978-1-61779-288-5 OR Gene expression profiling Methods and Protocols
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- MeSH
- časná diagnóza MeSH
- diagnostické techniky molekulární MeSH
- exprese genu MeSH
- genom lidský MeSH
- lidé MeSH
- messenger RNA analýza MeSH
- mikro RNA analýza MeSH
- polymerázová řetězová reakce MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
- stanovení celkové genové exprese MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- recenze MeSH
Methods in molecular biology, ISSN 1064-3745 822 Springer protocols
xi, 341 stran : ilustrace
BACKGROUND: The characterisation of dividing brain cells is fundamental for studies ranging from developmental and stem cell biology, to brain cancers. Whilst there is extensive anatomical data on these dividing cells, limited gene transcription data is available due to technical constraints. NEW METHOD: We focally isolated dividing cells whilst conserving RNA, from culture, primary neural tissue and xenografted glioma tumours, using a thymidine analogue that enables gene transcription analysis. RESULTS: 5-ethynyl-2-deoxyuridine labels the replicating DNA of dividing cells. Once labelled, cultured cells and tissues were dissociated, fluorescently tagged with a revised click chemistry technique and the dividing cells isolated using fluorescence-assisted cell sorting. RNA was extracted and analysed using real time PCR. Proliferation and maturation related gene expression in neurogenic tissues was demonstrated in acutely and 3 day old labelled cells, respectively. An elevated expression of marker and pathway genes was demonstrated in the dividing cells of xenografted brain tumours, with the non-dividing cells showing relatively low levels of expression. COMPARISON WITH EXISTING METHOD: BrdU "immune-labelling", the most frequently used protocol for detecting cell proliferation, causes complete denaturation of RNA, precluding gene transcription analysis. This EdU labelling technique, maintained cell integrity during dissociation, minimized copper exposure during labelling and used a cell isolation protocol that avoided cell lysis, thus conserving RNA. CONCLUSIONS: The technique conserves RNA, enabling the definition of cell proliferation-related changes in gene transcription of neural and pathological brain cells in cells harvested immediately after division, or following a period of maturation.
- MeSH
- analýza jednotlivých buněk metody MeSH
- čichová sliznice fyziologie MeSH
- click chemie MeSH
- deoxyuridin analogy a deriváty MeSH
- embryonální kmenové buňky fyziologie MeSH
- gliom patofyziologie MeSH
- kultivované buňky MeSH
- lidé MeSH
- mozek * fyziologie patofyziologie MeSH
- myši inbrední C57BL MeSH
- myši inbrední NOD MeSH
- myši SCID MeSH
- nádory mozku * patofyziologie MeSH
- nervové kmenové buňky fyziologie MeSH
- neurogeneze * fyziologie MeSH
- neurony * fyziologie MeSH
- RNA metabolismus MeSH
- stanovení celkové genové exprese metody MeSH
- transplantace nádorů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: One possible approach how to economically facilitate gene expression profiling is to use the L1000 platform which measures the expression of ∼1,000 landmark genes and uses a computational method to infer the expression of another ∼10,000 genes. One such method for the gene expression inference is a D-GEX which employs neural networks. RESULTS: We propose two novel D-GEX architectures that significantly improve the quality of the inference by increasing the capacity of a network without any increase in the number of trained parameters. The architectures partition the network into individual towers. Our best proposed architecture - a checkerboard architecture with a skip connection and five towers - together with minor changes in the training protocol improves the average mean absolute error of the inference from 0.134 to 0.128. CONCLUSIONS: Our proposed approach increases the gene expression inference accuracy without increasing the number of weights of the model and thus without increasing the memory footprint of the model that is limiting its usage.
Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common tissue specimen available after microscopic examination. Molecular methods, such as polymerase chain reaction (PCR) and gene expression examination, serve as a source of diagnostic and prognostic information but require high-quality RNA. However, the increasing application of RNA extracted from FFPE tissue frequently results in very small and degraded quantities of nucleic acid. This study targets gene expression analysis from FFPE specimens using real-time quantitative PCR. The whole protocol consists of several steps, that is, RNA extraction and its quality control, reverse transcription, and fluorescence detection during real-time quantitative PCR. We compared several methods in each step, chose the most effective, and with that combination we successfully examined 95% (62 from 65) FFPE samples for our genes of interest. We reached the best results with RNA isolation by using a commercial kit, carefully interpreted UV spectrophotometric values, and meticulously chose reverse transcriptase and TaqMan fluorescence detection. Our protocol improves the utility of FFPE tissue for molecular profiling studies.
- MeSH
- fixativa farmakologie MeSH
- formaldehyd farmakologie MeSH
- lidé MeSH
- odběr biologického vzorku metody MeSH
- patologie metody MeSH
- polymerázová řetězová reakce metody MeSH
- RNA genetika izolace a purifikace MeSH
- stanovení celkové genové exprese metody MeSH
- uchovávání tkání MeSH
- zalévání tkání do parafínu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- hodnotící studie MeSH
- práce podpořená grantem MeSH
The sampling procedure is a crucial step in every kind of experiment. This is also true in gene expression profiling experiments, where high quality and sufficient quantity of extracted RNA plays a significant role in the experimental outcome. We have compared five different RNA extraction protocols from peripheral blood/PBMCs with the aim to define the most suitable method for the miRNA expression profiling experiments. Convincing results in terms of highest quantity and quality were obtained by the TRIzol-chloroform extraction method. The total RNA obtained using this method contained the highest portion of good-quality miRNA molecules, which was also confirmed by gene-specific real-time PCR experiments.
- MeSH
- lidé MeSH
- mikro RNA genetika metabolismus MeSH
- molekulární biologie metody MeSH
- regulace genové exprese MeSH
- reprodukovatelnost výsledků MeSH
- stanovení celkové genové exprese * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- validační studie MeSH
OBJECTIVES: Small extracellular vesicles (EVs) contain various signaling molecules, thus playing a crucial role in cell-to-cell communication and emerging as a promising source of biomarkers. However, the lack of standardized procedures impedes their translation to clinical practice. Thus, we compared different approaches for high-throughput analysis of small EVs transcriptome. METHODS: Small EVs were isolated from 150 μL of serum. Quality and quantity were assessed by dynamic light scattering, transmission electron microscopy, and Western blot. Comparison of RNA extraction efficiency was performed, and expression of selected genes was analyzed by RT-qPCR. Whole transcriptome analysis was done using microarrays. RESULTS: Obtained data confirmed the suitability of size exclusion chromatography for isolation of small EVs. Analyses of gene expression showed the best results in case of samples isolated by Monarch Total RNA Miniprep Kit. Totally, 7,182 transcripts were identified to be deregulated between colorectal cancer patients and healthy controls. The majority of them were non-coding RNAs with more than 70 % being lncRNAs, while protein-coding genes represented the second most common gene biotype. CONCLUSIONS: We have optimized the protocol for isolation of small EVs and their RNA from low volume of sera and confirmed the suitability of Clariom D Pico Assays for transcriptome profiling.
- MeSH
- extracelulární vezikuly * genetika metabolismus MeSH
- gelová chromatografie MeSH
- lidé MeSH
- RNA MeSH
- stanovení celkové genové exprese * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Background and Objectives Two-dimensional SDS PAGE (sodium dodecyl sulfate polyacrylamidegel electrophoresis) coupled with mass spectrometry is still a mainstream approach to analysing multiple protein expression levels. The requirement for some sophisticated devices and the lack of quantitative measurements for low-abundant proteins (e.g. cytokines) greatly limit its broad application. Cytokines present in the pg/ml levels in non-stimulated biological samples are traditionally detected by ELISA. We used a cytokine antibody array, a highly sensitive protein chip, for simultaneous detection of multiple cytokine expression levels in rat sarcoma lysates and serum samples . Material and methods We present here an optimized protocol for preparation and handling of tumour tissue lysates in protein chip detection. The sarcoma samples were processed at low temperatures to prevent cytokine degradation. Tumour cryosections (8?10 mm) were used for extraction of cytokines. The addition of NaN3 destroyed a high endogenous peroxidase activity, which may interfere with protein chip assay and decrease the signal/noise ratio. The data for the protein matrix effect from sandwich ELISA can also affect the protein chip detection. The optimal dilution of samples must be found to prevent pitfalls due to the non-optimal signal-to-noise ratio. This also enables recovery of low amounts of cytokines from difficult samples. Results We report optimized procedures for extraction, sample handling, inhibition of endogenous peroxidase activity and prevention of the protein matrix effect in serum and tumour lysates by detection of cytokine expression using the cytokine antibody array protein chip.
The interest to analyze single and few cell samples is rapidly increasing. Numerous extraction protocols to purify nucleic acids are available, but most of them compromise severely on yield to remove contaminants and are therefore not suitable for the analysis of samples containing small numbers of transcripts only. Here, we evaluate 17 direct cell lysis protocols for transcript yield and compatibility with downstream reverse transcription quantitative real-time PCR. Four endogenously expressed genes are assayed together with RNA and DNA spikes in the samples. We found bovine serum albumin (BSA) to be the best lysis agent, resulting in efficient cell lysis, high RNA stability, and enhanced reverse transcription efficiency. Furthermore, we found direct cell lysis with BSA superior to standard column based extraction methods, when analyzing from 1 up to 512 mammalian cells. In conclusion, direct cell lysis protocols based on BSA can be applied with most cell collection methods and are compatible with most analytical workflows to analyze single-cells as well as samples composed of small numbers of cells.
- Publikační typ
- časopisecké články MeSH
Cell-free microRNAs (miRNAs) have become one of the novel promising diagnostic and prognostic biomarkers for various diseases recently. Blood serum and plasma along with urine are the most common sources of clinically well, almost noninvasively available samples containing various types of miRNAs. Here, we present a protocol for a small-scale study investigating expression of several candidate miRNAs. Small-scale experiments may be worth investigating in cases where no information is available on miRNAs expression in particular diseases, for validation of previously published miRNAs with promising diagnostic potential, particularly in situations where follow-up study is aimed at validating miRNAs coming from array or NGS experiments, or where funding for these large-scale experiments is not available.Using urine miRNAs expression as the novel diagnostic tools is challenging and currently this approach is still in its infancy. Therefore, various methods may result in different conclusions depending on clinical sample sets and differences among methods used for the miRNAs isolation and quantitation. In this protocol, we present the method evaluated in the study focused on cell-free urinary miRNAs in ovarian and endometrial cancers. We recommend using stabilization tubes for the urine collection, as this step may be necessary to stop activity of RNases. Further, routine real-time PCR methods are described. We demonstrate that assessment of urinary miRNAs expression may reveal as a feasible method to explore the potential for finding novel diagnostic and prognostic markers.
- MeSH
- analýza moči metody MeSH
- cirkulující mikroRNA genetika izolace a purifikace moč MeSH
- kvantitativní polymerázová řetězová reakce metody MeSH
- lidé MeSH
- nádory endometria genetika moč MeSH
- nádory vaječníků genetika moč MeSH
- polymerázová řetězová reakce s reverzní transkripcí metody MeSH
- regulace genové exprese u nádorů MeSH
- stanovení celkové genové exprese metody MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
