Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

EIF3a in Urinary Bladder Cancer M-bM-^@M-^S in vivo and in vitro insights

ABSTRACT: The eukaryotic translation initiation factor (eIF) 3a is described in various tumor entities as potential tumor marker involved in development and progression of cancer. eIF3a is the largest subunit of the eIF3 complex, a key functional entity in 80S establishment and translation initiation. We hypothesize that eIF3a is more a specific than global translation initiator and involved in signalling pathways that are frequently targeted in UBC therapy. Methods: In FFPE samples of UBC patients eIF3a expression was analysed together with overall survival. In cell culture we investigated proliferation, migration, clonogenicity and tumorgenicity of UBC cell lines with and without knockdown of eIF3a and compared the cytotoxicity of eIF3a knockdown with other translational inhibitors, including the chemotherapeutic Rapamycine. Detailed information on changed gene expression and global translation initiation were gathered by mRNA expresssion and polysomal profiling. Results: and Conclusion eIF3a is upregulated in UBC and high expression of eIF3a corresponds with longer overall survival in low grade tumors. Knockdown of eIF3a in UBC cell lines reduces their malignant phenotype, including reduced tumor growth in xenotransplanted mice. eIF3a regulates DNA damage response (ATM, ATR, CDC25A) on a translational level and we show that reduction in eIF3a expression does not hamper global translation initiation. The knockdown of eIF3a strongly influences proliferation of UBC cell lines without dramatically disturbing general translation as depicted in polysomal profiles. We therefore analysed potential changes on the mRNA level in eIF3a knockdown compared to control HT1197 cells. Differential expression of genes between eIF3a knock-down and control samples was assessed with the moderated t-test (Bioconductor's limma package). Raw p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg for a strong control of the false discovery rate.

ORGANISM(S): Homo sapiens

SUBMITTER: Johannes Rainer

PROVIDER: E-GEOD-45636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

eIF3a is over-expressed in urinary bladder cancer and influences its phenotype independent of translation initiation.

Spilka Rita R Ernst Christina C Bergler Helmut H Rainer Johannes J Flechsig Susanne S Vogetseder Alexander A Lederer Eva E Benesch Martin M Brunner Andrea A Geley Stephan S Eger Andreas A Bachmann Felix F Doppler Wolfgang W Obrist Peter P Haybaeck Johannes J

Cellular oncology (Dordrecht) 20140729 4

<h4>Purpose</h4>The eukaryotic translation initiation factor (eIF) 3a, the largest subunit of the eIF3 complex, is a key functional entity in ribosome establishment and translation initiation. In the past, aberrant eIF3a expression has been linked to the pathology of various cancer types but, so far, its expression has not been investigated in transitional cell carcinomas. Here, we investigated the impact of eIF3 expression on urinary bladder cancer (UBC) cell characteristics and UBC patient sur ...[more]

PMID: 25070653

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Project description:Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant; Goal: ; To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of; eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5â leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5â leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Experiment Overall Design: Polysomal and non-polysomal RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants. The translation state (ratio between the polysome and non-polysome, PL/NP) for each gene in the WT and in the mutant was separately established, and then the translation states between the genotype were compared.

Project description:Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. Comparison of translatome profile changes with corresponding transcriptome profile changes can provide a measure of the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. To provide a direct experimental evaluation of the phenomenon, we decided to study a classical example of transcriptional reprogramming of gene expression: Epidermal Growth Factor (EGF) treatment. This stimulus triggers a well known chain of intracellular transduction events, ultimately resulting in a multifaceted phenotypic spectrum of changes with prevalent induction of cell growth and proliferation. We subjected HeLa cells to serum starvation for 12h and then we added EGF at final concentration of 1 Î¼g/ml, profiling before and after 40 minutes of treatment the transcriptome, the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation, and also the mRNA content of the subpolysomal pool, expected not to be actively translated. Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, EGF starvation release. The comparison between transcriptional and polysomal profiling was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved HeLa cells transcriptome in response to EGF stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA, subpolysomal RNA and total RNA were isolated from HeLa cells serum starved and treated with EGF. Cells lysates were collected before (t = 0 min) and after (t = 40 min) EGF treatment. All experiments were run in triplicates.

Dataset Information

EIF3a in Urinary Bladder Cancer M-bM-^@M-^S in vivo and in vitro insights

Publications

eIF3a is over-expressed in urinary bladder cancer and influences its phenotype independent of translation initiation.

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