Intermediate Methyl Research Articles

DNA Methylation Classes of Stage II and III Primary Melanomas and Their Clinical and Prognostic Significance.

Patients with stage II and III cutaneous primary melanoma vary considerably in their risk of melanoma-related death. We explore the ability of methylation profiling to distinguish primary melanoma methylation classes and their associations with clinicopathologic characteristics and survival. InterMEL is a retrospective case-control study that assembled primary cutaneous melanomas from American Joint Committee on Cancer (AJCC) 8th edition stage II and III patients diagnosed between 1998 and 2015 in the United States and Australia. Cases are patients who died of melanoma within 5 years from original diagnosis. Controls survived longer than 5 years without evidence of melanoma recurrence or relapse. Methylation classes, distinguished by consensus clustering of 850K methylation data, were evaluated for their clinicopathologic characteristics, 5-year survival status, and differentially methylated gene sets. Among 422 InterMEL melanomas, consensus clustering revealed three primary melanoma methylation classes (MethylClasses): a CpG island methylator phenotype (CIMP) class, an intermediate methylation (IM) class, and a low methylation (LM) class. CIMP and IM were associated with higher AJCC stage (both P = .002), Breslow thickness (CIMP P = .002; IM P = .006), and mitotic index (both P < .001) compared with LM, while IM had higher N stage than CIMP (P = .01) and LM (P = .007). CIMP and IM had a 2-fold higher likelihood of 5-year death from melanoma than LM (CIMP odds ratio [OR], 2.16 [95% CI, 1.18 to 3.96]; IM OR, 2.00 [95% CI, 1.12 to 3.58]) in a multivariable model adjusted for age, sex, log Breslow thickness, ulceration, mitotic index, and N stage. Despite more extensive CpG island hypermethylation in CIMP, CIMP and IM shared similar patterns of differential methylation and gene set enrichment compared with LM. Melanoma MethylClasses may provide clinical value in predicting 5-year death from melanoma among patients with primary melanoma independent of other clinicopathologic factors.

DNA methylation at AHRR as a master predictor of smoke exposure and a biomarker for sleep and exercise

BackgroundDNA methylation profiling may provide a more accurate measure of the smoking status than self-report and may be useful in guiding clinical interventions and forensic investigations. In the current study, blood DNA methylation profiles of nearly 800 Polish individuals were assayed using Illuminia EPIC and the inference of smoking from epigenetic data was explored. In addition, we focused on the role of the AHRR gene as a top marker for smoking and investigated its responsiveness to other lifestyle behaviors.ResultsWe found > 450 significant CpGs associated with cigarette consumption, and overrepresented in various biological functions including cell communication, response to stress, blood vessel development, cell death, and atherosclerosis. The model consisting of cg05575921 in AHRR (p = 4.5 × 10–32) and three additional CpGs (cg09594361, cg21322436 in CNTNAP2 and cg09842685) was able to predict smoking status with a high accuracy of AUC = 0.8 in the test set. Importantly, a gradual increase in the probability of smoking was observed, starting from occasional smokers to regular heavy smokers. Furthermore, former smokers displayed the intermediate DNA methylation profiles compared to current and never smokers, and thus our results indicate the potential reversibility of DNA methylation after smoking cessation. The AHRR played a key role in a predictive analysis, explaining 21.5% of the variation in smoking. In addition, the AHRR methylation was analyzed for association with other modifiable lifestyle factors, and showed significance for sleep and physical activity. We also showed that the epigenetic score for smoking was significantly correlated with most of the epigenetic clocks tested, except for two first-generation clocks.ConclusionsOur study suggests that a more rapid return to never-smoker methylation levels after smoking cessation may be achievable in people who change their lifestyle in terms of physical activity and sleep duration. As cigarette smoking has been implicated in the literature as a leading cause of epigenetic aging and AHRR appears to be modifiable by multiple exogenous factors, it emerges as a promising target for intervention and investment.

Infrared Spectrum of the Adduct 2-Chloro-2-hydroperoxybut-3-ene [(C2H3)CCl(CH3)OOH] of the Reaction between the Criegee Intermediate Methyl Vinyl Ketone Oxide [C2H3C(CH3)OO] and HCl.

Methyl vinyl ketone oxide (MVKO, C2H3C(CH3)OO) is an important Criegee intermediate produced from ozonolysis of isoprene, which is the most abundant nonmethane hydrocarbon emitted into the atmosphere. Reactions between Criegee intermediate and hydrogen chloride (HCl) are important because of their large rate coefficients. In this work, we photolyzed a mixture of (Z)-(CH2I)HC═C(CH3)I/HCl/O2 at 248 nm to produce MVKO to carry out the reaction MVKO + HCl and recorded infrared spectra of transient species with a step-scan Fourier-transform infrared absorption spectrometer. Eleven bands near 1415, 1381, 1350, 1249, 1178, 1118, 1103, 1065, 978, 931, and 895 cm-1 were observed and assigned to the hydrogen-transferred adduct (C2H3)CCl(CH3)OOH (2-chloro-2-hydroperoxybut-3-ene, CHPB) according to the predicted IR spectrum using the B3LYP/aug-cc-pVTZ method; the conformation could not be definitively determined. According to calculations, most low-energy conformers can interconvert, and the most stable conformers anti-trans-CHPB and syn-trans-CHPB might have the major contributions. Four bands near 1423, 1360, 1220, and 1080 cm-1 were observed and tentatively assigned to the OH-decomposition products (C2H3)CCl(CH3)O (1-chloro-1-methyl-2-propenyloxy, CMP); both trans-CMP and cis-CMP might contribute. Unlike in the case of CH2OO + HCl and CH3CHOO + HCl, in which secondary reactions of the OH-decomposition products reacted readily with O2 to produce the dehydrated products HC(O)Cl and CH3C(O)Cl, respectively, the secondary reaction of CMP with O2 was not observed because there is no feasible H atom in CMP for O2 to abstract.

Clinical and methylomic features of spinal meningiomas.

The objective of our study was to analyze methylomic and clinical features of a cohort of spinal meningiomas (SMs) resected at our institution. This is a retrospective study of patients undergoing SM resection at our institution between 2010 and 2023. Clinical and radiographic characteristics were reviewed and analyzed with standard statistical methods. A Partitioning Around Medoids approach was used to cluster SMs with methylation data in a combined cohort from our institution and a publicly available dataset by methylation profiles. Clinical variables and pathway analyses were compared for the resulting clusters. Sixty-five SMs were resected in 53 patients with median radiographic follow-up of 34 months. Forty-six (87%) patients were female. The median age at surgery was 65 years and median tumor diameter was 1.9cm. The five-year progression-free survival rate was 90%, with subtotal resection being associated with recurrence or progression (p = .017). SMs clustered into hypermethylation, intermediate methylation, and hypomethylation subgroups. Tumors in the hypermethylated subgroup were associated with higher WHO grade (p = .046) and higher risk histological subtypes (p <.001), while tumors in the hypomethylated subgroup were least likely to present with copy-number loss in chromosome 22q (p <.0001). SMs classified as immune-enriched under a previously developed intracranial meningioma classifier did not have increased leukocyte fractions or hypomethylation of genes typically hypomethylated in immune-enriched tumors. SMs are more benign than their intracranial counterparts, and gross-total resection results in long term PFS. Methylation profiling identifies subgroups with differences in clinical variables.

Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

Unveiling hierarchy and spatial distribution of O6-methylguanine-DNA methyltransferase promoter methylation in World Health Organization grade 2-3 gliomas.

This study investigated the role of O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation hierarchy and heterogeneity in grade 2-3 gliomas, focusing on variations in chemotherapy benefits and resection dependency. A cohort of 668 newly diagnosed grade 2-3 gliomas, with comprehensive clinical, radiological, and molecular data, formed the basis of this analysis. The extent of resection was categorized into gross total resection (GTR ≥100%), subtotal resection (STR >90%), and partial resection (PR ≤90%). MGMTp methylation levels were examined using quantitative pyrosequencing. Our findings highlighted the critical role of GTR in improving the prognosis for astrocytomas (IDH1/2-mutant and 1p/19q non-codeleted), contrasting with its lesser significance for oligodendrogliomas (IDH1/2 mutation and 1p/19q codeletion). Oligodendrogliomas demonstrated the highest average MGMTp methylation levels (median: 28%), with a predominant percentage of methylated cases (average methylation levels >20%). Astrocytomas were more common in the low-methylated group (10%-20%), while IDH wild-type gliomas were mostly unmethylated (<10%). Spatial distribution analysis revealed a decrement in frontal lobe involvement from methylated, low-methylated to unmethylated cases (72.8%, 59.3%, and 47.8%, respectively). In contrast, low-methylated and unmethylated cases were more likely to invade the temporal-insular region (19.7%, 34.3%, and 40.4%, respectively). Astrocytomas with intermediate MGMTp methylation were notably associated with temporal-insular involvement, potentially indicating a moderate response to temozolomide and underscoring the importance of aggressive resection strategies. In conclusion, our study elucidates the complex interplay of MGMTp methylation hierarchy and heterogeneity among grade 2-3 gliomas, providing insights into why astrocytomas and IDH wild-type lower-grade glioma might derive less benefit from chemotherapy.

Catalytic C(&lt;i&gt;sp&lt;/i&gt;²)–C(&lt;i&gt;sp&lt;/i&gt;³) Cross-Electrophile Coupling in Ptᴵᴵ–NaI–C₂H₃I–CH₃I–acetone System

A new catalytic system for reductive C(sp²)–C(sp³) cross-electrophile coupling of was designed: Ptᴵᴵ iodo complexes in acetone solution containing an excess of NaI catalyzes the coupling of methyl iodide with vinyl iodide to form propylene. In parallel, the product of C(sp²)–C(sp²) coupling, 1,3-butadiene, is released in minor amounts. The total yield of the products based on the consumed vinyl iodide is almost quantitative. Under conditions of a large excess of methyl iodide, kinetics of vinyl iodide uptake follows pseudo-first-order law. The cross-coupling proceeds in a sequence of steps: oxidative addition of CH3I to Ptᴵᴵ iodo complexes to form methyl PtIV species – reduction of the latter with I– into the corresponding Ptᴵᴵ derivative – oxidative addition of C2H3I to the last one – reductive elimination of propylene from the intermediate methyl vinyl PtIV complex.

Global level of methylation in the sea lamprey (jawless vertebrate) genome is intermediate between invertebrate and jawed vertebrate genomes.

In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. In invertebrate, methylated cytosine generally located on specific genomic elements (e.g., gene bodies and silenced repetitive elements) to show a "mosaic" pattern. While in jawed vertebrate (teleost and tetrapod), highly methylated cytosine located genome-wide but only absence at regulatory regions (e.g., promoter and enhancer). Many studies imply that the evolution of DNA methylation reprogramming may have helped the transition from invertebrates to jawed vertebrates, but the detail remains largely elusive. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant agnathan (jawless) vertebrate. Strikingly, we found that the methylation level of the sea lamprey is very similar to that in sea urchin (a deuterostome) and sea squirt (a chordate) invertebrates. In sum, the global pattern in sea lamprey is intermediate methylation level (around 30%), that is higher than methylation level in the genomes of pre-bilaterians and protostomes (1%-10%), but lower than methylation level appeared in jawed vertebrates (around 70%, teleost and tetrapod). We anticipate that, in addition to genetic dynamics such as genome duplications, epigenetic dynamics such as global methylation reprograming was also orchestrated toward the emergence and evolution of vertebrates.

DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma

ABSTRACT Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (CpG ct ) in glioma tissues. We identified eight prognosis-related CpG ct to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight CpG ct might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient’s prognosis.

Synthesis and Study of the Structure-Activity Relationship of Antiproliferative N-Substituted Isosteviol-Based 1,3-Aminoalcohols.

Starting from isosteviol, a series of diterpenoid 1,3-aminoalcohol derivatives were prepared via stereoselective transformations. The acid-catalysed hydrolysis and rearrangement of natural stevioside produced isosteviol, which was transformed into the key intermediate methyl ester. In the next step, an 1,3-aminoalcohol library was prepared by the reductive amination of the intermediate 3-hydroxyaldehyde obtained from isosteviol in a two-step synthesis. To study the effect of the carboxylate ester function at position 4, the free carboxylic acid, benzyl ester and acryloyl ester analogues were prepared as elongated derivatives in comparison with our earlier results in this field. The antiproliferative activity of compounds against human tumour cell lines (A2780, HeLa, MCF-7 and MDA-MB-231) was investigated. In our preliminary study, the 1,3-aminoalcohol function with N-benzyl or (1H-imidazol-1-yl)-propyl substitution and benzyl ester moiety seemed essential for the reliable antiproliferative activity. The results obtained could be a good starting point to further functionalisation towards more efficient antiproliferative diterpenes.

Abstract C006: Combining the methylation and gene expression contiguous signals leads to better pancreatic cancer patient stratification and early detection

Abstract Background Pancreatic cancer (PAC) lacks methods for screening, patient stratification, resulting in late diagnosis and inadequate treatment of patients. Cell-free DNA (cfDNA) methylation patterns are signals representing real-time cancer characteristics such as early presence, tissue, and cell of origin. The aim of this study is to provide a better patient stratification based on differential patterns on the combined methylation and gene expression results in PAC and normal samples and provide proof-of-concept for early detection. Method Differential methylation region (DMR) analysis was performed on 180 TCGA PAAD and normal tissue samples using paired methylation and expression data. Validation was done on 143 Infiltrating duct carcinomas (IDC), (stage I, II, II), and 4 normal samples and the 4 probe clusters (FPC) were defined based on their methylation status: HM = high methylation, IM = intermediate methylation, LM = low methylation and MM = minimum methylation. 3-year and 5-year survival analysis with Kaplan-Meier was done. Gene ontology (GO) and Biological Pathway analyses (PA) were performed on DMRs of FPC. Integration analysis on paired methylation and expression data and the limma analysis was performed for significant genes in 5000 bp vicinities of the selected DMRs. Finally, selected 23 DMRs, were targeted in plasma cfDNA from 9 PAC patients (stage I-III) and 20 matching control samples. Results The survival analysis of FPC, shows the highest probability difference between HM and MM groups with p-values of 0.018 and 0.029 for 3-year and 5-year survival, respectively. Variability analysis shows 5740 significant CpG sites and 1135 significant DMRs comparing IDC tumor samples to controls. GO and PA on DRMs of FPC, indicated the most PAC specific pathways in the group of probes with MM status. Integration analysis on the methylation and mutation data of the selected genes of GO analysis shows potential to discriminate between normal and PAC patients and in between HM and MM groups and showed smaller mutation burden in MM and LM sample groups. Comparing MM to HM groups of patients, shows the highest significance in 5 downregulated genes in 5000 bp vicinity from Hypermethylated probes and 13 upregulated genes and 425 regions in 5000 base pairs vicinity from 170 hypomethylated probes. Survival analysis on the selected genes showed a very high correlation between the expression of the genes like SIX2, DNMT3A, ZFP91 and POR and the survival probability on FPC. Additionally, it has been shown that the selected DMRs, show good individual performance of AUC &amp;gt;0.95 in the in-house analysis of plasma cfDNA targeted data from 9 PAC patients (stage I-III) and 20 matching control samples. Conclusion Methylation markers carry distinct biological signals and combined with gene expression differentiate the PAC patient groups, showing potential of the methylation signals for better patient stratification outcomes for improved survival. High accuracy for cancer detection was observed for early-stage cancers when compared to cfDNA from matching controls. Citation Format: Pardis Saadatmand, Urban Kunej, Kristi Kruusmaa. Combining the methylation and gene expression contiguous signals leads to better pancreatic cancer patient stratification and early detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C006.

The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas

DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.

The Helicobacter pylori methylome is acid-responsive due to regulation by the two-component system ArsRS and the type I DNA methyltransferase HsdM1 (HP0463).

In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5'-TCAm6AVN6TGY-3' and 3'-AGTN6GAm6ACA-5'. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. IMPORTANCE This study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR~P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.

Hydrodeoxygenation of anisole over SBA-15-supported Ni, Pd, and Pt mono- and bimetallic catalysts: effect of the metal's nature on catalytic activity and selectivity.

Monometallic Ni, Pd and Pt and bimetallic catalysts formed by combinations of the above metals supported on SBA-15 silica were synthesized, characterized and tested in the hydrodeoxygenation reaction of anisole. The objective of the work was to detect the effect of the nature of metals on the activity of the catalysts at different steps of anisole hydrodeoxygenation: hydrogenation of the aromatic ring of anisole and C-O bond cleavage in the intermediate cyclohexyl methyl ether. The support and the catalysts were characterized by N2 physisorption, X-ray diffraction, UV-vis diffuse reflectance spectroscopy, temperature-programmed reduction, scanning electron microscopy-energy dispersive X-ray spectroscopy, transmission electron microscopy and HAADF-STEM. The catalytic activity tests were carried out in a batch reactor at 280 °C and 7.3 MPa pressure. The activity results show that the NiPd/SBA-15 catalyst had the greatest ability for hydrogenation of the aromatic ring of anisole, while its NiPt/SBA-15 analog resulted in better activity for C-O bond hydrogenolysis. The bimetallic NiPt/SBA-15 catalyst showed the best catalytic performance in the HDO of anisole ascribed to the formation of a Ni-Pt alloy. On the other hand, the combination of Pd and Pt metals in the PdPt/SBA-15 catalyst resulted in the formation of bimetallic particles with Pd-rich and Pt-rich domains, showing high selectivity for the formation of the cyclohexyl methyl ether, which can be useful for the hydrogenation of aromatic rings in O-containing reactants with the formation of saturated O-containing products. According to the characterization results (HAADF-STEM), the different catalytic behavior of NiPd/SBA-15, NiPt/SBA-15, and PdPt/SBA-15 catalysts could be attributed to different characteristics of the bimetallic active phases in them.

A comprehensive characterisation of phaeochromocytoma and paraganglioma tumours through histone protein profiling, DNA methylation and transcriptomic analysis genome wide

BackgroundPhaeochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumours. Pathogenic variants have been identified in more than 15 susceptibility genes; associated tumours are grouped into three Clusters, reinforced by their transcriptional profiles. Cluster 1A PPGLs have pathogenic variants affecting enzymes of the tricarboxylic acid cycle, including succinate dehydrogenase. Within inherited PPGLs, these are the most common. PPGL tumours are known to undergo epigenetic reprograming, and here, we report on global histone post-translational modifications and DNA methylation levels, alongside clinical phenotypes.ResultsOut of the 25 histone post-translational modifications examined, Cluster 1A PPGLs were distinguished from other tumours by a decrease in hyper-acetylated peptides and an increase in H3K4me2. DNA methylation was compared between tumours from individuals who developed metastatic disease versus those that did not. The majority of differentially methylated sites identified tended to be completely methylated or unmethylated in non-metastatic tumours, with low inter-sample variance. Metastatic tumours by contrast consistently had an intermediate DNA methylation state, including the ephrin receptor EPHA4 and its ligand EFNA3. Gene expression analyses performed to identify genes involved in metastatic tumour behaviour pin-pointed a number of genes previously described as mis-regulated in Cluster 1A tumours, as well as highlighting the tumour suppressor RGS22 and the pituitary tumour-transforming gene PTTG1.ConclusionsCombined transcriptomic and DNA methylation analyses revealed aberrant pathways, including ones that could be implicated in metastatic phenotypes and, for the first time, we report a decrease in hyper-acetylated histone marks in Cluster 1 PPGLs.

Synthesis and Evaluation of Glycosyl Luciferins.

Measuring glycosidase activity is important to monitor any aberrations in carbohydrate hydrolase activity, but also for the screening of potential glycosidase inhibitors. To this end, synthetic substrates are needed which provide an enzyme-dependent read-out upon hydrolysis by the glycosidase. Herein, we present two new routes for the synthesis of caged luminescent carbohydrates, which can be used for determining glycosidase activity with a luminescent reporter molecule. The substrates were validated with glycosidase and revealed a clear linear range and enzyme-dependent signal upon the in situ generation of the luciferin moiety from the corresponding nitrile precursors. Besides, we showed that these compounds could directly be synthesized from unprotected glycosyl-α-fluorides in a two-step procedure with yields up to 75 %. The intermediate methyl imidate appeared a key intermediate which also reacted with d-cysteine to give the corresponding d-luciferin substrate rendering this a highly attractive method for synthesizing glycosyl luciferins in good yields.

Efficient Visible‐Light‐Assisted Synthesis of Dimethyl Carbonate from CO2 and Methanol by Ce–Metal Organic Framework‐Derived CeO2 Nanoparticles

The conversion of carbon dioxide to dimethyl carbonate (DMC) is an attractive process, but thermodynamic limitations of the reaction hinder its further development. Herein, a simple solution coprecipitation strategy for the synthesis of a series of Ce–metal organic framework (MOF)‐derived CeO2 nanoparticles is proposed to rapidly break the thermodynamic equilibrium and achieve highly efficient activation of CO2/CH3OH under photothermal system. The CeO2–M–5, Ce(NO3)3·6H2O/2‐methylimidazoles molar ratio of 1:5, exhibits the highest DMC yield of 2.52 mmolDMC g−1cat under photothermal system, higher 3.26 times than CeO2–C (nanoparticle by high‐temperature calcination). Moreover, the DMC yield of CeO2–M–5 nanoparticles increases by 10% under the photothermal synergistic system compared to thermocatalytic system. This superior catalytic performance is attributed to the abundant Lewis acid–base sites, excellent light absorption capacity, and hydrophobicity. Besides, in situ diffuse reflectance infrared Fourier transform spectroscopy demonstrates that Ce–MOF‐derived CeO2 nanoparticles can effectively activate CO2/CH3OH to enhance the formation of the key intermediate methyl carbonate upon light irradiation. Finally, combining characterization and experimental results, the reaction mechanism of photothermal catalysis of CO2/CH3OH for DMC synthesis over Ce–MOF‐derived CeO2 nanoparticles is proposed. This work would provide new insights into the rational design of an effective catalyst for CO2 to produce high value‐added chemicals.

Epigenetic inheritance is unfaithful at intermediately methylated CpG sites

DNA methylation at the CpG dinucleotide is considered a stable epigenetic mark due to its presumed long-term inheritance through clonal expansion. Here, we perform high-throughput bisulfite sequencing on clonally derived somatic cell lines to quantitatively measure methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity, and is not coordinately maintained between neighbouring sites. We determine that the probabilistic changes that occur at intermediately methylated sites are likely due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the current epigenetic inheritance model and has direct implications for both the functional relevance and general interpretability of DNA methylation as a stable epigenetic mark.

Targeting the ADPKD methylome using nanoparticle-mediated combination therapy.

DNA methylation aberrancies are found in autosomal dominant polycystic kidney disease (ADPKD), which suggests the methylome to be a promising therapeutic target. However, the impact of combining DNA methylation inhibitors (DNMTi) and ADPKD drugs in treating ADPKD and on disease-associated methylation patterns has not been fully explored. To test this, ADPKD drugs, metformin and tolvaptan (MT), were delivered in combination with DNMTi 5-aza-2'-deoxycytidine (Aza) to 2D or 3D cystic Pkd1 heterozygous renal epithelial cells (PKD1-Het cells) as free drugs or within nanoparticles to enable direct delivery for future in vivo applications. We found Aza synergizes with MT to reduce cell viability and cystic growth. Reduced representation bisulfite sequencing (RRBS) was performed across four groups: PBS, Free-Aza (Aza), Free-Aza+MT (F-MTAza), and Nanoparticle-Aza+MT (NP-MTAza). Global methylation patterns showed that while Aza alone induces a unimodal intermediate methylation landscape, Aza+MT recovers the bimodality reminiscent of somatic methylomes. Importantly, site-specific methylation changes associated with F-MTAza and NP-MTAza were largely conserved including hypomethylation at ADPKD-associated genes. Notably, we report hypomethylation of cancer-associated genes implicated in ADPKD pathogenesis as well as new target genes that may provide additional therapeutic effects. Overall, this study motivates future work to further elucidate the regulatory mechanisms of observed drug synergy and apply these combination therapies in vivo.

Association of 4qA-Specific Distal D4Z4 Hypomethylation With Disease Severity and Progression in Facioscapulohumeral Muscular Dystrophy.

To examine whether the regional methylation levels at the most distal D4Z4 repeat units (RU) in the 4qA-permissive haplotype were associated with disease severity and progression in facioscapulohumeral muscular dystrophy type 1 (FSHD1). This was a 21-year, retrospective, and observational cohort study conducted at the Fujian Neuromedical Centre (FNMC) in China. Methylation levels of the most distal D4Z4 RU, including 10 CpGs, were assessed in all participants by bisulfite sequencing. FSHD1 patients were stratified into 4 groups based on methylation percentage quartiles, including LM1 (low methylation), LM2 (low to intermediate methylation), LM3 (intermediate to high methylation), and highest methylation levels (HM). Patients received evaluations of motor function focusing on lower extremity (LE) progression at baseline and in follow-ups. FSHD clinical score (CS), age-corrected clinical severity scale (ACSS), and modified Rankin Scale were used to assess motor function. The methylation levels of the 10 CpGs were significantly lower in all 823 genetically confirmed FSHD1 patients than in 341 healthy controls (HCs). CpG6 methylation levels could distinguish: 1) FSHD1 patients from HCs; 2) symptomatic from asymptomatic/unaffected patients; 3) patients with LE involvement from those without LE involvement, with AUCs (95% CI) of 0.9684 (0.9584-0.9785), 0.7417 (0.6903-0.7931), and 0.6386 (0.5816-0.6956), respectively. CpG6 methylation levels were negatively correlated with both CS (r = -0.392) and ACSS (r = -0.432), and positively correlated with onset age of first-ever muscle weakness (r = 0.297). For the LM1, LM2, LM3, and HM groups, the respective proportions of LE involvement were 52.9%, 44.2%, 36.9%, and 23.4%; and onset ages of LE involvement were 20, 26.5, 25, and 26.5 years. Cox regression analysis-adjusted for sex, age at examination, D4Z4 RU, and 4qA/B haplotype-showed that the LM1, LM2, and LM3 groups (i.e., groups with lower methylation levels) had a higher risk for independent ambulation loss, with HRs (95% CI) of 3.523 (1.565-7.930), 3.356 (1.458-7.727), and 2.956 (1.245-7.020), respectively. 4q35 distal D4Z4 hypomethylation is correlated with disease severity and progression to lower extremity involvement.