SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
- MeSH
- COVID-19 virologie MeSH
- CpG ostrůvky * MeSH
- genom virový MeSH
- lidé MeSH
- metylace DNA MeSH
- mutace * MeSH
- SARS-CoV-2 genetika MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Syncytin-1 is a captive envelope glycoprotein encoded by one of human endogenous retroviruses W. It is expressed exclusively in the placental trophoblast where it participates in cell-to-cell fusion during differentiation of syncytiotrophobast. In other tissues, however, syncytin-1 expression must be kept in check because inadvertent cell fusion might be dangerous for tissue organization and integrity. We describe here an inverse correlation between CpG methylation of syncytin-1 5' long terminal repeat and its expression. Hypomethylation of the syncytin-1 5' long terminal repeat in the placenta and in the choriocarcinoma-derived cell line BeWo was detected. However, other analyzed primary cells and cell lines non-expressing syncytin-1 contain proviruses heavily methylated in this sequence. CpG methylation of syncytin-1 is resistant to the effect of the demethylating agent 5-azacytidine. The inhibitory role of CpG methylation is further confirmed by transient transfection of in-vitro-methylated syncytin-1 promoter-driven reporter construct. Altogether, we conclude that CpG methylation plays a principal role in the transcriptional suppression of syncytin-1 in non-placental tissues, and, in contrast, demethylation of the syncytin-1 promoter in trophoblast is a prerequisite for its expression and differentiation of multinucleated syncytiotrophoblast.
- MeSH
- buněčné linie MeSH
- CpG ostrůvky fyziologie MeSH
- down regulace imunologie MeSH
- financování organizované MeSH
- genové produkty env antagonisté a inhibitory biosyntéza genetika MeSH
- HeLa buňky MeSH
- koncové repetice MeSH
- lidé MeSH
- metylace DNA MeSH
- placenta metabolismus MeSH
- promotorové oblasti (genetika) MeSH
- těhotenské proteiny antagonisté a inhibitory biosyntéza genetika MeSH
- transkripční faktory antagonisté a inhibitory biosyntéza genetika MeSH
- trofoblasty metabolismus MeSH
- Check Tag
- lidé MeSH
Unmethylated oligodeoxynucleotides containing guanine-cytidine dimers (CpG ODN) have been described as potent inducers of selected antitumour immune responses and the immunotherapeutic efficacy of CpG ODN has been examined either alone or as a vaccine adjuvant. We hypothesized that CpG ODN therapy could be an effective tool for immunotherapy of not only conventional MHC class I(+) tumours but also of those tumours that have lost MHC class I expression during their progression. To address this hypothesis, we employed the animal model resembling MHC class I-proficient and -deficient human papilloma virus (HPV) 16-associated tumours. A cell line transformed with HPV16 E6 and E7 oncogenes, TC-1, as a prototype of MHC class I-positive line, and its MHC class I-deficient sublines TC-1/A9 and TC-1/P3C10 were injected into syngeneic C57BL/6 mice and the growing tumours were subjected to immunotherapy with CpG ODN 1826. The therapy started either 1 day after the challenge with the tumour cells or later, when the tumours had reached a palpable size. In both settings, CpG ODN 1826 significantly reduced the growth of MHC class I-proficient and -deficient tumours. Furthermore, we demonstrated that CpG ODN 1585, whose mechanism of action preferably involves indirect activation of the natural killer cells, induced regression of the MHC class I-deficient tumours TC1/A9 but not of the MHC class I-proficient tumours TC-1. This study infers that synthetic CpG ODN have a potential for the therapy of both MHC class I-proficient and -deficient tumours and thus could be also used against tumours that tend to down-regulate their MHC class I expression.
- MeSH
- CpG ostrůvky MeSH
- down regulace MeSH
- financování organizované MeSH
- geny MHC třídy I MeSH
- imunoterapie metody MeSH
- infekce papilomavirem MeSH
- lidský papilomavirus 16 MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- nádory terapie virologie MeSH
- oligonukleotidy MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
Unmethylated CpG islands are known to keep adjacent promoters transcriptionally active. In the CpG island adjacent to the adenosine phosphoribosyltransferase gene, the protection against transcriptional silencing can be attributed to the short CpG-rich core element containing Sp1 binding sites. We report here the insertion of this CpG island core element, IE, into the long terminal repeat of a retroviral vector derived from Rous sarcoma virus, which normally suffers from progressive transcriptional silencing in mammalian cells. IE insertion into a specific position between enhancer and promoter sequences led to efficient protection of the integrated vector from silencing and gradual CpG methylation in rodent and human cells. Individual cell clones with IE-modified reporter vectors display high levels of reporter expression for a sustained period and without substantial variegation in the cell culture. The presence of Sp1 binding sites is important for the protective effect of IE, but at least some part of the entire antisilencing capacity is maintained in IE with mutated Sp1 sites. We suggest that this strategy of antisilencing protection by the CpG island core element may prove generally useful in retroviral vectors.
- MeSH
- biologické modely MeSH
- CpG ostrůvky MeSH
- financování organizované MeSH
- genetická transkripce MeSH
- koncové repetice MeSH
- lidé MeSH
- mutace MeSH
- průtoková cytometrie MeSH
- ptačí sarkom genetika virologie MeSH
- reportérové geny MeSH
- transkripční faktor Sp1 metabolismus MeSH
- umlčování genů MeSH
- vazebná místa MeSH
- virus ptačí leukózy metabolismus MeSH
- virus Rousova sarkomu metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
BACKGROUND: CpG Island Methylator Phenotype (CIMP) is an epigenetic phenotype in CRC characterized by hypermethylation of CpG islands in promoter regions of tumor suppressor genes, leading to their transcriptional silencing and loss of function. While the prevalence of CRC differs across geographical regions, no studies have compared prevalence of CIMP-High phenotype across regions. The purpose of this project was to compare the prevalence of CIMP across geographical regions after adjusting for variations in methodologies to measure CIMP in a meta-analysis. METHODS: We searched PubMed, Medline, and Embase for articles focusing on CIMP published from 2000 to 2018. Two reviewers independently identified 111 articles to be included in final meta-analysis. We classified methods used to quantify CIMP into 4 categories: a) Classical (MINT marker) Panel group b) Weisenberg-Ogino (W-O) group c) Human Methylation Arrays group and d) Miscellaneous group. We compared the prevalence of CIMP across geographical regions after correcting for methodological variations using meta-regression techniques. RESULTS: The pooled prevalence of CIMP-High across all studies was 22% (95% confidence interval:21-24%; I2 = 94.75%). Pooled prevalence of CIMP-H across Asia, Australia, Europe, North America and South America was 22, 21, 21, 27 and 25%, respectively. Meta-regression analysis identified no significant differences in the prevalence of CIMP-H across geographical regions after correction for methodological variations. In exploratory analysis, we observed variations in CIMP-H prevalence across countries. CONCLUSION: Although no differences were found for CIMP-H prevalence across countries, further studies are needed to compare the influence of demographic, lifestyle and environmental factors in relation to the prevalence of CIMP across geographical regions.
- MeSH
- CpG ostrůvky genetika MeSH
- fenotyp * MeSH
- genetická heterogenita MeSH
- kohortové studie MeSH
- kolorektální nádory genetika MeSH
- lidé MeSH
- metylace DNA genetika MeSH
- pití alkoholu škodlivé účinky genetika MeSH
- prevalence MeSH
- promotorové oblasti (genetika) genetika MeSH
- publikační zkreslení MeSH
- rizikové faktory MeSH
- umlčování genů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- metaanalýza MeSH
- systematický přehled MeSH
- Geografické názvy
- Česká republika MeSH
- Indie MeSH
Vzhledem k významnosti vztahu mezi stupněm metylace DNA a genovou aktivitou, zejména u nádorových onemocnění, byla popsána celá řada technik sledujících metylací DNA. Cílem této práce bylo zpracovat přehled o metodikách, které mohou být využívány k monitorování DNA metylačních změn. V práci je kladen důraz na monitorování změn metylace DNA v oblasti CpG ostrůvků promotorových oblastí genů. Přehled popisuje výhody, nevýhody a potenciální využití jednotlivých metod.
There is an important relationship between the degree of DNA methylation and gene activity in cancer. Number of techniques of DNA methylation analysis has been reported. The aim of this study was to review methodologies that can be used to monitoring DNA methylation changes. We reviewed techniques important for monitoring of DNA methylation changes of CpG islands in gene promoter regions. Advantages, disadvantages and potential use of these techniques are described.
- Klíčová slova
- MS-MLPA, MSP, modifikace hydrogensiřičitanem,
- MeSH
- CpG ostrůvky genetika MeSH
- genetické techniky MeSH
- lidé MeSH
- metylace DNA MeSH
- nádory genetika MeSH
- Check Tag
- lidé MeSH
Epigenetic modifications are essential regulators of biological processes. Decreased DNA methylation of OAS2 (2'-5'-Oligoadenylate Synthetase 2), encoding an antiviral protein, has been seen in psoriasis. To provide further insight into the epigenetic regulation of OAS2, we performed pyrosequencing to detect OAS2 DNA methylation status at 11 promoter and first exon located CpG sites in psoriasis (n = 12) and two common subtypes of squamous cell carcinoma (SCC) of the head and neck: tongue (n = 12) and tonsillar (n = 11). Compared to corresponding controls, a general hypomethylation was seen in psoriasis. In tongue and tonsillar SCC, hypomethylation was found at only two CpG sites, the same two sites that were least demethylated in psoriasis. Despite differences in the specific residues targeted for methylation/demethylation, OAS2 expression was upregulated in all conditions and correlations between methylation and expression were seen in psoriasis and tongue SCC. Distinctive methylation status at four successively located CpG sites within a genomic area of 63 bp reveals a delicately integrated epigenetic program and indicates that detailed analysis of individual CpGs provides additional information into the mechanisms of epigenetic regulation in specific disease states. Methylation analyses as clinical biomarkers need to be tailored according to disease-specific sites.
- MeSH
- 2',5'-oligoadenylátsynthetasa genetika metabolismus MeSH
- CpG ostrůvky * MeSH
- epigeneze genetická * MeSH
- lidé MeSH
- metylace DNA MeSH
- nádory hlavy a krku genetika metabolismus patologie MeSH
- nádory jazyka genetika metabolismus patologie MeSH
- promotorové oblasti (genetika) MeSH
- psoriáza genetika metabolismus patologie MeSH
- retrospektivní studie MeSH
- spinocelulární karcinom genetika metabolismus patologie MeSH
- studie případů a kontrol MeSH
- tonzilární nádory genetika metabolismus patologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.
- MeSH
- biologické markery analýza MeSH
- CpG ostrůvky genetika MeSH
- DNA nádorová genetika MeSH
- kohortové studie MeSH
- kojenec MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- lidé MeSH
- metylace DNA * MeSH
- nádorové buňky kultivované MeSH
- neuroblastom diagnóza genetika MeSH
- prognóza MeSH
- staging nádorů MeSH
- vazebná místa MeSH
- výpočetní biologie MeSH
- Check Tag
- kojenec MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Oligodeoxynucleotides containing guanine-cytidine dimers (CpG ODN) are potent inducers of anti-tumour immune responses. In this study, we analyzed the capacity of CpG ODN to inhibit the growth of both MHC class I-positive and -deficient tumours after debulking the tumour mass by chemotherapy or surgery. We employed an animal model resembling human papillomavirus (HPV) 16-associated tumours. Tumour cell lines with distinct cell surface expression of the MHC class I molecules were injected into syngeneic C57BL/6 mice, and the growing tumours were either subjected to cytoreductive chemotherapy with ifosfamide derivative, CBM-4A, or surgically removed. Subsequent treatment with synthetic CpG ODN significantly blocked the growth of the recurrent tumours. Our results indicate that the therapy with CpG ODN can be effective for the treatment of minimal residual tumour disease of the tumours that have escaped from the immune surveillance by downmodulating the MHC class I expression.
- MeSH
- CpG ostrůvky MeSH
- financování organizované MeSH
- geny MHC třídy I MeSH
- lidé MeSH
- lidský papilomavirus 16 metabolismus MeSH
- modely nemocí na zvířatech MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- nádory genetika terapie virologie MeSH
- oligonukleotidy chemie terapeutické užití MeSH
- recidiva MeSH
- reziduální nádor farmakoterapie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- zvířata MeSH
