functional profiling
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... Tumor staging and grading: A primer -- Clinical trial design in the age of molecular profiling -- Personalized ... ... clinical trials -- Reduction of preanalytical variability in specimen procurement for molecular profiling ... ... -- The human side of cancer biobanking -- Introduction to genomics -- Genomic profiling: cDNA arrays ... ... and oligoarrays -- Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue ... ... samples -- An overview of microRNA methods: expression profiling and target identification -- Antibody ...
Methods in molecular biology, ISSN 1064-3745 vol 823
xiii, 447 s. : il. ; 27 cm
- MeSH
- molekulární biologie MeSH
- Publikační typ
- laboratorní příručky MeSH
- příručky MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biologie
Vznik a progrese plicních karcinomů je stejně jako u ostatních solidních nádorů provázena celou řadou poruch (mutací) genomu. Tyto často charakteristické poruchy představují molekulární markery a jejich vyšetřování se stalo dnes již neodmyslitelnou součástí diagnosticko-terapeutického procesu. Doplnění klasické histopatologické klasifikace založené na morfologii o informaci o molekulárním profilu se stává zcela klíčovým nástrojem pro predikci úspěšnosti protinádorové léčby i odhadu prognózy onkologických pacientů. Novým směrem v moderní patologické diagnostice je metoda tzv. tekuté biopsie, neboli vyšetřování nádorových buněk a nádorové DNA uvolněných do periferního oběhu pacienta.
As in other solid tumours, the development and progression of lung cancer is accompanied by a whole number of genome disorders (mutations). These often characteristic disorders represent molecular markers and their investigation has now become an inseparable part of the diagnostic-therapeutic process. Supplementing the conventional morphology-based histopathological classification with information on the molecular profile is becoming a completely crucial tool for predicting the success rate of anticancer treatment as well as estimating the prognosis of cancer patients. A new trend in modern pathological diagnosis is the method of so-called liquid biopsy, or the investigation of cancer cells and tumour DNA released into the patient’s peripheral circulation.
- Klíčová slova
- nádorová genomika,
- MeSH
- adenokarcinom genetika MeSH
- cílená molekulární terapie MeSH
- cirkulující nádorová DNA MeSH
- DNA nádorová * genetika krev MeSH
- genomika MeSH
- geny nádorové MeSH
- lidé MeSH
- malobuněčný karcinom plic genetika MeSH
- mutace * MeSH
- mutační analýza DNA MeSH
- nádorová transformace buněk MeSH
- nádorové biomarkery genetika MeSH
- nádorové cirkulující buňky MeSH
- nádory plic * genetika MeSH
- nemalobuněčný karcinom plic genetika MeSH
- sekvenční analýza DNA MeSH
- spinocelulární karcinom genetika MeSH
- tekutá biopsie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
Polycomb repressive complex 2 (PRC2) is involved in maintaining transcriptionally silent chromatin states through methylating lysine 27 of histone H3 by the catalytic subunit enhancer of zeste [E(z)]. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. For the first time, we identify the putative ortholog of E(z) in Discoba, a lineage hypothetically proximal to the eukaryotic root, strongly supporting emergence of PRC2 before the diversification of eukaryotes. Analyzing 283 species, we robustly detect a common presence of E(z) and ESC, indicating a conserved functional core. Full-length Su(z)12 orthologs were identified in some lineages and species only, indicating, nonexclusively, high divergence of VEFS-Box-containing Su(z)12-like proteins, functional convergence of sequence-unrelated proteins, or Su(z)12 dispensability. Our results trace E(z) evolution within the SET-domain protein family, proposing a substrate specificity shift during E(z) evolution based on SET-domain and H3 histone interaction prediction.
BACKGROUND: The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry and are having potential biomedical applications. Several independent breeding programs around the world have been initiated to develop new cultivars with enriched lupulin and secondary metabolite contents but met with limited success due to several constraints. In the present work, a pioneering attempt has been made to overexpress master regulator binary transcription factor complex formed by HlWRKY1 and HlWDR1 using a plant expression vector to enhance the level of prenylflavonoid and bitter acid content in the hop. Subsequently, we performed transcriptional profiling using high-throughput RNA-Seq technology in leaves of resultant transformants and wild-type hop to gain in-depth information about the genome-wide functional changes induced by HlWRKY1 and HlWDR1 overexpression. RESULTS: The transgenic WW-lines exhibited an elevated expression of structural and regulatory genes involved in prenylflavonoid and bitter acid biosynthesis pathways. In addition, the comparative transcriptome analysis revealed a total of 522 transcripts involved in 30 pathways, including lipids and amino acids biosynthesis, primary carbon metabolism, phytohormone signaling and stress responses were differentially expressed in WW-transformants. It was apparent from the whole transcriptome sequencing that modulation of primary carbon metabolism and other pathways by HlWRKY1 and HlWDR1 overexpression resulted in enhanced substrate flux towards secondary metabolites pathway. The detailed analyses suggested that none of the pathways or genes, which have a detrimental effect on physiology, growth and development processes, were induced on a genome-wide scale in WW-transgenic lines. CONCLUSIONS: Taken together, our results suggest that HlWRKY1 and HlWDR1 simultaneous overexpression positively regulates the prenylflavonoid and bitter acid biosynthesis pathways in the hop and thus these transgenes are presented as prospective candidates for achieving enhanced secondary metabolite content in the hop.
BACKGROUND: Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is the colony biofilm, composed of surface ("aerial") and invasive ("root") cells. While surface cells have been partially analyzed before, we know little about invasive root cells. In particular, information on the metabolic, chemical and morphogenetic properties of invasive versus surface cells is lacking. In this study, we used a new strategy to isolate invasive cells from agar and extracellular matrix, and employed it to perform genome wide expression profiling and biochemical analyses of surface and invasive cells. RESULTS: RNA sequencing revealed expression differences in 1245 genes with high statistical significance, indicating large genetically regulated metabolic differences between surface and invasive cells. Functional annotation analyses implicated genes involved in stress defense, peroxisomal fatty acid β-oxidation, autophagy, protein degradation, storage compound metabolism and meiosis as being important in surface cells. In contrast, numerous genes with functions in nutrient transport and diverse synthetic metabolic reactions, including genes involved in ribosome biogenesis, biosynthesis and translation, were found to be important in invasive cells. Variation in gene expression correlated significantly with cell-type specific processes such as autophagy and storage compound accumulation as identified by microscopic and biochemical analyses. Expression profiling also provided indications of cell-specific regulations. Subsequent knockout strain analyses identified Gip2p, a regulatory subunit of type 1 protein phosphatase Glc7p, to be essential for glycogen accumulation in surface cells. CONCLUSIONS: This is the first study reporting genome wide differences between surface and invasive cells of yeast colony biofilms. New findings show that surface and invasive cells display very different physiology, adapting to different conditions in different colony areas and contributing to development and survival of the colony biofilm as a whole. Notably, surface and invasive cells of colony biofilms differ significantly from upper and lower cells of smooth colonies adapted to plentiful laboratory conditions.
OBJECTIVE: To identify novel genetic and epigenetic factors associated with Myasthenia gravis (MG) using an identical twins experimental study design. METHODS: The transcriptome and methylome of peripheral monocytes were compared between monozygotic (MZ) twins discordant and concordant for MG, as well as with MG singletons and healthy controls, all females. Sets of differentially expressed genes and differentially methylated CpGs were validated using RT-PCR for expression and target bisulfite sequencing for methylation on additional samples. RESULTS: >100 differentially expressed genes and ∼1800 differentially methylated CpGs were detected in peripheral monocytes between MG patients and controls. Several transcripts associated with immune homeostasis and inflammation resolution were reduced in MG patients. Only a relatively few genes differed between the discordant healthy and MG co-twins, and both their expression and methylation profiles demonstrated very high similarity. INTERPRETATION: This is the first study to characterize the DNA methylation profile in MG, and the expression profile of immune cells in MZ twins with MG. Results suggest that numerous small changes in gene expression or methylation might together contribute to disease. Impaired monocyte function in MG and decreased expression of genes associated with inflammation resolution could contribute to the chronicity of the disease. Findings may serve as potential new predictive biomarkers for disease and disease activity, as well as potential future targets for therapy development. The high similarity between the healthy and the MG discordant twins, suggests that a molecular signature might precede a clinical phenotype, and that genetic predisposition may have a stronger contribution to disease than previously assumed.
- MeSH
- CpG ostrůvky MeSH
- dospělí MeSH
- dvojčata monozygotní * MeSH
- epigeneze genetická MeSH
- genetická predispozice k nemoci MeSH
- genetické asociační studie MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA * MeSH
- mladý dospělý MeSH
- monocyty imunologie metabolismus MeSH
- myasthenia gravis genetika metabolismus MeSH
- receptor TREM-1 genetika metabolismus MeSH
- senioři MeSH
- signální transdukce MeSH
- stanovení celkové genové exprese MeSH
- studie případů a kontrol MeSH
- transkriptom * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- studie na dvojčatech MeSH
BACKGROUND: Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. RESULTS: In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. CONCLUSIONS: We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.
- MeSH
- bakteriofágy genetika MeSH
- butanoly metabolismus MeSH
- Clostridium beijerinckii genetika metabolismus virologie MeSH
- DNA virů genetika MeSH
- fermentace MeSH
- genetická transkripce MeSH
- kinetika MeSH
- pseudogeny genetika MeSH
- sekvenční analýza RNA * MeSH
- stanovení celkové genové exprese * MeSH
- Publikační typ
- časopisecké články MeSH
Best practice & research clinical haematology, ISSN 1521-6926 Vol. 22, no. 2, June 2009
S. 165-282 : il., tab.
Both antibody mediated (AMR) and T-cell mediated (TCMR) rejections either acute or chronic represent the main reason for late graft dysfunction. In this study we aimed to evaluate differences in the intrarenal expression patterns of immune system related genes in acute and chronic rejections. Graft biopsies were performed and evaluated according to Banff classification. Using the TaqMan Low Density Array, the intrarenal expressions of 376 genes relating to immune response (B-cell activation, T-cell activation, chemokines, growth factors, immune regulators, and apoptosis) were analyzed in the four rejection categories: chronic AMR, chronic TCMR, acute AMR, and acute TCMR. The set of genes significantly upregulated in acute TCMR as compared to acute AMR was identified, while no difference in gene expressions between chronic rejections groups was found. In comparison with functioning grafts, grafts that failed within the next 24 months after the chronic rejection morphological confirmation presented at biopsy already established severe graft injury (low eGFR, higher proteinuria), longer followup, higher expression of CDC20, CXCL6, DIABLO, GABRP, KIAA0101, ME2, MMP7, NFATC4, and TGFB3 mRNA, and lower expression of CCL19 and TRADD mRNA. In conclusion, both Banff 2007 chronic rejection categories did not differ in intrarenal expression of 376 selected genes associated with immune response.
- MeSH
- alografty imunologie metabolismus MeSH
- biopsie MeSH
- dospělí MeSH
- hodnocení výsledků pacienta MeSH
- ledviny imunologie metabolismus patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- prognóza MeSH
- regulace genové exprese MeSH
- rejekce štěpu genetika imunologie mortalita MeSH
- rizikové faktory MeSH
- ROC křivka MeSH
- shluková analýza MeSH
- stanovení celkové genové exprese * MeSH
- transkriptom MeSH
- transplantace ledvin škodlivé účinky MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
