission and budding yeast, across 300 My of evolution, demonstrating a deep conservation of S-phase DDR targets and suggesting that these targets may be critical for maintaining genome stability in response to S-phase DNA damage across eukaryotes.

scholarly journals A comparative microarray analysis identifies a conserved gene expression signature between airway injury and lung cancer

2016 ◽  
Author(s):  
Adam Giangreco
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Microarray Analysis ◽  
Gene Expression Signature ◽  
Lung Squamous Cell Carcinoma ◽  
Altered Expression ◽  
Lung Cancers ◽  
Expression Signature ◽  
Airway Injury ◽  
Cancer Pathogenesis

AbstractLung squamous cell carcinoma (SqCC) accounts for 30% of lung cancers, with over 400,000 deaths per year worldwide. Although evidence suggests that chronic lung injury drives carcinogenesis, a comprehensive understanding of this process remains elusive. Here, I used a comparative microarray analysis to identify gene expression differences shared between airway injury and squamous lung cancer. Of the 667 genes that exhibited differential expression following murine polidocanol and SO2 injury, 40.6% were additionally dysregulated in human SqCC. Among these, 150 genes were consistently upregulated and 54 downregulated relative to all controls. Examples included genes associated with increased cell cycling, aberrant cytokinesis and DNA repair, and enhanced tumour cell invasion and metastases. For 88.2% of identified genes, altered expression was associated with increased SqCC progression and patient mortality. These results establish a novel gene expression signature linking airway injury and lung cancer pathogenesis.

scholarly journals Antimicrobial activity of the quinoline derivative HT61, effective against non-dividing cells, in Staphylococcus aureus biofilms

2020 ◽  
Author(s):  
C.J. Frapwell ◽  
P.J. Skipp ◽  
R.P. Howlin ◽  
E.M. Angus ◽  
Y. Hu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Cellular Response ◽  
Treatment Success ◽  
Quinoline Derivative ◽  
Global Changes ◽  
Altered Expression ◽  
Wide Range ◽  
Dividing Cells ◽  
Biofilm Development

AbstractStaphylococcus aureus is an opportunistic pathogen responsible for a wide range of chronic infections. Disease chronicity is often associated with biofilm formation, a phenotype that confers enhanced tolerance towards antimicrobials, a trait which can be attributed to a dormant, non-dividing subpopulation within the biofilm. Development of antibiofilm agents that target these populations could therefore improve treatment success. HT61 is a quinoline derivative that has demonstrated efficacy towards non-dividing planktonic Staphylococcus spp. and therefore, in principal, could be effective against staphylococcal biofilms. In this study HT61 was tested on mature S. aureus biofilms, assessing both antimicrobial efficacy and characterising the cellular response to treatment. HT61 was found to be more effective than vancomycin in killing S. aureus biofilms (minimum bactericidal concentrations: HT61; 32 mg/L, vancomycin; 64 mg/L), and in reducing biofilm biomass. Scanning electron microscopy of HT61-treated biofilms also revealed disrupted cellular structure and biofilm architecture. HT61 treatment resulted in increased expression of proteins associated with the cell wall stress stimulon and dcw cluster, implying global changes in peptidoglycan and cell wall biosynthesis. Altered expression of metabolic and translational proteins following treatment also confirm a general adaptive response. These findings suggest that HT61 represents a new treatment for S. aureus biofilm-associated infections that are otherwise tolerant to conventional antibiotics targeting actively dividing cells.

scholarly journals Patterns of DNA Methylation and Gene Expression in Higher-Risk Myelodysplastic Syndromes: Predictors of Demethylating Therapy Response

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4803-4803
Author(s):  
Monika Belickova ◽  
Anna Jonasova ◽  
Jitka Vesela ◽  
Barbora Pejsova ◽  
Jiri Klema ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myelodysplastic Syndromes ◽  
Cellular Response ◽  
Methylation Status ◽  
Therapy Response ◽  
Control Group ◽  
Hypomethylating Agents ◽  
Altered Expression ◽  
Cd34 Cells ◽  
Methylation Profiling

Abstract Background: Standard therapies for patients with higher-risk myelodysplastic syndromes (MDS) include the hypomethylating agents as azacitidine (AZA) and decitabine, of which they benefit significantly. However, the therapy is effective only in 60% of patients. The aim of the project was to identify patients in whom demethylating therapy might be appropriate. Methods: We performed gene expression and methylation profiling in parallel in CD34+ cells from 33 MDS patients before AZA treatment. Control group included 10 healthy individuals. HumanMethylation27 BeadChips and HumanHT-12 v4 Expression BeadChips (Illumina) were used to generate the profiles. DNA and RNA were isolated from the same CD34+ cells separated from bone marrow by magnetic beads. The expression data were preprocessed in lumi package. T-test was applied for differential expression testing. The method of Holm was employed to adjust p-values for multiple comparisons. COHCAP package was used to study differential methylation of the individual genome sites. Beta-values of statistics were considered. Results: We used gene expression and methylation profiling methods to identify predictors of therapy response and prognosis. Overall, 10 patients (30.3%) showed progression (PD), 9 (27.3%) had stable disease (SD), and 14 (42.4%) achieved complete (CR) or partial remission (PR). There were no differences between clinical parameters of these groups before administration of the treatment. The main efficacy indicator of the therapy was duration of overall survival, CR was not the main criterion. Therefore, we divided the patients into two groups for further analysis: patients with and without disease progression. Median survival after initiation of AZA treatment in PD was 11.1 months and in other groups was 25.9 months (Fig. 1). Comparison of gene expression levels between the groups revealed 110 differentially expressed probes (FC >1.5; p<0.05) related to following biological processes (according to the DAVID database): immune response (14 genes), cellular response to stress (12), DNA metabolic process (10), and response to DNA damage stimulus (9).We found affected Mismatch repair pathways (p<0.05). Among the most deregulated genes were F13A1, AR, TM4SF1 and BIRC3 withincreased expression and CXCR4, IRF8, LY86 and FABP4 genes with decreased expression (Fig. 2). Between the patient groups, we found significant differences in methylation status only in 5 genes (p<0.05), namely CLP24, LILRA4, KCNS2, DAAM2 and DBC1 genes. None of the genes showed a negative correlation between the expression and methylation status. Most of these deregulated genes are associated with a worse prognosis in AML. Conclusions: Although the data in our study still require a more comprehensive examination in a larger confirmative cohort of patients, the genomic signatures we detected before hypomethylation therapy may help to stratify patients regarding their response to treatment and thus optimize use of hypomethylating agents in order to achieve maximal benefit. Based on the altered expression and methylation status of AML-related genes, we assume that if a certain degree of the progression process has already started in the patient with MDS, azacitidine therapy is no longer effective. Supported by grant (NT/13899, NT/14377, NT/14539, NT/13847), the project for conceptual development of research organization (00023736) MHCZ and CZ.2.16/3.1.00/28007. Disclosures No relevant conflicts of interest to declare.

Abstract 1: Nucleolar Proteins Controlling Cardiac Phenotype in Rat Myocytes and Zebrafish Revealed by Chromatin Proteomics

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Emma Monte ◽  
Kevin Mouillesseaux ◽  
Haodong Chen ◽  
Shuxun Ren ◽  
Yibin Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Cardiac Hypertrophy ◽  
Ribosome Biogenesis ◽  
Cardiac Cells ◽  
Global Changes ◽  
Cellular Plasticity ◽  
Rdna Transcription ◽  
Altered Expression ◽  
Cardiac Phenotype

Cardiac hypertrophy is a common precursor to heart failure, during which cardiomyocytes grow to compensate for an increased workload. Hypertrophic cardiomyocytes undergo significant changes in cellular plasticity by adopting the expression profile and some phenotypic aspects of more primitive (embryonic or fetal) cardiac cells. These global changes in gene expression, conserved between humans and animal models of heart failure, must be preceded by structural alterations to the chromatin. Specifically, chromatin regions must be architecturally modified to allow or deny access for transcriptional machinery. However, the proteins responsible for remodeling chromatin to accomplish these gene expression changes during cardiac hypertrophy and failure are largely unknown. We used a proteomics approach to identify proteins bound to cardiac chromatin and to quantify changes in their abundance during disease. Quantitative mass spectrometry and bioinformatics revealed that 366 of the chromatin-bound proteins detected in this study displayed altered expression in a mouse model of pressure overload cardiac hypertrophy and failure. This included the chromatin remodeling protein Nucleolin (Ncl), which exhibited increased association with chromatin in the hypertrophic heart. To examine its role in regulating cardiac morphology and function we performed morpholino based knockdown of Ncl in zebrafish embryos. Ncl knockdown promoted the expression of bmp4 (a fetal marker), inhibited normal cardiomyocyte differentiation and resulted in abnormal heart chamber formation and looping. Hearts in surviving fish exhibited functional deficits as measured by fluorescence imaging and line-scanning analysis. To investigate the actions of Ncl in the mammalian cardiomyocyte, knockdown was carried out in isolated rat ventricular myocytes using siRNA. Loss of Ncl induced heterochromatin formation (increased Histone H3 K9-trimethylation), suppressed rDNA transcription (52% decrease in pre-rRNA via qPCR) and promoted fetal gene expression (65% increase in ANF; 41% increase in β-MHC transcripts). Overall, this study identifies Ncl as a regulator of chromatin structure, cell growth via ribosome biogenesis and cellular plasticity in the cardiomyocyte.

scholarly journals Transcriptome analysis reveals the differences between cellular response to ribosomal stress and translational stress

2017 ◽  
Author(s):  
Md Shamsuzzaman ◽  
Brian Gregory ◽  
Vincent Bruno ◽  
Lasse Lindahl
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Cell Wall ◽  
Cell Division ◽  
Cell Growth ◽  
Cell Membrane ◽  
Ribosomal Protein ◽  
Ribosome Biogenesis ◽  
Responsive Gene ◽  
Ribosomal Stress

AbstractRibosome biogenesis is an essential metabolic process of a growing cell. Cells need to continuously synthesize new ribosomes in order to make new proteins than can support building biomass and cell division. It is obvious that in the absence of ribosome biogenesis, cell growth will stop and cell division will stall. However, it is not clear whether cell growth stops due to reduced protein synthesis capacity (translational stress) or due to activation of signaling specific to ribosome biogenesis abnormalities (ribosomal stress). To understand the signaling pathways leading to cell cycle arrest under ribosomal and translational stress conditions, we performed time series RNA-seq experiments of cells at different time of ribosomal and translational stress. We found that expression of ribosomal protein genes follow different course over the time of these two stress types. In addition, ribosomal stress is sensed early in the cell, as early as 2hr. Up-regulation of genes responsive to oxidative stress and over representation of mRNAs for transcription factors responsive to stress was detected in cell at 2hr of ribosomal protein depletion. Even though, we detected phenotypic similarities in terms of cell separation and accumulation in G1 phase cells during inhibition of ribosome formation and ribosome function, different gene expression patterns underlie these phenotypes, indicating a difference in causalities of these phenotypes. Both ribosomal and translational stress show common increased expression of stress responsive gene expression, like Crz1 target gene expression, signature of oxidative stress response and finally membrane or cell wall instability. We speculate that cell membrane and cell wall acts as major stress sensor in the cell and adjust cellular metabolism accordingly. Any change in membrane lipid composition, or membrane protein oxidation, or decrease or increase in intracellular turgor pressure causes stress in cell membrane. Cell membrane or cell wall stress activates and/or inactivates specific signaling pathway which triggers stress responsive gene expression and adaptation of cellular behavior accordingly.

Microarray analysis of gene expression in blood neutrophils of parturient cows

2004 ◽  
Vol 16 (2) ◽  
pp. 212-221 ◽  
Author(s):  
Sally A. Madsen ◽  
Ling-Chu Chang ◽  
Mary-Clare Hickey ◽  
Guilherme J. M. Rosa ◽  
Paul M. Coussens ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Mixed Model ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rt Pcr ◽  
Altered Expression ◽  
Mixed Model Approach ◽  
Blood Neutrophils ◽  
Induced Changes

It is well documented that blood neutrophils from parturient dairy cows do not perform as well as neutrophils from nonparturient cows in laboratory assays of adhesion, migration, or phagocytosis-induced respiratory burst. However, little is known about the possible molecular basis for parturition-induced changes in neutrophils. cDNA microarray analysis was used in the current study to explore parturition-induced changes in gene expression profiles in bovine blood neutrophils. Total RNA from isolated blood neutrophils of four parturient Holstein cows was obtained before, during, and after parturition, reverse transcribed into cDNA, and sequentially labeled with Cy3 or Cy5 dyes prior to paired hybridizations to 1,056 member bovine total leukocyte (BOTL-3) microarrays in a loop design. Resulting gene expression data were LOWESS normalized by array and analyzed using a mixed model approach. Results showed that expression profiles for 302 BOTL-3 genes were influenced by parturition. BLASTn analysis and preliminary clustering of affected genes by biological function indicated that the largest proportion (14%) of changed genes encode proteins critical to regulation of apoptosis. Independent confirmation of altered expression for 16 of these genes was achieved using quantitative real-time RT-PCR (Q-RT-PCR). A predominantly survival phenotype inferred from the microarray and Q-RT-PCR results was substantiated by monitoring apoptosis status of blood neutrophils from castrated male cattle cultured in the presence of sera from parturient cows. Thus our combined gene expression and apoptosis phenotyping results suggest that bovine parturition may induce prolonged survival in normally short-lived blood neutrophils.

scholarly journals Overexpression of Genes of the Cell Wall Stimulon in Clinical Isolates of Staphylococcus aureus Exhibiting Vancomycin-Intermediate- S. aureus-Type Resistance to Vancomycin

2006 ◽  
Vol 188 (3) ◽  
pp. 1120-1133 ◽  
Author(s):  
Fionnuala McAleese ◽  
Shang Wei Wu ◽  
Krzysztof Sieradzki ◽  
Paul Dunman ◽  
Ellen Murphy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Heart Valve ◽  
Genetic Relatedness ◽  
Expression Profiles ◽  
Altered Expression ◽  
Vancomycin Mics ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles in Staphylococcus aureus isolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes, srtA and srtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).

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