Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post-translational turnover, we devised a strategy combining pulse stable isotope-labeled amino acids in cells (pSILAC), data-independent acquisition mass spectrometry (DIA-MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome-wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.

• MeSH
• alternativní sestřih MeSH
• HeLa buňky MeSH
• hmotnostní spektrometrie MeSH
• izoformy RNA genetika   metabolismus   MeSH
• izotopové značení metody   MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• protein - isoformy analýza   metabolismus   MeSH
• proteiny analýza   metabolismus   MeSH
• proteolýza MeSH
• proteomika metody   MeSH
• průběh práce MeSH
• regulace genové exprese u nádorů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS: We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS: We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.

• MeSH
• biogeneze organel MeSH
• genetická variace MeSH
• iniciace translace peptidového řetězce * MeSH
• kardiomegalie genetika   metabolismus   patologie   MeSH
• krysa rodu rattus MeSH
• lokus kvantitativního znaku * MeSH
• malá jadérková RNA genetika   metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• myokard metabolismus   patologie   MeSH
• myši inbrední C57BL MeSH
• myši knockoutované MeSH
• myši MeSH
• potkani inbrední SHR MeSH
• potkani transgenní MeSH
• regulace genové exprese MeSH
• ribozomální proteiny genetika   metabolismus   MeSH
• ribozomy genetika   metabolismus   patologie   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• sarkomery metabolismus   patologie   MeSH
• stanovení celkové genové exprese MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

INTRODUCTION: Interferon-β (IFNß) is the first-line treatment for relapsing-remitting multiple sclerosis. Myxovirus resistance protein A (MxA) is a marker of IFNß bioactivity, which may be reduced by neutralizing antibodies (NAbs) against IFNß. The aim of the study was to analyze the kinetics of MxA mRNA expression during long-term IFNβ treatment and assess its predictive value. METHODS: A prospective, observational, open-label, non-randomized study was designed in multiple sclerosis patients starting IFNß treatment. MxA mRNA was assessed prior to initiation of IFNß therapy and every three months subsequently. NAbs were assessed every six months. Assessment of relapses was scheduled every three months during 24 months of follow up. The disease activity was correlated to the pretreatment baseline MxA mRNA value. In NAb negative patients, clinical status was correlated to MxA mRNA values. RESULTS: 119 patients were consecutively enrolled and 107 were included in the final analysis. There was no correlation of MxA mRNA expression levels between baseline and month three. Using survival analysis, none of the selected baseline MxA mRNA cut off points allowed prediction of time to first relapse on the treatment. In NAb negative patients, mean MxA mRNA levels did not significantly differ in patients irrespective of relapse status. CONCLUSION: Baseline MxA mRNA does not predict the response to IFNß treatment or the clinical status of the disease and the level of MxA mRNA does not correlate with disease activity in NAb negative patients.

• MeSH
• dospělí MeSH
• injekce intramuskulární MeSH
• injekce subkutánní MeSH
• interferon beta 1a aplikace a dávkování   terapeutické užití   MeSH
• kinetika MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA metabolismus   MeSH
• mladý dospělý MeSH
• neutralizující protilátky krev   MeSH
• plocha pod křivkou MeSH
• prospektivní studie MeSH
• protein Mx genetika   metabolismus   MeSH
• ROC křivka MeSH
• roztroušená skleróza farmakoterapie   metabolismus   patologie   MeSH
• senioři MeSH
• stupeň závažnosti nemoci MeSH
• výsledek terapie MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• klinické zkoušky MeSH

The aim of the study was to determine whether or not the tyrosine kinase receptor ERBB2 is overexpressed in synovial sarcomas (SSs). We also focused on the cell cycle-related nuclear protein-Ki-67. Thirty-two samples were available for immunohistochemistry and only 1 case revealed a weak diffuse membrane ERBB-2 staining. The remaining cases showed either no staining (20 cases) or weak focal membrane staining (9 cases). In our 3 highly overexpressed ERBB2 mRNA samples, fluorescence in situ hybridization showed no amplification of the ERBB2 gene. ERBB2 mRNA expression was present in all samples of SSs at a comparable level to that in breast carcinoma control group, with a 2+ or 3+ immunopositivity. The high level of ERBB2 mRNA expression correlated with a high level of Ki-67 mRNA. The level of Ki-67 mRNA correlated with Ki-67 protein expression. The study shows that ERBB2 mRNA expression is very strong in SSs, but the membrane ERBB-2 protein expression is practically absent.

• MeSH
• antigen Ki-67 analýza   genetika   metabolismus   MeSH
• dítě MeSH
• dospělí MeSH
• financování organizované MeSH
• hybridizace in situ fluorescenční MeSH
• imunohistochemie MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA analýza   metabolismus   MeSH
• mladiství MeSH
• předškolní dítě MeSH
• proliferace buněk MeSH
• receptor erbB-2 analýza   genetika   metabolismus   MeSH
• synoviom patologie   MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH

This paper describes a comparative systems level analysis of the developmental proteome and transcriptome in the model antibiotic-producing eubacterium Streptomyces coelicolor, cultured on different media. The analysis formulates expression as the superposition of effects of regulatory networks and biological processes which can be identified using singular value decomposition (SVD) of a data matrix formed by time series measurements of expression of individual genes throughout the cell cycle of the bacterium. SVD produces linearly orthogonal factors, each of which can represent an independent system behavior defined by a linear combination of the genes/proteins highly correlated with the corresponding factor. By using SVD of the developmental time series of gene expression, as measured by both protein and RNA levels, we show that on the highest level of control (representing the basic kinetic behavior of the population), the results are identical, regardless of the type of experiment or cultivation method. The results show that this approach is capable of identifying basic regulatory processes independent of the environment in which the organism lives. It also shows that these processes are manifested equally on protein and RNA levels. Biological interpretation of the correlation of the genes and proteins with significant eigenprofiles (representing the highest level kinetic behavior of protein and/or RNA synthesis) revealed their association with metabolic processes, stress responses, starvation, and secondary metabolite production.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• bakteriální RNA genetika   metabolismus   MeSH
• citrátový cyklus MeSH
• financování organizované MeSH
• interpretace statistických dat MeSH
• messenger RNA genetika   metabolismus   MeSH
• proteiny teplotního šoku genetika   metabolismus   MeSH
• proteomika metody   statistika a číselné údaje   MeSH
• stanovení celkové genové exprese metody   statistika a číselné údaje   MeSH
• Streptomyces genetika   metabolismus   růst a vývoj   MeSH
• systémová biologie MeSH
• Publikační typ
• srovnávací studie MeSH

In this paper, correlation analysis of protein and mRNA levels in the soil dwelling bacteria Streptomyces coelicolor (S. coelicolor M145) is presented during development of the population as it grew in liquid medium using three biological and two technical replicates, measured during exponential growth, and its entry into the stationary phase. The proteome synthesis time series are compared with the gene expression time series measured previously under identical experimental conditions. Results reveal that about one third of protein/mRNA synthesis profiles are well correlated while another third are correlated negatively. Functional analysis of the highly correlated groups is presented. Based on numerical simulation, the negative correlation between protein and mRNA is shown to be caused by the difference between the rate of translation and protein degradation.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• proteom analýza   metabolismus   MeSH
• půda chemie   MeSH
• regulace genové exprese u bakterií MeSH
• stanovení celkové genové exprese MeSH
• Streptomyces coelicolor genetika   růst a vývoj   metabolismus   MeSH
• transkriptom * MeSH
• vývojová regulace genové exprese * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

FUS-DDIT3 belongs to the FET (FUS, EWSR1, and TAF15) family of fusion oncogenes, which collectively are considered to be key players in tumor development. Even though over 90% of all myxoid liposarcomas (MLS) have a FUS-DDIT3 gene fusion, there is limited understanding of the signaling pathways that regulate its expression. In order to study cell proliferation and FUS-DDIT3 regulation at mRNA and protein levels, we first developed a direct cell lysis approach that allows DNA, mRNA, and protein to be analyzed in the same sample using quantitative PCR, reverse transcription quantitative qPCR and proximity ligation assay, respectively. We screened 70 well-characterized kinase inhibitors and determined their effects on cell proliferation and expression of FUS-DDIT3 and FUS at both mRNA and protein levels in the MLS 402-91 cell line, where twelve selected inhibitors were evaluated further in two additional MLS cell lines. Both FUS-DDIT3 and FUS mRNA expression correlated with cell proliferation and both transcripts were co-regulated in most conditions, indicating that the common 5' FUS promotor is important in transcriptional regulation. In contrast, FUS-DDIT3 and FUS protein levels displayed more cell line dependent expression. Furthermore, most JAK inhibitors caused FUS-DDIT3 downregulation at both mRNA and protein levels. In conclusion, defining factors that regulate FUS-DDIT3 expression opens new means to understand MLS development at the molecular level.

• MeSH
• DNA analýza   genetika   metabolismus   MeSH
• fúzní onkogenní proteiny analýza   genetika   metabolismus   MeSH
• lidé MeSH
• messenger RNA analýza   genetika   metabolismus   MeSH
• myxoidní liposarkom genetika   metabolismus   MeSH
• nádorové buněčné linie MeSH
• proliferace buněk účinky léků   MeSH
• protinádorové látky farmakologie   MeSH
• regulace genové exprese u nádorů účinky léků   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Sudan I (1-phenylazo-2-hydroxynaphthol) is a suspected human carcinogen causing tumors in the livers and urinary bladders of rats, mice, and rabbits. Here, we investigated for the first time the influence of Sudan I exposure on the expression of several biotransformation enzymes in the livers, kidneys, and lungs of rats concomitantly at the mRNA and protein levels and assayed their enzymatic activities. We also studied its effect on the formation of Sudan I-derived DNA adducts in vitro. Sudan I increased the total amounts of cytochrome P450 (P450) in all organs tested. Western blots using antibodies raised against various P450s, NADPH:P450 reductase, and NAD(P)H:quinone oxidoreductase 1 (NQO1) showed that the expression of P450 1A1 and NQO1 was induced in the liver, kidney, and lung of rats treated with Sudan I. The higher protein levels correlated with increased enzyme activities of P450 1A1/2 and NQO1. Furthermore, 9.9-, 5.9-, and 2.8-fold increases in the formation of Sudan I oxidative metabolites catalyzed by microsomes isolated from the liver, kidney, and lung, respectively, of rats treated with Sudan I were found. The relative amounts of P450 1A and NQO1 mRNA, measured by real-time polymerase chain reaction (RT-PCR) analysis, demonstrated that Sudan I induced the expression of P450 1A1 and NQO1 mRNA in the liver, kidney, and lung, and of P450 1A2 mRNA in kidney and lung. Finally, microsomes isolated from livers, kidneys, and lungs of Sudan I exposed rats more effectively catalyzed the formation of Sudan I-DNA adducts than microsomes from organs of control rats. This was attributable to the higher P450 1A1 expression. Because P450 1A1 is playing a major role in the bioactivation of Sudan I in rat and human systems, its induction by Sudan I may have a profound effect on cancer risk by this azo dye. In addition, the induction of P450 1A1/2 and NQO1 enzymes can influence individual human susceptibility to other environmental carcinogens and have an effect on cancer risk.

• MeSH
• adukty DNA účinky léků   metabolismus   MeSH
• barvicí látky metabolismus   MeSH
• cytochrom P-450 CYP1A1 genetika   metabolismus   MeSH
• cytosol účinky léků   enzymologie   MeSH
• játra účinky léků   enzymologie   MeSH
• karcinogeny metabolismus   MeSH
• krysa rodu rattus MeSH
• ledviny účinky léků   enzymologie   MeSH
• messenger RNA genetika   MeSH
• mikrozomy účinky léků   enzymologie   MeSH
• NAD(P)H dehydrogenasa (chinon) genetika   metabolismus   MeSH
• naftoly metabolismus   MeSH
• plíce účinky léků   enzymologie   MeSH
• potkani Wistar MeSH
• upregulace účinky léků   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• duktální karcinom genetika   MeSH
• finanční podpora výzkumu jako téma MeSH
• genová dávka MeSH
• geny erbB-2 MeSH
• lidé MeSH
• nádory prsu genetika   MeSH
• receptor erbB-2 genetika   metabolismus   MeSH
• regulace genové exprese u nádorů MeSH
• senioři MeSH
• Check Tag
• lidé MeSH
• senioři MeSH
• ženské pohlaví MeSH

Using the data of 723 chronic myeloid leukemia (CML) patients in the chronic phase, we analyzed the prognostic value of the Sokal, Euro, and EUTOS scores as well as the level of BCR-ABL1 and the achievement of complete cytogenetic response (CCgR) at 3 months of imatinib therapy in relation to the so-called current survival measures: the current cumulative incidence (CCI) reflecting the probability of being alive and in CCgR after starting imatinib therapy; the current leukemia-free survival (CLFS) reflecting the probability of being alive and in CCgR after achieving the first CCgR; and the overall survival. The greatest difference between the CCI curves at 5 years after initiating imatinib therapy was observed for the BCR-ABL1 transcripts at 3 months. The 5-year CCI was 94.3% in patients with BCR-ABL1 transcripts ≤ 10% and 57.1% in patients with BCR-ABL1 transcripts > 10% (P = 0.005). Therefore, the examination of BCR-ABL1 transcripts at 3 months may help in early identification of patients who are likely to perform poorly with imatinib. On the other hand, CLFS was not significantly affected by the considered stratifications. In conclusion, our results indicate that once the CCgR is achieved, the prognosis is good irrespective of the starting prognostic risks.

• MeSH
• analýza přežití MeSH
• bcr-abl fúzní proteiny genetika   metabolismus   MeSH
• benzamidy terapeutické užití   MeSH
• chronická fáze myeloidní leukemie diagnóza   farmakoterapie   genetika   mortalita   MeSH
• dospělí MeSH
• indukce remise MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• mladiství MeSH
• piperaziny terapeutické užití   MeSH
• prediktivní hodnota testů MeSH
• protinádorové látky terapeutické užití   MeSH
• pyrimidiny terapeutické užití   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• výsledek terapie MeSH
• výzkumný projekt MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH