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This work reports the first electrochemical bioplatforms developed for the determination of the total contents of either target miRNA or methylated target miRNA. The bioplatforms are based on the hybridization of the target miRNA with a synthetic biotinylated DNA probe, the capture of the formed DNA/miRNA heterohybrids on the surface of magnetic microcarriers, and their recognition with an antibody selective to these heterohybrids or to the N6-methyladenosine (m6A) epimark. The determination of the total or methylated target miRNA was accomplished by labeling such secondary antibodies with the horseradish peroxidase (HRP) enzyme. In both cases, amperometric transduction was performed on the surface of disposable electrodes after capturing the resulting HRP-tagged magnetic bioconjugates. Because of their increasing relevance in colorectal cancer (CRC) diagnosis and prognosis, miRNA let-7a and m6A methylation were selected. The proposed electrochemical bioplatforms showed attractive analytical and operational characteristics for the determination of the total and m6A-methylated target miRNA in less than 75 min. These bioplatforms, innovative in design and application, were applied to the analysis of total RNA samples extracted from cultured cancer cells with different metastatic profiles and from paired healthy and tumor tissues of patients diagnosed with CRC at different stages. The obtained results demonstrated, for the first time using electrochemical platforms, the potential of interrogating the target miRNA methylation level to discriminate the metastatic capacities of cancer cells and to identify tumor tissues and, in a pioneering way, the potential of the m6A methylation in miRNA let-7a to serve as a prognostic biomarker for CRC.
Methylation systems have been conserved during the divergence of plants and animals, although they are regulated by different pathways and enzymes. However, studies on the interactions of the epigenomes among evolutionarily distant organisms are lacking. To address this, we studied the epigenetic modification and gene expression of plant chromosome fragments (~30 Mb) in a human-Arabidopsis hybrid cell line. The whole-genome bisulfite sequencing results demonstrated that recombinant Arabidopsis DNA could retain its plant CG methylation levels even without functional plant methyltransferases, indicating that plant DNA methylation states can be maintained even in a different genomic background. The differential methylation analysis showed that the Arabidopsis DNA was undermethylated in the centromeric region and repetitive elements. Several Arabidopsis genes were still expressed, whereas the expression patterns were not related to the gene function. We concluded that the plant DNA did not maintain the original plant epigenomic landscapes and was under the control of the human genome. This study showed how two diverging genomes can coexist and provided insights into epigenetic modifications and their impact on the regulation of gene expressions between plant and animal genomes.
- MeSH
- Arabidopsis genetika MeSH
- buněčné linie MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná genetika MeSH
- epigeneze genetická genetika MeSH
- epigenom genetika MeSH
- epigenomika metody MeSH
- genom rostlinný genetika MeSH
- hybridní buňky fyziologie MeSH
- lidé MeSH
- methyltransferasy genetika MeSH
- metylace DNA genetika MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
- MeSH
- cervix uteri cytologie metabolismus MeSH
- epigenom MeSH
- epitel metabolismus MeSH
- genetická predispozice k nemoci MeSH
- lidé MeSH
- metylace DNA * MeSH
- nádory vaječníků genetika metabolismus MeSH
- protein BRCA1 genetika metabolismus MeSH
- protein BRCA2 genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- práce podpořená grantem MeSH
Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting control centers (ICRs) also alters the expression patterns and the majority of patients with rare IDs carries intact but either silenced or overexpressed imprinted genes. Canonical CRISPR/Cas9 editing relying on double-stranded DNA break repair has little to offer in terms of therapeutics for rare IDs. Instead CRISPR/Cas9 can be used in a more sophisticated way by targeting the epigenome. Catalytically dead Cas9 (dCas9) tethered with effector enzymes such as DNA de- and methyltransferases and histone code editors in addition to systems such as CRISPRa and CRISPRi have been shown to have high epigenome editing efficiency in eukaryotic cells. This new era of CRISPR epigenome editors could arguably be a game-changer for curing and treating rare IDs by refined activation and silencing of disturbed imprinted gene expression. This review describes major CRISPR-based epigenome editors and points out their potential use in research and therapy of rare imprinting diseases.
- MeSH
- Angelmanův syndrom genetika metabolismus MeSH
- CRISPR-Cas systémy * MeSH
- diabetes mellitus genetika metabolismus MeSH
- editace genu metody MeSH
- epigeneze genetická MeSH
- epigenom účinky léků genetika MeSH
- genomový imprinting genetika MeSH
- lidé MeSH
- metylace DNA MeSH
- nemoci novorozenců genetika metabolismus MeSH
- Praderův-Williho syndrom genetika metabolismus MeSH
- Silverův-Russellův syndrom genetika metabolismus MeSH
- vzácné nemoci genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
nestr.
Colorectal cancer (CRC) is the third common cancer worldwide. Since the majority of colorectal carcinomas evolve from adenomatous polyps, identification of these adenomas can reduce CRC mortality. Despite the removal of colonic polyps at an initial colonoscopy, some patients are still at an increased risk of developing CRC. However, not all individuals with colonic adenomas have a risk of developing CRC higher than that of the general population. In the present project, we will simultaneously profile transcriptome and DNA methylome in adenoma specimen in prospective study. Concomitant analysis of patient ́s microbiome is aimed at identifying specific characteristics capable of discriminating individuals at risk of developing CRC. Selected relevant characteristics will be validated in additional group of subjects with detail follow up as well as functionally tested in vitro. In summary, above markers could provide a sensitive tool in CRC risk prediction.
Nádory tlustého střeva a konečníku (CRC) patří mezi tři nejčastější maligní onemocnění na světě. Protože většina kolorektálních karcinomů se vyvíjí z adenomatózních polypů, časná identifikace těchto adenomů v konečném důsledku sniží úmrtnost na CRC. Navzdory časnému kolonoskopickému odstranění polypů přetrvává u některých pacientů zvýšené riziko vzniku CRC. Na druhou stranu ne všichni jedinci s adenomy tlustého střeva mají vyšší riziko rozvoje CRC ve srovnání s obecnou populací. V předkládaném projektu se v prospektivní studii zaměříme na současnou profilaci transkriptomu a DNA metylomu u adenomů tlustého střeva. Průvodní analýza mikrobiomu sledovaných pacientů s adenomy přispěje k dalšímu ustavení specifických charakteristik, poukazujících na individuální riziko vývoje CRC. Výše uvedené ukazatele budou validovány u nezávislé skupiny osob s adenomy, u kterých je k dispozici dlouhodobé sledování. Kandidátní marker budou podrobeny funkčnímu testování in vitro. Naše studie mohou přispět k nalezení citlivých ukazatelů, predikujících riziko vzniku CRC.
- Klíčová slova
- mikrobiom, transkriptom, microbiom, přechod adenom-karcinom, metylom, predikze rizika CRC, adenoma-carcinoma transition, methylom, transcriptom, CRC risk prediction,
- NLK Publikační typ
- závěrečné zprávy o řešení grantu AZV MZ ČR
BACKGROUND: The composition of the microbiome plays an important role in human health and disease. Whether there is a direct association between the cervicovaginal microbiome and the host's epigenome is largely unexplored. RESULTS: Here we analyzed a total of 448 cervicovaginal smear samples and studied both the DNA methylome of the host and the microbiome using the Illumina EPIC array and next-generation sequencing, respectively. We found that those CpGs that are hypo-methylated in samples with non-lactobacilli (O-type) dominating communities are strongly associated with gastrointestinal differentiation and that a signature consisting of 819 CpGs was able to discriminate lactobacilli-dominating (L-type) from O-type samples with an area under the receiver operator characteristic curve (AUC) of 0.84 (95% CI = 0.77-0.90) in an independent validation set. The performance found in samples with more than 50% epithelial cells was further improved (AUC 0.87) and in women younger than 50 years of age was even higher (AUC 0.91). In a subset of 96 women, the buccal but not the blood cell DNA showed the same trend as the cervicovaginal samples in discriminating women with L- from O-type cervicovaginal communities. CONCLUSIONS: These findings strongly support the view that the epithelial epigenome plays an essential role in hosting specific microbial communities.
- MeSH
- cervix uteri mikrobiologie MeSH
- CpG ostrůvky MeSH
- dospělí MeSH
- epigenom genetika MeSH
- epitelové buňky metabolismus MeSH
- Lactobacillus genetika růst a vývoj MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA MeSH
- mikrobiota genetika MeSH
- prediktivní hodnota testů MeSH
- vagina mikrobiologie MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
Diffuse midline gliomas (DMGs) bearing driver mutations of histone 3 lysine 27 (H3K27M) are incurable brain tumors with unique epigenomes. Here, we generated a syngeneic H3K27M mouse model to study the amino acid metabolic dependencies of these tumors. H3K27M mutant cells were highly dependent on methionine. Interrogating the methionine cycle dependency through a short-interfering RNA screen identified the enzyme methionine adenosyltransferase 2A (MAT2A) as a critical vulnerability in these tumors. This vulnerability was not mediated through the canonical mechanism of MTAP deletion; instead, DMG cells have lower levels of MAT2A protein, which is mediated by negative feedback induced by the metabolite decarboxylated S-adenosyl methionine. Depletion of residual MAT2A induces global depletion of H3K36me3, a chromatin mark of transcriptional elongation perturbing oncogenic and developmental transcriptional programs. Moreover, methionine-restricted diets extended survival in multiple models of DMG in vivo. Collectively, our results suggest that MAT2A presents an exploitable therapeutic vulnerability in H3K27M gliomas.
- MeSH
- epigenom MeSH
- gliom * genetika MeSH
- histony genetika MeSH
- methionin genetika MeSH
- methioninadenosyltransferasa metabolismus MeSH
- myši MeSH
- nádory mozku * genetika MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Odhadovat směřování jakéhokoliv vědního oboru je sice tématem velice přitažlivým, nicméně riskantním, a v dnešním pojetí něčím na způsob adrenalinového sportu. Zvláště posouzení rychlosti, kterou se biologické vědy budou pohybovat, může být ošidné, protože se stává stále méně závislou na lidských pozorovacích schopnostech, paměti a zručnosti, tedy na lidských mírách. Stáváme se stále více závislými na technickém pokroku, na tom, v čem nás předčí přístroje. I v genetice můžeme díky nim sledovat neustálé zrychlování, s jakou přibývají naše poznatky. Množí se proto i způsoby pohledu a po dlouhém období klasické genetiky založené na pozorováních fenotypových znaků jsme postupně dospěli až do období nejrůznějších „omics“. Za vrchol a předěl současné genetiky považujeme dokončení stanovení sekvence nukleotidů celého lidského genomu potažmo roky 2000–2003. Dnes máme již k dispozici genomové sekvence celé řady dalších organismů a věnujeme svou pozornost modifikacím, které, aniž by měnily sekvenci samu, dokážou dočasně měnit funkční vlastnosti genetických informací – potlačovat, anebo aktivovat jejich uvolňování. Další intenzivně studovanou oblastí jsou „mezigenové vztahy“, jejich sítivo, a zdá se, že nezbytným směrem našeho dalšího postupu bude návrat k fenotypu, ovšem na úrovni vyplývající ze současných znalostí funkce genetického aparátu. Tuto historickou cestu lze schematicky vyjádřit jako fenom › genom › fenom.
Though we start to speak about postgenomic era, the genomic era has not been finished yet and the structure, function and variability of our genome is being still intensively studied and these studies bring us continually new scientific information – more than we are able to digest. The classical genetics utilized phenotype observation for discovering the function of genetic information and proceeded to the molecular basis represented by nucleic acids. Determination of the nucleotide sequence of the human genome is the top outcome of the effort. At present, the function, regulatory pathways and genome modifications have become principal targets of our research. If we compare variability, it increases in the direction from human genome to transcriptome and to proteom reaching the highest level in phenome. Differences concern not only quantity, but also quality with the exception of genome which is relatively stable and „we hand over to our children what we have inherited from our parents“ - all other levels undergo dynamic changes, and from this point of view are much less stable and under continuous influence of environment. To understand enviromental factors shaping our phenome, a long-term monitoring of our living functions will be necessary and an instrumental approach has to be looked for.
- Klíčová slova
- metylom, fenom, epigenetika, remodelace chromatinu,
- MeSH
- epigeneze genetická MeSH
- genom lidský MeSH
- genom MeSH
- genomika MeSH
- lidé MeSH
- metabolom MeSH
- proteom MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
Genetic and non-genetic factors contribute to breast cancer development. An epigenome-based signature capturing these components in easily accessible samples could identify women at risk. Here, we analyse the DNA methylome in 2,818 cervical, 357 and 227 matched buccal and blood samples respectively, and 42 breast tissue samples from women with and without breast cancer. Utilising cervical liquid-based cytology samples, we develop the DNA methylation-based Women's risk IDentification for Breast Cancer index (WID-BC-index) that identifies women with breast cancer with an AUROC (Area Under the Receiver Operator Characteristic) of 0.84 (95% CI: 0.80-0.88) and 0.81 (95% CI: 0.76-0.86) in internal and external validation sets, respectively. CpGs at progesterone receptor binding sites hypomethylated in normal breast tissue of women with breast cancer or in BRCA mutation carriers are also hypomethylated in cervical samples of women with poor prognostic breast cancer. Our data indicate that a systemic epigenetic programming defect is highly prevalent in women who develop breast cancer. Further studies validating the WID-BC-index may enable clinical implementation for monitoring breast cancer risk.
- MeSH
- cervix uteri cytologie metabolismus MeSH
- CpG ostrůvky MeSH
- epigenom MeSH
- epigenomika metody MeSH
- epitelové buňky metabolismus MeSH
- lidé MeSH
- metylace DNA * MeSH
- mutace MeSH
- nádorové biomarkery genetika metabolismus MeSH
- nádory prsu genetika metabolismus MeSH
- prognóza MeSH
- prsy cytologie metabolismus MeSH
- ROC křivka MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
