Epigenetic DNA modifications are pivotal in eukaryotic gene expression, but their regulatory significance in bacteria is less understood. In Synechocystis 6803, the DNA methyltransferase M.Ssp6803II modifies the first cytosine in the GGCC motif, forming N4-methylcytosine (GGm4CC). Deletion of the sll0729 gene encoding M.Ssp6803II (∆sll0729) caused a bluish phenotype due to reduced chlorophyll levels, which was reversed by suppressor mutations. Re-sequencing of 7 suppressor clones revealed a common GGCC to GGTC mutation in the slr1790 promoter's discriminator sequence, encoding protoporphyrinogen IX oxidase, HemJ, crucial for tetrapyrrole biosynthesis. Transcriptomic and qPCR analyses indicated aberrant slr1790 expression in ∆sll0729 mutants. This aberration led to the accumulation of coproporphyrin III and protoporphyrin IX, indicative of impaired HemJ activity. To confirm the importance of DNA methylation in hemJ expression, hemJ promoter variants with varying discriminator sequences were introduced into the wild type, followed by sll0729 deletion. The sll0729 deletion segregated in strains with the GGTC discriminator motif, resulting in wild-type-like pigmentation, whereas freshly prepared ∆sll0729 mutants with the native hemJ promoter exhibited the bluish phenotype. These findings demonstrate that hemJ is tightly regulated in Synechocystis and that N4-methylcytosine is essential for proper hemJ expression. Thus, cytosine N4-methylation is a relevant epigenetic marker in Synechocystis and likely other cyanobacteria.
- MeSH
- bakteriální proteiny metabolismus genetika MeSH
- epigeneze genetická * MeSH
- metylace DNA * MeSH
- mutace MeSH
- promotorové oblasti (genetika) * MeSH
- regulace genové exprese u bakterií MeSH
- Synechocystis * genetika metabolismus MeSH
- tetrapyrroly * metabolismus biosyntéza MeSH
- Publikační typ
- časopisecké články MeSH
Biological mechanisms related to cancer development can leave distinct molecular fingerprints in tumours. By leveraging multi-omics and epidemiological information, we can unveil relationships between carcinogenesis processes that would otherwise remain hidden. Our integrative analysis of DNA methylome, transcriptome, and somatic mutation profiles of kidney tumours linked ageing, epithelial-mesenchymal transition (EMT), and xenobiotic metabolism to kidney carcinogenesis. Ageing process was represented by associations with cellular mitotic clocks such as epiTOC2, SBS1, telomere length, and PBRM1 and SETD2 mutations, which ticked faster as tumours progressed. We identified a relationship between BAP1 driver mutations and the epigenetic upregulation of EMT genes (IL20RB and WT1), correlating with increased tumour immune infiltration, advanced stage, and poorer patient survival. We also observed an interaction between epigenetic silencing of the xenobiotic metabolism gene GSTP1 and tobacco use, suggesting a link to genotoxic effects and impaired xenobiotic metabolism. Our pan-cancer analysis showed these relationships in other tumour types. Our study enhances the understanding of kidney carcinogenesis and its relation to risk factors and progression, with implications for other tumour types.
- MeSH
- DNA vazebné proteiny genetika metabolismus MeSH
- epigeneze genetická MeSH
- epitelo-mezenchymální tranzice * genetika MeSH
- glutathion-S-transferasa fí genetika metabolismus MeSH
- histonlysin-N-methyltransferasa genetika metabolismus MeSH
- karcinogeneze * genetika MeSH
- lidé MeSH
- metylace DNA * MeSH
- multiomika MeSH
- mutace * MeSH
- nádorové supresorové proteiny genetika metabolismus MeSH
- nádory ledvin * genetika patologie MeSH
- regulace genové exprese u nádorů MeSH
- stárnutí genetika MeSH
- thiolesterasa ubikvitinu MeSH
- transkripční faktory genetika metabolismus MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
INTRODUCTION: Studies have correlated living close to major roads with Alzheimer's disease (AD) risk. However, the mechanisms responsible for this link remain unclear. METHODS: We exposed olfactory mucosa (OM) cells of healthy individuals and AD patients to diesel emissions (DE). Cytotoxicity of exposure was assessed, mRNA, miRNA expression, and DNA methylation analyses were performed. The discovered altered pathways were validated using data from the human population-based Rotterdam Study. RESULTS: DE exposure resulted in an almost four-fold higher response in AD OM cells, indicating increased susceptibility to DE effects. Methylation analysis detected different DNA methylation patterns, revealing new exposure targets. Findings were validated by analyzing data from the Rotterdam Study cohort and demonstrated a key role of nuclear factor erythroid 2-related factor 2 signaling in responses to air pollutants. DISCUSSION: This study identifies air pollution exposure biomarkers and pinpoints key pathways activated by exposure. The data suggest that AD individuals may face heightened risks due to impaired cellular defenses. HIGHLIGHTS: Healthy and AD olfactory cells respond differently to DE exposure. AD cells are highly susceptible to DE exposure. The NRF2 oxidative stress response is highly activated upon air pollution exposure. DE-exposed AD cells activate the unfolded protein response pathway. Key findings are also confirmed in a population-based study.
- MeSH
- Alzheimerova nemoc * genetika metabolismus MeSH
- čichová sliznice metabolismus MeSH
- epigenomika MeSH
- faktor 2 související s NF-E2 genetika metabolismus MeSH
- látky znečišťující vzduch škodlivé účinky MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA * MeSH
- mikro RNA metabolismus genetika MeSH
- senioři MeSH
- stanovení celkové genové exprese MeSH
- transkriptom MeSH
- výfukové emise vozidel * toxicita MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Diffuse pediatric-type high-grade gliomas (pedHGG), H3- and IDH-wildtype, encompass three main DNA-methylation-based subtypes: pedHGG-MYCN, pedHGG-RTK1A/B/C, and pedHGG-RTK2A/B. Since their first description in 2017 tumors of pedHGG-RTK2A/B have not been comprehensively characterized and clinical correlates remain elusive. In a recent series of pedHGG with a Gliomatosis cerebri (GC) growth pattern, an increased incidence of pedHGG-RTK2A/B (n = 18) was observed. We added 14 epigenetically defined pedHGG-RTK2A/B tumors to this GC series and provided centrally reviewed radiological, histological, and molecular characterization. The final cohort of 32 pedHGG-RTK2A/B tumors consisted of 25 pedHGG-RTK2A (78%) and seven pedHGG-RTK2B (22%) cases. The median age was 11.6 years (range, 4-17) with a median overall survival of 16.0 months (range 10.9-28.2). Seven of 11 of the newly added cases with imaging available showed a GC phenotype at diagnosis or follow-up. PedHGG-RTK2B tumors exhibited frequent bithalamic involvement (6/7, 86%). Central neuropathology review confirmed a diffuse glial neoplasm in all tumors with prominent angiocentric features in both subclasses. Most tumors (24/27 with available data, 89%) diffusely expressed EGFR with focal angiocentric enhancement. PedHGG-RTK2A tumors lacked OLIG2 expression, whereas 43% (3/7) of pedHGG-RTK2B expressed this glial transcription factor. ATRX loss occurred in 3/6 pedHGG-RTK2B samples with available data (50%). DNA sequencing (pedHGG-RTK2A: n = 18, pedHGG-RTK2B: n = 5) found EGFR alterations (15/23, 65%; predominantly point mutations) in both subclasses. Mutations in BCOR (14/18, 78%), SETD2 (7/18, 39%), and the hTERT promoter (7/19, 37%) occurred exclusively in pedHGG-RTK2A tumors, while pedHGG-RTK2B tumors were enriched for TP53 alterations (4/5, 80%). In conclusion, pedHGG-RTK2A/B tumors are characterized by highly diffuse-infiltrating growth patterns and specific radiological and histo-molecular features. By comprehensively characterizing methylation-based tumors, the chance to develop specific and effective therapy concepts for these detrimental tumors increases.
- MeSH
- dítě MeSH
- fenotyp MeSH
- gliom * genetika patologie diagnostické zobrazování MeSH
- lidé MeSH
- metylace DNA * MeSH
- mladiství MeSH
- nádory mozku * genetika patologie diagnostické zobrazování MeSH
- neuroepitelové nádory * genetika patologie diagnostické zobrazování MeSH
- předškolní dítě MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Analysis of cell-free DNA methylation (cfDNAme), alone or combined with CA125, could help to detect ovarian cancers earlier and may reduce mortality. We assessed cfDNAme in regions of ZNF154, C2CD4D and WNT6 via targeted bisulfite sequencing in diagnostic and early detection (preceding diagnosis) settings. Diagnostic samples were obtained via prospective blood collection in cell-free DNA tubes in a convenience series of patients with a pelvic mass. Early detection samples were matched case-control samples derived from the UK Familial Ovarian Cancer Screening Study (UKFOCSS). In the diagnostic set (ncases = 27, ncontrols = 41), the specificity of cfDNAme was 97.6% (95% CI: 87.1%-99.9%). High-risk cancers were detected with a sensitivity of 80% (56.3%-94.3%). Combination of cfDNAme and CA125 resulted in a sensitivity of 94.4% (72.7%-99.9%) for high-risk cancers. Despite technical issues in the early detection set (ncases = 29, ncontrols = 29), the specificity of cfDNAme was 100% (88.1%-100.0%). We detected 27.3% (6.0%-61.0%) of high-risk cases with relatively lower genomic DNA (gDNA) contamination. The sensitivity rose to 33.3% (7.5%-70.1%) in samples taken <1 year before diagnosis. We detected ovarian cancer in several patients up to 1 year before diagnosis despite technical limitations associated with archival samples (UKFOCSS). Combined cfDNAme and CA125 assessment may improve ovarian cancer screening in high-risk populations, but future large-scale prospective studies will be required to validate current findings.
- MeSH
- antigen CA-125 MeSH
- časná detekce nádoru metody MeSH
- lidé MeSH
- metylace DNA * MeSH
- nádorové biomarkery genetika MeSH
- nádory vaječníků * diagnóza genetika MeSH
- prospektivní studie MeSH
- studie případů a kontrol MeSH
- transkripční faktory Krüppel-like genetika MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Myelodysplastic syndromes (MDS) are myeloid malignancies with heterogeneous genotypes and phenotypes, characterized by ineffective haematopoiesis and a high risk of progression towards acute myeloid leukaemia (AML). Prognosis for patients treated with hypomethylating agents (HMAs), as is azacytidine, the main drug used as frontline therapy for MDS is mostly based on cytogenetics and next generation sequencing (NGS) of the initial myeloid clone. Although the critical influence of the epigenetic landscape upon cancer cells survival and development as well on tumour environment establishment is currently recognized and approached within current clinical practice in MDS, the heterogenous response of the patients to epigenetic therapy is suggesting a more complex mechanism of action, as is the case of RNA methylation. In this sense, the newly emerging field of epitranscriptomics could provide a more comprehensive perspective upon the modulation of gene expression in malignancies, as is the proof-of-concept of MDS. We initially did RNA methylation sequencing on MDS patients (n = 6) treated with azacytidine and compared responders with non-responders. Afterwards, the genes identified were assessed in vitro and afterwards validated on a larger cohort of MDS patients treated with azacytidine (n = 58). Our data show that a more accurate prognosis could be based on analysing the methylome and thus we used methylation sequencing to differentially split high-grade MDS patients with identical demographical and cytogenetic features, between azacytidine responders and non-responders.
- MeSH
- antimetabolity antitumorózní terapeutické užití farmakologie MeSH
- azacytidin * farmakologie terapeutické užití MeSH
- epigeneze genetická účinky léků MeSH
- lidé středního věku MeSH
- lidé MeSH
- methylace RNA MeSH
- metylace DNA * účinky léků MeSH
- myelodysplastické syndromy * genetika farmakoterapie patologie MeSH
- prognóza MeSH
- sekvenční analýza RNA MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- stanovení celkové genové exprese MeSH
- transkriptom genetika účinky léků MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Obesity represents a growing problem due to its impacts on human health and reproduction. In this study, we analysed semen quality, sperm DNA integrity and gene-specific CpG methylation in 116 healthy men from normal population. The men were divided into three groups according to their body mass index (BMI), and their ejaculates were analysed using standard methods, sperm chromatin structure assay (SCSA), methylation next generation sequencing (NGS) and amplicon sequencing. The sperm methylation NGS revealed six significantly differentially methylated regions (DMRs). Using subsequent targeted amplicon sequencing in 116 men, two of the DMRs were proved as differentially methylated in sperm of men with normal BMI vs. BMI ≥ 25. The DMRs were located in the EPHA8 and ANKRD11 gene. Also, we detected a significant decline in the EPHA8, ANKRD11 and CFAP46 gene methylation in association with increasing BMI values. The genes EPHA8 and ANKRD11 are involved in the nervous system and brain development; the CFAP46 gene plays a role in a flagellar assembly and is associated with sperm motility. Significantly lower rates of motile and progressive motile sperm were observed in men with BMI ≥ 30. Our results show that excess body weight can modify CpG methylation of specific genes, affect sperm motility, and compromise sperm chromatin integrity. These factors can stand behind the observed reduced fertility in men with obesity. The methylation changes might be transmitted to their offspring through sperm, and become a basis for possible developmental and reproductive issues in the next generation.
- MeSH
- analýza spermatu * MeSH
- chromatin * metabolismus MeSH
- CpG ostrůvky MeSH
- dospělí MeSH
- index tělesné hmotnosti * MeSH
- lidé MeSH
- metylace DNA * MeSH
- mladý dospělý MeSH
- motilita spermií genetika MeSH
- obezita genetika MeSH
- spermie * metabolismus MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
V posledných desaťročiach sme zaznamenali výrazný nárast počtu cisárskych rezov. Hoci je pôrod cisárskym rezom život zachraňujúci, je spojený so zvýšeným rizikom nepriaznivých zdravotných následkov u novorodencov, vrátane respiračných a atopických ochorení, obezity, cukrovky a závažných autoimunitných ochorení. Presné mechanizmy, ktoré sú základom týchto spojitostí zostávajú nepochopené; epigenetické modifikácie sa však ukázali ako pravdepodobný molekulárny základ spájajúci perinatálne faktory s budúcou náchylnosťou na ochorenie. Tento prehľad spája súčasnú literatúru a odhaľuje, že spôsob pôrodu môže ovplyvniť epigenetické markery u novorodencov, predovšetkým prostredníctvom zmien globálnej metylácie DNA a génovo špecifických metylačných vzorcov.
Recent decades have seen a notable increase in cesarean section rates. Although lifesaving, cesarean delivery is associated with an elevated risk of adverse health outcomes in newborns, including respiratory diseases, atopic disorders, obesity, diabetes, and severe autoimmune conditions. The exact mechanisms underlying these associations remain elusive; however, epigenetic modifications have emerged as a plausible molecular basis linking perinatal factors with future disease susceptibility. This review summarizes current literature, revealing that the delivery method may influence epigenetic markers in neonates, primarily through alterations in global DNA methylation and gene-specific methylation patterns.
WHO klasifikácia nádorov CNS z roku 2021 (WHO CNS 2021) predstavuje zásadné zmeny v klasifikácii nádorov mozgu a miechy, ktoré vychádzajú z významných pokrokov v oblasti molekulovej patológie. Základom patologickej diagnostiky je stále histomorfologické vyšetrenie podporené imunohistochémiou, mnohé typy nádorov však nie je možné správne diagnostikovať bez genetickej analýzy, vrátane použitia novej techniky - metylačného profilovania. WHO CNS 2021 popisuje mnohé nové nádorové jednotky, predstavuje nový prístup ku gradingu, vrátane tzv. molekulového gradingu a zdôrazňuje dôležitosť tzv. integrovanej histologicko‐genetickej diagnózy. V prehľadovom článku sú zhrnuté niektoré hlavné zmeny vo WHO CNS 2021 a stručne je predstavená praktická diagnostika difúznych gliómov.
WHO classification of tumors of the central nervous system published in 2021 (WHO CNS 2021) introduces major changes in classification of tumors of the brain and the spinal cord which reflect major advances in the molecular genetics. Histology and immunohistochemistry still represent the cornerstone of diagnostics, but in many tumor types advanced molecular techniques, including methylation profiling, are required to arrive at correct diagnosis. WHO CNS 2021 introduces many new tumor types, establishes different approach to grading, including molecular grading, and emphasizes the importance of integrated diagnosis. This review summarizes some general changes in WHO CNS 2021 and briefly introduces practical diagnosis of diffuse gliomas.
- MeSH
- diagnostické techniky molekulární MeSH
- gliom diagnóza genetika patologie MeSH
- histologické techniky MeSH
- lidé MeSH
- metylace DNA MeSH
- nádory centrálního nervového systému * diagnóza genetika klasifikace MeSH
- nádory mozku diagnóza genetika klasifikace MeSH
- sekvenční analýza DNA MeSH
- stanovení celkové genové exprese MeSH
- stupeň nádoru MeSH
- Check Tag
- lidé MeSH
Neuropatologická diagnostika nádorů centrální nervové soustavy se v posledních letech výrazně posunula díky molekulárně biologickým poznatkům i novým metodám, jako je metylační profilování. V současné WHO klasifikaci se na jejich podkladě změnil jednak obecný přístup ke gradingu a reportování nádorů. Také byly vytvořeny nové skupiny nádorů a nové jednotky, zdůrazňující rozdíly mezi morfologicky obdobnými nádory s rozdílným molekulárně patologickým pozadím. Tento edukativní článek předkládá aktuální pohled na členění nejčastějších dětských nádorů CNS a jeho vliv na současné diagnostické postupy.
Neuropathological diagnostics of central nervous system tumours has advanced significantly in recent years thanks to molecular biological insights and new methods such as methylation profiling. In the current WHO classification, the general approach to grading and reporting of tumours has changed as a result. New tumour groups and new units have also been created, highlighting the differences between morphologically similar tumours with different molecular pathological backgrounds. This educative article gives actual view on groups of the most frequent pediatric CNS tumours and its impact on diagnostic approaches.
- MeSH
- diagnostické techniky molekulární MeSH
- ependymom diagnóza patologie MeSH
- gliom diagnóza genetika patologie MeSH
- lidé MeSH
- meduloblastom diagnóza patologie MeSH
- metylace DNA MeSH
- nádory centrálního nervového systému * diagnóza genetika klasifikace MeSH
- nádory mozku diagnóza genetika klasifikace MeSH
- stupeň nádoru MeSH
- Check Tag
- lidé MeSH
