AIM： To evaluate the clinical significance of CpG island methylator phenotype （CIMP） in plasma and its association with hepatocellular carcinoma （HCC） progress. METHODS： CIMP status of 108 HCC patients was analy...AIM： To evaluate the clinical significance of CpG island methylator phenotype （CIMP） in plasma and its association with hepatocellular carcinoma （HCC） progress. METHODS： CIMP status of 108 HCC patients was analyzed using a methylation marker panel in tumor tissues and plasma with methylation-specific polymerase chain reaction. Fifteen samples of non-neoplastic liver tissues and 60 of plasma from healthy persons were examined simultaneously. Examined genes included APC, WIF-1, RUNX-3, DI C-1, SFRP-1, DKK and E-cad.26/108, 24.07% in plasma; WIF-1, 53/108, 49.07% in tissue and 35/108, 32.41% in plasma; RUNX-3, 52/108, 48.14% in tissue and 42/108, 38.89% in plasma; DIC-1, 38/108, 35.18% in tissue and 23/108, 21.30% in plasma; SFRP-1, 40/108, 37.04% in tissue and 31/108, 28.7% in plasma; DKK, 39/108, 36.1% in tis- sue and 25/108, 23.14% in plasma; and E-cad, 37/108, 34.3% in tissue and 18/108, 16.67% in plasma. CIMP＋ （≥3 methylated genes） was detected in 68 （60.2%） tumor tissue samples and 62 （57.4%） plasma samples. CIMP was not detected in non-neoplastic liver tissues or plasma of healthy persons. CIMP status in tumor tissues differed significantly in gender, hepatitis B surface antigen, alpha-fetoprotein, and tumor-node- metastasis stage （P 〈 0.05）. Similar results were obtained with plasma samples （P 〈 0.05）. There was no difference in CIMP status in age, presence of hepatitis C virus antibody, cirrhosis, number of nodes, number of tumors, tumor size, or Edmondson-Steiner stage. A one-year follow-up found that the metastatic rate and recurrence rate in the CIMP＋ group were significantly higher than in the CIMP- group as assessed with plasma samples （P 〈 0.05）. CONCLUSION： Plasma DNA can be a reliable sample source for CIMP analysis. CIMP in plasma may serve as a molecular marker of late-stage and poor-prognosis HCC.展开更多
AIM： To investigate the association between the CpG island methylator phenotype （CIMP） and serum Helico- bacter pylori （H. pylori） levels for clinical prediction of gastric cancer （GC） progression. METHODS： We...AIM： To investigate the association between the CpG island methylator phenotype （CIMP） and serum Helico- bacter pylori （H. pylori） levels for clinical prediction of gastric cancer （GC） progression. METHODS： We analyzed the serum ClMP status of 75 patients with GC using a methylation marker panel and a methylation-specific polymerase chain reaction. Serum samples from 40 healthy persons were examined at the same time. The genes examined were APC, WIF-1, RUNX-3, DLC-1, SFRP-1, DKK and E-cad. H. pylori infec- tion in serum was assayed with an anti-H, pylori immu- noglobulin G antibody test and a rapid urease test. RESULTS： The frequencies of high-level methylation in GC tissues for the seven genes were： 48% for APC, 57.33% for WIF-1, 56% for RUNX-3, 50.67% for DLC-1, 52% for SFRP-1, 54.67% for DKK, and 48% for E-cad.The frequencies in GC serum were 30.67% for APC, 34.67% for WIF-1, 37.33% for RUNX-3, 29.33% for DLC-1, 33.33% for SFRP-1, 32% for DKK, and 26.67% for E-cad. CIMP＋ （defined as ≥ 3 methylated genes） was associated with 47 （62.67%） GC tissue samples and 44 （58.67%） GC serum samples. CIMP＋ was not associated with non-neoplastic mucosal tissues or the serum of healthy persons. Of the 75 GC cases, 51 （68%） were H. pylori＋, and 24 （32%） were H. pylori-. Of the 51 H. pylori＋ cases, 36 were CIMP＋ and 15 were CIMP-. In contrast, for the 24 H. pylori- cases, 11 were CIMP＋, and 13 were CIMP-. The difference was signifi- cant between the H. pylori＋ and H. pylori- groups χ2 = 4.27, P 〈 0.05）. Of the 51 H. pylori＋ GC patients, 34 were CIMP＋ and 17 were CIMP-, while among the 24 H. pylori- GC cases, 10 were CIMP＋ and 14 were CIMP-. The difference was significant between the H. pylori＋ and H. pylori- groups （χ2 = 4.21, P 〈 0.05）. A 2-year follow-up showed significant difference in the rates of metastasis and recurrence between H. pylori＋/CIMP＋ cases and the H. pylori＋/CIMP- cases or CIMP- cases associated with H. pylori assayed in serum （P 〈 0.05）. However, there were no significant differences in sur- vival rates between the two groups. CONCLUSION： H. pylori＋/CIMP＋ cases are associ- ated with higher rates of metastasis and recurrence thanH, pylori＋/CIMP- cases. Serum may be useful for examining CIMP status.展开更多
Over the last two decades, cancer-related alterations in DNA methylation that regulate transcription have been reported for a variety of tumors of the gastrointestinal tract. Due to its relevance for translational res...Over the last two decades, cancer-related alterations in DNA methylation that regulate transcription have been reported for a variety of tumors of the gastrointestinal tract. Due to its relevance for translational research, great emphasis has been placed on the analysis and molecular characterization of the CpG island methylator phenotype(CIMP), defined as widespread hypermethylation of CpG islands in clinically distinct subsets of cancer patients. Here, we present an overview of previous work in this field and also explore some open questions using crossplatform data for esophageal, gastric, and colorectal adenocarcinomas from The Cancer Genome Atlas. We provide a data-driven, pan-gastrointestinal stratification of individual samples based on CIMP status and we investigate correlations with oncogenic alterations, including somatic mutations and epigenetic silencing of tumor suppressor genes. Besides known events in CIMP such as BRAF V600 E mutation, CDKN2 A silencing or MLH1 inactivation, we discuss the potential role of emerging actors such as Wnt pathway deregulation through truncating mutations in RNF43 and epigenetic silencing of WIF1. Our results highlight the existence of molecular similarities that are superimposed over a larger backbone of tissue-specific features and can be exploited to reduce heterogeneity of response in clinical trials.展开更多
To identify whether CpG island methylator phenotype (CIMP) is predictive of response to neoadjuvant chemoradiotherapy (NACRT) and outcomes in rectal cancer. METHODSPatients undergoing NACRT and surgical resection for ...To identify whether CpG island methylator phenotype (CIMP) is predictive of response to neoadjuvant chemoradiotherapy (NACRT) and outcomes in rectal cancer. METHODSPatients undergoing NACRT and surgical resection for rectal cancer in a tertiary referral centre between 2002-2011 were identified. Pre-treatment tumour biopsies were analysed for CIMP status (high, intermediate or low) using methylation specific PCR. KRAS and BRAF status were also determined using pyrosequencing analysis. Clinical information was extracted from case records and cancer services databases. Response to radiotherapy was measured by tumour regression scores determined upon histological examination of the resected specimen. The relationship between these molecular features, response to NACRT and oncological outcomes were analysed. RESULTSThere were 160 patients analysed with a median follow-up time of 46.4 mo. Twenty-one (13%) patients demonstrated high levels of CIMP methylation (CIMP-H) and this was significantly associated with increased risk of extramural vascular invasion (EMVI) compared with CIMP-L [8/21 (38%) vs 15/99 (15%), P = 0.028]. CIMP status was not related to tumour regression after radiotherapy or survival, however EMVI was significantly associated with adverse survival (P < 0.001). Intermediate CIMP status was significantly associated with KRAS mutation (P = 0.01). There were 14 (9%) patients with a pathological complete response (pCR) compared to 116 (73%) patients having no or minimal regression after neoadjuvant chemoradiotherapy. Those patients with pCR had median survival of 106 mo compared to 65.8 mo with minimal regression, although this was not statistically significant (P = 0.26). Binary logistic regression analysis of the relationship between EMVI and other prognostic features revealed, EMVI positivity was associated with poor overall survival, advanced “T” stage and CIMP-H but not nodal status, age, sex, KRAS mutation status and presence of local or systemic recurrence. CONCLUSIONWe report a novel association of pre-treatment characterisation of CIMP-H with EMVI status which has prognostic implications and is not readily detectable on pre-treatment histological examination.展开更多
Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methyla...Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methylation,a process predominantly attributed to anaerobic bacteria.However,recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns,although the mechanisms remain poorly understood.“Blue holes”are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles.Here,we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem.Yongle Blue Hole(YBH),currently the world’s deepest known blue hole,was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment.Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation,driven by abundant and diverse Deltaproteobacteria.In the suboxic intermediate layer,Nitrospina and Myxococcota dominated the Hg-methylating community.Furthermore,Hg methylators were found to have different lifestyles(free-living or particle-associated)and to occupy distinct ecological niches within the YBH.In addition,the contribution of sinking particles to Hg methylation,especially in the deep anoxic water column,was highlighted.Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments.The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.展开更多
The yam Dioscorea alata L.is widely cultivated globally.Purple-fleshed varieties of this important crop have enhanced market value due to their high anthocyanin contents,but how anthocyanin biosynthesis in D.alata tub...The yam Dioscorea alata L.is widely cultivated globally.Purple-fleshed varieties of this important crop have enhanced market value due to their high anthocyanin contents,but how anthocyanin biosynthesis in D.alata tubers is regulated remains poorly understood.In this study,we identified and functionally validated key transcription factors that regulate anthocyanin biosynthesis based on a comparative transcriptome and metabolome analysis of three D.alata cultivars with different colored tubers(dark purple,light purple,and white).The anthocyanin glycoside cyanidin-3-O-(2′′-O-glucosyl)glucoside was abundant during early tuber development,and we determined that its accumulation is regulated in opposite manners by two R2R3-MYB transcription factors:DaMYB75 and DaMYB56.Yeast two-hybrid and bimolecular fluorescence complementation assays in Nicotiana benthamiana and co-expression assays in D.alata demonstrated that DaMYB75 promotes anthocyanin biosynthesis by specifically activating the promoter of the late anthocyanin biosynthesis gene DaANS and enhancing its expression through an interaction with DabHLH72.By contrast,DaMYB56 is a negative regulator of anthocyanin biosynthesis that binds to the DaANS promoter together with DabHLH72.Furthermore,the methylation levels of the DaMYB75 promoter were significantly lower in purple tubers than in white tubers.These findings shed light on the regulation of anthocyanin biosynthesis by MYBs and provide the basis for genetically improving anthocyanin content in D.alata.展开更多
Licochalcone A(LCA)is a characteristic compound in licorice Glycyrrhiza inflata and is widely utilized in pharmaceutical and cosmetic industries.However,the biosynthetic pathway and regulatory mechanisms of LCA remain...Licochalcone A(LCA)is a characteristic compound in licorice Glycyrrhiza inflata and is widely utilized in pharmaceutical and cosmetic industries.However,the biosynthetic pathway and regulatory mechanisms of LCA remain poorly understood.In this study,we first found the accumulation of LCA is induced by methyl jasmonate(MeJA).Given that MYB transcriptional factors are well-documented as key regulators of flavonoid biosynthesis,we identified a total of 147 GiR2R3-MYB genes in G.inflata,which were classified into 28 subgroups.The chromosome distributions,sequence characteristics,gene structures,duplication events and cis-acting elements were also investigated.Through integrated analysis of GiR2R3-MYBs expression patterns across different tissues and under MeJA treatment,along with phylogenetic relationship,we identified GiMYB76—a MeJA-inducible MYB transcription factor—as a potential regulator of LCA accumulation.Functional validation showed that transgenic hairy roots overexpressing GiMYB76 exhibited a significant increase in LCA content.DAP-seq analysis of GiMYB76 revealed potential target genes involved in flavonoid biosynthesis regulation.Subsequent promoter activity assay verified that GiMYB76 can bind to the promoter and activate the expression of GiCHS4.Consistently,overexpression of GiCHS4 in G.inflata hairy roots also significantly enhanced LCA production.This study not only clarifies that GiMYB76 transcriptionally activated GiCHS4 to promote LCA biosynthesis but also provides valuable insights for basic research on licorice and the development of related industries.展开更多
The development of methylation protocol has attracted intense attention owing to"magic methyl effect"in drug discovery.Meanwhile,the indole scaffold is prevalence in the natural products and pharmacophores.D...The development of methylation protocol has attracted intense attention owing to"magic methyl effect"in drug discovery.Meanwhile,the indole scaffold is prevalence in the natural products and pharmacophores.Despite the advances in other site selective methylation,there is scarce reports for C4 methylation of indoles and combination of a carbonyl group rearrangement with C—H methylation on indole ring.Herein,the C4 methylation of indoles and the steric controlled C4-methylation/carbonyl group migration are reported.The large steric hindrance at carbonyl group facilitates the carbonyl group migration,which provides a straightforward protocol for the synthesis of C2/C4 disubstituted indoles.展开更多
The escalating pace of industrialization has significantly intensified water pollution challenges,for instance,the persistent organic pollutants like methyl orange(MO).Conventional remediation techniques,such as adsor...The escalating pace of industrialization has significantly intensified water pollution challenges,for instance,the persistent organic pollutants like methyl orange(MO).Conventional remediation techniques,such as adsorption and biological degradation,are often hampered by low efficiency and the risk of secondary pollution.Photocatalysis emerges as a promising sustainable alternative;however,the benchmark material titanium dioxide(TiO_(2))suffers from its intrinsic limitations,notably its wide bandgap energy(≥3.4 eV)restricting its activity to the region of the ultraviolet light and its rapid recombination of photogenerated charge carriers.To overcome these constraints,this research focused on synthesizing novel TiO_(2)/Sn_(3)O_(4) heterojunction composite photocatalysts via a solvothermal approach.Comprehensive characterization techniques confirmed the successful formation of the composite,which revealed that ultrathin Sn3O4 nanosheets uniformly coated TiO_(2) nanospheres.This unique architecture effectively reduced the overall crystallinity and introduced the beneficial oxygen vacancies.Under visible-light irradiation(λ≥420 nm),the optimized TiO_(2)/Sn3O4 composite exhibited the exceptional photocatalytic performance,which achieved 96%degradation of MO within just 60 minutes.The calculated apparent kinetic rate constant(0.103 min^(-1))was remarkably(5.15 times)higher than that of pristine TiO_(2).ESR experiments identified that hydroxyl radicals(·OH)was the predominant active species driving the degradation.Furthermore,cyclic degradation tests demonstrated its excellent material stability,with the composite retaining 85%of its initial efficiency after four consecutive reuse cycles.This work underscored the synergistic effects within the TiO_(2)/Sn_(3)O_(4) heterojunction,which significantly enhanced the visible-light absorption,charge separation,and photocatalytic activity,which provided the valuable insights for designing efficient,stable catalysts for the advanced environmental remediation applications.展开更多
In vitro maturation(IvM)of human oocytes offers cost efficiency and minimal invasiveness,serving as a valuable supplementary tool in assisted reproduction for fertility preservation,ovarian hyperstimulation syndrome p...In vitro maturation(IvM)of human oocytes offers cost efficiency and minimal invasiveness,serving as a valuable supplementary tool in assisted reproduction for fertility preservation,ovarian hyperstimulation syndrome prevention,and other reproductive strategies.Despite its availability for three decades,the clinical use of IVM remains limited due to efficacy and safety concerns.This study examines the DNA methylation profile of IVM oocytes collected during laparoscopic/hysteroscopic surgeries compared to in vivo matured oocytes via reduced representation bisulfite sequencing.Results indicate IVM oocytes exhibit a higher global methylation level.Differentially methylated regions(DMRs)analysis reveals that the in vitro group displays more hypermethylated and fewer hypomethylated DMRs compared to the in vivo group.Additionally,the in vitro group exhibits a higher level of non-CpG methylation than the in vivo group.However,no significant correlation between methylation levels and transcriptional activity in these oocytes is found,especially for those specific imprinted genes or genes related to embryonic development.These findings shed light on the epigenetic landscape of IvM oocytes,contributing to the ongoing assessment of their clinical feasibility and safety in assisted reproduction.展开更多
DNA methylation is an important promising biomarker for cancer diagnosis and monitoring.Therefore,the assessment of DNA methylation levels is helpful for the prognosis and diagnosis of cancer.However,it is still a hug...DNA methylation is an important promising biomarker for cancer diagnosis and monitoring.Therefore,the assessment of DNA methylation levels is helpful for the prognosis and diagnosis of cancer.However,it is still a huge challenge to sensitively and accurately quantify the levels of DNA methylation in clinical sample.In this work,we proposed a protospacer adjacent motif(PAM)-free mediated CRISPR-Cas12a ultra-sensitive and quantitative DNA methylation detection method.Through recognizing the ds DNA with toehold region,CRISPR-Cas12a not only got rid of the limitation of PAM,but also improved its distinction ability for single Cp G site methylation,nearly 5-fold that of conventional PAM-containing ds DNA.We further introduced assist-strand and design an artificial mismatch to greatly improve the ability to distinguish single Cp G methylation site.Our results showed that the discrimination factor was >200.Then,we constructed toe-ds DNA by using “heating and freezing”,which made our method universally applicable and feasible.In addition,we greatly simplified the difficulty of primer design.Our method detected four highly methylated genes acyl carrier protein(ACP),CLV3/ESR-related(CLE),Disabled(DAB) and Homeobox(HOX) with a detection limit of 0.01 % and excellent linearity in DNA methylation standards.Then,we verified the clinical utility of this method in 29 hepatocellular carcinomas,11 ovarian cancers and4 health people.In conclusion,we have successfully constructed a PAM-free CRISPR-Cas12a DNA methylation quantification method,which achieves high congruence in sensitivity,specificity and universality,fully demonstrating its significant clinical application value.展开更多
Fig(Ficus carica L.)with purple-red peel cultivars are popular among consumers and exhibit better storability.While DNA methylation influences fruit ripening and color development,its specific role in fig fruit remain...Fig(Ficus carica L.)with purple-red peel cultivars are popular among consumers and exhibit better storability.While DNA methylation influences fruit ripening and color development,its specific role in fig fruit remains unclear.This study explores the impact of DNA methylation on the fig peel coloration.Enzymatic colorimetric detection revealed that the level of‘Purple Peel’fig DNA methylation decreases with fig fruit ripening and coloring.Treatment of young fruit with the DNA-methylation inhibitor azacytidine induced peel coloration,suggesting that a decrease in DNA-methylation level promotes fig peel coloration.Seven members of DNA methyltransferases and three members of DNA demethylases were identified from a high-level fig genome,highlighting FcMET1 and FcDRM2 as stable proteins,ensuring functional expression.Reference to the Arabidopsis protein interaction network map predicted that FcMET1 is in a central position,suggesting a crucial regulatory role in multiple biological processes.Correlation analysis revealed a positive correlation between FcMET1 expression during peel development and the level of total DNA methylation.Weighted gene co-expression network analysis identified co-expression of FcMET1 with the color-related transcription factors MYB,bHLH and WD40,as well as with eight structural genes in the flavonoid-biosynthesis pathway.The expression of FcUFGT3 was negatively correlated with that of FcMET1.McrBC-PCR and Bisulfite Sequencing detection showed that a low methylation level of the FcUFGT3 promoter corresponds with its high expression in colored fig.This investigation of the mechanism of DNA methylation provides a theoretical basis for understanding the role of DNA-methylation modifications in fig ripening and coloring.展开更多
In eukaryotic organisms,the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression.Previous studies have provided significant insights into CpG methyl...In eukaryotic organisms,the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression.Previous studies have provided significant insights into CpG methylation,chromatin accessibility,and the dynamics of 3D architecture.However,a systematic delineation of how these epigenomic features regulate transcriptional activity remains limited.In this study,we develop nanoCAM-seq,a single-molecule sequencing technique designed to simultaneously profile higher-order chromatin interactions,chromatin accessibility,and endogenous CpG methylation.This approach provides an integrative view of chromatin features associated with cis-regulatory elements and reveals their coordinated dynamics during transitions of A/B compartments.Single-molecule analyses using nanoCAM-seq further reveal that promoters characterized by low CpG methylation and high chromatin accessibility more frequently interact with multiple enhancers.Collectively,our findings establish nanoCAM-seq as a powerful approach for resolving the coordinated dynamics of chromatin architecture and epigenetic modifications,offering critical insights into the regulatory mechanisms underlying gene expression.展开更多
Methyl mercaptan(CH_(3)SH)is notorious for global air pollution owing to its odorous characteristics and adverse health effects.Although CeO_(2) is currently regarded as a promising catalyst for CH_(3)SH decomposition...Methyl mercaptan(CH_(3)SH)is notorious for global air pollution owing to its odorous characteristics and adverse health effects.Although CeO_(2) is currently regarded as a promising catalyst for CH_(3)SH decomposition,the high conversion temperature followed by high energy consumption is still a bottleneck.Herein,the cobalt-doped CeO_(2) catalyst was synthesized by a facile one-pot preparation strategy and successfully reduces the decomposition temperature from 450 to 250℃.Further studies demonstrate that the excellent low-temperature catalytic activity of Co_(0.6)Ce_(0.4)O_(2-σ)is attributed to its abundant oxygen vacancies and reactive oxygen species.Oxygen vacancies promote the adsorption and dissociation of CH_(3)SH,while reactive oxygen species facilitate the decomposition of CH_(3)SH.Moreover,Co acts as a sacrificial agent for the adsorption of sulfur species in CH_(3)SH,while Ce is responsible for the adsorption and activation of CH_(3)SH as the active metal phase.Furthermore,the migration and transformation mechanism of CH_(3)SH on the surface of Co_(0.6)Ce_(0.4)O_(2-δ)was determined via in situ diffuse reflectance infrared Fourier transform spectra(in situ-DRIFTS).This work provides a new strategy to synthesize highperformance catalysts for decomposing sulfur-containing volatile organic compounds(VOCs)at low temperatures,which is beneficial to decreasing the energy consumption.展开更多
Alterations in RNA methylation may affect the initiation and development of Alzheimer’s disease.However,the exact nature of the relationship between RNA methylation and Alzheimer’s disease remains unclear.In this st...Alterations in RNA methylation may affect the initiation and development of Alzheimer’s disease.However,the exact nature of the relationship between RNA methylation and Alzheimer’s disease remains unclear.In this study,RNA methylation levels were analyzed by bulk transcriptomic and single-cell RNA sequencing.The expression levels of RNA methylation regulators were confirmed using molecular biology techniques.Co-expression network analysis was used to identify relevant long non-coding RNAs.Molecular subtypes related to RNA methylation were classified,and variations in clinical characteristics,biological behavior,and immune signatures between subtypes were assessed.Machine learning approaches were applied to identify methylation-associated long non-coding RNAs,which were used to construct a risk model and nomogram for Alzheimer’s disease.Potential therapeutic agents for different risk groups were predicted,and in vitro experiments were conducted to identify key RNA methylation events.Single-cell analysis demonstrated enhanced RNA methylation in patients with Alzheimer’s disease,particularly within T cells,B cells,and NK cells.Quantitative reverse transcription-polymerase chain reaction and western blot confirmed alterations in RNA methylation regulators in neurons treated with amyloid-βoligomers in vitro.This evidence supported the classification of patients with Alzheimer’s disease into heterogeneous subtypes.Specifically,subtype 1 was identified as the immune-active subtype,while subtype 2 was characterized by a metabolic phenotype.Machine learning algorithms identified five significant methylation-associated long non-coding RNAs-LINC01007,MAP4K3-DT,MIR302CHG,VAC14-AS1,and TGFB2-OT1-that accurately predict clinical outcomes for patients with Alzheimer’s disease.These patients were classified into low-and high-risk categories;the latter group displayed higher immune infiltration,upregulated immune regulatory gene expression,and elevated immune scores and responded better to treatment with arachidonic-trifluoroethane.These findings suggest that dysregulated RNA methylation alters the immune microenvironment in Alzheimer’s disease and is closely associated with its progression.This phenomenon provides novel insights into potential therapeutic strategies for Alzheimer’s disease that target RNA methylation.展开更多
Glutamate receptors and schizophrenia:Schizophrenia is a chronic mental disorder affecting approximately 1%of the global population,with 70%-80%heritability.It has a multifactorial etiology involving both environmenta...Glutamate receptors and schizophrenia:Schizophrenia is a chronic mental disorder affecting approximately 1%of the global population,with 70%-80%heritability.It has a multifactorial etiology involving both environmental factors and a complex polygenic genetic architecture.Over the last two decades,large-scale genome-wide approaches revealed contributions of common variants with individually small effect sizes and of rare copy number variants with a large effect size.N-methy l-D-a spar tat e receptor(NMDAR)hypofunction has been implicated as a central mechanism in the pathophysiology of schizophrenia(Coyle et al.,2020).展开更多
Neurodegenerative diseases are characterized by a decline in brain structure and function.Their pathology involves multiple cell death pathways,including ferroptosis,cuproptosis,and pyroptosis.These pathways are intri...Neurodegenerative diseases are characterized by a decline in brain structure and function.Their pathology involves multiple cell death pathways,including ferroptosis,cuproptosis,and pyroptosis.These pathways are intricately linked to genes associated with metabolism,antioxidant defense,lipid metabolism,chronic inflammation,and nerve regeneration processes.Key regulators of atypical cell death pathways show aberrant N^(6)-methyladenosine modification levels under pathological conditions.As the most abundant and dynamic RNA modification in brain tissue,N^(6)-methyladenosine plays crucial functional roles.Notably,there exists an intricate interplay between N^(6)-methyladenosine modifications and these cell death pathways,both of which are robustly associated with the pathogenesis of neurodegenerative diseases.However,the molecular mechanisms underlying this association remain unclear.This paper reviews the correlation between N^(6)-methyladenosine and various cell death patterns in neurodegenerative diseases,with emphasis on the molecular mechanisms underlying the interaction between N^(6)-methyladenosine epigenetic regulation and ferroptosis,cuproptosis,and pyroptosis in cognitive impairment.N^(6)-methyladenosine-modified ferroptosis plays an important role in neurodegenerative diseases.There is also a close association between N^(6)-methyladenosine modification and key molecules related to cuproptosis,which may promote the deposition of copper in the brain.Chronic inflammation,a hallmark of neurodegenerative diseases,is related to pyroptosis and N^(6)-methyladenosine modification.It is widely thought that ferroptosis,cuproptosis,and pyroptosis are interconnected processes that may share a common pathway affecting the pathogenesis of neurodegenerative diseases,and are related to key molecules involved in N^(6)-methyladenosine epigenetic modification.This suggests a great potential for future neurodegenerative diseases treatment strategies regulated by N^(6)-methyladenosine modification.N^(6)-methyladenosine modification plays a dual role in nerve injury and regeneration by dynamically regulating processes such as ferroptosis,cuproptosis,and pyroptosis and their key molecules.It maintains the“death-regeneration”balance in oxidative stress and inflammation while selectively promoting axon regeneration through the modulation of methylases.This mechanism indicates a considerable therapeutic target for neurological disorders.展开更多
N^(6)-methyladenosine RNA methylation,an essential post-transcriptional modification,dynamically regulates RNA metabolism and plays a crucial role in neuronal function.Growing evidence suggests that dysregulated N^(6)...N^(6)-methyladenosine RNA methylation,an essential post-transcriptional modification,dynamically regulates RNA metabolism and plays a crucial role in neuronal function.Growing evidence suggests that dysregulated N^(6)-methyladenosine modification contributes to the pathogenesis of neurodegenerative diseases,including Alzheimer’s disease,Parkinson’s disease,multiple sclerosis,and amyotrophic lateral sclerosis.However,the precise mechanisms by which N^(6)-methyladenosine modification influences these conditions remain unclear.This review summarizes the role of m6A modification and its associated regulators in neurodegeneration,focusing on their involvement in key pathological processes.In Alzheimer’s disease,m6A modification contributes to synaptic dysfunction,mitochondrial damage,and neuronal apoptosis.Evidence from APP/PS1,5xFAD,tau transgenic,and Drosophila models demonstrates that regulators such as methyltransferase-like 3 and fat mass and obesity-associated protein influence Alzheimer’s disease progression through neuroinflammation,circular RNAs dysregulation,and autophagy-related mechanisms.In Parkinson’s disease,altered N^(6)-methyladenosine regulator expression affects dopaminergic neuron survival and stress responses by modulating mRNA stability and autophagy-related lncRNAs.In multiple sclerosis and amyotrophic lateral sclerosis,N^(6)-methyladenosine affects immune activation,myelin repair,and the regulation of disease-associated genes such as TDP-43.Beyond N^(6)-methyladenosine,other RNA methylation modifications-such as m1A,m5C,m7G,uracil,and pseudouridine-are implicated in neurodegenerative diseases through their regulation of mitochondrial function,RNA metabolism,and neuronal stress responses.Additionally,N^(6)-methyladenosine exhibits cell type-specific functions:in microglia,it regulates inflammatory activation and phagocytic function;in astrocytes,it modulates metabolic homeostasis and glutamate-associated neurotoxicity;in neurons,it affects synaptic function and neurodegeneration-related gene expression;and in adult neural stem cells,it controls differentiation,neurogenesis,and cognitive plasticity.Recently,several small-molecule inhibitors targeting methyltransferase-like 3 or fat mass and obesity-associated protein have been developed to modulate N^(6)-methyladenosine modification,providing new opportunities for disease intervention,with the targeting of N⁶-methyladenosine-related pathways emerging as a promising therapeutic strategy.However,challenges persist in optimizing the specificity and delivery of these therapeutic approaches.展开更多
Stroke is classified as ischemic or hemorrhagic,and there are few effective treatments for either type.Immunologic mechanisms play a critical role in secondary brain injury following a stroke,which manifests as cytoki...Stroke is classified as ischemic or hemorrhagic,and there are few effective treatments for either type.Immunologic mechanisms play a critical role in secondary brain injury following a stroke,which manifests as cytokine release,blood–brain barrier disruption,neuronal cell death,and ultimately behavioral impairment.Suppressing the inflammatory response has been shown to mitigate this cascade of events in experimental stroke models.However,in clinical trials of anti-inflammatory agents,longterm immunosuppression has not demonstrated significant clinical benefits for patients.This may be attributable to the dichotomous roles of inflammation in both tissue injury and repair,as well as the complex pathophysiologic inflammatory processes in stroke.Inhibiting acute harmful inflammatory responses or inducing a phenotypic shift from a pro-inflammatory to an anti-inflammatory state at specific time points after a stroke are alternative and promising therapeutic strategies.Identifying agents that can modulate inflammation requires a detailed understanding of the inflammatory processes of stroke.Furthermore,epigenetic reprogramming plays a crucial role in modulating post-stroke inflammation and can potentially be exploited for stroke management.In this review,we summarize current findings on the epigenetic regulation of the inflammatory response in stroke,focusing on key signaling pathways including nuclear factor-kappa B,Janus kinase/signal transducer and activator of transcription,and mitogen-activated protein kinase as well as inflammasome activation.We also discuss promising molecular targets for stroke treatment.The evidence to date indicates that therapeutic targeting of the epigenetic regulation of inflammation can shift the balance from inflammation-induced tissue injury to repair following stroke,leading to improved post-stroke outcomes.展开更多
Salsolinol(1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline,Sal)is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine,an environme...Salsolinol(1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline,Sal)is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine,an environmental toxin that causes Parkinson's disease.However,the mechanism by which Sal mediates dopaminergic neuronal death remains unclear.In this study,we found that Sal significantly enhanced the global level of N~6-methyladenosine(m~6A)RNA methylation in PC12 cells,mainly by inducing the downregulation of the expression of m~6A demethylases fat mass and obesity-associated protein(FTO)and alk B homolog 5(ALKBH5).RNA sequencing analysis showed that Sal downregulated the Hippo signaling pathway.The m~6A reader YTH domain-containing family protein 2(YTHDF2)promoted the degradation of m~6A-containing Yes-associated protein 1(YAP1)mRNA,which is a downstream key effector in the Hippo signaling pathway.Additionally,downregulation of YAP1 promoted autophagy,indicating that the mutual regulation between YAP1 and autophagy can lead to neurotoxicity.These findings reveal the role of Sal on m~6A RNA methylation and suggest that Sal may act as an RNA methylation inducer mediating dopaminergic neuronal death through YAP1 and autophagy.Our results provide greater insights into the neurotoxic effects of catechol isoquinolines compared with other studies and may be a reference for assessing the involvement of RNA methylation in the pathogenesis of Parkinson's disease.展开更多
基金Supported by The Department of Health of Jiangsu Province,China,No.H200957
文摘AIM： To evaluate the clinical significance of CpG island methylator phenotype （CIMP） in plasma and its association with hepatocellular carcinoma （HCC） progress. METHODS： CIMP status of 108 HCC patients was analyzed using a methylation marker panel in tumor tissues and plasma with methylation-specific polymerase chain reaction. Fifteen samples of non-neoplastic liver tissues and 60 of plasma from healthy persons were examined simultaneously. Examined genes included APC, WIF-1, RUNX-3, DI C-1, SFRP-1, DKK and E-cad.26/108, 24.07% in plasma; WIF-1, 53/108, 49.07% in tissue and 35/108, 32.41% in plasma; RUNX-3, 52/108, 48.14% in tissue and 42/108, 38.89% in plasma; DIC-1, 38/108, 35.18% in tissue and 23/108, 21.30% in plasma; SFRP-1, 40/108, 37.04% in tissue and 31/108, 28.7% in plasma; DKK, 39/108, 36.1% in tis- sue and 25/108, 23.14% in plasma; and E-cad, 37/108, 34.3% in tissue and 18/108, 16.67% in plasma. CIMP＋ （≥3 methylated genes） was detected in 68 （60.2%） tumor tissue samples and 62 （57.4%） plasma samples. CIMP was not detected in non-neoplastic liver tissues or plasma of healthy persons. CIMP status in tumor tissues differed significantly in gender, hepatitis B surface antigen, alpha-fetoprotein, and tumor-node- metastasis stage （P 〈 0.05）. Similar results were obtained with plasma samples （P 〈 0.05）. There was no difference in CIMP status in age, presence of hepatitis C virus antibody, cirrhosis, number of nodes, number of tumors, tumor size, or Edmondson-Steiner stage. A one-year follow-up found that the metastatic rate and recurrence rate in the CIMP＋ group were significantly higher than in the CIMP- group as assessed with plasma samples （P 〈 0.05）. CONCLUSION： Plasma DNA can be a reliable sample source for CIMP analysis. CIMP in plasma may serve as a molecular marker of late-stage and poor-prognosis HCC.
基金Supported by Department of Health of Jiangsu Province o China,No.H200957
文摘AIM： To investigate the association between the CpG island methylator phenotype （CIMP） and serum Helico- bacter pylori （H. pylori） levels for clinical prediction of gastric cancer （GC） progression. METHODS： We analyzed the serum ClMP status of 75 patients with GC using a methylation marker panel and a methylation-specific polymerase chain reaction. Serum samples from 40 healthy persons were examined at the same time. The genes examined were APC, WIF-1, RUNX-3, DLC-1, SFRP-1, DKK and E-cad. H. pylori infec- tion in serum was assayed with an anti-H, pylori immu- noglobulin G antibody test and a rapid urease test. RESULTS： The frequencies of high-level methylation in GC tissues for the seven genes were： 48% for APC, 57.33% for WIF-1, 56% for RUNX-3, 50.67% for DLC-1, 52% for SFRP-1, 54.67% for DKK, and 48% for E-cad.The frequencies in GC serum were 30.67% for APC, 34.67% for WIF-1, 37.33% for RUNX-3, 29.33% for DLC-1, 33.33% for SFRP-1, 32% for DKK, and 26.67% for E-cad. CIMP＋ （defined as ≥ 3 methylated genes） was associated with 47 （62.67%） GC tissue samples and 44 （58.67%） GC serum samples. CIMP＋ was not associated with non-neoplastic mucosal tissues or the serum of healthy persons. Of the 75 GC cases, 51 （68%） were H. pylori＋, and 24 （32%） were H. pylori-. Of the 51 H. pylori＋ cases, 36 were CIMP＋ and 15 were CIMP-. In contrast, for the 24 H. pylori- cases, 11 were CIMP＋, and 13 were CIMP-. The difference was signifi- cant between the H. pylori＋ and H. pylori- groups χ2 = 4.27, P 〈 0.05）. Of the 51 H. pylori＋ GC patients, 34 were CIMP＋ and 17 were CIMP-, while among the 24 H. pylori- GC cases, 10 were CIMP＋ and 14 were CIMP-. The difference was significant between the H. pylori＋ and H. pylori- groups （χ2 = 4.21, P 〈 0.05）. A 2-year follow-up showed significant difference in the rates of metastasis and recurrence between H. pylori＋/CIMP＋ cases and the H. pylori＋/CIMP- cases or CIMP- cases associated with H. pylori assayed in serum （P 〈 0.05）. However, there were no significant differences in sur- vival rates between the two groups. CONCLUSION： H. pylori＋/CIMP＋ cases are associ- ated with higher rates of metastasis and recurrence thanH, pylori＋/CIMP- cases. Serum may be useful for examining CIMP status.
基金funded by the Intramural program of the National Human Genome Research Institute,the National Institutes of Health
文摘Over the last two decades, cancer-related alterations in DNA methylation that regulate transcription have been reported for a variety of tumors of the gastrointestinal tract. Due to its relevance for translational research, great emphasis has been placed on the analysis and molecular characterization of the CpG island methylator phenotype(CIMP), defined as widespread hypermethylation of CpG islands in clinically distinct subsets of cancer patients. Here, we present an overview of previous work in this field and also explore some open questions using crossplatform data for esophageal, gastric, and colorectal adenocarcinomas from The Cancer Genome Atlas. We provide a data-driven, pan-gastrointestinal stratification of individual samples based on CIMP status and we investigate correlations with oncogenic alterations, including somatic mutations and epigenetic silencing of tumor suppressor genes. Besides known events in CIMP such as BRAF V600 E mutation, CDKN2 A silencing or MLH1 inactivation, we discuss the potential role of emerging actors such as Wnt pathway deregulation through truncating mutations in RNF43 and epigenetic silencing of WIF1. Our results highlight the existence of molecular similarities that are superimposed over a larger backbone of tissue-specific features and can be exploited to reduce heterogeneity of response in clinical trials.
文摘To identify whether CpG island methylator phenotype (CIMP) is predictive of response to neoadjuvant chemoradiotherapy (NACRT) and outcomes in rectal cancer. METHODSPatients undergoing NACRT and surgical resection for rectal cancer in a tertiary referral centre between 2002-2011 were identified. Pre-treatment tumour biopsies were analysed for CIMP status (high, intermediate or low) using methylation specific PCR. KRAS and BRAF status were also determined using pyrosequencing analysis. Clinical information was extracted from case records and cancer services databases. Response to radiotherapy was measured by tumour regression scores determined upon histological examination of the resected specimen. The relationship between these molecular features, response to NACRT and oncological outcomes were analysed. RESULTSThere were 160 patients analysed with a median follow-up time of 46.4 mo. Twenty-one (13%) patients demonstrated high levels of CIMP methylation (CIMP-H) and this was significantly associated with increased risk of extramural vascular invasion (EMVI) compared with CIMP-L [8/21 (38%) vs 15/99 (15%), P = 0.028]. CIMP status was not related to tumour regression after radiotherapy or survival, however EMVI was significantly associated with adverse survival (P < 0.001). Intermediate CIMP status was significantly associated with KRAS mutation (P = 0.01). There were 14 (9%) patients with a pathological complete response (pCR) compared to 116 (73%) patients having no or minimal regression after neoadjuvant chemoradiotherapy. Those patients with pCR had median survival of 106 mo compared to 65.8 mo with minimal regression, although this was not statistically significant (P = 0.26). Binary logistic regression analysis of the relationship between EMVI and other prognostic features revealed, EMVI positivity was associated with poor overall survival, advanced “T” stage and CIMP-H but not nodal status, age, sex, KRAS mutation status and presence of local or systemic recurrence. CONCLUSIONWe report a novel association of pre-treatment characterisation of CIMP-H with EMVI status which has prognostic implications and is not readily detectable on pre-treatment histological examination.
基金supported by The University of Melbourne’s Research Computing Services and the Petascale Campus Initiative.
文摘Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methylation,a process predominantly attributed to anaerobic bacteria.However,recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns,although the mechanisms remain poorly understood.“Blue holes”are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles.Here,we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem.Yongle Blue Hole(YBH),currently the world’s deepest known blue hole,was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment.Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation,driven by abundant and diverse Deltaproteobacteria.In the suboxic intermediate layer,Nitrospina and Myxococcota dominated the Hg-methylating community.Furthermore,Hg methylators were found to have different lifestyles(free-living or particle-associated)and to occupy distinct ecological niches within the YBH.In addition,the contribution of sinking particles to Hg methylation,especially in the deep anoxic water column,was highlighted.Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments.The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.
基金supported by the National Natural Science Foundation of China(32460767)Jiangxi Provincial Key Research and Development Program(20232BBF60007)Jiangxi Provincial Natural Science Foundation(20224BAB205024).
文摘The yam Dioscorea alata L.is widely cultivated globally.Purple-fleshed varieties of this important crop have enhanced market value due to their high anthocyanin contents,but how anthocyanin biosynthesis in D.alata tubers is regulated remains poorly understood.In this study,we identified and functionally validated key transcription factors that regulate anthocyanin biosynthesis based on a comparative transcriptome and metabolome analysis of three D.alata cultivars with different colored tubers(dark purple,light purple,and white).The anthocyanin glycoside cyanidin-3-O-(2′′-O-glucosyl)glucoside was abundant during early tuber development,and we determined that its accumulation is regulated in opposite manners by two R2R3-MYB transcription factors:DaMYB75 and DaMYB56.Yeast two-hybrid and bimolecular fluorescence complementation assays in Nicotiana benthamiana and co-expression assays in D.alata demonstrated that DaMYB75 promotes anthocyanin biosynthesis by specifically activating the promoter of the late anthocyanin biosynthesis gene DaANS and enhancing its expression through an interaction with DabHLH72.By contrast,DaMYB56 is a negative regulator of anthocyanin biosynthesis that binds to the DaANS promoter together with DabHLH72.Furthermore,the methylation levels of the DaMYB75 promoter were significantly lower in purple tubers than in white tubers.These findings shed light on the regulation of anthocyanin biosynthesis by MYBs and provide the basis for genetically improving anthocyanin content in D.alata.
基金supported by the Guangdong Basic and Applied Basic Research Foundation (2025A1515012679)Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources (PFGR202502)
文摘Licochalcone A(LCA)is a characteristic compound in licorice Glycyrrhiza inflata and is widely utilized in pharmaceutical and cosmetic industries.However,the biosynthetic pathway and regulatory mechanisms of LCA remain poorly understood.In this study,we first found the accumulation of LCA is induced by methyl jasmonate(MeJA).Given that MYB transcriptional factors are well-documented as key regulators of flavonoid biosynthesis,we identified a total of 147 GiR2R3-MYB genes in G.inflata,which were classified into 28 subgroups.The chromosome distributions,sequence characteristics,gene structures,duplication events and cis-acting elements were also investigated.Through integrated analysis of GiR2R3-MYBs expression patterns across different tissues and under MeJA treatment,along with phylogenetic relationship,we identified GiMYB76—a MeJA-inducible MYB transcription factor—as a potential regulator of LCA accumulation.Functional validation showed that transgenic hairy roots overexpressing GiMYB76 exhibited a significant increase in LCA content.DAP-seq analysis of GiMYB76 revealed potential target genes involved in flavonoid biosynthesis regulation.Subsequent promoter activity assay verified that GiMYB76 can bind to the promoter and activate the expression of GiCHS4.Consistently,overexpression of GiCHS4 in G.inflata hairy roots also significantly enhanced LCA production.This study not only clarifies that GiMYB76 transcriptionally activated GiCHS4 to promote LCA biosynthesis but also provides valuable insights for basic research on licorice and the development of related industries.
基金Project supported by the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province(No.UNPYSCT-2017124)。
文摘The development of methylation protocol has attracted intense attention owing to"magic methyl effect"in drug discovery.Meanwhile,the indole scaffold is prevalence in the natural products and pharmacophores.Despite the advances in other site selective methylation,there is scarce reports for C4 methylation of indoles and combination of a carbonyl group rearrangement with C—H methylation on indole ring.Herein,the C4 methylation of indoles and the steric controlled C4-methylation/carbonyl group migration are reported.The large steric hindrance at carbonyl group facilitates the carbonyl group migration,which provides a straightforward protocol for the synthesis of C2/C4 disubstituted indoles.
文摘The escalating pace of industrialization has significantly intensified water pollution challenges,for instance,the persistent organic pollutants like methyl orange(MO).Conventional remediation techniques,such as adsorption and biological degradation,are often hampered by low efficiency and the risk of secondary pollution.Photocatalysis emerges as a promising sustainable alternative;however,the benchmark material titanium dioxide(TiO_(2))suffers from its intrinsic limitations,notably its wide bandgap energy(≥3.4 eV)restricting its activity to the region of the ultraviolet light and its rapid recombination of photogenerated charge carriers.To overcome these constraints,this research focused on synthesizing novel TiO_(2)/Sn_(3)O_(4) heterojunction composite photocatalysts via a solvothermal approach.Comprehensive characterization techniques confirmed the successful formation of the composite,which revealed that ultrathin Sn3O4 nanosheets uniformly coated TiO_(2) nanospheres.This unique architecture effectively reduced the overall crystallinity and introduced the beneficial oxygen vacancies.Under visible-light irradiation(λ≥420 nm),the optimized TiO_(2)/Sn3O4 composite exhibited the exceptional photocatalytic performance,which achieved 96%degradation of MO within just 60 minutes.The calculated apparent kinetic rate constant(0.103 min^(-1))was remarkably(5.15 times)higher than that of pristine TiO_(2).ESR experiments identified that hydroxyl radicals(·OH)was the predominant active species driving the degradation.Furthermore,cyclic degradation tests demonstrated its excellent material stability,with the composite retaining 85%of its initial efficiency after four consecutive reuse cycles.This work underscored the synergistic effects within the TiO_(2)/Sn_(3)O_(4) heterojunction,which significantly enhanced the visible-light absorption,charge separation,and photocatalytic activity,which provided the valuable insights for designing efficient,stable catalysts for the advanced environmental remediation applications.
基金supported by funding from the National Natural Science Foundation of China(81971349 and 81300456).
文摘In vitro maturation(IvM)of human oocytes offers cost efficiency and minimal invasiveness,serving as a valuable supplementary tool in assisted reproduction for fertility preservation,ovarian hyperstimulation syndrome prevention,and other reproductive strategies.Despite its availability for three decades,the clinical use of IVM remains limited due to efficacy and safety concerns.This study examines the DNA methylation profile of IVM oocytes collected during laparoscopic/hysteroscopic surgeries compared to in vivo matured oocytes via reduced representation bisulfite sequencing.Results indicate IVM oocytes exhibit a higher global methylation level.Differentially methylated regions(DMRs)analysis reveals that the in vitro group displays more hypermethylated and fewer hypomethylated DMRs compared to the in vivo group.Additionally,the in vitro group exhibits a higher level of non-CpG methylation than the in vivo group.However,no significant correlation between methylation levels and transcriptional activity in these oocytes is found,especially for those specific imprinted genes or genes related to embryonic development.These findings shed light on the epigenetic landscape of IvM oocytes,contributing to the ongoing assessment of their clinical feasibility and safety in assisted reproduction.
基金financially supported by the Natural Science Foundation of Wuhan City (Chenguang Project) (No.2024040801020331)the Natural Science Foundation of Hubei Province of China (No.2023AFB402)+1 种基金the National Key Research and Development Program of China (No.2023YFE0210200)Interdisciplinary Research Program of HUST。
文摘DNA methylation is an important promising biomarker for cancer diagnosis and monitoring.Therefore,the assessment of DNA methylation levels is helpful for the prognosis and diagnosis of cancer.However,it is still a huge challenge to sensitively and accurately quantify the levels of DNA methylation in clinical sample.In this work,we proposed a protospacer adjacent motif(PAM)-free mediated CRISPR-Cas12a ultra-sensitive and quantitative DNA methylation detection method.Through recognizing the ds DNA with toehold region,CRISPR-Cas12a not only got rid of the limitation of PAM,but also improved its distinction ability for single Cp G site methylation,nearly 5-fold that of conventional PAM-containing ds DNA.We further introduced assist-strand and design an artificial mismatch to greatly improve the ability to distinguish single Cp G methylation site.Our results showed that the discrimination factor was >200.Then,we constructed toe-ds DNA by using “heating and freezing”,which made our method universally applicable and feasible.In addition,we greatly simplified the difficulty of primer design.Our method detected four highly methylated genes acyl carrier protein(ACP),CLV3/ESR-related(CLE),Disabled(DAB) and Homeobox(HOX) with a detection limit of 0.01 % and excellent linearity in DNA methylation standards.Then,we verified the clinical utility of this method in 29 hepatocellular carcinomas,11 ovarian cancers and4 health people.In conclusion,we have successfully constructed a PAM-free CRISPR-Cas12a DNA methylation quantification method,which achieves high congruence in sensitivity,specificity and universality,fully demonstrating its significant clinical application value.
基金supported by 111 Project(Grant No.B17043)China Postdoctoral Science Foundation(Grant No.2022M723425).
文摘Fig(Ficus carica L.)with purple-red peel cultivars are popular among consumers and exhibit better storability.While DNA methylation influences fruit ripening and color development,its specific role in fig fruit remains unclear.This study explores the impact of DNA methylation on the fig peel coloration.Enzymatic colorimetric detection revealed that the level of‘Purple Peel’fig DNA methylation decreases with fig fruit ripening and coloring.Treatment of young fruit with the DNA-methylation inhibitor azacytidine induced peel coloration,suggesting that a decrease in DNA-methylation level promotes fig peel coloration.Seven members of DNA methyltransferases and three members of DNA demethylases were identified from a high-level fig genome,highlighting FcMET1 and FcDRM2 as stable proteins,ensuring functional expression.Reference to the Arabidopsis protein interaction network map predicted that FcMET1 is in a central position,suggesting a crucial regulatory role in multiple biological processes.Correlation analysis revealed a positive correlation between FcMET1 expression during peel development and the level of total DNA methylation.Weighted gene co-expression network analysis identified co-expression of FcMET1 with the color-related transcription factors MYB,bHLH and WD40,as well as with eight structural genes in the flavonoid-biosynthesis pathway.The expression of FcUFGT3 was negatively correlated with that of FcMET1.McrBC-PCR and Bisulfite Sequencing detection showed that a low methylation level of the FcUFGT3 promoter corresponds with its high expression in colored fig.This investigation of the mechanism of DNA methylation provides a theoretical basis for understanding the role of DNA-methylation modifications in fig ripening and coloring.
基金supported by grants from the Key Project Fund of National Natural Science Foundation of China(82230031)the Regional Innovation and Development Joint Fund of the National Natural Science Foundation of China(No.U24A200954)+4 种基金the Key Special Project of‘Cutting-Edge Biotechnology’in the National Key Research and Development Program of China(2024YFC3406200)Sanming Project of Medicine in Shenzhen(SZSM202411007)Guangdong Basic and Applied Basic Research Foundation Regional Joint Fund Key Program(2023B1515120051)Shenzhen Bay Laboratory Basic Research(SZBK2021080601009)to Wei Chithe Youth Fund of the National Natural Science Foundation of China(No.32300515)to Longjian Niu.
文摘In eukaryotic organisms,the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression.Previous studies have provided significant insights into CpG methylation,chromatin accessibility,and the dynamics of 3D architecture.However,a systematic delineation of how these epigenomic features regulate transcriptional activity remains limited.In this study,we develop nanoCAM-seq,a single-molecule sequencing technique designed to simultaneously profile higher-order chromatin interactions,chromatin accessibility,and endogenous CpG methylation.This approach provides an integrative view of chromatin features associated with cis-regulatory elements and reveals their coordinated dynamics during transitions of A/B compartments.Single-molecule analyses using nanoCAM-seq further reveal that promoters characterized by low CpG methylation and high chromatin accessibility more frequently interact with multiple enhancers.Collectively,our findings establish nanoCAM-seq as a powerful approach for resolving the coordinated dynamics of chromatin architecture and epigenetic modifications,offering critical insights into the regulatory mechanisms underlying gene expression.
基金Project supported by the National Natural Science Foundation of China(22306081,42030712,42477109,21966018 and 22106055)National Key R&D Program of China(2023YFB3810800)Yunnan Major Scientific and Technological Projects(202302AG050002)。
文摘Methyl mercaptan(CH_(3)SH)is notorious for global air pollution owing to its odorous characteristics and adverse health effects.Although CeO_(2) is currently regarded as a promising catalyst for CH_(3)SH decomposition,the high conversion temperature followed by high energy consumption is still a bottleneck.Herein,the cobalt-doped CeO_(2) catalyst was synthesized by a facile one-pot preparation strategy and successfully reduces the decomposition temperature from 450 to 250℃.Further studies demonstrate that the excellent low-temperature catalytic activity of Co_(0.6)Ce_(0.4)O_(2-σ)is attributed to its abundant oxygen vacancies and reactive oxygen species.Oxygen vacancies promote the adsorption and dissociation of CH_(3)SH,while reactive oxygen species facilitate the decomposition of CH_(3)SH.Moreover,Co acts as a sacrificial agent for the adsorption of sulfur species in CH_(3)SH,while Ce is responsible for the adsorption and activation of CH_(3)SH as the active metal phase.Furthermore,the migration and transformation mechanism of CH_(3)SH on the surface of Co_(0.6)Ce_(0.4)O_(2-δ)was determined via in situ diffuse reflectance infrared Fourier transform spectra(in situ-DRIFTS).This work provides a new strategy to synthesize highperformance catalysts for decomposing sulfur-containing volatile organic compounds(VOCs)at low temperatures,which is beneficial to decreasing the energy consumption.
基金supported by the Elderly Health Research Project of Jiangsu Province,No.LKM2023043(to XZ).
文摘Alterations in RNA methylation may affect the initiation and development of Alzheimer’s disease.However,the exact nature of the relationship between RNA methylation and Alzheimer’s disease remains unclear.In this study,RNA methylation levels were analyzed by bulk transcriptomic and single-cell RNA sequencing.The expression levels of RNA methylation regulators were confirmed using molecular biology techniques.Co-expression network analysis was used to identify relevant long non-coding RNAs.Molecular subtypes related to RNA methylation were classified,and variations in clinical characteristics,biological behavior,and immune signatures between subtypes were assessed.Machine learning approaches were applied to identify methylation-associated long non-coding RNAs,which were used to construct a risk model and nomogram for Alzheimer’s disease.Potential therapeutic agents for different risk groups were predicted,and in vitro experiments were conducted to identify key RNA methylation events.Single-cell analysis demonstrated enhanced RNA methylation in patients with Alzheimer’s disease,particularly within T cells,B cells,and NK cells.Quantitative reverse transcription-polymerase chain reaction and western blot confirmed alterations in RNA methylation regulators in neurons treated with amyloid-βoligomers in vitro.This evidence supported the classification of patients with Alzheimer’s disease into heterogeneous subtypes.Specifically,subtype 1 was identified as the immune-active subtype,while subtype 2 was characterized by a metabolic phenotype.Machine learning algorithms identified five significant methylation-associated long non-coding RNAs-LINC01007,MAP4K3-DT,MIR302CHG,VAC14-AS1,and TGFB2-OT1-that accurately predict clinical outcomes for patients with Alzheimer’s disease.These patients were classified into low-and high-risk categories;the latter group displayed higher immune infiltration,upregulated immune regulatory gene expression,and elevated immune scores and responded better to treatment with arachidonic-trifluoroethane.These findings suggest that dysregulated RNA methylation alters the immune microenvironment in Alzheimer’s disease and is closely associated with its progression.This phenomenon provides novel insights into potential therapeutic strategies for Alzheimer’s disease that target RNA methylation.
文摘Glutamate receptors and schizophrenia:Schizophrenia is a chronic mental disorder affecting approximately 1%of the global population,with 70%-80%heritability.It has a multifactorial etiology involving both environmental factors and a complex polygenic genetic architecture.Over the last two decades,large-scale genome-wide approaches revealed contributions of common variants with individually small effect sizes and of rare copy number variants with a large effect size.N-methy l-D-a spar tat e receptor(NMDAR)hypofunction has been implicated as a central mechanism in the pathophysiology of schizophrenia(Coyle et al.,2020).
基金supported by The Youth Talent Support Program of China Association of Chinese Medicine(2024-2026),No.CACM-2024-QNRC2-B36(to QX)The Central High-level Hospital of Traditional Chinese Medicine:Beijing University of Traditional Chinese Medicine Dongzhimen Hospital Talent Training Program-Youth Reserve Talent Project,No.DZMG-QNHB0010(to QX)the Natural Science Foundation of Heilongjiang Province(Outstanding Youth Program),No.YQ2022H003(to DW).
文摘Neurodegenerative diseases are characterized by a decline in brain structure and function.Their pathology involves multiple cell death pathways,including ferroptosis,cuproptosis,and pyroptosis.These pathways are intricately linked to genes associated with metabolism,antioxidant defense,lipid metabolism,chronic inflammation,and nerve regeneration processes.Key regulators of atypical cell death pathways show aberrant N^(6)-methyladenosine modification levels under pathological conditions.As the most abundant and dynamic RNA modification in brain tissue,N^(6)-methyladenosine plays crucial functional roles.Notably,there exists an intricate interplay between N^(6)-methyladenosine modifications and these cell death pathways,both of which are robustly associated with the pathogenesis of neurodegenerative diseases.However,the molecular mechanisms underlying this association remain unclear.This paper reviews the correlation between N^(6)-methyladenosine and various cell death patterns in neurodegenerative diseases,with emphasis on the molecular mechanisms underlying the interaction between N^(6)-methyladenosine epigenetic regulation and ferroptosis,cuproptosis,and pyroptosis in cognitive impairment.N^(6)-methyladenosine-modified ferroptosis plays an important role in neurodegenerative diseases.There is also a close association between N^(6)-methyladenosine modification and key molecules related to cuproptosis,which may promote the deposition of copper in the brain.Chronic inflammation,a hallmark of neurodegenerative diseases,is related to pyroptosis and N^(6)-methyladenosine modification.It is widely thought that ferroptosis,cuproptosis,and pyroptosis are interconnected processes that may share a common pathway affecting the pathogenesis of neurodegenerative diseases,and are related to key molecules involved in N^(6)-methyladenosine epigenetic modification.This suggests a great potential for future neurodegenerative diseases treatment strategies regulated by N^(6)-methyladenosine modification.N^(6)-methyladenosine modification plays a dual role in nerve injury and regeneration by dynamically regulating processes such as ferroptosis,cuproptosis,and pyroptosis and their key molecules.It maintains the“death-regeneration”balance in oxidative stress and inflammation while selectively promoting axon regeneration through the modulation of methylases.This mechanism indicates a considerable therapeutic target for neurological disorders.
基金supported by the National Nature Science Foundation of China(General Program),Nos.82271237,82071218(both to JC),and 82230042(to ZY)the Foundation of Key Laboratory of Neurology,Hebei Medical University,Ministry of Education,China,No.2023001(to JC).
文摘N^(6)-methyladenosine RNA methylation,an essential post-transcriptional modification,dynamically regulates RNA metabolism and plays a crucial role in neuronal function.Growing evidence suggests that dysregulated N^(6)-methyladenosine modification contributes to the pathogenesis of neurodegenerative diseases,including Alzheimer’s disease,Parkinson’s disease,multiple sclerosis,and amyotrophic lateral sclerosis.However,the precise mechanisms by which N^(6)-methyladenosine modification influences these conditions remain unclear.This review summarizes the role of m6A modification and its associated regulators in neurodegeneration,focusing on their involvement in key pathological processes.In Alzheimer’s disease,m6A modification contributes to synaptic dysfunction,mitochondrial damage,and neuronal apoptosis.Evidence from APP/PS1,5xFAD,tau transgenic,and Drosophila models demonstrates that regulators such as methyltransferase-like 3 and fat mass and obesity-associated protein influence Alzheimer’s disease progression through neuroinflammation,circular RNAs dysregulation,and autophagy-related mechanisms.In Parkinson’s disease,altered N^(6)-methyladenosine regulator expression affects dopaminergic neuron survival and stress responses by modulating mRNA stability and autophagy-related lncRNAs.In multiple sclerosis and amyotrophic lateral sclerosis,N^(6)-methyladenosine affects immune activation,myelin repair,and the regulation of disease-associated genes such as TDP-43.Beyond N^(6)-methyladenosine,other RNA methylation modifications-such as m1A,m5C,m7G,uracil,and pseudouridine-are implicated in neurodegenerative diseases through their regulation of mitochondrial function,RNA metabolism,and neuronal stress responses.Additionally,N^(6)-methyladenosine exhibits cell type-specific functions:in microglia,it regulates inflammatory activation and phagocytic function;in astrocytes,it modulates metabolic homeostasis and glutamate-associated neurotoxicity;in neurons,it affects synaptic function and neurodegeneration-related gene expression;and in adult neural stem cells,it controls differentiation,neurogenesis,and cognitive plasticity.Recently,several small-molecule inhibitors targeting methyltransferase-like 3 or fat mass and obesity-associated protein have been developed to modulate N^(6)-methyladenosine modification,providing new opportunities for disease intervention,with the targeting of N⁶-methyladenosine-related pathways emerging as a promising therapeutic strategy.However,challenges persist in optimizing the specificity and delivery of these therapeutic approaches.
基金supported by the National Natural Science Foundation of China,Nos.32070735(to QL),82371321(to QL),82171270(to ZL)Public Service Platform for Artificial Intelligence Screening and Auxiliary Diagnosis for the Medical and Health Industry,Ministry of Industry and Information Technology of the People's Republic of China,No.2020-0103-3-1(to ZL)+2 种基金the Natural Science Foundation of Beijing,No.Z200016(to ZL)Beijing Talents Project,No.2018000021223ZK03(to ZL)Beijing Municipal Committee of Science and Technology,No.Z201100005620010(to ZL)。
文摘Stroke is classified as ischemic or hemorrhagic,and there are few effective treatments for either type.Immunologic mechanisms play a critical role in secondary brain injury following a stroke,which manifests as cytokine release,blood–brain barrier disruption,neuronal cell death,and ultimately behavioral impairment.Suppressing the inflammatory response has been shown to mitigate this cascade of events in experimental stroke models.However,in clinical trials of anti-inflammatory agents,longterm immunosuppression has not demonstrated significant clinical benefits for patients.This may be attributable to the dichotomous roles of inflammation in both tissue injury and repair,as well as the complex pathophysiologic inflammatory processes in stroke.Inhibiting acute harmful inflammatory responses or inducing a phenotypic shift from a pro-inflammatory to an anti-inflammatory state at specific time points after a stroke are alternative and promising therapeutic strategies.Identifying agents that can modulate inflammation requires a detailed understanding of the inflammatory processes of stroke.Furthermore,epigenetic reprogramming plays a crucial role in modulating post-stroke inflammation and can potentially be exploited for stroke management.In this review,we summarize current findings on the epigenetic regulation of the inflammatory response in stroke,focusing on key signaling pathways including nuclear factor-kappa B,Janus kinase/signal transducer and activator of transcription,and mitogen-activated protein kinase as well as inflammasome activation.We also discuss promising molecular targets for stroke treatment.The evidence to date indicates that therapeutic targeting of the epigenetic regulation of inflammation can shift the balance from inflammation-induced tissue injury to repair following stroke,leading to improved post-stroke outcomes.
基金supported by the National Natural Science Foundation of China,Nos.82271283(to XC),91854115(to JW),31970044(to JW)the Natural Science Foundation of Beijing,No.7202001(to XC)the Scientific Research Project of Beijing Educational Committee,No.KM202010005022(to XC)。
文摘Salsolinol(1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline,Sal)is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine,an environmental toxin that causes Parkinson's disease.However,the mechanism by which Sal mediates dopaminergic neuronal death remains unclear.In this study,we found that Sal significantly enhanced the global level of N~6-methyladenosine(m~6A)RNA methylation in PC12 cells,mainly by inducing the downregulation of the expression of m~6A demethylases fat mass and obesity-associated protein(FTO)and alk B homolog 5(ALKBH5).RNA sequencing analysis showed that Sal downregulated the Hippo signaling pathway.The m~6A reader YTH domain-containing family protein 2(YTHDF2)promoted the degradation of m~6A-containing Yes-associated protein 1(YAP1)mRNA,which is a downstream key effector in the Hippo signaling pathway.Additionally,downregulation of YAP1 promoted autophagy,indicating that the mutual regulation between YAP1 and autophagy can lead to neurotoxicity.These findings reveal the role of Sal on m~6A RNA methylation and suggest that Sal may act as an RNA methylation inducer mediating dopaminergic neuronal death through YAP1 and autophagy.Our results provide greater insights into the neurotoxic effects of catechol isoquinolines compared with other studies and may be a reference for assessing the involvement of RNA methylation in the pathogenesis of Parkinson's disease.
